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These force fields are only enabled through interfaces to other programs. This includes: + +- The UFF and MMFF94 force fields via openbabel. +- The GFN-FF force field via xtb-python. + +One of the easiest ways to do this is to create a conda environment that includes the external program(s) you require. + +## Creating an avogadro conda environment + +Assuming conda is already installed on your system, the following will create a new environment named avogadro that contains both the openbabel and xtb-python packages. + + conda create -c conda-forge --name avogadro openbabel xtb-python + +When desired, this environment can then be activated as: + + conda activate avogadro + +```{warning} +Additional packages may need to be added to your conda environment in order for the force field scripts to run. For example, xtb-python may require the typing_extensions package. +``` + +## Setting the Python path + +It is also necessary to set the Python path correctly for Avogadro to be able to interface with the Python modules. To do this, go to the "Extensions" menu and select "Set Python Path...". + +![](../../_static/python-path.png) + +In the dialogue box, browse to (or copy and paste) the Python executable from the corresponding conda environment. Assuming a Linux or macOS system, you can find this by typing `which python` from a terminal (with the conda environment active). Once this is set, select OK. + +![](../../_static/set-path.png) + +You must now restart Avogadro for changes to take effect. If you now go to the "Extensions" menu, and under "Calculate", select "Setup Force Field..." you should be able to select the additional force fields. + +![](../../_static/ff-selector.png) + diff --git a/_sources/docs/optimizing-geometry/index.md.txt b/_sources/docs/optimizing-geometry/index.md.txt index 37d67a25..43c3bc5e 100644 --- a/_sources/docs/optimizing-geometry/index.md.txt +++ b/_sources/docs/optimizing-geometry/index.md.txt @@ -7,6 +7,7 @@ caption: Optimization --- +enabling-ff constraints conformers force-fields diff --git a/_sources/index.md.txt b/_sources/index.md.txt index 15d93907..bb07d486 100644 --- a/_sources/index.md.txt +++ b/_sources/index.md.txt @@ -141,6 +141,7 @@ install/index docs/index develop/index contrib/index +teach/index ``` [avogadro discussion]: https://discuss.avogadro.cc/ diff --git a/_sources/teach/acid_base.md.txt b/_sources/teach/acid_base.md.txt new file mode 100644 index 00000000..b3301100 --- /dev/null +++ b/_sources/teach/acid_base.md.txt @@ -0,0 +1,29 @@ +# Acid-Base Properties of Amino Acids + +Investigate the pH-dependent protonation of amino acids. + +## Tasks + +1. Create and optimize the geometry of a glycine molecule (H2NCH2COOH). Open the "Build" menu and select "Add Hydrogens for pH...". Choose different values of pH (1, 2, 3, ..., 13) and note the effect of pH shift on the electrical charge of glycine. +2. In a new View, create a (glutamic acid - lysine) dipeptide using the "Build" menu, then "Insert", then "Peptides...". Set the pH to 3 and calculate the corresponding electrical charge of the dipeptide. Do the same for pH 7 and pH 13. + +When performing a paper electrophoresis at these pHs, in which direction will the dipeptide move (towards the anode or cathode)? + +## Solution + +1. Glycine electrical charge according to pH shift: + - pH < 5: NH3+-CH2-COO-H+; net charge = +1. + - 5 ≤ pH < 10: NH3+-CH2-COO-; net charge = 0. + - 10 ≤ pH ≤ 13: NH2-CH2-COO-; net charge = -1. +2. Glu-Lys dipeptide: + +| pH | ![](../_static/Glu-Lys_dipeptideatph3.png) | ![](../_static/Glu-Lys_dipeptideatph7.png) | ![](../_static/Glu-Lys_dipeptideatph13.png) | +| ----------- | ----------- | ------------- | ---------- | +| Net charge | +1 | -1 | -2 | +| Electrophoresis | → cathode (-) | → anode (+) | →→ anode (+) | + + +## Further reading + +- [The acid-base behaviour of amino acids (chemguide.co.uk)](https://www.chemguide.co.uk/organicprops/aminoacids/acidbase.html) +- [Isoelectric point (wikipedia)](https://en.wikipedia.org/wiki/Isoelectric_point) diff --git a/_sources/teach/alkene_isomers.md.txt b/_sources/teach/alkene_isomers.md.txt new file mode 100644 index 00000000..27eeb1c2 --- /dev/null +++ b/_sources/teach/alkene_isomers.md.txt @@ -0,0 +1,15 @@ +# Alkene Isomers + +Investigate the stability of alkene isomers due to steric interactions. + +## Task + +Build and optimize the geometry of isomeric alkenes and compare their relative energies to confirm empirical rules for evaluating alkene stability: Zaitsef’s rule, cis- vs trans-, isolate vs conjugated dienes. + +Examples: +- Compare: 1-hexene, 2-hexene (cis and trans), 2-methyl-2-pentene, 2,3-dimethyl-2-butene. +- Compare: 1,4-pentadiene and 1,3-pentadiene. + +## See also + +[Markovnikov's Rule](markovnikovs_rule) \ No newline at end of file diff --git a/_sources/teach/basic_vsepr.md.txt b/_sources/teach/basic_vsepr.md.txt new file mode 100644 index 00000000..2ff3c344 --- /dev/null +++ b/_sources/teach/basic_vsepr.md.txt @@ -0,0 +1,33 @@ +# Basic VSEPR + +Investigate molecular geometries using VSEPR rules. + +## Task + +Build and optimize the geometry of simple molecules to illustrate VSEPR theory. + +- For organic-type molecules, use the MMFF94 forcefield. + +Examples: methane, water, ammonia, etc. + +- For octahedral-based geometries, use the UFF forcefield which is optimized for all elements. + +Examples: SF6, IF5, XeF4, etc. + +- Try even 7, 8, or 9 atoms around a central metal - how do the VSEPR rules extend beyond octahedral molecules? + +## See also + +[Organic Hybridization](organic_hybridization) + +## Further reading + +[VSEPR theory (wikipedia)](https://en.wikipedia.org/wiki/VSEPR_theory) + +```{warning} +Geometries derived from the trigonal bipyramidal geometry are not currently reliable. +``` + +```{tip} +When using the Draw tool, you may wish to uncheck the “Adjust Hydrogens” box. +``` diff --git a/_sources/teach/diaxial_interactions.md.txt b/_sources/teach/diaxial_interactions.md.txt new file mode 100644 index 00000000..7f9c84a7 --- /dev/null +++ b/_sources/teach/diaxial_interactions.md.txt @@ -0,0 +1,17 @@ +# 1,3-diaxial interactions + +Investigate steric interactions in cyclohexane derivatives. + +## Tasks + +1. Create and optimize the geometry of a cyclohexane molecule. +2. Add methyl substituents to the 1 and 3 positions in a diequatorial arrangement, optimize the geometry and note the energy. +3. Delete the diequatorial substituents to return to cyclohexane, and optimize the geometry again. +4. Place methyl substituents in 1,3-diaxial positions, optimize the geometry and note the movement of the groups and the energy. + +## Solution + +| | ![](../_static/TeachDiaxial_cyclohexane.png) | ![](../_static/TeachDiaxial_diequatorial.png) | ![](../_static/TeachDiaxial_diaxial.png) | +| ----------- | ----------- | ------------- | ---------- | +| Molecule | Cyclohexane | Diequatorial | Diaxial | +| Energy | 30 kJ/mol | 40 kJ/mol | 98 kJ/mol | diff --git a/_sources/teach/hcn_dipole.md.txt b/_sources/teach/hcn_dipole.md.txt new file mode 100644 index 00000000..eccd17fd --- /dev/null +++ b/_sources/teach/hcn_dipole.md.txt @@ -0,0 +1,11 @@ +# HCN dipole + +Investigate polar intermolecular interactions using HCN. + +## Task + +Create two molecules of HCN, run a force field geometry optimization. Check the orientation of the molecules, note the energy of interaction. Find primary dipoles, compare length of interatomic and intermolecular bonds. + +## See also + +[Water](water) diff --git a/_sources/teach/hydrogen_clusters.md.txt b/_sources/teach/hydrogen_clusters.md.txt new file mode 100644 index 00000000..2ff04687 --- /dev/null +++ b/_sources/teach/hydrogen_clusters.md.txt @@ -0,0 +1,35 @@ +# Hydrogen Clusters + +Investigate the intermolecular interactions of solid hydrogen. + +## Task + +Create 7 molecules of hydrogen. Optimize the geometry using the UFF forcefield and correct figure until all molecules are standing in a flat hexagonal order. Check the energy of interaction and distance between molecules. + +## Solution + + + +| Cell parameters | a | b | c | α | β | γ | +| ----------- | ----------- | ------------- | ---------- | ------- | ------- | ------- | +| Webelements | 470 pm | 470 pm | 340 pm | 90.0° | 90.0° | 120.0° | +| UFF | 486-496 pm | 486-496 pm | 324 pm | 90.0° | 90.0° | 120.0° | + +- Space group: P63/mmc (Space group number: 194). +- Structure: hcp (hexagonal close-packed). + +## Issues + +Melting of this cluster is poorly controllable. + +Cluster is a bit deformed, with long optimization some molecules tend to rotate and stand skew to neighbours. + +Since UFF does not properly include quantum mechanical effects and hydrogen bonding, the configuration and size of the unit cell are somewhat different than the experimental configuration. + +## See also + +[Hydrogen Molecule](hydrogen_molecule) + +## Sources + +[Webelements data on hydrogen clusters](https://www.webelements.com/hydrogen/crystal_structure.html) diff --git a/_sources/teach/hydrogen_molecule.md.txt b/_sources/teach/hydrogen_molecule.md.txt new file mode 100644 index 00000000..3c27309d --- /dev/null +++ b/_sources/teach/hydrogen_molecule.md.txt @@ -0,0 +1,31 @@ +# Hydrogen Molecule + +Investigate the hydrogen molecule and its bond length using different force fields. + +## Task + +- Create the H2 molecule using the drawing tool. +- Optimize the geometry with a variety of force fields and tabulate the resulting bond lengths. +- Enable display of its orbitals (?) + +## Solution + +![](../_static/Hydrogen_molecule.png) + +| Force field | Bond length (Å) | +| ----------- | ----------- | +| GAFF | 1.10 | +| Ghemical | 1.01 | +| MMFF | Error | +| UFF | 0.71 | + +An accurate bond length (see sources) for the molecule is 0.074 nm, so the UFF force field should be used. + +## See also + +[Hydrogen Clusters](hydrogen_clusters) + +## Sources + +[Hyperphysics data on the hydrogen molecule](http://hyperphysics.phy-astr.gsu.edu/hbase/molecule/hmol.html) + diff --git a/_sources/teach/index.md.txt b/_sources/teach/index.md.txt new file mode 100644 index 00000000..464f6168 --- /dev/null +++ b/_sources/teach/index.md.txt @@ -0,0 +1,71 @@ +(teach)= + +# Teach + +```{warning} +This section is in the process of being migrated from the original Avogadro documentation. Some instructions and screenshots may be out of date. +``` + +Avogadro is intended not only for molecular modeling research, but also for educational use. This category is intended to help educators around the world find lessons and tips for using Avogadro 2 in teaching chemistry. If you have an exercise or article that you would like to list here, please get in touch via [Avogadro Discussion](https://discuss.avogadro.cc). + +[1,3-diaxial interactions](diaxial_interactions) + +Investigate steric interactions in cyclohexane derivatives. + +[Alkene Isomers](alkene_isomers) + +Investigate the stability of alkene isomers due to steric interactions. + +[Basic VSEPR](basic_vsepr) + +Investigate molecular geometries using VSEPR rules. + +[HCN dipole](hcn_dipole) + +Investigate polar intermolecular interactions using HCN. + +[Hydrogen Clusters](hydrogen_clusters) + +Investigate the intermolecular interactions of solid hydrogen. + +[Hydrogen Molecule](hydrogen_molecule) + +Investigate the hydrogen molecule and its bond length using different force fields. + +[Markovnikov's Rule](markovnikovs_rule) + +Investigate the stability of reactions using Markovnikov's rule. + +[Organic Hybridization](organic_hybridization) + +Illustrate the geometry and bond lengths in sp3, sp2 and sp hybridized carbons. + +[Water](water) + +Investigate the geometry of water and hydrogen bonding between molecules. + +[Acid-Base Properties of Amino Acids](acid_base) + +Investigate the pH-dependent protonation of amino acids. + +```{toctree} +--- +caption: Teach +hidden: true +--- + +diaxial_interactions +alkene_isomers +basic_vsepr +hcn_dipole +hydrogen_clusters +hydrogen_molecule +markovnikovs_rule +organic_hybridization +water +acid_base + +``` + +[avogadro forum]: https://discuss.avogadro.cc +[github tracker]: https://github.com/OpenChemistry/avogadrolibs/issues diff --git a/_sources/teach/markovnikovs_rule.md.txt b/_sources/teach/markovnikovs_rule.md.txt new file mode 100644 index 00000000..5d69fdfe --- /dev/null +++ b/_sources/teach/markovnikovs_rule.md.txt @@ -0,0 +1,31 @@ +# Markovnikov's Rule + +Investigate the stability of reactions using Markovnikov's rule. + +## Task + +Build a propene molecule and optimize its geometry. Compare the relative energy of bromine-hydrogen substitution at either the 1-carbon or 2-carbon of the carbon-carbon double bond. Which of these two bromopropane compounds will be the major product of a propene bromination reaction? + +![](../_static/Markovnikovs_rule.png) + +## Solution + +![](../_static/Markovnikovs_rule_mechanistic.png) + +Results of relative energies expressed in kJ/mol (need confirmation in literature). + +| Force field | Intermediate primary carbocation (1') | Intermediate secondary carbocation (2') | 1-bromopropane (1) | 2-bromopropane (2) | +| ----------- | ----------- | ------------- | ---------- | ---------- | +| Ghemical | -2.24 | -2.06 | -2.39 | -1.87 | +| MMFF94 | -9.88 | -3.84 | -8.96 | +2.70 | +| UFF | +4.05 | +3.63 | +4.15 | +4.86 | + +UFF data is considered in this case, the secondary carbocation intermediate requires less energy (2') than the primary carbocation intermediate (1') (resp. 3.6 vs 4 kJ/mol). So compound (2) will be the major form. This is called the Markovnikov’s rule: “the major product of the addition of HX (where X is some atom more electronegative than H, the bromine in our case) to an alkene (here the propene) has the hydrogen atom in the less substituted position and X in the more substituted position”. Mechanisms which avoid the carbocation intermediate such as the presence of dialkyl peroxides will reverse the reaction result and compound (1) becomes the major product (Anti-Markovnikov rule). + +## See also + +[Alkene Isomers](alkene_isomers) + +## Further reading + +[Markovnikov's rule (wikipedia)](https://en.wikipedia.org/wiki/Markovnikov's_rule) diff --git a/_sources/teach/organic_hybridization.md.txt b/_sources/teach/organic_hybridization.md.txt new file mode 100644 index 00000000..d9cf28a6 --- /dev/null +++ b/_sources/teach/organic_hybridization.md.txt @@ -0,0 +1,27 @@ +# Organic Hybridization + +Illustrate the geometry and bond lengths in sp3, sp2 and sp hybridized carbons. + +## Task + +For each of ethane, ethylene and ethyne, build the molecule and optimize the geometry. Use the measurement tool to examine bond lengths and bond angles. + +## Solution + +![](../_static/Hybridisation.png) + +![](../_static/Molecular_hybridisation.png) + +Results using the MMFF94 forcefield: + +- sp3 - ethane bond angle: 110°; C-C bond length: 1.5 Å. +- sp2 - ethylene bond angle: 121°; C-C bond length: 1.336 Å. +- sp - ethyne bond angle: 180°; C-C bond length: 1.200 Å. + +## See also + +[Basic VSEPR](basic_vsepr) + +## Further reading + +[Orbital hybridization (wikipedia)](https://en.wikipedia.org/wiki/Orbital_hybridisation) diff --git a/_sources/teach/water.md.txt b/_sources/teach/water.md.txt new file mode 100644 index 00000000..873b329b --- /dev/null +++ b/_sources/teach/water.md.txt @@ -0,0 +1,38 @@ +# Water + +Investigate the geometry of water and hydrogen bonding between molecules. + +## Task + +Create a water molecule and optimize its geometry. Use the measurement tool to check the bond lengths and angle. + +Add another water molecule and use the same force field to optimize the geometry of the resulting dimer. Check the bond lengths in both molecules, and the angles between the bonds. Check how the molecules are oriented to each other. Calculate the energy of interaction, pay attention to the role of hydrogen bonds. Measure the deformation of bonds. + +## Solution + +| Force field | Bond length (Å) | Angle (°) | +| ----------- | ----------- | ------------- | +| GAFF | 1.10 | 102.8 | +| Ghemical | 0.95 | 109.5 | +| MMFF94 | 0.97 | 104.0 | +| UFF | 0.96 | 104.5 | + +Wikipedia gives an experimental O-H bond length of 95.84 pm, and a H-O-H bond angle of 104.45°, so both MMFF94 and UFF perform reasonably. + +![](../_static/Water_molecules.png) + +Note that there is a significant electrostatic interaction between the positively charged hydrogen atom and the oxygen on neighboring molecules. + +![](../_static/Water_molecules_with_electrostatic_potential.png) + +```{warning} +Only the MMFF94 force field includes hydrogen bonding terms, so two water molecules may not attract each other using the other force fields. +``` + +## See also + +[HCN dipole](hcn_dipole) + +## Sources + +[Wikipedia page on the properties of water](https://en.wikipedia.org/wiki/Properties_of_water) diff --git a/_static/Glu-Lys_dipeptideatph13.png b/_static/Glu-Lys_dipeptideatph13.png new file mode 100644 index 00000000..96b77cab Binary files /dev/null and b/_static/Glu-Lys_dipeptideatph13.png differ diff --git a/_static/Glu-Lys_dipeptideatph3.png b/_static/Glu-Lys_dipeptideatph3.png new file mode 100644 index 00000000..875dded1 Binary files /dev/null and b/_static/Glu-Lys_dipeptideatph3.png differ diff --git a/_static/Glu-Lys_dipeptideatph7.png b/_static/Glu-Lys_dipeptideatph7.png new file mode 100644 index 00000000..1c0a64ec Binary files /dev/null and b/_static/Glu-Lys_dipeptideatph7.png differ diff --git a/_static/Hybridisation.png b/_static/Hybridisation.png new file mode 100644 index 00000000..4fa5e1e1 Binary files /dev/null and b/_static/Hybridisation.png differ diff --git a/_static/Hydrogen_molecule.png b/_static/Hydrogen_molecule.png new file mode 100644 index 00000000..1b40fb7e Binary files /dev/null and b/_static/Hydrogen_molecule.png differ diff --git a/_static/Markovnikovs_rule.png b/_static/Markovnikovs_rule.png new file mode 100644 index 00000000..d7eef890 Binary files /dev/null and b/_static/Markovnikovs_rule.png differ diff --git a/_static/Markovnikovs_rule_mechanistic.png b/_static/Markovnikovs_rule_mechanistic.png new file mode 100644 index 00000000..4ecd2c43 Binary files /dev/null and b/_static/Markovnikovs_rule_mechanistic.png differ diff --git a/_static/Molecular_hybridisation.png b/_static/Molecular_hybridisation.png new file mode 100644 index 00000000..1890c1d9 Binary files /dev/null and b/_static/Molecular_hybridisation.png differ diff --git a/_static/TeachDiaxial_cyclohexane.png b/_static/TeachDiaxial_cyclohexane.png new file mode 100644 index 00000000..a89105ba Binary files /dev/null and b/_static/TeachDiaxial_cyclohexane.png differ diff --git a/_static/TeachDiaxial_diaxial.png b/_static/TeachDiaxial_diaxial.png new file mode 100644 index 00000000..2608017c Binary files /dev/null and b/_static/TeachDiaxial_diaxial.png differ diff --git a/_static/TeachDiaxial_diequatorial.png b/_static/TeachDiaxial_diequatorial.png new file mode 100644 index 00000000..f7e4707b Binary files /dev/null and b/_static/TeachDiaxial_diequatorial.png differ diff --git a/_static/Water_molecules.png b/_static/Water_molecules.png new file mode 100644 index 00000000..5131206d Binary files /dev/null and b/_static/Water_molecules.png differ diff --git a/_static/Water_molecules_with_electrostatic_potential.png b/_static/Water_molecules_with_electrostatic_potential.png new file mode 100644 index 00000000..11795844 Binary files /dev/null and b/_static/Water_molecules_with_electrostatic_potential.png differ diff --git a/_static/ff-selector.png b/_static/ff-selector.png new file mode 100644 index 00000000..0713719f Binary files /dev/null and b/_static/ff-selector.png differ diff --git a/_static/python-path.png b/_static/python-path.png new file mode 100644 index 00000000..1a435bb2 Binary files /dev/null and b/_static/python-path.png differ diff --git a/_static/set-path.png b/_static/set-path.png new file mode 100644 index 00000000..2767070b Binary files /dev/null and b/_static/set-path.png differ diff --git a/contrib/code-docs.html b/contrib/code-docs.html index f3984975..4d07859c 100644 --- a/contrib/code-docs.html +++ b/contrib/code-docs.html @@ -48,6 +48,7 @@ + @@ -168,12 +169,27 @@ + + + + @@ -323,12 +339,27 @@ + + + + @@ -569,6 +600,15 @@

Coding Style (C++)

+ +
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next

+

Teach

+
+ +
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175, 178, 181, 183, 193, 197, 198, 200, 205, 209, 213, 214, 219, 220, 222, 228, 230, 232, 235, 236, 240, 241], "should": [1, 2, 5, 8, 20, 22, 27, 28, 39, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 68, 72, 73, 75, 82, 84, 85, 89, 90, 91, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 117, 121, 123, 133, 134, 167, 168, 169, 172, 173, 175, 176, 178, 182, 202, 205, 212, 236, 240, 244], "minimum": [1, 22, 28, 41, 49, 62, 82, 84, 176, 178, 212, 244], "brief": [1, 175], "one": [1, 2, 5, 13, 15, 19, 22, 24, 26, 27, 37, 48, 62, 75, 78, 82, 85, 95, 115, 117, 120, 134, 136, 168, 173, 178, 181, 182, 190, 191, 192, 198, 202, 207, 211, 213, 219, 234, 244], "two": [1, 15, 26, 75, 84, 142, 166, 167, 171, 182, 186, 202, 211, 213, 216, 239, 240, 242, 243, 244], "sentenc": 1, "explain": 1, "what": [1, 28, 43, 85, 95, 180, 197, 207, 211, 224], "intend": [1, 23, 51, 172, 178], "purpos": [1, 2, 5, 51, 65, 115, 126, 136, 167, 178, 207], "i": [1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 75, 78, 81, 82, 84, 85, 88, 89, 90, 91, 92, 93, 94, 95, 96, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 121, 123, 124, 126, 127, 128, 129, 132, 133, 134, 136, 138, 142, 145, 157, 158, 159, 160, 161, 164, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 178, 179, 181, 182, 183, 185, 186, 187, 188, 191, 192, 193, 197, 198, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 212, 213, 214, 216, 217, 219, 220, 222, 223, 224, 225, 227, 229, 230, 232, 234, 235, 236, 240, 241, 242, 243, 244], "goe": [1, 5, 62, 82, 173, 236], "here": [1, 62, 81, 82, 166, 170, 171, 176, 178, 181, 182, 183, 185, 186, 187, 188, 190, 191, 207, 213, 228], "void": [1, 5, 7, 8, 12, 13, 15, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28, 31, 33, 35, 36, 37, 39, 41, 42, 43, 44, 48, 51, 57, 61, 62, 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45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 69, 82, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 157, 159, 161, 173, 232, 242], "simplest": 1, "wai": [1, 85, 95, 178, 182, 188, 197, 203, 205, 207, 234, 235], "possibl": [1, 5, 21, 22, 49, 84, 171, 178, 204, 236], "molequeu": [1, 2, 82, 159, 166, 173, 236, 239], "jsonrpcclient": 1, "h": [1, 2, 5, 19, 24, 49, 61, 63, 64, 65, 66, 67, 68, 71, 74, 76, 78, 82, 83, 89, 92, 98, 105, 107, 115, 116, 118, 120, 122, 125, 127, 141, 159, 160, 161, 167, 173, 178, 183, 185, 209, 214, 239, 243], "client": [1, 66, 159, 163, 178], "The": [1, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72, 73, 74, 75, 76, 78, 79, 80, 81, 82, 83, 84, 85, 87, 89, 90, 91, 92, 95, 96, 97, 99, 100, 101, 102, 103, 104, 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190, 193, 197, 198, 200, 202, 203, 207, 210, 211, 212, 213, 216, 217, 218, 219, 220, 224, 225, 229, 230, 231, 234, 235, 236, 242, 243, 244], "rpc": [1, 65, 68, 161, 239], "server": [1, 4, 61, 65, 66, 68, 92, 166, 227], "json": [1, 45, 62, 65, 75, 82, 83, 100, 113, 161, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 239, 244], "2": [1, 5, 15, 17, 19, 28, 62, 65, 82, 84, 132, 142, 159, 160, 166, 169, 173, 176, 180, 182, 185, 190, 193, 200, 209, 212, 221, 223, 233, 234, 235, 236, 239, 242, 243], "0": [1, 5, 8, 10, 13, 14, 15, 18, 19, 21, 23, 26, 28, 39, 41, 43, 48, 62, 65, 72, 73, 75, 82, 95, 96, 100, 101, 102, 105, 118, 132, 134, 138, 140, 141, 142, 159, 160, 166, 167, 169, 171, 173, 175, 176, 179, 182, 185, 193, 200, 204, 217, 232, 234, 238, 241], "author": [1, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 47, 48, 49, 51, 53, 55, 57, 58, 59, 60, 62, 70, 74, 75, 76, 82, 84, 86, 87, 89, 97, 98, 100, 101, 102, 104, 113, 115, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 168, 173, 175, 178], "marcu": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "d": [1, 3, 7, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 62, 70, 75, 76, 82, 84, 86, 87, 89, 92, 97, 98, 102, 104, 107, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 159, 160, 178, 240, 242, 243], "hanwel": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "provid": [1, 13, 14, 18, 21, 22, 24, 25, 27, 28, 31, 36, 38, 41, 43, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 74, 79, 82, 83, 85, 90, 91, 102, 103, 104, 118, 121, 123, 126, 129, 139, 145, 161, 167, 169, 170, 173, 175, 178, 186, 197, 198, 200, 203, 204, 205, 206, 207, 208, 211, 217, 220, 225, 229, 231, 234, 244], "To": [1, 11, 16, 51, 63, 65, 74, 168, 171, 178, 181, 202, 209, 218, 219, 236], "creat": [1, 12, 17, 19, 21, 26, 28, 33, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 66, 78, 82, 83, 85, 90, 91, 95, 102, 104, 106, 107, 109, 110, 111, 112, 113, 114, 117, 130, 133, 134, 144, 169, 170, 173, 175, 176, 178, 182, 184, 187, 189, 198, 201, 205, 206, 208, 209, 211, 221, 228, 229, 230, 234, 236, 240, 242, 244], "connect": [1, 26, 61, 66, 68, 84, 95, 127, 166, 171, 178, 227, 228, 243], "method": [1, 5, 12, 17, 21, 23, 28, 42, 48, 51, 62, 63, 65, 67, 75, 78, 82, 84, 85, 90, 91, 95, 100, 102, 104, 117, 118, 134, 158, 167, 169, 173, 214, 215, 234, 239, 242, 244], "follow": [1, 5, 19, 62, 82, 92, 142, 167, 168, 169, 170, 171, 172, 173, 176, 178, 185, 188, 213, 236], "done": [1, 13, 24, 37, 39, 65, 117, 123, 133, 159, 163, 169, 171, 217, 230], "new": [1, 2, 4, 5, 6, 7, 12, 17, 26, 27, 28, 33, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 66, 68, 75, 79, 81, 82, 89, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 127, 128, 141, 158, 159, 166, 169, 171, 172, 174, 177, 180, 181, 189, 190, 196, 200, 202, 204, 205, 209, 210, 216, 217, 230, 239, 240, 242, 243, 244], "connecttoserv": 1, "myrpcserv": 1, "qjsonobject": [1, 61, 62, 82], "emptyrequest": 1, "qlatin1str": 1, "listqueu": 1, "sendrequest": 1, "endcod": 1, "signal": [1, 2, 61, 66, 67, 68, 69, 70, 75, 77, 82, 84, 85, 86, 87, 88, 89, 92, 95, 96, 98, 100, 103, 104, 157], "order": [1, 7, 13, 17, 21, 28, 62, 75, 79, 82, 85, 89, 92, 95, 103, 105, 123, 133, 134, 142, 159, 160, 167, 168, 171, 173, 176, 198, 200, 220, 223, 228, 236, 240, 244], "act": [1, 95, 171, 236], "result": [1, 5, 12, 13, 18, 21, 25, 38, 62, 65, 68, 82, 83, 105, 124, 134, 141, 161, 168, 171, 172, 176, 178, 181, 182, 183, 228, 236], "notif": 1, "error": [1, 12, 48, 49, 51, 61, 63, 65, 68, 69, 78, 92, 104, 117, 123, 133, 134, 142, 159, 162, 163, 164, 165, 178, 242, 243, 244], "receiv": [1, 61, 82, 178], "respons": [1, 3, 61, 87, 95, 123, 170, 171, 244], "set": [1, 12, 14, 15, 17, 18, 21, 22, 24, 25, 26, 27, 28, 33, 37, 38, 39, 41, 42, 43, 48, 51, 61, 62, 63, 64, 65, 68, 69, 73, 75, 78, 79, 80, 82, 84, 90, 91, 92, 95, 96, 100, 103, 104, 107, 116, 118, 121, 123, 126, 127, 128, 129, 132, 133, 134, 136, 140, 146, 157, 158, 159, 160, 161, 164, 166, 167, 168, 170, 173, 178, 181, 182, 183, 186, 187, 190, 197, 198, 207, 209, 214, 215, 217, 236, 239, 241, 242, 244], "public": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 158, 240], "qobject": [1, 61, 62, 66, 67, 69, 74, 75, 79, 82, 84, 85, 86, 88, 92, 95, 96, 98, 99, 100, 101, 103], "end": [1, 2, 5, 7, 28, 43, 81, 95, 115, 116, 120, 121, 124, 130, 136, 144, 159, 160, 165, 182, 185, 197, 218, 219], "complet": [1, 27, 51, 61, 65, 68, 84, 117, 127, 163, 167, 168, 175, 185], "constructor": [1, 7, 15, 18, 24, 27, 28, 37, 62, 67, 72, 73, 82, 84, 85, 88, 89, 92], "more": [1, 2, 5, 24, 27, 37, 48, 62, 75, 82, 85, 95, 103, 104, 105, 115, 120, 123, 126, 134, 136, 161, 168, 172, 173, 174, 175, 178, 190, 197, 198, 203, 207, 210, 211, 213, 214, 217, 229, 234, 235, 239, 240, 243, 244], "construct": [1, 18, 19, 61, 64, 79, 83, 89, 95, 202, 205], "describ": [1, 13, 15, 62, 68, 82, 117, 167, 169, 172, 173, 178], "paramet": [1, 7, 13, 14, 15, 18, 21, 22, 24, 25, 27, 28, 32, 37, 38, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 63, 64, 65, 67, 68, 74, 75, 78, 81, 83, 84, 85, 89, 90, 91, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 139, 141, 142, 168, 169, 188, 207, 213, 214, 217, 230, 243], "input": [1, 8, 13, 21, 23, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 83, 84, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 130, 144, 157, 161, 162, 167, 168, 169, 172, 174, 175, 176, 180, 182, 192, 207, 234, 239, 240, 241, 243, 244], "job": [1, 61, 62, 63, 64, 65, 68, 82, 173], "param": [1, 166], "filenam": [1, 48, 49, 51, 62, 69, 77, 78, 82, 108, 159, 162, 163, 164, 166, 169, 173, 175, 244], "appear": [1, 62, 78, 82, 95, 173, 175, 181, 188, 207], "work": [1, 3, 4, 6, 24, 103, 168, 178, 182, 190, 193, 204, 207, 210, 213, 234, 235, 236, 243, 244], "directori": [1, 29, 30, 78, 156, 161, 236, 240], "content": [1, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 84, 104, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 121, 127, 128, 136, 139, 157, 166, 173, 178], "specifi": [1, 13, 18, 19, 21, 22, 25, 27, 28, 33, 38, 48, 49, 51, 64, 79, 83, 85, 90, 91, 92, 95, 104, 124, 126, 127, 128, 129, 134, 142, 167, 169, 170, 171, 172, 176, 178, 181, 183, 185, 186, 210], "return": [1, 5, 8, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72, 73, 74, 75, 78, 79, 81, 82, 84, 85, 87, 89, 90, 91, 92, 95, 96, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 126, 127, 128, 129, 134, 136, 142, 158, 167, 170, 171, 205, 227], "true": [1, 5, 8, 12, 14, 15, 17, 21, 24, 25, 26, 27, 28, 31, 36, 37, 38, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 75, 82, 84, 85, 90, 91, 92, 95, 96, 100, 104, 106, 107, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 142, 159, 164, 167, 168, 169, 170, 171, 176], "wa": [1, 27, 28, 61, 62, 65, 68, 69, 73, 75, 82, 84, 85, 100, 104, 124, 126, 173, 186, 188, 197, 202, 204, 229, 232, 234, 240], "successfulli": [1, 51, 61, 62, 65, 66, 75, 82, 84, 236, 243], "fals": [1, 5, 14, 15, 21, 24, 25, 27, 28, 31, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 75, 82, 84, 85, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 159, 164, 167, 169, 171, 173], "otherwis": [1, 14, 15, 21, 24, 25, 28, 37, 38, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 75, 82, 95, 100, 106, 109, 110, 111, 112, 113, 114, 126, 172, 173, 178, 212, 227], "bool": [1, 7, 8, 12, 14, 15, 17, 21, 22, 24, 25, 26, 27, 28, 31, 33, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 75, 77, 82, 84, 85, 86, 90, 91, 92, 95, 96, 98, 99, 100, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 121, 123, 124, 126, 129, 131, 132, 133, 134, 140, 142, 157, 158, 159, 160], "setinputfil": 1, "const": [1, 2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 72, 73, 75, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 144, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157], "qstring": [1, 2, 61, 62, 63, 64, 65, 67, 68, 69, 74, 75, 77, 78, 79, 80, 82, 83, 87, 92, 95, 96, 99, 100, 101, 102, 104, 108], "don": [2, 5, 68, 217, 240, 244], "t": [2, 5, 7, 8, 20, 37, 42, 44, 68, 129, 142, 147, 178, 183, 185, 193, 197, 207, 217, 240, 241, 244], "except": [2, 5, 167, 169, 178, 244], "assert": [2, 178], "product": [2, 197], "never": [2, 169, 178], "crash": [2, 62, 82, 168, 173, 232, 234, 240, 242, 243, 244], "prefer": [2, 49, 62, 82, 134, 167, 171, 173, 192, 205, 207, 212, 243], "solut": 2, "from": [2, 3, 7, 15, 18, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 37, 39, 43, 48, 49, 51, 61, 62, 65, 67, 68, 69, 75, 78, 81, 82, 83, 84, 85, 90, 91, 95, 100, 104, 107, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 137, 138, 156, 158, 161, 166, 168, 169, 171, 172, 173, 174, 175, 176, 178, 180, 181, 182, 183, 186, 187, 189, 190, 192, 195, 197, 198, 200, 202, 204, 206, 207, 208, 211, 213, 216, 218, 219, 220, 228, 229, 230, 231, 232, 234, 235, 236, 237, 239, 240, 241, 242, 243, 244], "librari": [2, 4, 51, 103, 142, 175, 181, 236, 240, 244], "over": [2, 182, 186, 192, 193, 196, 217, 227, 232, 234, 239, 240], "boost": [2, 236], "depend": [2, 3, 105, 171, 181, 198, 207, 217, 236, 239], "In": [2, 6, 27, 62, 82, 84, 168, 171, 173, 178, 182, 185, 200, 204, 220, 228, 234, 236, 237], "11": [2, 31, 178, 182], "17": [2, 36, 236], "where": [2, 5, 18, 22, 23, 24, 26, 27, 37, 62, 72, 73, 82, 104, 161, 166, 170, 171, 173, 178, 183, 194, 202, 211, 214, 225, 229, 234, 236, 244], "necessari": [2, 5, 7, 96, 178, 211, 217], "offer": [2, 3, 95, 173, 178, 204, 235], "avo_overrid": 2, "avo_fin": 2, "defin": [2, 41, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 82, 87, 106, 109, 110, 111, 112, 113, 114, 115, 121, 136, 140, 141, 142, 168, 170, 173, 178, 181, 182, 185, 205, 234], "overrid": [2, 24, 28, 32, 37, 40, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 72, 73, 75, 76, 77, 79, 82, 83, 84, 85, 86, 87, 88, 89, 92, 95, 96, 97, 98, 99, 100, 104, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 122, 124, 125, 126, 127, 128, 130, 136, 137, 138, 139, 143, 144, 146, 158, 173, 243], "final": [2, 61, 95, 168, 171, 190, 197, 244], "minim": [2, 62, 82, 140, 173, 190], "third": [2, 182, 236], "parti": [2, 178, 236], "think": [2, 167, 235], "carefulli": [2, 75], "befor": [2, 5, 12, 17, 24, 37, 51, 62, 66, 82, 85, 92, 95, 107, 176, 178, 187, 197, 212, 213, 217, 230, 236, 244], "ad": [2, 6, 24, 26, 28, 33, 37, 48, 61, 62, 81, 82, 85, 102, 120, 124, 126, 127, 128, 159, 164, 176, 188, 189, 190, 198, 200, 220, 227, 234, 239, 244], "templat": [2, 6, 7, 8, 9, 12, 13, 17, 20, 42, 44, 62, 64, 65, 68, 82, 90, 91, 117, 129, 134, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 173, 240, 244], "sens": [2, 68], "alwai": [2, 5, 68, 174, 178, 212, 240, 242, 243], "form": [2, 14, 26, 83, 95, 104, 127, 167, 168, 169, 172, 173, 178, 197, 213, 214, 240, 242, 243], "project": [2, 4, 5, 29, 30, 118, 138, 156, 159, 165, 182, 185, 206, 209, 235, 236, 240, 244], "someth": [2, 84, 100, 204], "type": [2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 20, 21, 22, 24, 25, 28, 32, 33, 37, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 71, 75, 77, 78, 81, 82, 85, 89, 90, 91, 95, 96, 99, 102, 103, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 121, 124, 126, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 159, 160, 165, 168, 170, 172, 173, 174, 175, 176, 180, 181, 189, 190, 191, 194, 197, 200, 202, 203, 205, 207, 209, 210, 213, 216, 220, 224, 225, 228, 229, 234, 240], "myclass": 2, "sourc": [2, 3, 5, 84, 133, 159, 161, 165, 183, 204, 235, 237, 239, 243], "special": [2, 75, 178], "first": [2, 7, 19, 22, 23, 24, 27, 28, 44, 51, 62, 65, 68, 79, 82, 84, 85, 95, 104, 127, 128, 142, 168, 169, 173, 182, 187, 202, 207, 210, 229, 243], "myapihead": 2, "our": [2, 3, 6, 115, 116, 120, 121, 124, 126, 127, 128, 129, 136, 137, 138, 167, 178, 183, 190, 235], "molecul": [2, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 25, 27, 32, 33, 35, 38, 39, 40, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 69, 71, 75, 81, 86, 90, 91, 95, 96, 100, 103, 104, 106, 109, 110, 111, 112, 113, 114, 121, 131, 157, 159, 160, 161, 164, 165, 166, 167, 168, 169, 171, 177, 180, 181, 182, 191, 192, 196, 199, 201, 202, 203, 205, 206, 209, 210, 213, 214, 215, 216, 217, 218, 219, 221, 222, 224, 225, 226, 229, 231, 232, 234, 235, 239, 240, 242, 244], "differ": [2, 4, 22, 28, 42, 43, 85, 99, 176, 178, 180, 199, 200, 214, 220, 228, 234], "modul": [2, 170, 175, 234, 236], "qtcore": 2, "vector": [2, 7, 18, 20, 21, 22, 24, 26, 27, 28, 33, 34, 35, 37, 39, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 81, 84, 95, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 120, 124, 134, 142, 182, 183, 231], "stl": [2, 7], "do": [2, 5, 12, 17, 84, 95, 122, 125, 130, 134, 144, 145, 171, 172, 178, 183, 190, 200, 202, 220, 236, 239, 244], "avogadrorenderingexport": 2, "ar": [2, 3, 4, 5, 6, 13, 14, 15, 18, 21, 23, 24, 25, 26, 28, 37, 39, 41, 48, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 75, 78, 79, 80, 81, 82, 84, 92, 95, 103, 104, 115, 117, 120, 121, 124, 128, 134, 136, 140, 142, 161, 167, 168, 169, 172, 173, 174, 175, 176, 178, 181, 185, 187, 200, 202, 203, 211, 212, 216, 217, 219, 220, 223, 225, 227, 234, 235, 236, 237, 239, 240, 242, 243, 244], "denot": [2, 121, 129], "_p": 2, "camel": [2, 5], "case": [2, 5, 15, 24, 37, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 72, 73, 82, 84, 106, 109, 110, 111, 112, 113, 114, 166, 169, 171, 173, 178, 197, 200, 210, 219, 220, 242, 243, 244], "qtgui": [2, 28, 62, 63, 64, 103, 104, 157, 159, 161], "instead": [2, 39, 75, 167, 168, 169, 243], "being": [2, 5, 15, 24, 27, 48, 84, 90, 91, 104, 120, 124, 157, 158, 198, 217, 219, 224, 236], "wrong": [2, 5, 240], "qdialog": [2, 63, 65, 71], "correct": [2, 5, 49, 62, 82, 123, 126, 173, 190, 236, 244], "open": [2, 3, 4, 5, 48, 51, 65, 68, 75, 78, 159, 161, 162, 163, 166, 169, 181, 182, 184, 185, 186, 187, 193, 198, 201, 204, 207, 209, 211, 227, 230, 231, 234, 235, 236, 239, 241, 242, 243, 244], "chemistri": [2, 3, 4, 5, 204, 228, 230, 231, 235, 236, 239], "nest": [2, 190], "everyth": [2, 206, 210, 216], "insid": [2, 5, 175, 236], "mongochem": [2, 244], "contain": [2, 5, 7, 8, 12, 15, 17, 18, 20, 21, 22, 24, 26, 27, 28, 33, 37, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 70, 75, 78, 82, 86, 87, 90, 91, 92, 95, 98, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 120, 124, 126, 130, 132, 134, 136, 142, 144, 146, 158, 159, 160, 167, 168, 169, 171, 172, 173, 175, 212, 236, 243], "most": [2, 15, 61, 62, 72, 73, 75, 78, 82, 125, 126, 164, 168, 173, 178, 204, 205, 207, 211, 214, 217, 228, 229, 234, 236], "overspecifi": 2, "e": [2, 5, 19, 26, 27, 28, 33, 37, 43, 48, 62, 64, 74, 75, 82, 84, 85, 88, 89, 92, 95, 100, 132, 134, 138, 142, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 185, 190, 192, 193, 200, 212, 220, 227, 231, 232, 234, 236, 239, 240, 243, 244], "doesn": [2, 193, 197, 217], "slot": [2, 61, 62, 63, 65, 66, 68, 69, 71, 75, 77, 82, 85, 86, 87, 88, 89, 92, 95, 98, 100, 103, 104, 157], "moc": 2, "often": [2, 183, 214], "littl": 2, "help": [2, 3, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 106, 109, 110, 111, 112, 113, 114, 161, 167, 169, 172, 204, 205, 214, 229, 234, 235, 240, 242, 243], "onli": [2, 5, 15, 21, 23, 28, 43, 51, 62, 65, 68, 81, 82, 85, 95, 104, 117, 121, 124, 133, 167, 168, 169, 171, 172, 173, 178, 190, 197, 198, 202, 207, 210, 214, 217, 219, 228, 234, 236, 241, 242, 243, 244], "specif": [2, 11, 16, 19, 28, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 106, 109, 110, 111, 112, 113, 114, 159, 160, 171, 172, 173, 182, 197, 207, 210, 213, 214, 216, 217, 218, 229, 239, 244], "symbol": [2, 19, 23, 39, 40, 72, 73, 159, 160, 173, 200, 220, 242], "avoid": [2, 5, 22, 84, 178, 236, 243, 244], "static_cast": 2, "dynamic_cast": [2, 129], "const_cast": 2, "reinterpret_cast": [2, 5], "For": [2, 4, 5, 15, 19, 23, 51, 61, 95, 134, 161, 167, 169, 170, 171, 172, 173, 176, 178, 182, 188, 191, 198, 204, 206, 207, 210, 211, 213, 217, 219, 222, 223, 236], "deriv": [2, 15, 20, 21, 25, 38, 48, 85, 100, 104, 126, 158, 178, 228], "qobject_cast": 2, "enum": [2, 15, 19, 21, 22, 24, 33, 37, 39, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 95, 96, 107, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155], "": [2, 12, 13, 17, 19, 21, 24, 26, 28, 37, 41, 42, 43, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 75, 79, 80, 81, 82, 84, 85, 95, 104, 106, 107, 109, 110, 111, 112, 113, 114, 118, 121, 129, 142, 157, 159, 160, 162, 166, 168, 169, 170, 172, 173, 178, 180, 183, 190, 200, 205, 207, 211, 213, 215, 216, 217, 218, 219, 220, 224, 228, 229, 234, 236, 239, 244], "constant": [2, 23, 84, 207], "static": [2, 14, 21, 23, 28, 39, 41, 48, 49, 61, 65, 66, 68, 71, 74, 78, 81, 84, 99, 103, 116, 127, 128, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 214], "int": [2, 5, 12, 15, 17, 18, 21, 22, 24, 25, 27, 28, 33, 34, 37, 38, 41, 42, 44, 48, 51, 61, 62, 65, 67, 68, 72, 73, 74, 75, 79, 81, 82, 84, 85, 86, 88, 89, 92, 95, 98, 104, 105, 107, 118, 123, 127, 128, 134, 140, 141, 142, 158, 159, 160, 171], "verbos": 2, "argument": [2, 28, 43, 62, 65, 82, 85, 167, 168, 169, 171, 172, 173, 236], "id": [2, 26, 27, 28, 33, 49, 61, 65, 68, 85, 90, 91, 95, 115, 119, 131, 135, 136, 166, 236, 240], "show": [2, 28, 65, 78, 89, 181, 185, 187, 190, 191, 202, 207, 219, 227, 228, 234, 243], "autocomplet": 2, "It": [2, 14, 15, 18, 21, 24, 27, 28, 37, 43, 49, 62, 81, 82, 85, 95, 121, 168, 170, 171, 173, 194, 202, 204, 208, 232, 234, 235, 236], "look": [2, 5, 49, 118, 171, 175, 183, 202, 211, 234, 236], "better": [2, 4, 204, 212, 217, 234, 235, 244], "poor": 2, "peopl": [2, 204], "guess": [2, 23], "abbrevi": [2, 5], "ambigu": 2, "can": [2, 7, 13, 20, 21, 23, 25, 27, 28, 38, 48, 49, 51, 61, 62, 64, 65, 66, 67, 68, 75, 78, 81, 82, 84, 85, 90, 91, 95, 100, 103, 115, 121, 130, 132, 133, 134, 136, 144, 157, 158, 161, 166, 167, 168, 169, 170, 172, 173, 174, 175, 176, 178, 182, 183, 185, 186, 187, 188, 189, 190, 191, 193, 194, 196, 197, 198, 200, 202, 203, 204, 205, 206, 207, 210, 211, 213, 214, 216, 217, 218, 219, 220, 224, 225, 228, 229, 230, 234, 235, 236, 237, 239, 240, 242, 243], "afford": 2, "few": [2, 175, 190, 194, 232, 234, 244], "extra": [2, 62, 82, 168, 173, 182], "byte": [2, 51, 105, 141], "like": [3, 15, 24, 37, 61, 65, 78, 162, 166, 169, 171, 172, 190, 211, 212, 234, 235, 236, 240, 241, 242, 243, 244], "mani": [3, 24, 37, 161, 167, 204, 207, 219, 222, 232, 233, 234, 239, 240, 241, 242, 243, 244], "fundament": 3, "commun": [3, 4, 66, 166, 178], "aim": [3, 228], "develop": [3, 4, 204, 228, 232, 234, 235, 239, 240, 242, 243], "contributor": [3, 232, 239, 240, 241, 242, 243, 244], "alik": [3, 179], "hope": 3, "build": [3, 21, 29, 30, 95, 98, 156, 168, 170, 180, 181, 196, 209, 214, 227, 232, 234, 235, 237, 239, 240, 242, 243, 244], "top": [3, 75, 105, 118, 120, 123, 138, 141, 198, 222, 236, 242], "framework": [3, 234, 243, 244], "so": [3, 18, 21, 24, 37, 41, 51, 62, 82, 84, 95, 134, 142, 157, 158, 161, 166, 171, 173, 175, 178, 183, 190, 196, 197, 198, 207, 217, 236], "veri": [3, 4, 22, 31, 36, 161, 183, 202, 240, 242, 243], "grate": 3, "shahzad": 3, "ali": 3, "michael": 3, "banck": 3, "ross": 3, "braithwait": 3, "jame": 3, "bunt": 3, "donald": 3, "curti": 3, "naomi": 3, "fox": 3, "geoff": [3, 74], "hutchison": [3, 74, 175, 204], "beno\u00eet": 3, "jacob": 3, "jordan": 3, "mantha": 3, "thoma": [3, 239], "margraf": 3, "carsten": 3, "niehau": 3, "simon": 3, "ochsenreith": 3, "konstantin": 3, "tokarev": 3, "allison": [3, 51, 60, 100, 101], "vacanti": [3, 51, 60, 100, 101], "tim": [3, 115], "vandermeersch": [3, 115], "translat": [3, 4, 22, 41, 67, 74, 118, 159, 162, 165, 167, 169, 172, 176, 178, 182, 183, 185, 189, 190, 202, 204, 216, 222, 235, 238, 239], "support": [3, 4, 12, 24, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 74, 78, 82, 95, 102, 106, 109, 110, 111, 112, 113, 114, 115, 117, 123, 134, 142, 161, 166, 167, 168, 169, 170, 172, 173, 175, 202, 227, 228, 234, 235, 236, 239, 240, 242, 243, 244], "its": [3, 8, 14, 26, 39, 49, 51, 72, 73, 81, 95, 126, 161, 170, 171, 178, 197, 205, 224], "ha": [3, 4, 13, 14, 15, 21, 24, 26, 28, 37, 41, 51, 64, 66, 68, 75, 85, 95, 96, 100, 123, 132, 134, 171, 178, 185, 187, 188, 191, 193, 197, 198, 200, 202, 205, 207, 208, 214, 217, 219, 220, 229, 231, 234, 236, 239, 244], "come": [3, 193, 198, 214, 219, 235], "would": [3, 75, 126, 134, 190, 202, 204, 232, 234, 235, 236], "particularli": [3, 214, 232, 233, 240, 242, 243], "googl": [3, 240, 242, 243], "summer": [3, 204, 239, 240, 242, 243], "2007": 3, "2008": 3, "2011": 3, "2016": 3, "2018": 3, "2019": [3, 242], "2021": [3, 239, 240, 241], "2022": [3, 204, 242, 243], "kitwar": [3, 236], "inc": 3, "univers": [3, 204, 214, 217], "pittsburgh": [3, 204], "u": [3, 4, 7, 8, 20, 104, 126, 185, 190, 235, 239, 240, 242, 243], "depart": 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183, 185, 186, 187, 188, 190, 205, 210, 228, 233, 234, 242, 244], "pybind11": 3, "chemic": [3, 23, 28, 33, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 161, 172, 173, 194, 202, 206, 208, 210, 227, 234], "structur": [3, 21, 22, 23, 24, 26, 28, 37, 75, 170, 171, 183, 189, 190, 194, 196, 198, 200, 206, 211, 214, 217, 220, 234, 239, 240, 242], "databas": [3, 4, 23, 174, 189, 196, 208, 227], "cmake": [3, 236, 244], "eigen": [3, 5, 28, 37, 107, 118, 134, 236], "softwar": [3, 207, 228], "babel": [3, 162, 169, 202, 234, 239, 242, 243], "And": [3, 167], "cours": [3, 189], "johann": 3, "loschmidt": 3, "amedeo": 3, "made": [4, 6, 7, 23, 26, 81, 100, 178, 179, 196, 197, 198, 202, 203, 208, 210, 211, 214, 225, 239], "who": 4, "want": [4, 7, 168, 185, 189, 190, 197, 200, 202, 212, 213, 220, 222, 228, 229, 235], "back": [4, 7, 83, 159, 160, 205, 211, 239, 240, 242], "great": [4, 235, 236], "place": [4, 5, 39, 49, 72, 73, 171, 173, 178, 183, 198, 206, 207, 211, 217, 222, 224, 235, 236], "start": [4, 5, 24, 26, 92, 116, 120, 180, 181, 182, 189, 190, 205, 215, 217, 218, 221, 226, 231, 235, 240, 244], "fellow": 4, "forum": [4, 6], "question": [4, 235], "level": [4, 62, 75, 82, 173, 236], "post": [4, 213], "mai": [4, 18, 28, 39, 51, 62, 64, 67, 75, 82, 95, 96, 100, 104, 105, 117, 126, 134, 167, 168, 171, 173, 175, 176, 178, 181, 183, 185, 189, 190, 191, 194, 204, 212, 217, 227, 228, 230, 232, 236], "find": [4, 14, 22, 29, 30, 41, 51, 78, 84, 95, 99, 156, 170, 171, 180, 202, 215, 230, 234, 235, 243], "experi": 4, "valuabl": 4, "bug": [4, 6, 193, 235, 238], "pleas": [4, 6, 235, 239, 240, 242, 243], "take": [4, 22, 28, 49, 62, 69, 72, 73, 75, 82, 87, 104, 122, 123, 137, 171, 181, 194, 198, 207, 211, 217, 222, 224, 230], "moment": [4, 190, 230], "tracker": [4, 235], "issu": [4, 6, 235, 239, 244], "code": [4, 6, 24, 37, 62, 82, 84, 88, 161, 167, 169, 170, 171, 173, 183, 190, 191, 193, 207, 230, 231, 234, 235, 237, 239, 240, 242, 243, 244], "while": [4, 5, 26, 62, 82, 84, 95, 100, 168, 169, 173, 182, 187, 213, 217, 227, 243], "move": [4, 28, 104, 138, 142, 178, 185, 193, 196, 202, 217, 222, 234, 244], "around": [4, 5, 15, 22, 31, 36, 63, 65, 69, 185, 187, 190, 196, 198, 202, 213, 222, 234], "fit": [4, 5, 28, 51, 104, 123, 157, 178], "particular": [4, 23, 51, 62, 75, 82, 166, 167, 169, 173, 178, 189, 204], "compon": [4, 18, 22, 23, 26, 28, 127, 128, 132, 140, 142, 161], "itself": 4, "section": [4, 21, 62, 67, 82, 95, 173, 175, 198, 203, 204, 205, 207, 213, 217, 222, 234], "discuss": [4, 6, 168, 207, 235, 239, 240, 242, 243], "idea": [4, 235], "plan": 4, "direct": [4, 18, 41, 62, 82, 115, 118, 119, 120, 121, 124, 128, 136, 142, 159, 165, 173, 178, 193, 218, 236, 242], "progress": [4, 27, 84, 208], "etc": [4, 5, 17, 24, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 100, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 120, 133, 134, 136, 142, 157, 161, 168, 169, 170, 173, 176, 198, 202, 207, 227, 228, 231, 234, 235, 236, 239, 244], "both": [4, 15, 26, 51, 63, 64, 161, 167, 169, 172, 173, 175, 176, 187, 235], "python": [4, 92, 99, 161, 168, 171, 174, 175, 235, 236, 238, 240, 242, 243, 244], "script": [4, 63, 64, 75, 83, 92, 99, 100, 162, 172, 235, 239, 240, 241, 243, 244], "util": [4, 64, 92, 99, 118, 175, 188, 198, 207], "tell": [4, 100, 166], "friend": [4, 27, 41, 67, 79, 95, 115, 116, 120, 121, 127, 128, 129, 136, 139], "cite": 4, "paper": [4, 21, 192, 235], "write": [4, 5, 7, 15, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 78, 82, 92, 103, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 170, 173, 242, 243, 244], "edit": [4, 14, 64, 95, 161, 180, 188, 197, 198, 200, 202, 207, 209, 210, 211, 220, 222, 231, 232, 234, 236, 242, 243, 244], "tutori": [4, 180, 181, 198, 207, 234, 235], "site": [4, 234, 235], "up": [4, 24, 26, 27, 37, 49, 51, 84, 98, 104, 118, 142, 157, 161, 166, 170, 181, 185, 188, 189, 190, 193, 194, 196, 197, 202, 207, 208, 210, 211, 212, 223, 227, 229, 232, 234, 243, 244], "lesson": [4, 185], "activ": [4, 24, 70, 75, 86, 87, 88, 89, 96, 100, 103, 104, 234, 236], "teacher": 4, "send": [4, 61, 66, 92, 161, 166, 173, 239], "fragment": [4, 133, 134, 159, 165, 180, 192, 195, 203, 205, 222, 225, 234, 239, 244], "report": [4, 6, 62, 82, 173, 183, 235, 240, 241, 242, 243], "encount": [4, 6, 48, 51, 104], "about": [4, 19, 23, 39, 62, 82, 118, 173, 197, 207, 211, 213, 224, 235, 242, 243], "improv": [4, 6, 232, 234, 238, 241], "languag": [4, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 167, 168, 169, 170, 173, 210, 235, 243], "donat": 4, "pai": [4, 204], "host": [4, 242, 243, 244], "meet": 4, "bounti": 4, "when": [5, 7, 8, 13, 15, 18, 20, 24, 28, 37, 49, 51, 61, 62, 63, 64, 65, 66, 68, 69, 75, 78, 82, 88, 89, 92, 95, 100, 104, 123, 127, 128, 157, 168, 169, 170, 171, 173, 175, 187, 188, 197, 198, 202, 203, 205, 207, 211, 212, 222, 230, 236, 240, 243, 244], 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12, 17, 23, 26, 28, 51, 62, 82, 95, 166, 178, 186, 234, 240], "80": 5, "charact": [5, 19, 48, 62, 82, 168, 173], "wide": [5, 204, 207, 234], "each": [5, 13, 19, 24, 26, 27, 32, 37, 40, 48, 51, 61, 62, 63, 82, 95, 134, 142, 161, 169, 170, 173, 175, 176, 212, 236], "separ": [5, 142, 168, 173, 178, 228, 233], "g": [5, 19, 24, 28, 33, 48, 62, 74, 75, 82, 88, 89, 92, 100, 134, 138, 140, 142, 159, 160, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 190, 192, 193, 200, 212, 220, 227, 231, 234, 236, 239, 244], "nmbr": 5, "singl": [5, 17, 28, 51, 62, 64, 66, 70, 82, 84, 95, 116, 142, 173, 190, 191, 197, 203, 225, 243], "fine": [5, 62, 82, 173], "counter": [5, 62, 82, 92], "temporari": [5, 169], "obviou": 5, "wait": [5, 64, 67, 92], "until": [5, 7, 64, 65, 205, 217], "unus": [5, 15, 24, 37], "ones": 5, "incorrect": [5, 240, 243, 244], "f": [5, 24, 37, 70, 87, 107, 121, 134, 136, 138, 157, 159, 160, 169, 178, 214, 240], "lower": [5, 26, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 106, 109, 110, 111, 112, 113, 114, 142, 211], "letter": [5, 23, 191, 242], "word": 5, "acronym": 5, "cmlformat": [5, 48, 159, 162], "doubl": [5, 14, 17, 23, 24, 25, 28, 37, 38, 39, 42, 51, 89, 95, 107, 116, 157, 158, 159, 160, 190, 191, 200, 203, 220, 224, 225, 243], "cntr": 5, "std": [5, 7, 8, 9, 10, 12, 15, 19, 20, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 37, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 81, 85, 95, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 120, 121, 123, 124, 126, 130, 133, 134, 136, 139, 141, 142, 144], "string": [5, 6, 12, 15, 19, 22, 23, 24, 27, 28, 32, 33, 34, 39, 40, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 68, 69, 75, 78, 79, 80, 82, 95, 100, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 117, 123, 130, 133, 134, 139, 141, 142, 144, 159, 160, 162, 166, 168, 171, 173, 192], "rawxml": 5, "char": [5, 12, 17, 23, 24, 28, 33, 39, 42, 85, 95, 100, 105, 127, 128, 134, 139, 140, 141, 142, 147, 149, 150, 151, 152, 154, 155, 159, 160], "list_delimit": 5, "center": [5, 28, 115, 118, 125, 132, 136, 159, 165, 185, 189, 190, 191, 197, 198, 209, 225, 234, 240, 244], "listdelimit": 5, "upper": [5, 137], "m_": 5, "blank": [5, 176, 211], "togeth": [5, 95, 126, 175], "after": [5, 28, 48, 51, 62, 63, 65, 68, 82, 89, 117, 168, 169, 176, 181, 185, 186, 187, 188, 190, 194, 196, 197, 200, 205, 207, 208, 213, 220, 222, 229, 231, 239], "curli": 5, "blah": [5, 62, 82, 176], "explod": 5, "5": [5, 14, 39, 41, 62, 82, 95, 159, 160, 176, 185, 221, 236, 243, 244], "pointer": [5, 7, 23, 27, 42, 44, 65, 78, 121, 124, 126, 129, 159, 160], "refer": [5, 7, 12, 17, 42, 44, 63, 65, 66, 67, 78, 79, 85, 90, 91, 103, 104, 115, 117, 118, 120, 124, 126, 134, 136, 142, 157, 159, 160, 170, 178, 213, 216, 217, 241], "between": [5, 14, 22, 23, 26, 28, 41, 42, 43, 84, 85, 95, 166, 171, 172, 181, 182, 198, 207, 213, 217, 223, 244], "x": [5, 19, 21, 22, 27, 28, 123, 169, 172, 173, 182, 198, 205, 207, 211, 216, 218, 234, 236, 244], "mystr": 5, "y": [5, 19, 22, 28, 118, 123, 169, 173, 198, 205, 207, 211, 216, 218, 236], "whoah": 5, "surround": [5, 229], "binari": [5, 236, 243], "oper": [5, 7, 12, 13, 17, 20, 21, 27, 28, 33, 34, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 69, 71, 78, 79, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 127, 128, 131, 134, 136, 139, 140, 142, 159, 160, 162, 164, 165, 168, 170, 172, 182], "No": [5, 21, 26, 167, 178, 243], "memoryblock": 5, "malloc": 5, "data": [5, 7, 8, 15, 18, 20, 22, 23, 24, 25, 26, 27, 28, 33, 37, 38, 39, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 75, 82, 84, 85, 86, 92, 95, 98, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 132, 134, 141, 142, 146, 157, 159, 160, 163, 164, 166, 167, 171, 172, 180, 195, 206, 209, 210, 228, 234, 239], "size": [5, 7, 18, 20, 26, 27, 43, 51, 84, 115, 117, 120, 134, 136, 142, 159, 160, 165, 181, 182, 198, 211, 239, 244], "left": [5, 51, 62, 82, 105, 118, 137, 141, 142, 173, 200, 202, 203, 205, 211, 216, 217, 219, 220, 225, 236], "normal": [5, 7, 24, 27, 28, 37, 62, 75, 82, 84, 89, 115, 119, 120, 121, 124, 128, 134, 136, 159, 160, 164, 165, 173, 187, 202], "same": [5, 12, 17, 21, 26, 51, 61, 63, 127, 128, 167, 178, 197, 211, 214, 236], "foo": 5, "run": [5, 13, 27, 61, 64, 67, 68, 82, 83, 84, 103, 159, 160, 164, 167, 168, 169, 170, 172, 175, 202, 209, 231, 234, 241, 243], "implement": [5, 11, 13, 16, 21, 32, 40, 45, 46, 47, 51, 53, 54, 55, 58, 59, 60, 62, 75, 82, 84, 89, 92, 95, 105, 113, 117, 122, 134, 139, 141, 142, 161, 166, 172, 242, 243], "myfun": 5, "cout": 5, "suppli": [5, 22, 23, 24, 28, 37, 48, 49, 62, 63, 75, 78, 82, 84, 95, 96, 107, 118, 121, 124, 133, 134, 136, 157, 167, 168, 169, 178, 202], "endl": 5, "bar": [5, 207, 211, 222, 224, 230], "bodi": 5, "condit": [5, 21, 190], "also": [5, 26, 27, 39, 48, 62, 72, 73, 82, 95, 104, 115, 132, 136, 161, 167, 169, 171, 173, 174, 175, 178, 181, 185, 187, 189, 190, 191, 193, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 214, 217, 218, 220, 223, 224, 225, 228, 234, 235, 236, 243], "complex": [5, 126, 234, 244], "42": 5, "var": [5, 170], "parent": [5, 44, 61, 65, 67, 69, 70, 71, 75, 78, 81, 84, 86, 87, 88, 95, 96, 98, 100, 101, 104, 121, 126, 129, 143, 159, 160, 163, 164, 165], "doe": [5, 7, 12, 14, 21, 28, 39, 51, 85, 92, 95, 104, 118, 134, 158, 167, 168, 169, 178, 186, 207, 214, 222], "wrap": [5, 41, 95, 142, 158, 159, 165], "isvalid": [5, 12, 15, 17, 24, 25, 37, 38, 62, 82, 85, 90, 91, 104, 123, 131, 159, 160, 163, 164, 165], "agooddai": 5, "ani": [5, 7, 12, 13, 17, 22, 26, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 68, 75, 78, 79, 80, 82, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 117, 118, 124, 134, 166, 167, 168, 169, 171, 172, 173, 175, 176, 178, 194, 202, 205, 208, 211, 219, 232, 236, 244], "els": 5, "block": [5, 19, 62, 82, 168, 176], "element": [5, 7, 19, 20, 24, 26, 27, 28, 32, 40, 71, 72, 73, 74, 88, 89, 95, 122, 128, 130, 132, 134, 142, 144, 159, 160, 164, 167, 169, 170, 171, 173, 176, 178, 181, 188, 199, 200, 205, 209, 214, 220, 234, 240, 243], "cover": [5, 168, 204, 227], "b": [5, 19, 21, 26, 28, 41, 47, 53, 59, 85, 91, 95, 105, 140, 159, 160, 169, 173, 178, 191, 242, 244], "empti": [5, 7, 19, 24, 26, 28, 33, 39, 42, 43, 48, 49, 51, 75, 78, 79, 95, 117, 123, 133, 134, 159, 160, 168, 187, 239], "express": [5, 62, 82, 173, 178], "intent": 5, "clearer": 5, "label": [5, 12, 19, 28, 62, 82, 95, 107, 138, 159, 160, 164, 168, 170, 173, 176, 178, 199, 213, 234, 239, 240, 242, 244], "column": [5, 21, 41, 67, 86, 98], "everi": [5, 26, 28, 178, 227], "must": [5, 15, 24, 25, 28, 37, 51, 62, 65, 75, 78, 82, 84, 95, 105, 117, 119, 127, 128, 133, 134, 141, 142, 167, 168, 169, 171, 172, 173, 175, 178, 205, 236], "indic": [5, 19, 22, 26, 27, 28, 62, 63, 65, 67, 68, 75, 78, 81, 82, 85, 95, 103, 104, 115, 128, 134, 136, 167, 168, 169, 171, 172, 173, 175, 176, 178, 181, 185, 211, 213, 219, 241], "omiss": 5, "anoth": [5, 39, 51, 169, 183, 188, 198, 200, 203, 220, 234], "immedi": [5, 175], "myenum": 5, "drawlin": [5, 116, 159, 165], "vertex": [5, 26, 27, 84, 116, 127, 128, 133, 134, 159, 160, 165, 223], "drawdot": 5, "fall": [5, 239, 240, 242], "default": [5, 15, 19, 23, 24, 25, 27, 28, 33, 37, 48, 51, 62, 64, 75, 78, 82, 95, 96, 104, 118, 127, 128, 132, 133, 138, 142, 168, 170, 173, 176, 191, 198, 200, 202, 211, 212, 217, 220, 230, 234, 244], "drawdefault": 5, "shorter": 5, "insert": [5, 7, 28, 62, 82, 159, 160, 168, 176, 180, 181, 185, 189, 190, 191, 192, 195, 209, 222, 234, 239, 240, 242, 244], "comma": [5, 167, 169], "broken": 5, "begin": [5, 7, 43, 84, 95, 105, 130, 141, 144, 159, 160, 165, 200, 203, 219, 220, 229, 231], "verylongexpress": 5, "anotherevenlongerexpress": 5, "justwhenyouthoughtitcouldntgetlong": 5, "vector3d": [5, 107], "posit": [5, 7, 12, 14, 21, 22, 25, 28, 38, 81, 84, 95, 115, 118, 119, 125, 132, 134, 135, 136, 138, 159, 160, 165, 185, 189, 190, 205, 211, 222, 234], "currentposit": 5, "offset": [5, 84, 134, 159, 164], "reimplement": [5, 64, 104], "put": [5, 234, 244], "discourag": 5, "prefix": [5, 12, 17, 62, 78, 82, 172, 175, 176, 236], "clear": [5, 7, 13, 26, 27, 42, 43, 48, 62, 82, 84, 86, 89, 98, 104, 115, 116, 120, 121, 125, 126, 127, 128, 132, 136, 139, 157, 159, 160, 162, 164, 165, 182, 203, 209, 225, 239], "cpp": [5, 84], "extens": [5, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 76, 78, 82, 106, 109, 110, 111, 112, 113, 114, 161, 166, 167, 168, 169, 172, 173, 180, 182, 198, 200, 209, 210, 213, 217, 220, 228, 229, 234, 235, 239, 242, 243, 244], "As": [5, 6, 166, 168, 189, 198, 209, 216, 223, 227, 236, 239, 242], "feel": [5, 235], "free": [5, 51, 104, 168, 173, 178, 204, 235, 236], "bad": 5, "local": [6, 62, 74, 82, 84, 168, 173, 175, 176, 235, 239, 242, 244], "avail": [6, 25, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 66, 67, 68, 75, 82, 84, 100, 104, 106, 109, 110, 111, 112, 113, 114, 133, 158, 167, 168, 169, 170, 172, 173, 176, 178, 179, 234, 235, 243], "weblat": [6, 239, 240, 241, 242, 243, 244], "autom": [6, 49, 175, 234, 242, 243], "task": [6, 214, 234], "phrase": 6, "whenev": 6, "allow": [6, 7, 27, 31, 36, 42, 62, 78, 82, 161, 162, 167, 169, 172, 173, 178, 181, 182, 185, 187, 188, 189, 190, 192, 193, 198, 200, 202, 203, 205, 207, 208, 210, 211, 213, 217, 218, 219, 222, 223, 224, 225, 228, 230, 231, 234, 239, 243, 244], "time": [6, 51, 62, 82, 92, 95, 104, 117, 126, 161, 178, 181, 186, 190, 244], "freez": [6, 28], "least": [6, 75, 95, 212, 223, 229, 234, 243], "week": 6, "advanc": [6, 62, 82, 173, 235, 236], "releas": [6, 51, 117, 134, 142, 159, 165, 175, 204, 232, 236, 237, 238], "typenam": [7, 8, 9, 13, 20, 42, 44, 90, 91, 129, 147], "copi": [7, 12, 17, 22, 27, 28, 42, 49, 78, 85, 105, 141, 185, 192, 209, 239, 242, 244], "semant": 7, "effect": [7, 118, 178], "share": [7, 12, 17, 26, 36, 175, 178, 179, 234, 236], "without": [7, 26, 49, 51, 65, 68, 161, 178, 202, 204, 207, 208, 232, 236, 240], "expos": 7, "access": [7, 18, 51, 64, 66, 67, 83, 103, 117, 134, 142, 169, 178, 193, 198, 208, 243], "amount": [7, 185, 207], "non": [7, 8, 23, 28, 62, 82, 95, 126, 169, 171, 173, 178, 239, 240, 243, 244], "trigger": [7, 104, 171], "detach": [7, 134, 159, 160, 209, 242], "op": 7, "count": [7, 12, 28], "1": [7, 12, 15, 17, 18, 19, 21, 22, 24, 26, 28, 51, 62, 65, 68, 82, 85, 95, 105, 118, 132, 134, 141, 142, 159, 160, 167, 169, 171, 173, 175, 176, 182, 183, 185, 187, 190, 191, 193, 200, 204, 209, 212, 221, 223, 232, 234, 236, 237, 238, 239, 244], "perform": [7, 13, 15, 21, 42, 51, 63, 84, 95, 104, 134, 168, 170, 171, 178, 182, 188, 202, 207, 212, 234, 236, 238], "deep": [7, 229, 236], "greater": 7, "unnam": [7, 12, 17, 19, 28, 41, 61, 63, 64, 65, 66, 68, 69, 78, 85, 92, 95, 100, 104, 105, 116, 121, 122, 123, 127, 128, 134, 137, 138, 139, 140, 142, 157], "typedef": [7, 11, 12, 13, 16, 17, 21, 28, 33, 43, 44, 48, 61, 78, 85, 90, 91, 95, 140], "value_typ": [7, 44, 117, 134, 142, 159, 160], "compat": [7, 78, 178, 207], "allocator_typ": [7, 44, 159, 160], "const_refer": [7, 44, 159, 160], "const_point": [7, 44, 159, 160], "iter": [7, 13, 43, 44, 159, 160], "const_iter": [7, 43, 44, 159, 160], "reverse_iter": [7, 44, 159, 160], "const_reverse_iter": [7, 44, 159, 160], "difference_typ": [7, 44, 159, 160], "size_typ": [7, 44, 142, 159, 160], "intern": [7, 13, 39, 51, 61, 63, 65, 66, 78, 89, 139, 142, 159, 160, 167, 169, 172, 235], "arrayrefcontain": [7, 159, 160], "valuetyp": [7, 8, 9, 10, 13, 44, 159, 160], "inlin": [7, 8, 9, 10, 11, 15, 16, 18, 19, 20, 22, 24, 25, 27, 28, 33, 34, 37, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 68, 69, 70, 75, 77, 79, 80, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 97, 100, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139, 140, 142, 144, 145, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 158], "explicit": [7, 13, 25, 26, 32, 35, 38, 40, 41, 44, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 75, 77, 79, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 104, 122, 126, 127, 128, 133, 143], "size_t": [7, 12, 26, 28, 35, 43, 44, 51, 81, 95, 115, 116, 120, 124, 126, 127, 128, 134, 136, 140], "n": [7, 15, 19, 24, 26, 27, 37, 44, 126, 128, 173, 189, 190, 214], "valu": [7, 8, 9, 15, 18, 19, 21, 22, 24, 25, 27, 28, 33, 37, 38, 42, 43, 44, 48, 49, 51, 61, 65, 67, 77, 78, 81, 84, 85, 86, 92, 96, 98, 104, 117, 118, 121, 126, 128, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 159, 160, 167, 169, 170, 172, 173, 175, 207], "inputiter": [7, 44], "last": [7, 22, 44, 62, 68, 82, 92, 206, 240], "note": [7, 24, 28, 62, 82, 118, 128, 134, 142, 166, 169, 173, 175, 176, 183, 185, 186, 187, 190, 198, 202, 204, 236, 238], "detachwithcopi": [7, 159, 160], "explicitli": [7, 166], "implicitli": 7, "ensur": [7, 21, 28, 62, 66, 82, 85, 95, 123, 132, 173, 207, 236, 239, 244], "retriev": [7, 15, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 82, 106, 109, 110, 111, 112, 113, 114], "underli": [7, 18, 64, 83, 90, 91], "constdata": [7, 159, 160], "max_siz": [7, 159, 160], "capac": [7, 159, 160], "reserv": [7, 13, 27, 159, 160, 178], "sz": 7, "resiz": [7, 20, 51, 89, 104, 123, 159, 160, 165], "rbegin": [7, 159, 160], "rend": [7, 159, 160], "front": [7, 159, 160], "assign": [7, 26, 27, 28, 32, 40, 85, 95, 159, 160, 167, 234, 242, 243], "val": 7, "push_back": [7, 159, 160], "v": [7, 39, 41, 42, 43, 127, 128, 134, 176, 178, 193, 236, 244], "pop_back": [7, 159, 160], "eras": [7, 159, 160], "idx": [7, 67, 79], "othert": 7, "swap": [7, 26, 41, 79, 115, 116, 120, 121, 127, 128, 136, 139, 140, 159, 160, 164, 165], "swapandpop": [7, 159, 160], "index": [7, 11, 12, 13, 16, 17, 19, 20, 22, 24, 26, 28, 33, 37, 62, 67, 79, 82, 85, 86, 90, 91, 93, 94, 95, 98, 115, 117, 120, 124, 126, 127, 128, 131, 133, 134, 136, 142, 159, 160, 163, 164, 165, 171, 173, 176, 190, 244], "delet": [7, 49, 51, 69, 95, 104, 124, 126, 133, 157, 168, 182, 200, 205, 211, 220, 240, 242, 244], "valid": [7, 15, 24, 25, 27, 37, 38, 48, 62, 68, 82, 85, 90, 91, 95, 104, 123, 128, 129, 133, 159, 160, 172, 173, 176, 236, 244], "pop": [7, 170, 188, 194, 196, 197, 207, 208, 210, 211, 229], "preserv": [7, 21, 26, 51, 95, 187], "protect": [7, 8, 13, 15, 18, 22, 28, 32, 33, 40, 48, 67, 79, 84, 88, 89, 92, 95, 96, 104, 121, 124, 126, 129, 133, 134, 139, 158, 178], "attribut": [7, 8, 13, 15, 18, 22, 28, 33, 61, 62, 68, 82, 84, 92, 95, 96, 116, 117, 121, 124, 126, 127, 128, 129, 133, 134, 139, 158, 173, 175, 179], "arrai": [8, 13, 18, 20, 21, 22, 26, 27, 28, 39, 51, 62, 82, 84, 85, 95, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 159, 160, 167, 169, 172, 173, 176], "store": [8, 18, 20, 23, 24, 25, 28, 37, 38, 39, 42, 51, 62, 63, 64, 79, 80, 82, 95, 115, 116, 117, 118, 121, 127, 136, 142, 208, 244], "figur": [8, 73, 213], "subclass": [8, 10, 15, 28, 45, 48, 66, 121, 126, 127, 128, 129, 131, 139, 141, 145], "coordinateset": [8, 159, 160], "istyp": [8, 159, 160], "match": [8, 23, 28, 39, 49, 62, 65, 67, 68, 78, 79, 80, 82, 117, 168, 173, 230, 236], "placehold": [8, 9, 63, 159, 160], "m_content": [8, 9, 159, 160], "m_data": [8, 18, 22, 28, 159, 160], "holder": [8, 10, 159, 160, 178], "type_info": [8, 9, 10], "clone": [8, 9, 10, 15, 24, 37, 159, 160], "atomtempl": [11, 93, 159, 160], "repres": [11, 12, 16, 17, 18, 21, 23, 26, 28, 33, 39, 42, 49, 63, 64, 66, 67, 83, 95, 121, 131, 161, 171, 198, 232, 234], "moleculeclass": [11, 16], "atomtyp": [11, 17, 28, 32, 40, 85, 90, 95, 159, 160, 164], "m": [11, 12, 16, 17, 24, 35, 37, 41, 64, 77, 90, 91, 93, 94, 95, 178, 187, 190], "molecule_t": [12, 17, 90, 91], "setatomicnumb": [12, 28, 95, 159, 160, 164], "unsign": [12, 14, 15, 17, 21, 22, 23, 24, 27, 28, 37, 39, 42, 44, 61, 65, 68, 84, 85, 95, 100, 105, 107, 127, 128, 134, 139, 140, 141, 142, 159, 160], "num": [12, 24, 28, 95, 171], "proton": [12, 72, 229], "atom": [12, 13, 15, 17, 19, 21, 23, 24, 28, 32, 33, 37, 39, 40, 62, 74, 81, 82, 85, 90, 95, 96, 107, 131, 138, 159, 160, 161, 164, 165, 169, 170, 171, 173, 180, 181, 182, 183, 185, 188, 197, 199, 200, 203, 205, 209, 210, 211, 212, 213, 216, 217, 218, 219, 220, 222, 223, 224, 225, 226, 227, 229, 231, 232, 234, 239, 240, 242, 243, 244], "atomicnumb": [12, 23, 28, 85, 95, 159, 160, 164], "setposition2d": [12, 159, 160], "vector2": [12, 28, 95], "po": [12, 22, 28, 84, 95, 119, 135], "2d": [12, 28, 211, 239], "Not": 12, "current": [12, 13, 17, 26, 27, 28, 48, 51, 55, 61, 63, 64, 65, 68, 74, 75, 84, 87, 89, 95, 100, 103, 105, 115, 116, 118, 120, 121, 122, 123, 127, 128, 129, 132, 133, 134, 136, 139, 141, 166, 168, 185, 198, 208, 210, 211, 212, 222, 234, 235], "moleculetyp": [12, 17, 90, 91, 159, 160, 164], "compil": [12, 133, 134, 159, 165, 236], "position2d": [12, 159, 160], "setposition3d": [12, 159, 160], "vector3": [12, 21, 22, 25, 28, 38, 39, 41, 81, 85, 95], "3d": [12, 22, 28, 95, 104, 118, 127, 128, 134, 161, 169, 171, 192, 202, 211, 234, 243], "position3d": [12, 28, 85, 95, 159, 160], "sethybrid": [12, 28, 95, 159, 160, 164], "atomhybrid": [12, 28, 95], "hyb": [12, 28, 95], "hybrid": [12, 28, 95, 159, 160, 164], "coordin": [12, 19, 20, 21, 24, 28, 39, 41, 62, 82, 95, 107, 116, 118, 123, 134, 137, 138, 142, 159, 160, 162, 182, 183, 186, 187, 205, 239, 240, 244], "setformalcharg": [12, 28, 95, 159, 160, 164], "sign": [12, 28, 95, 134, 236, 242], "charg": [12, 28, 62, 82, 95, 173, 174, 175, 207, 214, 229, 234, 240, 242, 243, 244], "formal": [12, 28, 95, 242, 244], "formalcharg": [12, 28, 95, 159, 160, 164], "setcolor": [12, 27, 28, 33, 95, 127, 128, 131, 159, 160, 164, 165], "vector3ub": [12, 28, 33, 95, 115, 119, 120, 127, 128, 130, 131, 134, 135, 136, 140, 144], "color": [12, 18, 23, 27, 28, 33, 62, 82, 95, 115, 120, 127, 128, 131, 132, 136, 140, 142, 157, 159, 160, 164, 165, 173, 174, 176, 180, 185, 198, 199, 207, 209, 229, 234, 239, 240, 242, 243, 244], "setlay": [12, 28, 95, 159, 160, 164], "layer": [12, 28, 85, 95, 159, 160, 164, 240, 241, 242, 243, 244], "invalid": [12, 17, 28, 39, 48, 68, 85, 90, 91, 95, 131, 159, 165, 240], "object": [12, 13, 17, 18, 24, 27, 28, 42, 43, 49, 51, 61, 62, 63, 64, 67, 68, 72, 75, 78, 82, 83, 84, 85, 90, 91, 95, 100, 103, 104, 105, 107, 115, 116, 117, 118, 120, 121, 123, 124, 127, 128, 131, 134, 136, 141, 145, 158, 164, 167, 168, 169, 172, 173, 197, 213, 239], "increment": [12, 17], "self": [12, 17, 243], "check": [12, 15, 17, 21, 25, 27, 28, 38, 39, 48, 62, 68, 75, 82, 85, 92, 95, 104, 123, 126, 170, 171, 175, 176, 200, 211, 213, 217, 219, 220, 224, 239, 243, 244], "postfix": [12, 17], "decrement": [12, 17], "setselect": [12, 159, 160], "select": [12, 28, 65, 68, 78, 85, 89, 95, 159, 160, 164, 176, 180, 181, 182, 185, 188, 189, 190, 191, 192, 193, 194, 196, 198, 199, 200, 201, 202, 205, 208, 209, 211, 213, 214, 216, 218, 219, 220, 221, 222, 223, 227, 229, 230, 231, 239, 240, 241, 242, 243, 244], "setforcevector": [12, 28, 95, 159, 160, 164], "forc": [12, 28, 85, 95, 139, 161, 174, 175, 190, 199, 209, 213, 214, 215, 231, 236, 244], "forcevector": [12, 28, 95, 159, 160, 164], "setlabel": [12, 28, 95, 159, 160, 164], "outputtyp": 13, "interfac": [13, 14, 23, 39, 61, 62, 64, 75, 82, 83, 84, 92, 96, 100, 141, 161, 168, 170, 171, 173, 180, 202, 204, 207, 217, 243, 244], "list": [13, 21, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 66, 67, 68, 75, 78, 79, 102, 104, 106, 109, 110, 111, 112, 113, 114, 124, 126, 167, 168, 169, 170, 171, 173, 175, 178, 207, 208, 236, 239, 243], "identifi": [13, 15, 23, 28, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 68, 82, 85, 90, 91, 101, 106, 109, 110, 111, 112, 113, 114, 115, 119, 120, 121, 123, 124, 131, 134, 135, 136, 142, 159, 162, 164, 165, 173], "mol": [13, 14, 19, 21, 22, 25, 32, 33, 38, 39, 40, 56, 58, 61, 62, 63, 64, 69, 71, 75, 82, 95, 100, 167, 168, 169, 171, 207], "nullptr": [13, 25, 28, 32, 35, 38, 40, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 75, 77, 78, 79, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 121, 122, 124, 126, 129, 143, 157, 240], "setmolecul": [13, 15, 19, 35, 63, 64, 69, 75, 100, 104, 157, 159, 160, 163, 164, 177], "obtain": [13, 28, 31, 36, 67, 81, 85, 90, 91, 95, 128, 171], "lookup": [13, 49, 243], "been": [13, 28, 49, 51, 66, 68, 75, 95, 96, 132, 134, 171, 178, 185, 188, 197, 198, 200, 207, 208, 211, 214, 217, 220, 223, 229, 230, 231, 234, 236], "previous": [13, 207, 208, 211, 223], "cach": [13, 51, 62, 66, 82, 92, 175, 243, 244], "There": [13, 62, 81, 82, 173, 191, 192, 193, 203, 211, 225, 235, 236], "correspond": [13, 15, 24, 28, 61, 62, 82, 95, 173, 175, 176, 178, 182, 217], "reset": [13, 48, 51, 62, 82, 90, 91, 92, 96, 104, 118, 123, 157, 159, 160, 163, 164, 185, 209, 218, 222, 223, 224, 239, 240], "typer": 13, "state": [13, 48, 51, 61, 62, 65, 68, 82, 90, 91, 95, 96, 125, 158, 176, 178, 240], "m_type": [13, 133, 159, 160, 165], "initi": [13, 23, 24, 26, 37, 62, 65, 68, 78, 82, 84, 85, 95, 104, 123, 159, 160, 164, 165, 175, 176, 200, 202, 205, 220, 224, 227, 228, 239, 241, 242, 243, 244], "setup": [13, 61, 169, 209, 242], "prior": [13, 61, 178], "enough": [13, 51], "room": 13, "determin": [13, 32, 40, 49, 51, 61, 62, 82, 117, 125, 175, 187, 188, 190, 207, 219, 223, 228, 229, 244], "m_molecul": [13, 15, 95, 159, 160, 164], "popul": [13, 15, 21, 25, 51, 95], "spglib": [14, 39, 95, 183, 239], "short": [14, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 92, 95, 106, 109, 110, 111, 112, 113, 114, 142, 159, 160], "gethallnumb": [14, 159, 160], "carttol": [14, 39, 95], "1e": [14, 39, 95], "hall": [14, 39, 95], "crystal": [14, 39, 41, 180, 184, 188, 198, 205, 207, 209, 234, 240, 244], "unit": [14, 19, 21, 23, 28, 39, 41, 62, 82, 95, 173, 176, 180, 181, 184, 187, 188, 190, 193, 209, 211, 240, 244], "cell": [14, 19, 21, 28, 39, 41, 95, 173, 180, 181, 184, 185, 188, 190, 193, 209, 211, 240, 244], "exist": [14, 22, 26, 28, 43, 51, 65, 67, 85, 95, 102, 126, 134, 168, 172, 173, 217, 232, 240], "algorithm": [14, 21, 84, 95, 186, 207, 212], "fail": [14, 42, 51, 62, 65, 66, 82, 95, 127, 128, 169, 173, 178], "succe": 14, "handl": [14, 21, 48, 49, 63, 68, 75, 78, 88, 89, 92, 100, 104, 117, 133, 142, 159, 162, 163, 164, 165, 167, 168, 169, 172, 234, 239, 244], "cartesian": [14, 19, 21, 24, 37, 39, 41, 95, 169, 173, 182, 183, 186, 187, 198, 209], "toler": [14, 28, 39, 95, 183, 186, 243], "reducetoprimit": [14, 159, 160], "reduc": [14, 21, 39, 95, 178, 180, 184], "primit": [14, 24, 37, 95, 96, 115, 119, 120, 121, 123, 124, 132, 135, 136, 159, 165, 180, 184], "unless": [14, 18, 178], "miss": [14, 232, 240, 243], "conventionalizecel": [14, 95, 159, 160, 164], "refin": [14, 214], "convention": [14, 95], "symmetr": [14, 95, 159, 160, 187, 234], "basi": [15, 24, 25, 28, 37, 38, 62, 82, 107, 108, 173, 178, 207, 244], "gaussianset": [15, 25, 37, 38, 108, 159, 160], "slaterset": [15, 159, 160], "capabl": [15, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95, 106, 109, 110, 111, 112, 113, 114, 115, 136, 172, 173, 205, 208, 214], "calcul": [15, 24, 25, 27, 28, 37, 38, 62, 63, 64, 68, 82, 84, 105, 118, 141, 163, 173, 181, 182, 183, 185, 188, 190, 209, 214, 223, 228, 229, 231, 234, 243], "electrontyp": [15, 24, 25, 37, 159, 160], "electron": [15, 23, 24, 25, 28, 38, 207, 228, 229, 243], "pair": [15, 24, 25, 26, 27, 28, 34, 37, 62, 82, 85, 95, 116, 159, 160, 173, 175, 176, 207, 228, 234, 243], "alpha": [15, 24, 25, 41, 140, 142, 159, 160, 165, 169, 239, 243], "beta": [15, 24, 25, 41, 159, 160, 169, 232], "cannot": [15, 21, 29, 30, 49, 51, 68, 156, 178, 234], "enumer": [15, 19, 21, 22, 24, 33, 37, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 96, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 171], "destructor": [15, 24, 27, 37, 51, 84], "setelectroncount": [15, 159, 160], "electroncount": [15, 159, 160], "molecule_": 15, "get": [15, 22, 24, 28, 39, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 84, 85, 87, 90, 91, 95, 102, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 157, 158, 161, 167, 169, 171, 180, 235, 236, 239], "belong": [15, 67, 85, 90, 91], "setnam": [15, 22, 27, 159, 160], "settheorynam": [15, 159, 160], "theorynam": [15, 159, 160], "molecularorbitalcount": [15, 24, 37, 159, 160], "molecular": [15, 24, 25, 28, 37, 38, 62, 82, 104, 161, 166, 167, 168, 169, 170, 171, 173, 180, 192, 194, 195, 198, 202, 209, 211, 213, 215, 217, 226, 228, 232, 234, 235, 243, 244], "orbit": [15, 24, 25, 37, 38, 107, 159, 160, 161, 180, 198, 209, 226, 234, 240], "homo": [15, 159, 160], "given": [15, 22, 23, 24, 26, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 67, 78, 83, 85, 95, 104, 106, 109, 110, 111, 112, 113, 114, 167, 170], "mo": [15, 22, 24, 25, 37, 159, 160, 244], "lumo": [15, 159, 160], "m_electron": [15, 159, 160], "total": [15, 28, 61, 244], "close": [15, 48, 51, 64, 70, 159, 162, 178, 209, 213, 229, 230, 240, 242, 243], "shell": [15, 24, 37, 107, 159, 162], "doubli": 15, "occupi": [15, 51], "hold": [15, 84, 107, 171, 192, 196, 202, 203, 217], "possibli": 15, "bond": [15, 17, 28, 33, 62, 81, 82, 85, 91, 95, 131, 159, 160, 161, 164, 165, 171, 173, 180, 182, 188, 190, 199, 200, 203, 205, 207, 211, 212, 214, 217, 220, 221, 222, 223, 225, 228, 241, 242, 243, 244], "read": [15, 28, 36, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 75, 78, 82, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 171, 173, 175, 178, 195, 205, 228, 239, 240, 241, 242, 244], "output": [15, 19, 21, 24, 29, 30, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 68, 82, 92, 106, 107, 109, 110, 111, 112, 113, 114, 156, 162, 163, 167, 168, 169, 172, 173, 206, 213, 214, 228, 230, 231, 243, 244], "necessarili": 15, "m_name": [15, 22, 159, 160], "usual": [15, 171, 236], "standard": [15, 62, 70, 82, 90, 91, 92, 95, 117, 134, 158, 166, 167, 168, 169, 171, 172, 173, 178, 198, 208, 240, 244], "m_theorynam": [15, 159, 160], "theori": [15, 62, 82, 173, 178, 199, 209, 244], "bondtempl": [16, 94, 159, 160], "bondtyp": [16, 28, 85, 91, 95, 159, 160, 164], "atom1": [17, 28, 85, 95, 159, 160], "atom2": [17, 28, 85, 95, 159, 160], "setord": [17, 159, 160], "o": [17, 92, 118, 126, 136, 158, 167, 200, 206, 214, 220, 236], "getotheratom": [17, 159, 160], "represent": [18, 21, 41, 62, 82, 134, 172, 173, 178, 198, 206], "rgb": [18, 62, 82, 140, 173], "three": [18, 23, 24, 37, 127, 128, 142, 198, 203, 205, 223, 225], "float": [18, 22, 27, 42, 84, 115, 118, 119, 120, 121, 123, 124, 125, 127, 130, 132, 134, 135, 136, 138, 139, 140, 142, 144, 159, 160, 167, 169, 171, 243], "rang": [18, 21, 62, 82, 124, 126, 128, 134, 140, 142, 167, 169, 173, 176, 207, 234, 243], "intens": [18, 28, 243], "red": [18, 140, 142, 159, 160, 165, 198, 216, 229, 234], "green": [18, 140, 142, 159, 160, 165, 198, 216], "memori": [18, 24, 51, 95, 134, 242], "3": [18, 27, 62, 82, 84, 127, 128, 134, 140, 142, 159, 160, 167, 169, 176, 182, 186, 190, 200, 209, 212, 213, 221, 236, 239], "pass": [18, 22, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 68, 75, 82, 83, 84, 92, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 122, 134, 166, 168, 173, 240, 243], "directli": [18, 49, 67, 167, 178, 189, 191, 195, 228], "opengl": [18, 123, 132, 161, 236, 242, 243, 244], "conveni": [18, 28, 43, 48, 49, 51, 66, 67, 85, 161, 205, 210, 244], "written": [18, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 82, 84, 106, 109, 110, 111, 112, 113, 114, 168, 173, 176, 178, 229], "emphasi": 18, "effici": [18, 210, 240], "layout": [18, 65, 87], "black": [18, 132, 200, 203, 220, 224, 225], "integ": [18, 22, 27, 142, 173], "255": [18, 62, 82, 134, 140, 173], "expect": [18, 23, 24, 27, 62, 82, 84, 103, 168, 169, 173, 178, 236, 244], "align": [19, 21, 132, 140, 173, 180, 181, 182, 185, 190, 191, 209, 221, 244], "see": [19, 28, 51, 62, 64, 78, 82, 85, 95, 105, 134, 142, 161, 168, 172, 173, 183, 186, 187, 190, 191, 207, 228], "setspecif": [19, 159, 160], "detail": [19, 21, 48, 51, 61, 62, 64, 65, 72, 82, 161, 167, 168, 169, 170, 172, 173, 207], "distanceunit": [19, 159, 160], "distanc": [19, 39, 41, 118, 138, 159, 160, 165, 181, 182, 207, 213, 223, 243, 244], "angstrom": [19, 21, 41, 159, 160, 190, 205, 213], "bohr": [19, 159, 160, 190, 205], "setdistanceunit": [19, 159, 160], "spec": 19, "inform": [19, 24, 28, 39, 62, 82, 95, 104, 123, 134, 168, 173, 175, 178, 187, 197, 198, 203, 205, 207, 209, 210, 213, 214, 217, 222, 235, 242], "z": [19, 22, 28, 169, 173, 181, 185, 190, 191, 198, 205, 207, 211, 216, 218, 239], "6": [19, 21, 27, 62, 74, 82, 84, 123, 158, 159, 160, 167, 169, 171, 173, 190, 213, 221, 236, 244], "carbon": [19, 23, 28, 74, 170, 171, 173, 175, 180, 185, 201, 205, 219, 220, 224], "l": [19, 119, 178, 236], "c1": [19, 244], "gamess": [19, 107, 173, 207, 243, 244], "lattic": [19, 21, 41, 95, 173, 186, 187], "requir": [19, 24, 49, 62, 65, 82, 123, 142, 158, 167, 168, 171, 172, 173, 175, 178, 230, 232], "A": [19, 21, 24, 26, 28, 31, 36, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 70, 75, 78, 79, 81, 82, 85, 86, 87, 90, 91, 92, 95, 96, 98, 99, 100, 102, 104, 106, 109, 110, 111, 112, 113, 114, 115, 122, 124, 126, 132, 133, 134, 136, 142, 161, 168, 173, 176, 178, 179, 182, 188, 189, 191, 193, 194, 196, 200, 203, 205, 207, 211, 212, 219, 220, 224, 229, 230, 234, 236], "liter": [19, 62, 82, 173], "optim": [19, 28, 62, 82, 169, 173, 176, 180, 182, 190, 200, 209, 214, 220, 234, 242, 243, 244], "flag": [19, 21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 78, 82, 86, 98, 106, 109, 110, 111, 112, 113, 114, 140, 159, 163, 164, 168, 170, 173], "_": [19, 173], "__szxyz110": [19, 173], "replac": [19, 28, 79, 95, 168, 170, 171, 173, 178, 205, 236, 240], "text": [19, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 79, 80, 95, 105, 106, 109, 110, 111, 112, 113, 114, 122, 123, 130, 137, 138, 139, 140, 141, 144, 159, 165, 167, 169, 170, 172, 173, 178, 182, 192, 193, 205, 206, 244], "126214": [19, 173], "765886": [19, 173], "000000": [19, 173], "819345": [19, 173], "564955": [19, 173], "598383": [19, 173], "795127": [19, 173], "310706": [19, 173], "370165": [19, 173], "16": [19, 84, 173, 240], "285330": [19, 173], "757144": [19, 173], "130424": [19, 173], "185837": [19, 173], "548377": [19, 173], "375303": [19, 173], "033768": [19, 173], "794407": [19, 173], "396173": [19, 173], "450760": [19, 173], "generatecoordinateblock": [19, 159, 160], "arrayset": [20, 159, 160], "concret": 20, "_size": 20, "_index": 20, "collect": [21, 61, 62, 64, 65, 82, 104, 115, 120, 121, 124, 132, 136, 161, 171, 173, 178], "common": [21, 48, 62, 82, 121, 124, 126, 129, 145, 167, 168, 173, 179, 196, 207, 214, 234], "crystallograph": [21, 183], "option": [21, 48, 49, 51, 61, 63, 64, 65, 68, 72, 73, 75, 83, 92, 95, 100, 115, 134, 136, 140, 142, 159, 160, 162, 163, 164, 166, 167, 169, 170, 171, 172, 176, 182, 185, 190, 207, 209, 215, 216, 217, 229, 234, 240], "bitwis": [21, 49, 65, 140], "variou": [21, 24, 37, 62, 82, 168, 173, 197, 198, 207, 208, 210, 229, 231, 234, 235, 236, 242], "none": [21, 22, 24, 28, 39, 48, 49, 61, 78, 102, 126, 133, 134, 159, 160, 162, 163, 165, 209, 242], "transformatom": [21, 95, 159, 160], "transform": [21, 39, 95, 118, 143, 178], "along": [21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 72, 73, 95, 106, 109, 110, 111, 112, 113, 114, 161, 167, 169, 172, 185, 190, 202], "wrapatomstounitcel": [21, 159, 160], "adjust": [21, 41, 81, 95, 159, 164, 187, 197, 198, 200, 205, 207, 211, 213, 217, 218, 220, 221, 222, 230, 231, 239, 244], "fraction": [21, 39, 41, 95, 187, 205], "success": [21, 24, 25, 27, 28, 31, 36, 37, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 68, 69, 82, 85, 95, 106, 109, 110, 111, 112, 113, 114, 134, 159, 164, 169], "rotatetostandardorient": [21, 159, 160], "opt": [21, 61, 95, 142, 170, 171], "rotat": [21, 95, 118, 140, 159, 165, 180, 181, 185, 189, 202, 212, 216, 219, 222, 224, 234, 239, 244], "axi": [21, 28, 118, 120, 132, 181, 182, 185, 190, 211, 216], "xy": [21, 37, 159, 160, 181, 185, 190], "plane": [21, 28, 118, 137, 181, 185, 190, 211, 214, 219], "trig": 21, "sinc": [21, 51, 167, 169, 171, 175, 176, 183, 186, 189, 193, 227, 234], "fragil": 21, "neg": [21, 81, 234], "angl": [21, 41, 118, 200, 207, 211, 213, 220, 221, 223, 242, 243, 244], "found": [21, 28, 39, 43, 49, 62, 67, 78, 79, 80, 82, 84, 85, 124, 126, 161, 170, 173, 198, 203, 205, 206, 207, 210, 225, 227, 230, 235, 236, 239, 240, 241, 242, 243], "http": [21, 51, 84, 172, 175, 178, 190, 193, 194, 207, 236, 239, 240, 242, 243], "xtalopt": [21, 166], "openmolecul": 21, "net": [21, 198], "misc": 21, "rotatetostdorient": 21, "pdf": 21, "setvolum": [21, 159, 160], "real": [21, 41, 42, 169, 244], "newvolum": [21, 95], "isotrop": 21, "scale": [21, 95, 118, 159, 165, 180, 184, 218, 224, 243], "volum": [21, 41, 95, 157, 159, 160, 180, 184, 186], "cubic": [21, 41], "failur": [21, 24, 25, 28, 31, 36, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 95, 106, 109, 110, 111, 112, 113, 114, 134, 178, 241], "nigglireduc": [21, 159, 160], "niggli": [21, 95, 186], "reduct": [21, 95, 186], "produc": [21, 64, 122, 172, 178, 190], "canon": 21, "strive": 21, "gross": 21, "kunstlev": 21, "rw": 21, "sauter": 21, "nk": 21, "adam": 21, "pd": 21, "numer": [21, 62, 82, 115, 134, 136, 167, 168, 169, 173, 239], "stabl": [21, 27, 159, 160], "comput": [21, 118, 167, 202, 204, 207, 211, 217, 234, 235], "acta": 21, "crystallographica": 21, "foundat": 21, "crystallographi": [21, 181, 188, 193], "2003": 21, "60": 21, "modifi": [21, 27, 28, 49, 64, 81, 85, 95, 104, 118, 157, 159, 164, 168, 170, 171, 178, 188, 202, 209, 227, 234, 235], "extend": [21, 161, 174, 235, 239], "isnigglireduc": [21, 159, 160], "alreadi": [21, 39, 66, 85, 95, 107, 172, 188, 200, 220, 244], "gruber": 21, "cryst": 21, "1973": 21, "29": 21, "4": [21, 84, 105, 128, 140, 141, 159, 160, 166, 169, 179, 181, 186, 190, 212, 217, 221, 234], "433": 21, "440": [21, 239], "buildsupercel": [21, 95, 159, 160, 164], "supercel": [21, 95, 180, 181, 184, 186], "expand": [21, 65, 68, 187, 188, 211], "upon": [21, 95, 126, 178], "zero": [21, 23, 28, 62, 79, 82, 95, 118, 169, 173, 176, 218, 244], "setcellmatrix": [21, 41, 159, 160], "matrix3": [21, 41, 95], "newcellcolmatrix": 21, "ignor": [21, 28, 62, 82, 95, 96, 104, 142, 159, 164, 173, 175, 209, 213, 236, 243], "fractionalcoordin": [21, 159, 160], "unitcel": [21, 28, 85, 159, 160, 164, 169], "cart": [21, 41], "frac": [21, 41], "coord": [21, 28, 62, 82, 169, 171, 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"referencing-members"]], "File Naming": [[5, "file-naming"]], "Breaking Rules": [[5, "breaking-rules"]], "Class Avogadro::Core::Cube": [[22, "class-avogadro-core-cube"]], "Class Avogadro::Core::AtomTemplate": [[12, "class-avogadro-core-atomtemplate"]], "Contributing Code": [[0, "contributing-code"], [0, null]], "Thanks": [[3, "thanks"], [204, "thanks"]], "Code": [[3, "code"]], "Funding": [[3, "funding"]], "Other Projects": [[3, "other-projects"]], "Class Avogadro::Core::CrystalTools": [[21, "class-avogadro-core-crystaltools"]], "Class Avogadro::Core::Bond": [[16, "class-avogadro-core-bond"]], "Class Avogadro::Core::ArraySet::PlaceHolder": [[10, "class-avogadro-core-arrayset-placeholder"]], "Coding Conventions (C++)": [[2, "coding-conventions-c"]], "C++ Features": [[2, "c-features"]], "Including Headers": [[2, "including-headers"]], "Export Macro Headers": [[2, "export-macro-headers"]], "Private Headers": [[2, "private-headers"]], "Qt Headers": [[2, "qt-headers"]], "Namespaces": [[2, "namespaces"]], "Casting": [[2, "casting"]], "Aesthetics": [[2, "aesthetics"]], "Translations": [[6, "translations"]], "Current Status": [[6, "current-status"]], "Credits": [[6, "credits"], [241, "credits"], [240, "credits"], [243, "credits"], [242, "credits"], [244, "credits"], [239, "credits"]], "Class Avogadro::Core::Array": [[7, "class-avogadro-core-array"]], "Documenting Code": [[1, "documenting-code"]], "Class Descriptions": [[1, "class-descriptions"]], "Function Descriptions": [[1, "function-descriptions"]], "Class Avogadro::Core::AtomTyper": [[13, "class-avogadro-core-atomtyper"]], "Class Avogadro::Core::ArraySet": [[8, "class-avogadro-core-arrayset"]], "Class Avogadro::Core::AvoSpglib": [[14, "class-avogadro-core-avospglib"]], "Class Avogadro::Core::CoordinateBlockGenerator": [[19, "class-avogadro-core-coordinateblockgenerator"]], "Class Avogadro::Core::BondTemplate": [[17, "class-avogadro-core-bondtemplate"]], "Class Avogadro::Core::Elements": [[23, 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"\ud83d\ude80 Performance Improvements": [[243, "performance-improvements"], [244, "performance-improvements"]], "Release Notes v1.96.0": [[242, "release-notes-v1-96-0"]], "\ud83d\ude80 Performance Fixes": [[242, "performance-fixes"]], "Release Notes v1.98.0": [[244, "release-notes-v1-98-0"]], "Class Avogadro::Io::MMTFFormat": [[54, "class-avogadro-io-mmtfformat"]], "Class Avogadro::Io::OutcarFormat": [[56, "class-avogadro-io-outcarformat"]], "Class Avogadro::Io::PdbFormat": [[57, "class-avogadro-io-pdbformat"]], "Class Avogadro::Io::XyzFormat": [[60, "class-avogadro-io-xyzformat"]], "Class Avogadro::Io::LammpsDataFormat": [[52, "class-avogadro-io-lammpsdataformat"]], "Class Avogadro::Io::MdlFormat": [[55, "class-avogadro-io-mdlformat"]], "Class Avogadro::MoleQueue::InputGeneratorWidget": [[64, "class-avogadro-molequeue-inputgeneratorwidget"]], "Class Avogadro::Io::Hdf5DataFormat": [[51, "class-avogadro-io-hdf5dataformat"]], "Class Avogadro::MoleQueue::MoleQueueManager": [[66, 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"class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md22"], [173, "syntax-highlighting"]], "Requesting Full Structure of Current Molecule": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md9"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md23"], [173, "requesting-full-structure-of-current-molecule"]], "Handling User Selections: \u2013generate-input": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md10"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md24"]], "Automatic Generation of Geometry": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md11"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md25"], [173, "automatic-generation-of-geometry"]], "Error Handling": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md12"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md26"], [173, "error-handling"]], "Debugging": [[62, 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"class-avogadro-io-lammpstrajectoryformat"]], "Class Avogadro::Io::PoscarFormat": [[58, "class-avogadro-io-poscarformat"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[69, "class-avogadro-qtgui-backgroundfileformat"]], "Class Avogadro::MoleQueue::MoleQueueDialog": [[65, "class-avogadro-molequeue-molequeuedialog"]], "Class Avogadro::Io::FileFormat": [[48, "class-avogadro-io-fileformat"]], "Class Avogadro::QtGui::FileFormatDialog": [[78, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::ElementTranslator": [[74, "class-avogadro-qtgui-elementtranslator"]], "Class Avogadro::QtGui::InterfaceScript": [[82, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::RWMolecule": [[95, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::HydrogenTools": [[81, "class-avogadro-qtgui-hydrogentools"]], "Class Avogadro::QtGui::ExtensionPlugin": [[75, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::MoleculeModel": [[86, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::PeriodicTableView": [[89, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::InterfaceWidget": [[83, "class-avogadro-qtgui-interfacewidget"]], "Class Avogadro::QtGui::PeriodicTableScene": [[88, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[76, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::MeshGenerator": [[84, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::FileBrowseWidget": [[77, "class-avogadro-qtgui-filebrowsewidget"]], "Class Avogadro::QtGui::ElementDetail": [[72, "class-avogadro-qtgui-elementdetail"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[80, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::PersistentBond": [[91, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::GenericHighlighter": [[79, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::ElementItem": [[73, "class-avogadro-qtgui-elementitem"]], "Class Avogadro::QtGui::RWBond": [[94, "class-avogadro-qtgui-rwbond"]], "Class Avogadro::QtGui::MultiViewWidget": [[87, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::PythonScript": [[92, "class-avogadro-qtgui-pythonscript"]], "Class Avogadro::QtGui::PersistentAtom": [[90, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::Molecule": [[85, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::RWAtom": [[93, "class-avogadro-qtgui-rwatom"]], "Class Avogadro::Core::Variant": [[42, "class-avogadro-core-variant"]], "Class Avogadro::Core::SymbolAtomTyper": [[40, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::Mutex": [[31, "class-avogadro-core-mutex"]], "Class Avogadro::Core::SharedMutex": [[36, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::Molecule": [[28, "class-avogadro-core-molecule"]], "Class Avogadro::Core::SlaterSetTools": [[38, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::VariantMap": [[43, "class-avogadro-core-variantmap"]], "Class Avogadro::Core::NameAtomTyper": [[32, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::MoleculeSerializer": [[30, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::SlaterSet": [[37, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::MoleculeDeserializer": [[29, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Io::CmlFormat": [[46, "class-avogadro-io-cmlformat"]], "Class Avogadro::Core::SpaceGroups": [[39, "class-avogadro-core-spacegroups"]], "Class Avogadro::Core::Mesh": [[27, "class-avogadro-core-mesh"]], "Class Avogadro::Core::GaussianSetTools": [[25, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Io::CjsonFormat": [[45, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Core::ResidueData": [[34, "class-avogadro-core-residuedata"]], "Class Avogadro::Io::DcdFormat": [[47, "class-avogadro-io-dcdformat"]], "Class Avogadro::Core::Residue": [[33, "class-avogadro-core-residue"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[44, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Core::GaussianSet": [[24, "class-avogadro-core-gaussianset"]], "Class Avogadro::Core::UnitCell": [[41, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::RingPerceiver": [[35, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::Graph": [[26, "class-avogadro-core-graph"]], "Drawing Molecules": [[200, "drawing-molecules"]], "Creating Carbon Dioxide": [[200, "creating-carbon-dioxide"]], "Making Selections": [[203, "making-selections"]], "Insert Molecular Fragments": [[196, "insert-molecular-fragments"]], "Importing from the Protein Data Bank (PDB)": [[193, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[193, "importing-directly"]], "Reading a Downloaded PDB file": [[193, "reading-a-downloaded-pdb-file"]], "Getting Started": [[201, "getting-started"], [201, null]], "Finding Conformers of Molecules": [[212, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[212, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[212, "optimize-the-geometry"]], "Change the force field options": [[212, "change-the-force-field-options"]], "Set the conformer search options": [[212, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[212, "pick-a-search-method-and-start-the-search"]], "View Menu": [[211, "view-menu"]], "New View": [[211, "new-view"]], "Duplicate View": [[211, "duplicate-view"]], "Detach View": [[211, "detach-view"]], "Close View": [[211, "close-view"]], "Center": [[211, "center"]], "Align View to Axes": [[211, "align-view-to-axes"]], "Full Screen": [[211, "full-screen"]], "Reset Display Types": [[211, "reset-display-types"]], "Set Background Color\u2026": [[211, "set-background-color"]], "Projection": [[211, "projection"]], "Display Axes": [[211, "display-axes"]], "Debug Information": [[211, "debug-information"]], "Use Quick Render": [[211, "use-quick-render"]], "All Molecules in File\u2026": [[211, "all-molecules-in-file"]], "Crystal View Options\u2026": [[211, "crystal-view-options"]], "Properties": [[211, "properties"]], "Importing Molecules by Name": [[194, "importing-molecules-by-name"]], "Menus": [[209, "menus"], [209, null]], "Extension Menu": [[207, "extension-menu"]], "Animation": [[207, "animation"]], "Optimize Geometry": [[207, "optimize-geometry"]], "Molecular Mechanics": [[207, "molecular-mechanics"]], "Setup Force Field\u2026": [[207, "setup-force-field"]], "Calculate Energy": [[207, "calculate-energy"]], "Conformer Search": [[207, "conformer-search"]], "Constraints": [[207, "constraints"], [213, "constraints"]], "Ignore Selection": [[207, "ignore-selection"]], "Fix Selected Atoms": [[207, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[207, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[207, "general-how-to-for-plugins"]], "Running Gaussian": [[207, "running-gaussian"]], "Molecular Orbitals": [[207, "molecular-orbitals"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[207, "qtaim-quantum-theory-of-atoms-in-molecules"], [198, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Spectra\u2026": [[207, "spectra"]], "Create Surfaces\u2026": [[207, "create-surfaces"]], "Select Menu": [[210, "select-menu"]], "Select All": [[210, "select-all"], [206, "select-all"]], "Select None": [[210, "select-none"], [206, "select-none"]], "Invert Selection": [[210, "invert-selection"]], "Select SMARTS\u2026": [[210, "select-smarts"]], "Select by Element\u2026": [[210, "select-by-element"]], "Select by Residue\u2026": [[210, "select-by-residue"]], "Select Solvent": [[210, "select-solvent"]], "Add Name Selection\u2026": [[210, "add-name-selection"]], "Introduction to Molecular Mechanics": [[214, "introduction-to-molecular-mechanics"]], "UFF": [[214, "uff"]], "MMFF94(s)": [[214, "mmff94-s"]], "GAFF": [[214, "gaff"]], "Coloring Part of a Molecules": [[197, "coloring-part-of-a-molecules"]], "Hemoglobin": [[197, "hemoglobin"]], "Select by Residue": [[197, "select-by-residue"]], "Select by Element": [[197, "select-by-element"]], "Optimizing Geometry": [[215, "optimizing-geometry"]], "Optimization": [[215, null]], "Different Display Styles": [[198, "different-display-styles"]], "Locating Display Types": [[198, "locating-display-types"]], "Axes": [[198, "axes"]], "Ball and Stick": [[198, "ball-and-stick"]], "Cartoon": [[198, "cartoon"]], "Dipole": [[198, "dipole"]], "Force": [[198, "force"]], "Hydrogen Bond": [[198, "hydrogen-bond"]], "Label": [[198, "label"]], "Polygon": [[198, "polygon"]], "Ribbon": [[198, "ribbon"]], "Ring": [[198, "ring"]], "Stick": [[198, "stick"]], "Surfaces": [[198, "surfaces"]], "Van der Waals Spheres": [[198, "van-der-waals-spheres"]], "Wireframe": [[198, "wireframe"]], "File Menu": [[208, "file-menu"]], "New": [[208, "new"]], "Open": [[208, "open"]], "Open Recent": [[208, "open-recent"]], "Close": [[208, "close"]], "Save": [[208, "save"]], "Save As\u2026": [[208, "save-as"]], "Revert to Saved": [[208, "revert-to-saved"]], "Import": [[208, "import"]], "Export": [[208, "export"]], "Geometry Constraints": [[213, "geometry-constraints"]], "Example": [[213, "example"]], "Optimizations": [[213, "optimizations"]], "Example cont.": [[213, "example-cont"]], "Display Types": [[199, "display-types"], [199, null]], "Introduction": [[202, "introduction"]], "Opening a File": [[202, "opening-a-file"]], "Navigation": [[202, "navigation"]], "Edit Menu": [[206, "edit-menu"]], "Undo": [[206, "undo"]], "Redo": [[206, "redo"]], "Cut": [[206, "cut"]], "Copy": [[206, "copy"]], "Copy As": [[206, "copy-as"]], "Paste": [[206, "paste"]], "Clear": [[206, "clear"]], "User Guide": [[204, "user-guide"]], "Avogadro: Molecular Editor and Visualization": [[204, "avogadro-molecular-editor-and-visualization"], [179, "avogadro-molecular-editor-and-visualization"]], "Avogadro 2": [[204, "avogadro-2"]], "Build Menu": [[205, "build-menu"]], "Cartesian Editor\u2026": [[205, "cartesian-editor"]], "1. Sort by\u2026": [[205, "sort-by"]], "2. Unit of Measure": [[205, "unit-of-measure"]], "3. Editing & Modifying Data": [[205, "editing-modifying-data"]], "Change H to Methyl": [[205, "change-h-to-methyl"]], "Add Hydrogens": [[205, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[205, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[205, "remove-hydrogens"]], "Insert": [[205, "insert"]], "Invert Chirality": [[205, "invert-chirality"]], "Super Cell Builder\u2026": [[205, "super-cell-builder"]], "Nanotube Builder\u2026": [[205, "nanotube-builder"]], "Building with SMILES": [[192, "building-with-smiles"]], "Building Molecules": [[195, "building-molecules"], [195, null]], "Align Tool": [[216, "align-tool"]], "Viewing Electrostatic Potential Maps": [[229, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[229, "changing-surface-settings"]], "Auto-Optimize Tool": [[217, "auto-optimize-tool"]], "Force Fields & Algorithms": [[217, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[217, "fixing-ignoring-selections"]], "Selection Tool": [[225, "selection-tool"]], "What\u2019s New in Avogadro 2": [[232, "whats-new-in-avogadro-2"]], "Naming a Molecule": [[227, "naming-a-molecule"]], "Auto-Rotate Tool": [[218, "auto-rotate-tool"]], "Using QTAIM (Atoms in Molecules) Analysis": [[228, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[228, "start-with-a-wfn-file"]], "Tools": [[221, "tools"], [221, null]], "Release Notes v1.94.0": [[239, "release-notes-v1-94-0"]], "Features": [[239, "features"], [235, "features"]], "\ud83d\udc0d Python Improvements": [[239, "python-improvements"]], "Viewing Vibrations": [[231, "viewing-vibrations"]], "Tutorials": [[226, "tutorials"], [226, null]], "Interface Changes": [[233, "interface-changes"]], "Version History": [[238, "version-history"], [238, null]], "Measure Tool": [[223, "measure-tool"]], "Navigate Tool": [[224, "navigate-tool"]], "Manipulate Tool": [[222, "manipulate-tool"]], "Install": [[237, "install"], [235, "install"]], "Building Source Code": [[236, "building-source-code"]], "Cloning Repositories": [[236, "cloning-repositories"]], "Updating": [[236, "updating"]], "Prerequisites": [[236, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[236, "debian-based-distribution-or-ubuntu"]], "Building": [[236, "building"]], "Finding Qt, Windows Generators": [[236, "finding-qt-windows-generators"]], "Normal Development": [[236, "normal-development"]], "Build Tree Layout": [[236, "build-tree-layout"]], "Running Executables": [[236, "running-executables"]], "Building Packages": [[236, "building-packages"]], "Draw Tool": [[220, "draw-tool"]], "1. Creating a Molecule": [[220, "creating-a-molecule"]], "2.": [[220, "id1"]], "3.": [[220, "id2"]], "4.": [[220, "id3"]], "5.": [[220, "id4"]], "6.": [[220, "id5"]], "7.": [[220, "id6"]], "8.": [[220, "id7"]], "9.": [[220, "id8"]], "Bond-Centric Manipulate Tool": [[219, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[219, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[219, "adjusting-bonds-and-torsion-angles"]], "Resources": [[235, "resources"]], "Connecting with the Avogadro community": [[235, "connecting-with-the-avogadro-community"]], "Major New Features": [[234, "major-new-features"]], "Speed and Stability": [[234, "speed-and-stability"]], "Rendering": [[234, "rendering"]], "New real-time shadows and depth effects": [[234, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[234, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[234, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[234, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[234, "layers"]], "Symmetry Properties": [[234, "symmetry-properties"]], "Template Tool": [[234, "template-tool"]], "Solvent Accessible and Solvent Excluded Surfaces": [[234, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[234, "flexible-electrostatics-models"]], "New Analysis Tools": [[234, "new-analysis-tools"]], "Python Commands / Plugins": [[234, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[234, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[234, "new-and-updated-interfaces-to-external-programs"]], "Viewing Molecular Orbitals": [[230, "viewing-molecular-orbitals"]], "Configure": [[230, "configure"]], "Building DNA or RNA": [[191, "building-dna-or-rna"]], "Example Plugin Script - Part 2": [[171, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[171, "providing-input-to-run-command"]], "runCommand() Function": [[171, "runcommand-function"]], "Operation Function": [[171, "operation-function"]], "Retrieving necessary components": [[171, "retrieving-necessary-components"]], "Support for Selection": [[171, "support-for-selection"]], "Sample Input and Output": [[171, "sample-input-and-output"]], "Building a Peptide": [[189, "building-a-peptide"]], "Making a Crystal Surface Slab": [[181, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[181, "import-the-appropriate-crystal-structure"]], "Script Interfaces": [[176, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[176, "fixed-string-lists-pop-up-menus"]], "Integer Values": [[176, "integer-values"]], "Floating-point values": [[176, "floating-point-values"]], "Table of contents": [[180, "table-of-contents"]], "License": [[178, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[178, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[178, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[178, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[178, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[178, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[178, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[178, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[178, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[178, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[178, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[178, "section-8-interpretation"]], "Building a Supercell": [[188, "building-a-supercell"]], "Creating a Surface": [[188, "creating-a-surface"]], "Script Plugins": [[174, "script-plugins"], [161, "script-plugins"]], "Scaling Crystal Cell Volume": [[187, "scaling-crystal-cell-volume"]], "Installing Script Plugins": [[175, "installing-script-plugins"]], "Directories": [[175, "directories"]], "Plugin Packages and Repositories": [[175, "plugin-packages-and-repositories"]], "Adding to the Plugin Directory": [[175, "adding-to-the-plugin-directory"]], "Example Plugin Script - Part 1": [[170, "example-plugin-script-part-1"]], "The Main function:": [[170, "the-main-function"]], "Input Arguments": [[170, "input-arguments"]], "getOptions() Function": [[170, "getoptions-function"]], "Perceiving Crystall Symmetry": [[183, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[183, "open-a-crystal-file"]], "File Formats": [[172, "file-formats"]], "Identify the Format with --metadata": [[172, "identify-the-format-with-metadata"]], "Reading a format with --read": [[172, "reading-a-format-with-read"]], "Writing a format with --write": [[172, "writing-a-format-with-write"]], "Building Materials": [[184, "building-materials"], [184, null]], "Command Scripts": [[168, "command-scripts"]], "Specifying UI options with \u2013print-options": [[168, "specifying-ui-options-with-print-options"]], "Returning Data": [[168, "returning-data"]], "Returning Data in a Specific File Format": [[168, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[168, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[168, "bonding-new-atoms"]], "Selected Atoms": [[168, "selected-atoms"]], "VTK Classes": [[177, "vtk-classes"]], "Building Molecule-Surface Interactions": [[185, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[185, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[185, "new-window-create-our-molecule"]], "Reducing Crystals to a Primitive Unit Cell": [[186, "reducing-crystals-to-a-primitive-unit-cell"]], "Input Generators": [[173, "input-generators"]], "Specifying parameters with --print-options": [[173, "specifying-parameters-with-print-options"]], "Handling User Selections: --generate-input": [[173, "handling-user-selections-generate-input"]], "Coordinate Blocks": [[173, "coordinate-blocks"]], "Building Carbon Nanotubes": [[190, "building-carbon-nanotubes"]], "Energy / Force Fields": [[169, "energy-force-fields"]], "Identify the Script with --metadata": [[169, "identify-the-script-with-metadata"], [167, "identify-the-script-with-metadata"]], "Calculating Energies and Gradients": [[169, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[169, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[169, "lattice-vectors-and-fractional-coordinates"]], "Building a Polymer Unit Cell": [[182, "building-a-polymer-unit-cell"]], "Core Classes": [[160, "core-classes"]], "QtGui Classes": [[164, "qtgui-classes"]], "Charges / Electrostatics": [[167, "charges-electrostatics"]], "Calculating Atomic Partial Charges with --charge": [[167, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials with --potential": [[167, "generating-electrostatic-potentials-with-potential"]], "Class Avogadro::Rendering::Visitor": [[145, "class-avogadro-rendering-visitor"]], "Class Avogadro::TypeTraits": [[147, "class-avogadro-typetraits"]], "Class Avogadro::Rendering::VolumeGeometry": [[146, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::TypeTraits< unsigned int >": [[154, "class-avogadro-typetraits-unsigned-int"]], "Class List": [[159, "class-list"]], "Class Avogadro::TypeTraits< unsigned short >": [[155, "class-avogadro-typetraits-unsigned-short"]], "Class Avogadro::TypeTraits< int >": [[151, "class-avogadro-typetraits-int"]], "Class Avogadro::TypeTraits< float >": [[150, "class-avogadro-typetraits-float"]], "Avogadro Remote Procedure Call (RPC)": [[166, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[166, "rpc-protocol"]], "Methods": [[166, "methods"]], "Class vtkAvogadroActor": [[158, "class-vtkavogadroactor"]], "Class Avogadro::TypeTraits< unsigned char >": [[153, "class-avogadro-typetraits-unsigned-char"]], "Develop": [[161, "develop"]], "External Scripting": [[161, "external-scripting"]], "Libraries": [[161, "libraries"]], "Main Classes": [[161, "main-classes"]], "Class Avogadro::TypeTraits< char >": [[148, "class-avogadro-typetraits-char"]], "Class Avogadro::Rendering::VRMLVisitor": [[144, "class-avogadro-rendering-vrmlvisitor"]], "MoleQueue Classes": [[163, "molequeue-classes"]], "Rendering Classes": [[165, "rendering-classes"]], "Class Avogadro::TypeTraits< short >": [[152, "class-avogadro-typetraits-short"]], "IO Classes": [[162, "io-classes"]], "Class Avogadro::VTK::vtkGLWidget": [[157, "class-avogadro-vtk-vtkglwidget"]], "Class Avogadro::VTK::VtkPlot": [[156, "class-avogadro-vtk-vtkplot"]], "Class Avogadro::TypeTraits< double >": [[149, "class-avogadro-typetraits-double"]], "Class Avogadro::QuantumIO::GaussianCube": [[109, "class-avogadro-quantumio-gaussiancube"]], "Class Avogadro::QtGui::ScenePlugin": [[96, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::Rendering::ArrowGeometry": [[116, "class-avogadro-rendering-arrowgeometry"]], "Class Avogadro::QtGui::ToolPluginFactory": [[101, "class-avogadro-qtgui-toolpluginfactory"]], "Class Avogadro::QtOpenGL::QtTextRenderStrategy": [[105, "class-avogadro-qtopengl-qttextrenderstrategy"]], "Class Avogadro::QtGui::ViewFactory": [[102, "class-avogadro-qtgui-viewfactory"]], "Class Avogadro::QuantumIO::MoldenFile": [[111, "class-avogadro-quantumio-moldenfile"]], "Class Avogadro::QuantumIO::MopacAux": [[112, "class-avogadro-quantumio-mopacaux"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[107, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::QtGui::ScenePluginFactory": [[97, "class-avogadro-qtgui-scenepluginfactory"]], "Class Avogadro::QtOpenGL::GLWidget": [[104, "class-avogadro-qtopengl-glwidget"]], "Class Avogadro::QtGui::ToolPlugin": [[100, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::Rendering::Camera": [[118, "class-avogadro-rendering-camera"]], "Class Avogadro::Rendering::BufferObject": [[117, "class-avogadro-rendering-bufferobject"]], "Class Avogadro::QuantumIO::GamessukOut": [[108, "class-avogadro-quantumio-gamessukout"]], "Class Avogadro::QuantumIO::GaussianFchk": [[110, "class-avogadro-quantumio-gaussianfchk"]], "Class Avogadro::QuantumIO::NWChemJson": [[113, "class-avogadro-quantumio-nwchemjson"]], "Class Avogadro::QtGui::ScenePluginModel": [[98, "class-avogadro-qtgui-scenepluginmodel"]], "Class Avogadro::QuantumIO::NWChemLog": [[114, 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"docs/tools/selection-tool.md", "docs/tutorials/index.md", "docs/tutorials/naming-a-molecule.md", "docs/tutorials/using-qtaim-and-wfn.md", "docs/tutorials/viewing-electrostatic-potential.md", "docs/tutorials/viewing-molecular-orbitals.md", "docs/tutorials/viewing-vibrations.md", "docs/whats-new-in-avogadro-2/index.md", "docs/whats-new-in-avogadro-2/interface-changes.md", "docs/whats-new-in-avogadro-2/major-new-features.md", "index.md", "install/build.md", "install/index.md", "install/versions/index.md", "install/versions/v194.md", "install/versions/v195.md", "install/versions/v1951.md", "install/versions/v196.md", "install/versions/v197.md", "install/versions/v198.md", "teach/acid_base.md", "teach/alkene_isomers.md", "teach/basic_vsepr.md", "teach/diaxial_interactions.md", "teach/hcn_dipole.md", "teach/hydrogen_clusters.md", "teach/hydrogen_molecule.md", "teach/index.md", "teach/markovnikovs_rule.md", "teach/organic_hybridization.md", "teach/water.md"], "titles": ["Contributing Code", 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Avogadro::QtGui::GenericHighlighter::Rule", "Class Avogadro::QtGui::HydrogenTools", "Class Avogadro::QtGui::InterfaceScript", "Class Avogadro::QtGui::InterfaceWidget", "Class Avogadro::QtGui::MeshGenerator", "Class Avogadro::QtGui::Molecule", "Class Avogadro::QtGui::MoleculeModel", "Class Avogadro::QtGui::MultiViewWidget", "Class Avogadro::QtGui::PeriodicTableScene", "Class Avogadro::QtGui::PeriodicTableView", "Class Avogadro::QtGui::PersistentAtom", "Class Avogadro::QtGui::PersistentBond", "Class Avogadro::QtGui::PythonScript", "Class Avogadro::QtGui::RWAtom", "Class Avogadro::QtGui::RWBond", "Class Avogadro::QtGui::RWMolecule", "Class Avogadro::QtGui::ScenePlugin", "Class Avogadro::QtGui::ScenePluginFactory", "Class Avogadro::QtGui::ScenePluginModel", "Class Avogadro::QtGui::ScriptLoader", "Class Avogadro::QtGui::ToolPlugin", "Class Avogadro::QtGui::ToolPluginFactory", "Class Avogadro::QtGui::ViewFactory", "Class Avogadro::QtOpenGL::ActiveObjects", "Class Avogadro::QtOpenGL::GLWidget", "Class Avogadro::QtOpenGL::QtTextRenderStrategy", "Class Avogadro::QuantumIO::GAMESSUSOutput", "Class Avogadro::QuantumIO::GUKBasisSet", "Class Avogadro::QuantumIO::GamessukOut", "Class Avogadro::QuantumIO::GaussianCube", "Class Avogadro::QuantumIO::GaussianFchk", "Class Avogadro::QuantumIO::MoldenFile", "Class Avogadro::QuantumIO::MopacAux", "Class Avogadro::QuantumIO::NWChemJson", "Class Avogadro::QuantumIO::NWChemLog", "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry", "Class Avogadro::Rendering::ArrowGeometry", "Class Avogadro::Rendering::BufferObject", "Class Avogadro::Rendering::Camera", "Class Avogadro::Rendering::Cylinder", "Class Avogadro::Rendering::CylinderGeometry", "Class Avogadro::Rendering::Drawable", "Class Avogadro::Rendering::GLRenderVisitor", "Class Avogadro::Rendering::GLRenderer", "Class Avogadro::Rendering::GeometryNode", "Class Avogadro::Rendering::GeometryVisitor", "Class Avogadro::Rendering::GroupNode", "Class 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186, 187, 200, 206, 214, 215, 221, 236, 237, 245, 251, 255], "well": [0, 26, 168, 175, 178, 190, 191, 207, 208, 213, 215, 235, 237, 243], "need": [0, 2, 5, 13, 19, 21, 28, 51, 62, 81, 82, 84, 95, 100, 103, 161, 166, 169, 172, 173, 175, 176, 178, 181, 183, 185, 186, 188, 190, 196, 200, 207, 213, 214, 218, 221, 231, 237, 241, 245, 254], "document": [0, 2, 4, 19, 62, 64, 78, 82, 161, 172, 173, 185, 206, 208, 236, 240, 241, 243, 244, 253], "your": [0, 1, 4, 5, 169, 175, 178, 187, 188, 192, 193, 196, 200, 202, 203, 205, 207, 208, 210, 211, 213, 214, 216, 217, 218, 220, 221, 223, 226, 228, 230, 235, 236, 237, 244], "comment": [0, 5, 62, 82, 173, 240, 241, 243, 244], "doxygen": [0, 1, 29, 30, 156], "api": [0, 1, 48, 49, 75, 95, 121, 126, 129, 145, 236], "doc": [0, 29, 30, 51, 105, 156, 171, 240], "which": [0, 4, 13, 18, 28, 51, 62, 64, 68, 72, 73, 81, 82, 104, 121, 122, 125, 127, 130, 132, 144, 145, 167, 168, 169, 170, 171, 172, 173, 175, 176, 178, 182, 185, 186, 187, 202, 210, 214, 228, 229, 235, 237, 241, 245, 246, 248, 254], "ultim": 0, "becom": [0, 100, 142, 254], "part": [0, 27, 90, 91, 166, 168, 173, 178, 180, 199, 207, 234, 235, 240, 241, 243, 244], "thi": [0, 1, 2, 4, 5, 7, 8, 12, 13, 15, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 33, 37, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 69, 71, 72, 73, 74, 75, 78, 79, 80, 81, 82, 84, 85, 88, 89, 92, 95, 96, 100, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 117, 118, 121, 122, 123, 124, 125, 126, 127, 128, 130, 132, 133, 134, 136, 144, 157, 158, 161, 166, 168, 169, 170, 171, 172, 173, 176, 178, 179, 181, 182, 183, 185, 186, 187, 188, 191, 197, 198, 200, 202, 203, 204, 205, 206, 207, 210, 211, 213, 214, 215, 218, 220, 221, 223, 226, 229, 230, 231, 232, 235, 236, 237, 241, 242, 243, 244, 251, 253, 254], "websit": [0, 190, 192, 193, 207, 243, 244], "featur": [0, 4, 6, 103, 123, 161, 180, 181, 185, 197, 198, 203, 204, 205, 206, 207, 210, 211, 215, 218, 231, 232, 233, 239], "header": [0, 1, 5, 33, 240, 244], "export": [0, 161, 188, 209, 240, 245], "macro": [0, 95, 158], "privat": [0, 78, 241], "qt": [0, 1, 3, 5, 67, 70, 86, 87, 98, 105, 157, 164, 240, 244, 245], "namespac": [0, 1, 5, 161], "cast": [0, 3, 5, 20, 42, 75, 129, 159, 165, 218, 243], "aesthet": 0, "indent": [0, 158], "line": [0, 48, 62, 82, 83, 116, 127, 167, 168, 169, 170, 171, 172, 173, 182, 192, 220, 235, 244, 245], "width": [0, 104, 118, 123, 127, 142, 159, 165, 244], "declar": [0, 1, 2, 169, 245], "variabl": [0, 65, 85, 92, 95, 170, 213, 237], "whitespac": 0, "brace": 0, "parenthes": 0, "switch": [0, 182, 185, 202, 212, 240, 244, 245], "statement": 0, "break": [0, 171], "inherit": 0, "virtual": [0, 8, 9, 10, 13, 15, 24, 28, 32, 33, 37, 40, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 64, 75, 85, 96, 100, 101, 102, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 121, 122, 124, 125, 126, 127, 128, 129, 130, 136, 137, 138, 139, 141, 144, 145], "keyword": [0, 62, 82, 173, 207, 232], "referenc": [0, 15, 65, 85], "member": [0, 8, 9, 27, 28, 42, 43, 44, 62, 82, 85, 107, 123, 126, 127, 128, 131, 158, 161, 167, 169, 172, 173, 178, 198], "file": [0, 1, 2, 4, 6, 15, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 68, 69, 75, 78, 92, 106, 109, 110, 111, 112, 113, 114, 130, 144, 159, 161, 162, 163, 166, 167, 169, 173, 174, 175, 180, 181, 184, 185, 186, 188, 194, 195, 197, 198, 201, 206, 207, 209, 210, 227, 231, 232, 235, 240, 241, 243, 244, 245], "name": [0, 1, 2, 15, 19, 22, 23, 24, 27, 28, 32, 33, 34, 43, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 69, 72, 74, 75, 82, 95, 96, 99, 100, 102, 104, 106, 109, 110, 111, 112, 113, 114, 134, 147, 148, 149, 150, 151, 152, 153, 154, 155, 159, 160, 162, 164, 167, 168, 169, 170, 171, 172, 173, 175, 176, 178, 180, 181, 195, 197, 209, 213, 214, 227, 237, 244, 245], "rule": [0, 62, 79, 82, 159, 164, 173, 247, 248, 253], "class": [0, 2, 5, 173, 235, 241, 245], "descript": [0, 4, 13, 21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 75, 82, 95, 96, 100, 106, 109, 110, 111, 112, 113, 114, 159, 162, 163, 164, 167, 169, 172, 173, 175, 243], "function": [0, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 158, 161, 174, 175, 207, 215, 235, 245], "us": [1, 2, 5, 7, 8, 11, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 33, 37, 38, 39, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 74, 75, 78, 79, 82, 83, 84, 85, 90, 91, 95, 100, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 122, 123, 126, 127, 128, 131, 132, 134, 136, 138, 139, 140, 142, 157, 161, 164, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 180, 181, 182, 183, 185, 186, 190, 191, 193, 194, 198, 200, 202, 203, 204, 205, 207, 209, 210, 212, 214, 215, 217, 218, 220, 221, 224, 225, 227, 228, 233, 235, 236, 237, 240, 241, 243, 244, 245, 246, 248, 250, 251, 252, 253, 254, 255, 256], "gener": [1, 2, 6, 13, 19, 20, 23, 24, 27, 28, 39, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 81, 83, 84, 92, 95, 103, 104, 106, 109, 110, 111, 112, 113, 114, 139, 141, 157, 161, 168, 174, 175, 176, 180, 181, 188, 190, 200, 203, 209, 210, 211, 215, 218, 221, 233, 235, 240, 241, 242, 243, 244, 245], "javadoc": 1, "thei": [1, 2, 4, 6, 13, 51, 62, 64, 82, 84, 115, 136, 173, 175, 176, 178, 185, 189, 215, 218, 237], "go": [1, 5, 75, 81, 100, 191, 193, 197, 213, 214, 218, 223, 237], "next": [1, 62, 82, 139, 169, 176, 182, 197, 212, 230, 233, 235], "all": [1, 3, 4, 5, 7, 8, 12, 21, 22, 23, 24, 26, 27, 28, 41, 48, 49, 51, 62, 65, 68, 75, 78, 81, 82, 89, 92, 95, 99, 103, 104, 121, 124, 126, 127, 128, 129, 132, 143, 145, 159, 161, 162, 165, 168, 171, 173, 175, 178, 181, 183, 193, 197, 198, 200, 205, 209, 213, 215, 220, 221, 223, 229, 231, 233, 236, 237, 241, 242, 248, 251], "should": [1, 2, 5, 8, 20, 22, 27, 28, 39, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 68, 72, 73, 75, 82, 84, 85, 89, 90, 91, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 117, 121, 123, 133, 134, 167, 168, 169, 172, 173, 175, 176, 178, 182, 202, 205, 212, 214, 237, 241, 245, 252], "minimum": [1, 22, 28, 41, 49, 62, 82, 84, 176, 178, 212, 245], "brief": [1, 175], "one": [1, 2, 5, 13, 15, 19, 22, 24, 26, 27, 37, 48, 62, 75, 78, 82, 85, 95, 115, 117, 120, 134, 136, 168, 173, 178, 181, 182, 190, 191, 192, 198, 202, 207, 211, 213, 220, 235, 245], "two": [1, 15, 26, 75, 84, 142, 166, 167, 171, 182, 186, 202, 211, 213, 217, 240, 241, 243, 244, 245, 250, 254, 256], "sentenc": 1, "explain": 1, "what": [1, 28, 43, 85, 95, 180, 197, 207, 211, 225], "intend": [1, 23, 51, 172, 178, 253], "purpos": [1, 2, 5, 51, 65, 115, 126, 136, 167, 178, 207], "i": [1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 75, 78, 81, 82, 84, 85, 88, 89, 90, 91, 92, 93, 94, 95, 96, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 121, 123, 124, 126, 127, 128, 129, 132, 133, 134, 136, 138, 142, 145, 157, 158, 159, 160, 161, 164, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 178, 179, 181, 182, 183, 185, 186, 187, 188, 191, 192, 193, 197, 198, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 212, 213, 214, 215, 217, 218, 220, 221, 223, 224, 225, 226, 228, 230, 231, 233, 235, 236, 237, 241, 242, 243, 244, 245, 248, 251, 252, 253, 254, 256], "goe": [1, 5, 62, 82, 173, 237], "here": [1, 62, 81, 82, 166, 170, 171, 176, 178, 181, 182, 183, 185, 186, 187, 188, 190, 191, 207, 213, 229, 253, 254], "void": [1, 5, 7, 8, 12, 13, 15, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28, 31, 33, 35, 36, 37, 39, 41, 42, 43, 44, 48, 51, 57, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 75, 77, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 100, 103, 104, 105, 107, 108, 110, 112, 114, 115, 116, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 144, 145, 157, 158], "dosometh": [1, 5], "overview": [1, 5], "add": [1, 6, 22, 24, 26, 27, 28, 33, 37, 48, 49, 62, 79, 80, 81, 82, 85, 95, 96, 100, 104, 115, 116, 120, 124, 126, 127, 128, 136, 157, 159, 161, 164, 175, 176, 182, 187, 188, 207, 209, 211, 213, 215, 226, 235, 237, 240, 241, 242, 243, 244, 245, 246, 249, 256], "path": [1, 48, 51, 62, 63, 64, 72, 73, 75, 78, 82, 83, 92, 99, 166, 168, 170, 173, 175, 176, 216, 235, 237, 241, 243, 244, 245], "user": [1, 3, 4, 23, 28, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 63, 64, 65, 68, 75, 78, 83, 84, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 162, 167, 168, 169, 170, 171, 172, 175, 176, 211, 236, 237, 241, 242, 243, 244, 245], "appropri": [1, 5, 11, 16, 51, 62, 74, 82, 168, 170, 173, 176, 202, 237, 243], "point": [1, 5, 22, 41, 43, 63, 64, 71, 78, 83, 84, 104, 115, 118, 120, 121, 124, 128, 132, 134, 136, 137, 138, 140, 167, 170, 185, 205, 211, 217, 229, 237, 244, 245, 246], "out": [1, 8, 15, 28, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 73, 82, 92, 106, 109, 110, 111, 112, 113, 114, 118, 124, 126, 176, 178, 182, 183, 202, 204, 213, 215, 219, 225, 234, 235, 245, 253], "altern": [1, 169], "similar": [1, 19, 95, 173, 178, 198, 202], "ideal": [1, 14], "give": [1, 4, 7, 8, 20, 23, 39, 48, 118, 171, 178, 211, 245, 256], "some": [1, 4, 23, 28, 62, 64, 82, 85, 95, 115, 136, 161, 166, 167, 171, 173, 175, 176, 181, 183, 186, 198, 242, 244, 245, 251, 253, 254], "simpl": [1, 23, 31, 32, 36, 39, 40, 50, 62, 82, 176, 188, 198, 205, 237, 248], "exampl": [1, 4, 19, 117, 134, 161, 167, 168, 169, 172, 173, 178, 182, 183, 188, 198, 202, 206, 207, 210, 211, 214, 216, 220, 224, 230, 235, 237, 240, 244, 247, 248], "demonstr": [1, 198, 210], "core": [1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 69, 82, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 157, 159, 161, 173, 233, 243], "simplest": 1, "wai": [1, 85, 95, 178, 182, 188, 197, 203, 205, 207, 214, 235, 236], "possibl": [1, 5, 21, 22, 49, 84, 171, 178, 204, 237], "molequeu": [1, 2, 82, 159, 166, 173, 237, 240], "jsonrpcclient": 1, "h": [1, 2, 5, 19, 24, 49, 61, 63, 64, 65, 66, 67, 68, 71, 74, 76, 78, 82, 83, 89, 92, 98, 105, 107, 115, 116, 118, 120, 122, 125, 127, 141, 159, 160, 161, 167, 173, 178, 183, 185, 209, 215, 240, 244, 246, 252, 254, 256], "client": [1, 66, 159, 163, 178], "The": [1, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72, 73, 74, 75, 76, 78, 79, 80, 81, 82, 83, 84, 85, 87, 89, 90, 91, 92, 95, 96, 97, 99, 100, 101, 102, 103, 104, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 132, 134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 158, 161, 162, 164, 167, 168, 169, 171, 172, 173, 175, 176, 178, 181, 182, 185, 187, 189, 190, 191, 196, 197, 198, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 213, 214, 215, 217, 218, 219, 220, 223, 224, 225, 226, 228, 230, 235, 237, 246], "submit": [1, 4, 61, 63, 64, 65, 68, 159, 163, 175, 182, 185], "call": [1, 7, 12, 13, 17, 18, 25, 27, 48, 51, 62, 63, 67, 68, 69, 72, 73, 75, 82, 84, 88, 89, 92, 95, 100, 104, 123, 127, 128, 134, 161, 162, 168, 169, 170, 171, 172, 173, 176, 204, 235, 237, 240, 243, 245, 254], "an": [1, 2, 4, 5, 11, 13, 14, 17, 18, 19, 22, 23, 24, 26, 27, 28, 31, 33, 36, 37, 39, 42, 43, 48, 49, 51, 61, 62, 64, 65, 67, 68, 69, 78, 79, 82, 83, 84, 85, 88, 89, 90, 91, 92, 95, 103, 104, 105, 107, 115, 136, 137, 141, 157, 158, 161, 162, 167, 168, 169, 171, 172, 173, 175, 176, 178, 182, 183, 185, 188, 189, 190, 193, 197, 198, 200, 202, 203, 207, 210, 211, 212, 213, 216, 217, 218, 219, 220, 221, 225, 226, 230, 231, 232, 235, 236, 237, 243, 244, 245, 252, 253, 254, 256], "rpc": [1, 65, 68, 161, 240], "server": [1, 4, 61, 65, 66, 68, 92, 166, 228], "json": [1, 45, 62, 65, 75, 82, 83, 100, 113, 161, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 240, 245], "2": [1, 5, 15, 17, 19, 28, 62, 65, 82, 84, 132, 142, 159, 160, 166, 169, 173, 176, 180, 182, 185, 190, 193, 200, 209, 212, 222, 224, 234, 235, 236, 237, 240, 243, 244, 246, 247, 252, 253, 254, 255], "0": [1, 5, 8, 10, 13, 14, 15, 18, 19, 21, 23, 26, 28, 39, 41, 43, 48, 62, 65, 72, 73, 75, 82, 95, 96, 100, 101, 102, 105, 118, 132, 134, 138, 140, 141, 142, 159, 160, 166, 167, 169, 171, 173, 175, 176, 179, 182, 185, 193, 200, 204, 218, 233, 235, 239, 242, 246, 251, 252, 256], "author": [1, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 47, 48, 49, 51, 53, 55, 57, 58, 59, 60, 62, 70, 74, 75, 76, 82, 84, 86, 87, 89, 97, 98, 100, 101, 102, 104, 113, 115, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 168, 173, 175, 178], "marcu": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "d": [1, 3, 7, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 62, 70, 75, 76, 82, 84, 86, 87, 89, 92, 97, 98, 102, 104, 107, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 159, 160, 178, 241, 243, 244], "hanwel": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "provid": [1, 13, 14, 18, 21, 22, 24, 25, 27, 28, 31, 36, 38, 41, 43, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 74, 79, 82, 83, 85, 90, 91, 102, 103, 104, 118, 121, 123, 126, 129, 139, 145, 161, 167, 169, 170, 173, 175, 178, 186, 197, 198, 200, 203, 204, 205, 206, 207, 208, 211, 218, 221, 226, 230, 232, 235, 245], "To": [1, 11, 16, 51, 63, 65, 74, 168, 171, 178, 181, 202, 209, 214, 219, 220, 237], "creat": [1, 12, 17, 19, 21, 26, 28, 33, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 66, 78, 82, 83, 85, 90, 91, 95, 102, 104, 106, 107, 109, 110, 111, 112, 113, 114, 117, 130, 133, 134, 144, 169, 170, 173, 175, 176, 178, 182, 184, 187, 189, 198, 201, 205, 206, 208, 209, 211, 216, 222, 229, 230, 231, 235, 237, 241, 243, 245, 246, 249, 250, 251, 252, 256], "connect": [1, 26, 61, 66, 68, 84, 95, 127, 166, 171, 178, 228, 229, 244], "method": [1, 5, 12, 17, 21, 23, 28, 42, 48, 51, 62, 63, 65, 67, 75, 78, 82, 84, 85, 90, 91, 95, 100, 102, 104, 117, 118, 134, 158, 167, 169, 173, 215, 216, 235, 240, 243, 245], "follow": [1, 5, 19, 62, 82, 92, 142, 167, 168, 169, 170, 171, 172, 173, 176, 178, 185, 188, 213, 214, 237], "done": [1, 13, 24, 37, 39, 65, 117, 123, 133, 159, 163, 169, 171, 218, 231], "new": [1, 2, 4, 5, 6, 7, 12, 17, 26, 27, 28, 33, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 66, 68, 75, 79, 81, 82, 89, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 127, 128, 141, 158, 159, 166, 169, 171, 172, 174, 177, 180, 181, 189, 190, 196, 200, 202, 204, 205, 209, 210, 214, 217, 218, 231, 240, 241, 243, 244, 245, 246], "connecttoserv": 1, "myrpcserv": 1, "qjsonobject": [1, 61, 62, 82], "emptyrequest": 1, "qlatin1str": 1, "listqueu": 1, "sendrequest": 1, "endcod": 1, "signal": [1, 2, 61, 66, 67, 68, 69, 70, 75, 77, 82, 84, 85, 86, 87, 88, 89, 92, 95, 96, 98, 100, 103, 104, 157], "order": [1, 7, 13, 17, 21, 28, 62, 75, 79, 82, 85, 89, 92, 95, 103, 105, 123, 133, 134, 142, 159, 160, 167, 168, 171, 173, 176, 198, 200, 214, 221, 224, 229, 237, 241, 245, 251], "act": [1, 95, 171, 237], "result": [1, 5, 12, 13, 18, 21, 25, 38, 62, 65, 68, 82, 83, 105, 124, 134, 141, 161, 168, 171, 172, 176, 178, 181, 182, 183, 229, 237, 252, 254, 255, 256], "notif": 1, "error": [1, 12, 48, 49, 51, 61, 63, 65, 68, 69, 78, 92, 104, 117, 123, 133, 134, 142, 159, 162, 163, 164, 165, 178, 243, 244, 245, 252], "receiv": [1, 61, 82, 178], "respons": [1, 3, 61, 87, 95, 123, 170, 171, 245], "set": [1, 12, 14, 15, 17, 18, 21, 22, 24, 25, 26, 27, 28, 33, 37, 38, 39, 41, 42, 43, 48, 51, 61, 62, 63, 64, 65, 68, 69, 73, 75, 78, 79, 80, 82, 84, 90, 91, 92, 95, 96, 100, 103, 104, 107, 116, 118, 121, 123, 126, 127, 128, 129, 132, 133, 134, 136, 140, 146, 157, 158, 159, 160, 161, 164, 166, 167, 168, 170, 173, 178, 181, 182, 183, 186, 187, 190, 197, 198, 207, 209, 215, 216, 218, 237, 240, 242, 243, 245, 246], "public": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 158, 241], "qobject": [1, 61, 62, 66, 67, 69, 74, 75, 79, 82, 84, 85, 86, 88, 92, 95, 96, 98, 99, 100, 101, 103], "end": [1, 2, 5, 7, 28, 43, 81, 95, 115, 116, 120, 121, 124, 130, 136, 144, 159, 160, 165, 182, 185, 197, 219, 220], "complet": [1, 27, 51, 61, 65, 68, 84, 117, 127, 163, 167, 168, 175, 185], "constructor": [1, 7, 15, 18, 24, 27, 28, 37, 62, 67, 72, 73, 82, 84, 85, 88, 89, 92], "more": [1, 2, 5, 24, 27, 37, 48, 62, 75, 82, 85, 95, 103, 104, 105, 115, 120, 123, 126, 134, 136, 161, 168, 172, 173, 174, 175, 178, 190, 197, 198, 203, 207, 210, 211, 213, 214, 215, 218, 230, 235, 236, 240, 241, 244, 245, 254], "construct": [1, 18, 19, 61, 64, 79, 83, 89, 95, 202, 205], "describ": [1, 13, 15, 62, 68, 82, 117, 167, 169, 172, 173, 178], "paramet": [1, 7, 13, 14, 15, 18, 21, 22, 24, 25, 27, 28, 32, 37, 38, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 63, 64, 65, 67, 68, 74, 75, 78, 81, 83, 84, 85, 89, 90, 91, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 139, 141, 142, 168, 169, 188, 207, 213, 215, 218, 231, 244, 251], "input": [1, 8, 13, 21, 23, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 83, 84, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 130, 144, 157, 161, 162, 167, 168, 169, 172, 174, 175, 176, 180, 182, 192, 207, 235, 240, 241, 242, 244, 245], "job": [1, 61, 62, 63, 64, 65, 68, 82, 173], "param": [1, 166], "filenam": [1, 48, 49, 51, 62, 69, 77, 78, 82, 108, 159, 162, 163, 164, 166, 169, 173, 175, 245], "appear": [1, 62, 78, 82, 95, 173, 175, 181, 188, 207], "work": [1, 3, 4, 6, 24, 103, 168, 178, 182, 190, 193, 204, 207, 210, 213, 235, 236, 237, 244, 245], "directori": [1, 29, 30, 78, 156, 161, 237, 241], "content": [1, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 84, 104, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 121, 127, 128, 136, 139, 157, 166, 173, 178], "specifi": [1, 13, 18, 19, 21, 22, 25, 27, 28, 33, 38, 48, 49, 51, 64, 79, 83, 85, 90, 91, 92, 95, 104, 124, 126, 127, 128, 129, 134, 142, 167, 169, 170, 171, 172, 176, 178, 181, 183, 185, 186, 210], "return": [1, 5, 8, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72, 73, 74, 75, 78, 79, 81, 82, 84, 85, 87, 89, 90, 91, 92, 95, 96, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 126, 127, 128, 129, 134, 136, 142, 158, 167, 170, 171, 205, 228, 249], "true": [1, 5, 8, 12, 14, 15, 17, 21, 24, 25, 26, 27, 28, 31, 36, 37, 38, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 75, 82, 84, 85, 90, 91, 92, 95, 96, 100, 104, 106, 107, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 142, 159, 164, 167, 168, 169, 170, 171, 176], "wa": [1, 27, 28, 61, 62, 65, 68, 69, 73, 75, 82, 84, 85, 100, 104, 124, 126, 173, 186, 188, 197, 202, 204, 230, 233, 235, 241], "successfulli": [1, 51, 61, 62, 65, 66, 75, 82, 84, 237, 244], "fals": [1, 5, 14, 15, 21, 24, 25, 27, 28, 31, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 75, 82, 84, 85, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 159, 164, 167, 169, 171, 173], "otherwis": [1, 14, 15, 21, 24, 25, 28, 37, 38, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 75, 82, 95, 100, 106, 109, 110, 111, 112, 113, 114, 126, 172, 173, 178, 212, 228], "bool": [1, 7, 8, 12, 14, 15, 17, 21, 22, 24, 25, 26, 27, 28, 31, 33, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 75, 77, 82, 84, 85, 86, 90, 91, 92, 95, 96, 98, 99, 100, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 121, 123, 124, 126, 129, 131, 132, 133, 134, 140, 142, 157, 158, 159, 160], "setinputfil": 1, "const": [1, 2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 72, 73, 75, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 144, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157], "qstring": [1, 2, 61, 62, 63, 64, 65, 67, 68, 69, 74, 75, 77, 78, 79, 80, 82, 83, 87, 92, 95, 96, 99, 100, 101, 102, 104, 108], "don": [2, 5, 68, 218, 241, 245], "t": [2, 5, 7, 8, 20, 37, 42, 44, 68, 129, 142, 147, 178, 183, 185, 193, 197, 207, 218, 241, 242, 245], "except": [2, 5, 167, 169, 178, 245], "assert": [2, 178], "product": [2, 197, 254], "never": [2, 169, 178], "crash": [2, 62, 82, 168, 173, 233, 235, 241, 243, 244, 245], "prefer": [2, 49, 62, 82, 134, 167, 171, 173, 192, 205, 207, 212, 244], "solut": 2, "from": [2, 3, 7, 15, 18, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 37, 39, 43, 48, 49, 51, 61, 62, 65, 67, 68, 69, 75, 78, 81, 82, 83, 84, 85, 90, 91, 95, 100, 104, 107, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 137, 138, 156, 158, 161, 166, 168, 169, 171, 172, 173, 174, 175, 176, 178, 180, 181, 182, 183, 186, 187, 189, 190, 192, 195, 197, 198, 200, 202, 204, 206, 207, 208, 211, 213, 214, 217, 219, 220, 221, 229, 230, 231, 232, 233, 235, 236, 237, 238, 240, 241, 242, 243, 244, 245, 248, 253], "librari": [2, 4, 51, 103, 142, 175, 181, 237, 241, 245], "over": [2, 182, 186, 192, 193, 196, 218, 228, 233, 235, 240, 241], "boost": [2, 237], "depend": [2, 3, 105, 171, 181, 198, 207, 218, 237, 240, 246, 253], "In": [2, 6, 27, 62, 82, 84, 168, 171, 173, 178, 182, 185, 200, 204, 214, 221, 229, 235, 237, 238, 246], "11": [2, 31, 178, 182], "17": [2, 36, 237], "where": [2, 5, 18, 22, 23, 24, 26, 27, 37, 62, 72, 73, 82, 104, 161, 166, 170, 171, 173, 178, 183, 194, 202, 211, 215, 226, 230, 235, 237, 245, 254], "necessari": [2, 5, 7, 96, 178, 211, 214, 218], "offer": [2, 3, 95, 173, 178, 204, 236], "avo_overrid": 2, "avo_fin": 2, "defin": [2, 41, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 82, 87, 106, 109, 110, 111, 112, 113, 114, 115, 121, 136, 140, 141, 142, 168, 170, 173, 178, 181, 182, 185, 205, 235], "overrid": [2, 24, 28, 32, 37, 40, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 72, 73, 75, 76, 77, 79, 82, 83, 84, 85, 86, 87, 88, 89, 92, 95, 96, 97, 98, 99, 100, 104, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 122, 124, 125, 126, 127, 128, 130, 136, 137, 138, 139, 143, 144, 146, 158, 173, 244], "final": [2, 61, 95, 168, 171, 190, 197, 245], "minim": [2, 62, 82, 140, 173, 190], "third": [2, 182, 237], "parti": [2, 178, 237], "think": [2, 167, 236], "carefulli": [2, 75], "befor": [2, 5, 12, 17, 24, 37, 51, 62, 66, 82, 85, 92, 95, 107, 176, 178, 187, 197, 212, 213, 218, 231, 237, 245], "ad": [2, 6, 24, 26, 28, 33, 37, 48, 61, 62, 81, 82, 85, 102, 120, 124, 126, 127, 128, 159, 164, 176, 188, 189, 190, 198, 200, 214, 221, 228, 235, 240, 245], "templat": [2, 6, 7, 8, 9, 12, 13, 17, 20, 42, 44, 62, 64, 65, 68, 82, 90, 91, 117, 129, 134, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 173, 241, 245], "sens": [2, 68], "alwai": [2, 5, 68, 174, 178, 212, 241, 243, 244], "form": [2, 14, 26, 83, 95, 104, 127, 167, 168, 169, 172, 173, 178, 197, 213, 215, 241, 243, 244, 254], "project": [2, 4, 5, 29, 30, 118, 138, 156, 159, 165, 182, 185, 206, 209, 236, 237, 241, 245], "someth": [2, 84, 100, 204], "type": [2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 20, 21, 22, 24, 25, 28, 32, 33, 37, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 71, 75, 77, 78, 81, 82, 85, 89, 90, 91, 95, 96, 99, 102, 103, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 121, 124, 126, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 159, 160, 165, 168, 170, 172, 173, 174, 175, 176, 180, 181, 189, 190, 191, 194, 197, 200, 202, 203, 205, 207, 209, 210, 213, 214, 217, 221, 225, 226, 229, 230, 235, 241, 248], "myclass": 2, "sourc": [2, 3, 5, 84, 133, 159, 161, 165, 183, 204, 236, 238, 240, 244], "special": [2, 75, 178], "first": [2, 7, 19, 22, 23, 24, 27, 28, 44, 51, 62, 65, 68, 79, 82, 84, 85, 95, 104, 127, 128, 142, 168, 169, 173, 182, 187, 202, 207, 210, 230, 244], "myapihead": 2, "our": [2, 3, 6, 115, 116, 120, 121, 124, 126, 127, 128, 129, 136, 137, 138, 167, 178, 183, 190, 236, 254], "molecul": [2, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 25, 27, 32, 33, 35, 38, 39, 40, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 69, 71, 75, 81, 86, 90, 91, 95, 96, 100, 103, 104, 106, 109, 110, 111, 112, 113, 114, 121, 131, 157, 159, 160, 161, 164, 165, 166, 167, 168, 169, 171, 177, 180, 181, 182, 191, 192, 196, 199, 201, 202, 203, 205, 206, 209, 210, 213, 215, 216, 217, 218, 219, 220, 222, 223, 225, 226, 227, 230, 232, 233, 235, 236, 240, 241, 243, 245, 246, 248, 249, 250, 251, 253, 254, 255, 256], "differ": [2, 4, 22, 28, 42, 43, 85, 99, 176, 178, 180, 199, 200, 214, 215, 221, 229, 235, 246, 251, 252, 253], "modul": [2, 170, 175, 214, 235, 237], "qtcore": 2, "vector": [2, 7, 18, 20, 21, 22, 24, 26, 27, 28, 33, 34, 35, 37, 39, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 81, 84, 95, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 120, 124, 134, 142, 182, 183, 232], "stl": [2, 7], "do": [2, 5, 12, 17, 84, 95, 122, 125, 130, 134, 144, 145, 171, 172, 178, 183, 190, 200, 202, 214, 221, 237, 240, 245, 246, 248], "avogadrorenderingexport": 2, "ar": [2, 3, 4, 5, 6, 13, 14, 15, 18, 21, 23, 24, 25, 26, 28, 37, 39, 41, 48, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 75, 78, 79, 80, 81, 82, 84, 92, 95, 103, 104, 115, 117, 120, 121, 124, 128, 134, 136, 140, 142, 161, 167, 168, 169, 172, 173, 174, 175, 176, 178, 181, 185, 187, 200, 202, 203, 211, 212, 214, 217, 218, 220, 221, 224, 226, 228, 235, 236, 237, 238, 240, 241, 243, 244, 245, 248, 251, 256], "denot": [2, 121, 129], "_p": 2, "camel": [2, 5], "case": [2, 5, 15, 24, 37, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 72, 73, 82, 84, 106, 109, 110, 111, 112, 113, 114, 166, 169, 171, 173, 178, 197, 200, 210, 220, 221, 243, 244, 245, 254], "qtgui": [2, 28, 62, 63, 64, 103, 104, 157, 159, 161], "instead": [2, 39, 75, 167, 168, 169, 244], "being": [2, 5, 15, 24, 27, 48, 84, 90, 91, 104, 120, 124, 157, 158, 198, 218, 220, 225, 237, 253], "wrong": [2, 5, 241], "qdialog": [2, 63, 65, 71], "correct": [2, 5, 49, 62, 82, 123, 126, 173, 190, 237, 245, 251], "open": [2, 3, 4, 5, 48, 51, 65, 68, 75, 78, 159, 161, 162, 163, 166, 169, 181, 182, 184, 185, 186, 187, 193, 198, 201, 204, 207, 209, 211, 228, 231, 232, 235, 236, 237, 240, 242, 243, 244, 245, 246], "chemistri": [2, 3, 4, 5, 204, 229, 231, 232, 236, 237, 240, 253], "nest": [2, 190], "everyth": [2, 206, 210, 217], "insid": [2, 5, 175, 237], "mongochem": [2, 245], "contain": [2, 5, 7, 8, 12, 15, 17, 18, 20, 21, 22, 24, 26, 27, 28, 33, 37, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 70, 75, 78, 82, 86, 87, 90, 91, 92, 95, 98, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 120, 124, 126, 130, 132, 134, 136, 142, 144, 146, 158, 159, 160, 167, 168, 169, 171, 172, 173, 175, 212, 214, 237, 244], "most": [2, 15, 61, 62, 72, 73, 75, 78, 82, 125, 126, 164, 168, 173, 178, 204, 205, 207, 211, 215, 218, 229, 230, 235, 237], "overspecifi": 2, "e": [2, 5, 19, 26, 27, 28, 33, 37, 43, 48, 62, 64, 74, 75, 82, 84, 85, 88, 89, 92, 95, 100, 132, 134, 138, 142, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 185, 190, 192, 193, 200, 212, 221, 228, 232, 233, 235, 237, 240, 241, 244, 245], "doesn": [2, 193, 197, 218], "slot": [2, 61, 62, 63, 65, 66, 68, 69, 71, 75, 77, 82, 85, 86, 87, 88, 89, 92, 95, 98, 100, 103, 104, 157], "moc": 2, "often": [2, 183, 215], "littl": 2, "help": [2, 3, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 106, 109, 110, 111, 112, 113, 114, 161, 167, 169, 172, 204, 205, 215, 230, 235, 236, 241, 243, 244, 253], "onli": [2, 5, 15, 21, 23, 28, 43, 51, 62, 65, 68, 81, 82, 85, 95, 104, 117, 121, 124, 133, 167, 168, 169, 171, 172, 173, 178, 190, 197, 198, 202, 207, 210, 214, 215, 218, 220, 229, 235, 237, 242, 243, 244, 245, 253, 256], "specif": [2, 11, 16, 19, 28, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 106, 109, 110, 111, 112, 113, 114, 159, 160, 171, 172, 173, 182, 197, 207, 210, 213, 215, 217, 218, 219, 230, 240, 245], "symbol": [2, 19, 23, 39, 40, 72, 73, 159, 160, 173, 200, 221, 243], "avoid": [2, 5, 22, 84, 178, 237, 244, 245, 254], "static_cast": 2, "dynamic_cast": [2, 129], "const_cast": 2, "reinterpret_cast": [2, 5], "For": [2, 4, 5, 15, 19, 23, 51, 61, 95, 134, 161, 167, 169, 170, 171, 172, 173, 176, 178, 182, 188, 191, 198, 204, 206, 207, 210, 211, 213, 214, 218, 220, 223, 224, 237, 248, 255], "deriv": [2, 15, 20, 21, 25, 38, 48, 85, 100, 104, 126, 158, 178, 229, 248, 249, 253], "qobject_cast": 2, "enum": [2, 15, 19, 21, 22, 24, 33, 37, 39, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 95, 96, 107, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155], "": [2, 12, 13, 17, 19, 21, 24, 26, 28, 37, 41, 42, 43, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 75, 79, 80, 81, 82, 84, 85, 95, 104, 106, 107, 109, 110, 111, 112, 113, 114, 118, 121, 129, 142, 157, 159, 160, 162, 166, 168, 169, 170, 172, 173, 178, 180, 183, 190, 200, 205, 207, 211, 213, 214, 216, 217, 218, 219, 220, 221, 225, 229, 230, 235, 237, 240, 245, 247, 253], "constant": [2, 23, 84, 207], "static": [2, 14, 21, 23, 28, 39, 41, 48, 49, 61, 65, 66, 68, 71, 74, 78, 81, 84, 99, 103, 116, 127, 128, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 215], "int": [2, 5, 12, 15, 17, 18, 21, 22, 24, 25, 27, 28, 33, 34, 37, 38, 41, 42, 44, 48, 51, 61, 62, 65, 67, 68, 72, 73, 74, 75, 79, 81, 82, 84, 85, 86, 88, 89, 92, 95, 98, 104, 105, 107, 118, 123, 127, 128, 134, 140, 141, 142, 158, 159, 160, 171], "verbos": 2, "argument": [2, 28, 43, 62, 65, 82, 85, 167, 168, 169, 171, 172, 173, 237], "id": [2, 26, 27, 28, 33, 49, 61, 65, 68, 85, 90, 91, 95, 115, 119, 131, 135, 136, 166, 237, 241], "show": [2, 28, 65, 78, 89, 181, 185, 187, 190, 191, 202, 207, 220, 228, 229, 235, 244], "autocomplet": 2, "It": [2, 14, 15, 18, 21, 24, 27, 28, 37, 43, 49, 62, 81, 82, 85, 95, 121, 168, 170, 171, 173, 194, 202, 204, 208, 214, 233, 235, 236, 237], "look": [2, 5, 49, 118, 171, 175, 183, 202, 211, 235, 237], "better": [2, 4, 204, 212, 218, 235, 236, 245], "poor": 2, "peopl": [2, 204], "guess": [2, 23], "abbrevi": [2, 5], "ambigu": 2, "can": [2, 7, 13, 20, 21, 23, 25, 27, 28, 38, 48, 49, 51, 61, 62, 64, 65, 66, 67, 68, 75, 78, 81, 82, 84, 85, 90, 91, 95, 100, 103, 115, 121, 130, 132, 133, 134, 136, 144, 157, 158, 161, 166, 167, 168, 169, 170, 172, 173, 174, 175, 176, 178, 182, 183, 185, 186, 187, 188, 189, 190, 191, 193, 194, 196, 197, 198, 200, 202, 203, 204, 205, 206, 207, 210, 211, 213, 214, 215, 217, 218, 219, 220, 221, 225, 226, 229, 230, 231, 235, 236, 237, 238, 240, 241, 243, 244], "afford": 2, "few": [2, 175, 190, 194, 233, 235, 245], "extra": [2, 62, 82, 168, 173, 182], "byte": [2, 51, 105, 141], "like": [3, 15, 24, 37, 61, 65, 78, 162, 166, 169, 171, 172, 190, 211, 212, 235, 236, 237, 241, 242, 243, 244, 245, 253], "mani": [3, 24, 37, 161, 167, 204, 207, 220, 223, 233, 234, 235, 240, 241, 242, 243, 244, 245], "fundament": 3, "commun": [3, 4, 66, 166, 178], "aim": [3, 229], "develop": [3, 4, 204, 229, 233, 235, 236, 240, 241, 243, 244], "contributor": [3, 233, 240, 241, 242, 243, 244, 245], "alik": [3, 179], "hope": 3, "build": [3, 21, 29, 30, 95, 98, 156, 168, 170, 180, 181, 196, 209, 215, 228, 233, 235, 236, 238, 240, 241, 243, 244, 245, 246, 247, 248, 254, 255], "top": [3, 75, 105, 118, 120, 123, 138, 141, 198, 223, 237, 243], "framework": [3, 235, 244, 245], "so": [3, 18, 21, 24, 37, 41, 51, 62, 82, 84, 95, 134, 142, 157, 158, 161, 166, 171, 173, 175, 178, 183, 190, 196, 197, 198, 207, 218, 237, 252, 254, 256], "veri": [3, 4, 22, 31, 36, 161, 183, 202, 241, 243, 244], "grate": 3, "shahzad": 3, "ali": 3, "michael": 3, "banck": 3, "ross": 3, "braithwait": 3, "jame": 3, "bunt": 3, "donald": 3, "curti": 3, "naomi": 3, "fox": 3, "geoff": [3, 74], "hutchison": [3, 74, 175, 204], "beno\u00eet": 3, "jacob": 3, "jordan": 3, "mantha": 3, "thoma": [3, 240], "margraf": 3, "carsten": 3, "niehau": 3, "simon": 3, "ochsenreith": 3, "konstantin": 3, "tokarev": 3, "allison": [3, 51, 60, 100, 101], "vacanti": [3, 51, 60, 100, 101], "tim": [3, 115], "vandermeersch": [3, 115], "translat": [3, 4, 22, 41, 67, 74, 118, 159, 162, 165, 167, 169, 172, 176, 178, 182, 183, 185, 189, 190, 202, 204, 217, 223, 236, 239, 240], "support": [3, 4, 12, 24, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 74, 78, 82, 95, 102, 106, 109, 110, 111, 112, 113, 114, 115, 117, 123, 134, 142, 161, 166, 167, 168, 169, 170, 172, 173, 175, 202, 228, 229, 235, 236, 237, 240, 241, 243, 244, 245], "its": [3, 8, 14, 26, 39, 49, 51, 72, 73, 81, 95, 126, 161, 170, 171, 178, 197, 205, 225, 252, 253, 254, 256], "ha": [3, 4, 13, 14, 15, 21, 24, 26, 28, 37, 41, 51, 64, 66, 68, 75, 85, 95, 96, 100, 123, 132, 134, 171, 178, 185, 187, 188, 191, 193, 197, 198, 200, 202, 205, 207, 208, 215, 218, 220, 221, 230, 232, 235, 237, 240, 245, 254], "come": [3, 193, 198, 214, 215, 220, 236], "would": [3, 75, 126, 134, 190, 202, 204, 233, 235, 236, 237, 253], "particularli": [3, 215, 233, 234, 241, 243, 244], "googl": [3, 241, 243, 244], "summer": [3, 204, 240, 241, 243, 244], "2007": 3, "2008": 3, "2011": 3, "2016": 3, "2018": 3, "2019": [3, 243], "2021": [3, 240, 241, 242], "2022": [3, 204, 243, 244], "kitwar": [3, 237], "inc": 3, "univers": [3, 204, 215, 218], "pittsburgh": [3, 204], "u": [3, 4, 7, 8, 20, 104, 126, 185, 190, 236, 240, 241, 243, 244], "depart": [3, 204], "defens": 3, "dod": 3, "through": [3, 4, 5, 6, 13, 64, 68, 75, 95, 100, 161, 164, 169, 171, 174, 175, 178, 181, 182, 186, 187, 188, 191, 192, 197, 198, 200, 202, 207, 208, 210, 214, 218, 221, 229, 235, 237, 240, 245], "pettt": 3, "program": [3, 65, 66, 67, 68, 134, 159, 163, 166, 167, 168, 173, 182, 188, 208, 214, 233, 243], "research": [3, 190, 236, 253], "corpor": [3, 178], "cottrel": 3, "scholar": 3, "award": 3, "reli": 3, "number": [3, 5, 12, 14, 15, 17, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 37, 38, 39, 51, 61, 62, 63, 72, 73, 74, 79, 81, 82, 84, 85, 95, 115, 120, 126, 128, 134, 136, 142, 166, 167, 169, 171, 173, 175, 176, 185, 191, 198, 200, 202, 205, 207, 212, 213, 218, 221, 237, 251], "infrastructur": 3, "blue": [3, 18, 23, 140, 142, 159, 160, 165, 197, 198, 217, 220, 230, 235], "obelisk": [3, 23], "group": [3, 5, 7, 12, 17, 19, 28, 39, 41, 61, 62, 63, 64, 65, 66, 68, 69, 78, 82, 85, 92, 95, 100, 104, 105, 116, 121, 122, 123, 126, 127, 128, 134, 136, 137, 138, 139, 140, 142, 157, 173, 183, 185, 186, 187, 188, 190, 205, 210, 229, 234, 235, 243, 245, 249, 251], "pybind11": 3, "chemic": [3, 23, 28, 33, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 161, 172, 173, 194, 202, 206, 208, 210, 214, 228, 235], "structur": [3, 21, 22, 23, 24, 26, 28, 37, 75, 170, 171, 183, 189, 190, 194, 196, 198, 200, 206, 211, 215, 218, 221, 235, 240, 241, 243, 251], "databas": [3, 4, 23, 174, 189, 196, 208, 228], "cmake": [3, 237, 245], "eigen": [3, 5, 28, 37, 107, 118, 134, 237], "softwar": [3, 207, 229], "babel": [3, 162, 169, 202, 235, 240, 243, 244], "And": [3, 167], "cours": [3, 189], "johann": 3, "loschmidt": 3, "amedeo": 3, "made": [4, 6, 7, 23, 26, 81, 100, 178, 179, 196, 197, 198, 202, 203, 208, 210, 211, 215, 226, 240], "who": 4, "want": [4, 7, 168, 185, 189, 190, 197, 200, 202, 212, 213, 221, 223, 229, 230, 236], "back": [4, 7, 83, 159, 160, 205, 211, 240, 241, 243], "great": [4, 236, 237], "place": [4, 5, 39, 49, 72, 73, 171, 173, 178, 183, 198, 206, 207, 211, 218, 223, 225, 236, 237, 249], "start": [4, 5, 24, 26, 92, 116, 120, 180, 181, 182, 189, 190, 205, 216, 218, 219, 222, 227, 232, 236, 241, 245], "fellow": 4, "forum": [4, 6], "question": [4, 236], "level": [4, 62, 75, 82, 173, 237], "post": [4, 213], "mai": [4, 18, 28, 39, 51, 62, 64, 67, 75, 82, 95, 96, 100, 104, 105, 117, 126, 134, 167, 168, 171, 173, 175, 176, 178, 181, 183, 185, 189, 190, 191, 194, 204, 212, 214, 218, 228, 229, 231, 233, 237, 248, 253, 256], "find": [4, 14, 22, 29, 30, 41, 51, 78, 84, 95, 99, 156, 170, 171, 180, 202, 214, 216, 231, 235, 236, 244, 250, 253], "experi": 4, "valuabl": 4, "bug": [4, 6, 193, 236, 239], "pleas": [4, 6, 236, 240, 241, 243, 244, 253], "take": [4, 22, 28, 49, 62, 69, 72, 73, 75, 82, 87, 104, 122, 123, 137, 171, 181, 194, 198, 207, 211, 214, 218, 223, 225, 231], "moment": [4, 190, 231], "tracker": [4, 236], "issu": [4, 6, 236, 240, 245], "code": [4, 6, 24, 37, 62, 82, 84, 88, 161, 167, 169, 170, 171, 173, 183, 190, 191, 193, 207, 231, 232, 235, 236, 238, 240, 241, 243, 244, 245], "while": [4, 5, 26, 62, 82, 84, 95, 100, 168, 169, 173, 182, 187, 213, 218, 228, 244], "move": [4, 28, 104, 138, 142, 178, 185, 193, 196, 202, 218, 223, 235, 245, 246], "around": [4, 5, 15, 22, 31, 36, 63, 65, 69, 185, 187, 190, 196, 198, 202, 213, 223, 235, 248, 253], "fit": [4, 5, 28, 51, 104, 123, 157, 178], "particular": [4, 23, 51, 62, 75, 82, 166, 167, 169, 173, 178, 189, 204], "compon": [4, 18, 22, 23, 26, 28, 127, 128, 132, 140, 142, 161], "itself": 4, "section": [4, 21, 62, 67, 82, 95, 173, 175, 198, 203, 204, 205, 207, 213, 218, 223, 235, 253], "discuss": [4, 6, 168, 207, 236, 240, 241, 243, 244, 253], "idea": [4, 236], "plan": 4, "direct": [4, 18, 41, 62, 82, 115, 118, 119, 120, 121, 124, 128, 136, 142, 159, 165, 173, 178, 193, 219, 237, 243, 246], "progress": [4, 27, 84, 208], "etc": [4, 5, 17, 24, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 100, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 120, 133, 134, 136, 142, 157, 161, 168, 169, 170, 173, 176, 198, 202, 207, 228, 229, 232, 235, 236, 237, 240, 245, 248], "both": [4, 15, 26, 51, 63, 64, 161, 167, 169, 172, 173, 175, 176, 187, 214, 236, 256], "python": [4, 92, 99, 161, 168, 171, 174, 175, 216, 236, 237, 239, 241, 243, 244, 245], "script": [4, 63, 64, 75, 83, 92, 99, 100, 162, 172, 214, 236, 240, 241, 242, 244, 245], "util": [4, 64, 92, 99, 118, 175, 188, 198, 207], "tell": [4, 100, 166], "friend": [4, 27, 41, 67, 79, 95, 115, 116, 120, 121, 127, 128, 129, 136, 139], "cite": 4, "paper": [4, 21, 192, 236, 246], "write": [4, 5, 7, 15, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 78, 82, 92, 103, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 170, 173, 243, 244, 245], "edit": [4, 14, 64, 95, 161, 180, 188, 197, 198, 200, 202, 207, 209, 210, 211, 221, 223, 232, 233, 235, 237, 243, 244, 245], "tutori": [4, 180, 181, 198, 207, 235, 236], "site": [4, 235, 236], "up": [4, 24, 26, 27, 37, 49, 51, 84, 98, 104, 118, 142, 157, 161, 166, 170, 181, 185, 188, 189, 190, 193, 194, 196, 197, 202, 207, 208, 210, 211, 212, 224, 228, 230, 233, 235, 244, 245], "lesson": [4, 185, 253], "activ": [4, 24, 70, 75, 86, 87, 88, 89, 96, 100, 103, 104, 214, 235, 237], "teacher": 4, "send": [4, 61, 66, 92, 161, 166, 173, 240], "fragment": [4, 133, 134, 159, 165, 180, 192, 195, 203, 205, 223, 226, 235, 240, 245], "report": [4, 6, 62, 82, 173, 183, 236, 241, 242, 243, 244], "encount": [4, 6, 48, 51, 104], "about": [4, 19, 23, 39, 62, 82, 118, 173, 197, 207, 211, 213, 225, 236, 243, 244], "improv": [4, 6, 233, 235, 239, 242], "languag": [4, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 167, 168, 169, 170, 173, 210, 236, 244], "donat": 4, "pai": [4, 204, 256], "host": [4, 243, 244, 245], "meet": 4, "bounti": 4, "when": [5, 7, 8, 13, 15, 18, 20, 24, 28, 37, 49, 51, 61, 62, 63, 64, 65, 66, 68, 69, 75, 78, 82, 88, 89, 92, 95, 100, 104, 123, 127, 128, 157, 168, 169, 170, 171, 173, 175, 187, 188, 197, 198, 202, 203, 205, 207, 211, 212, 214, 223, 231, 237, 241, 244, 245, 246, 248], "base": [5, 7, 8, 13, 15, 19, 28, 33, 48, 62, 75, 76, 78, 79, 82, 85, 97, 100, 101, 116, 120, 121, 122, 124, 125, 129, 130, 144, 145, 161, 169, 171, 173, 175, 176, 178, 190, 191, 205, 207, 210, 235, 244, 245, 248, 253], "larg": [5, 7, 51, 181, 185, 186, 189, 190, 202, 235, 237], "kde": 5, "format": [5, 19, 33, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 75, 78, 79, 80, 82, 106, 109, 110, 111, 112, 113, 114, 140, 142, 161, 162, 166, 167, 169, 170, 171, 173, 174, 175, 178, 179, 193, 207, 229, 231, 235, 240, 241, 242, 243, 244, 245], "enforc": [5, 178], "clang": [5, 244], "tool": [5, 25, 38, 75, 100, 101, 104, 159, 164, 180, 182, 185, 189, 190, 196, 198, 200, 202, 203, 204, 213, 233, 236, 240, 242, 243, 245, 248, 252, 255, 256], "space": [5, 19, 21, 22, 25, 27, 28, 38, 39, 51, 95, 146, 159, 160, 169, 173, 181, 183, 185, 186, 187, 188, 211, 243, 245, 251], "tab": [5, 211, 241, 244], "keep": [5, 26, 51, 65, 67, 95, 103, 105, 213, 237], "less": [5, 12, 17, 23, 28, 95, 207, 230, 235, 254], "than": [5, 7, 12, 17, 23, 26, 28, 51, 62, 82, 95, 166, 178, 186, 235, 241, 251, 254], "80": 5, "charact": [5, 19, 48, 62, 82, 168, 173], "wide": [5, 204, 207, 235], "each": [5, 13, 19, 24, 26, 27, 32, 37, 40, 48, 51, 61, 62, 63, 82, 95, 134, 142, 161, 169, 170, 173, 175, 176, 212, 237, 255, 256], "separ": [5, 142, 168, 173, 178, 229, 234], "g": [5, 19, 24, 28, 33, 48, 62, 74, 75, 82, 88, 89, 92, 100, 134, 138, 140, 142, 159, 160, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 190, 192, 193, 200, 212, 221, 228, 232, 235, 237, 240, 245], "nmbr": 5, "singl": [5, 17, 28, 51, 62, 64, 66, 70, 82, 84, 95, 116, 142, 173, 190, 191, 197, 203, 226, 244], "fine": [5, 62, 82, 173], "counter": [5, 62, 82, 92], "temporari": [5, 169], "obviou": 5, "wait": [5, 64, 67, 92], "until": [5, 7, 64, 65, 205, 218, 251], "unus": [5, 15, 24, 37], "ones": 5, "incorrect": [5, 241, 244, 245], "f": [5, 24, 37, 70, 87, 107, 121, 134, 136, 138, 157, 159, 160, 169, 178, 215, 241], "lower": [5, 26, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 106, 109, 110, 111, 112, 113, 114, 142, 211], "letter": [5, 23, 191, 243], "word": 5, "acronym": 5, "cmlformat": [5, 48, 159, 162], "doubl": [5, 14, 17, 23, 24, 25, 28, 37, 38, 39, 42, 51, 89, 95, 107, 116, 157, 158, 159, 160, 190, 191, 200, 203, 221, 225, 226, 244, 254], "cntr": 5, "std": [5, 7, 8, 9, 10, 12, 15, 19, 20, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 37, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 81, 85, 95, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 120, 121, 123, 124, 126, 130, 133, 134, 136, 139, 141, 142, 144], "string": [5, 6, 12, 15, 19, 22, 23, 24, 27, 28, 32, 33, 34, 39, 40, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 68, 69, 75, 78, 79, 80, 82, 95, 100, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 117, 123, 130, 133, 134, 139, 141, 142, 144, 159, 160, 162, 166, 168, 171, 173, 192], "rawxml": 5, "char": [5, 12, 17, 23, 24, 28, 33, 39, 42, 85, 95, 100, 105, 127, 128, 134, 139, 140, 141, 142, 147, 149, 150, 151, 152, 154, 155, 159, 160], "list_delimit": 5, "center": [5, 28, 115, 118, 125, 132, 136, 159, 165, 185, 189, 190, 191, 197, 198, 209, 226, 235, 241, 245], "listdelimit": 5, "upper": [5, 137], "m_": 5, "blank": [5, 176, 211], "togeth": [5, 95, 126, 175], "after": [5, 28, 48, 51, 62, 63, 65, 68, 82, 89, 117, 168, 169, 176, 181, 185, 186, 187, 188, 190, 194, 196, 197, 200, 205, 207, 208, 213, 221, 223, 230, 232, 240], "curli": 5, "blah": [5, 62, 82, 176], "explod": 5, "5": [5, 14, 39, 41, 62, 82, 95, 159, 160, 176, 185, 222, 237, 244, 245, 246, 248, 255, 256], "pointer": [5, 7, 23, 27, 42, 44, 65, 78, 121, 124, 126, 129, 159, 160], "refer": [5, 7, 12, 17, 42, 44, 63, 65, 66, 67, 78, 79, 85, 90, 91, 103, 104, 115, 117, 118, 120, 124, 126, 134, 136, 142, 157, 159, 160, 170, 178, 213, 217, 218, 242], "between": [5, 14, 22, 23, 26, 28, 41, 42, 43, 84, 85, 95, 166, 171, 172, 181, 182, 198, 207, 213, 218, 224, 245, 251, 253, 256], "x": [5, 19, 21, 22, 27, 28, 123, 169, 172, 173, 182, 198, 205, 207, 211, 217, 219, 235, 237, 245, 254], "mystr": 5, "y": [5, 19, 22, 28, 118, 123, 169, 173, 198, 205, 207, 211, 217, 219, 237], "whoah": 5, "surround": [5, 230], "binari": [5, 237, 244], "oper": [5, 7, 12, 13, 17, 20, 21, 27, 28, 33, 34, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 69, 71, 78, 79, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 127, 128, 131, 134, 136, 139, 140, 142, 159, 160, 162, 164, 165, 168, 170, 172, 182], "No": [5, 21, 26, 167, 178, 244], "memoryblock": 5, "malloc": 5, "data": [5, 7, 8, 15, 18, 20, 22, 23, 24, 25, 26, 27, 28, 33, 37, 38, 39, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 75, 82, 84, 85, 86, 92, 95, 98, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 132, 134, 141, 142, 146, 157, 159, 160, 163, 164, 166, 167, 171, 172, 180, 195, 206, 209, 210, 229, 235, 240, 251, 252, 254], "size": [5, 7, 18, 20, 26, 27, 43, 51, 84, 115, 117, 120, 134, 136, 142, 159, 160, 165, 181, 182, 198, 211, 240, 245, 251], "left": [5, 51, 62, 82, 105, 118, 137, 141, 142, 173, 200, 202, 203, 205, 211, 217, 218, 220, 221, 226, 237], "normal": [5, 7, 24, 27, 28, 37, 62, 75, 82, 84, 89, 115, 119, 120, 121, 124, 128, 134, 136, 159, 160, 164, 165, 173, 187, 202], "same": [5, 12, 17, 21, 26, 51, 61, 63, 127, 128, 167, 178, 197, 211, 215, 237, 246, 256], "foo": 5, "run": [5, 13, 27, 61, 64, 67, 68, 82, 83, 84, 103, 159, 160, 164, 167, 168, 169, 170, 172, 175, 202, 209, 214, 232, 235, 242, 244, 250], "implement": [5, 11, 13, 16, 21, 32, 40, 45, 46, 47, 51, 53, 54, 55, 58, 59, 60, 62, 75, 82, 84, 89, 92, 95, 105, 113, 117, 122, 134, 139, 141, 142, 161, 166, 172, 243, 244], "myfun": 5, "cout": 5, "suppli": [5, 22, 23, 24, 28, 37, 48, 49, 62, 63, 75, 78, 82, 84, 95, 96, 107, 118, 121, 124, 133, 134, 136, 157, 167, 168, 169, 178, 202], "endl": 5, "bar": [5, 207, 211, 223, 225, 231], "bodi": 5, "condit": [5, 21, 190], "also": [5, 26, 27, 39, 48, 62, 72, 73, 82, 95, 104, 115, 132, 136, 161, 167, 169, 171, 173, 174, 175, 178, 181, 185, 187, 189, 190, 191, 193, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 214, 215, 218, 219, 221, 224, 225, 226, 229, 235, 236, 237, 244, 253], "complex": [5, 126, 235, 245], "42": 5, "var": [5, 170], "parent": [5, 44, 61, 65, 67, 69, 70, 71, 75, 78, 81, 84, 86, 87, 88, 95, 96, 98, 100, 101, 104, 121, 126, 129, 143, 159, 160, 163, 164, 165], "doe": [5, 7, 12, 14, 21, 28, 39, 51, 85, 92, 95, 104, 118, 134, 158, 167, 168, 169, 178, 186, 207, 215, 223, 251], "wrap": [5, 41, 95, 142, 158, 159, 165], "isvalid": [5, 12, 15, 17, 24, 25, 37, 38, 62, 82, 85, 90, 91, 104, 123, 131, 159, 160, 163, 164, 165], "agooddai": 5, "ani": [5, 7, 12, 13, 17, 22, 26, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 68, 75, 78, 79, 80, 82, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 117, 118, 124, 134, 166, 167, 168, 169, 171, 172, 173, 175, 176, 178, 194, 202, 205, 208, 211, 220, 233, 237, 245], "els": 5, "block": [5, 19, 62, 82, 168, 176], "element": [5, 7, 19, 20, 24, 26, 27, 28, 32, 40, 71, 72, 73, 74, 88, 89, 95, 122, 128, 130, 132, 134, 142, 144, 159, 160, 164, 167, 169, 170, 171, 173, 176, 178, 181, 188, 199, 200, 205, 209, 215, 221, 235, 241, 244, 248], "cover": [5, 168, 204, 228], "b": [5, 19, 21, 26, 28, 41, 47, 53, 59, 85, 91, 95, 105, 140, 159, 160, 169, 173, 178, 191, 243, 245, 251], "empti": [5, 7, 19, 24, 26, 28, 33, 39, 42, 43, 48, 49, 51, 75, 78, 79, 95, 117, 123, 133, 134, 159, 160, 168, 187, 240], "express": [5, 62, 82, 173, 178, 254], "intent": 5, "clearer": 5, "label": [5, 12, 19, 28, 62, 82, 95, 107, 138, 159, 160, 164, 168, 170, 173, 176, 178, 199, 213, 235, 240, 241, 243, 245], "column": [5, 21, 41, 67, 86, 98], "everi": [5, 26, 28, 178, 228], "must": [5, 15, 24, 25, 28, 37, 51, 62, 65, 75, 78, 82, 84, 95, 105, 117, 119, 127, 128, 133, 134, 141, 142, 167, 168, 169, 171, 172, 173, 175, 178, 205, 214, 237], "indic": [5, 19, 22, 26, 27, 28, 62, 63, 65, 67, 68, 75, 78, 81, 82, 85, 95, 103, 104, 115, 128, 134, 136, 167, 168, 169, 171, 172, 173, 175, 176, 178, 181, 185, 211, 213, 220, 242], "omiss": 5, "anoth": [5, 39, 51, 169, 183, 188, 198, 200, 203, 221, 235, 256], "immedi": [5, 175], "myenum": 5, "drawlin": [5, 116, 159, 165], "vertex": [5, 26, 27, 84, 116, 127, 128, 133, 134, 159, 160, 165, 224], "drawdot": 5, "fall": [5, 240, 241, 243], "default": [5, 15, 19, 23, 24, 25, 27, 28, 33, 37, 48, 51, 62, 64, 75, 78, 82, 95, 96, 104, 118, 127, 128, 132, 133, 138, 142, 168, 170, 173, 176, 191, 198, 200, 202, 211, 212, 218, 221, 231, 235, 245], "drawdefault": 5, "shorter": 5, "insert": [5, 7, 28, 62, 82, 159, 160, 168, 176, 180, 181, 185, 189, 190, 191, 192, 195, 209, 223, 235, 240, 241, 243, 245, 246], "comma": [5, 167, 169], "broken": 5, "begin": [5, 7, 43, 84, 95, 105, 130, 141, 144, 159, 160, 165, 200, 203, 220, 221, 230, 232], "verylongexpress": 5, "anotherevenlongerexpress": 5, "justwhenyouthoughtitcouldntgetlong": 5, "vector3d": [5, 107], "posit": [5, 7, 12, 14, 21, 22, 25, 28, 38, 81, 84, 95, 115, 118, 119, 125, 132, 134, 135, 136, 138, 159, 160, 165, 185, 189, 190, 205, 211, 223, 235, 249, 254, 256], "currentposit": 5, "offset": [5, 84, 134, 159, 164], "reimplement": [5, 64, 104], "put": [5, 235, 245], "discourag": 5, "prefix": [5, 12, 17, 62, 78, 82, 172, 175, 176, 237], "clear": [5, 7, 13, 26, 27, 42, 43, 48, 62, 82, 84, 86, 89, 98, 104, 115, 116, 120, 121, 125, 126, 127, 128, 132, 136, 139, 157, 159, 160, 162, 164, 165, 182, 203, 209, 226, 240], "cpp": [5, 84], "extens": [5, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 76, 78, 82, 106, 109, 110, 111, 112, 113, 114, 161, 166, 167, 168, 169, 172, 173, 180, 182, 198, 200, 209, 210, 213, 214, 218, 221, 229, 230, 235, 236, 240, 243, 244, 245], "As": [5, 6, 166, 168, 189, 198, 209, 217, 224, 228, 237, 240, 243], "feel": [5, 236], "free": [5, 51, 104, 168, 173, 178, 204, 236, 237], "bad": 5, "local": [6, 62, 74, 82, 84, 168, 173, 175, 176, 236, 240, 243, 245], "avail": [6, 25, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 66, 67, 68, 75, 82, 84, 100, 104, 106, 109, 110, 111, 112, 113, 114, 133, 158, 167, 168, 169, 170, 172, 173, 176, 178, 179, 235, 236, 244], "weblat": [6, 240, 241, 242, 243, 244, 245], "autom": [6, 49, 175, 235, 243, 244], "task": [6, 215, 235], "phrase": 6, "whenev": 6, "allow": [6, 7, 27, 31, 36, 42, 62, 78, 82, 161, 162, 167, 169, 172, 173, 178, 181, 182, 185, 187, 188, 189, 190, 192, 193, 198, 200, 202, 203, 205, 207, 208, 210, 211, 213, 218, 219, 220, 223, 224, 225, 226, 229, 231, 232, 235, 240, 244, 245], "time": [6, 51, 62, 82, 92, 95, 104, 117, 126, 161, 178, 181, 186, 190, 245], "freez": [6, 28], "least": [6, 75, 95, 212, 224, 230, 235, 244], "week": 6, "advanc": [6, 62, 82, 173, 236, 237], "releas": [6, 51, 117, 134, 142, 159, 165, 175, 204, 233, 237, 238, 239], "typenam": [7, 8, 9, 13, 20, 42, 44, 90, 91, 129, 147], "copi": [7, 12, 17, 22, 27, 28, 42, 49, 78, 85, 105, 141, 185, 192, 209, 214, 240, 243, 245], "semant": 7, "effect": [7, 118, 178, 214, 246, 251], "share": [7, 12, 17, 26, 36, 175, 178, 179, 235, 237], "without": [7, 26, 49, 51, 65, 68, 161, 178, 202, 204, 207, 208, 233, 237, 241], "expos": 7, "access": [7, 18, 51, 64, 66, 67, 83, 103, 117, 134, 142, 169, 178, 193, 198, 208, 244], "amount": [7, 185, 207], "non": [7, 8, 23, 28, 62, 82, 95, 126, 169, 171, 173, 178, 240, 241, 244, 245], "trigger": [7, 104, 171], "detach": [7, 134, 159, 160, 209, 243], "op": 7, "count": [7, 12, 28], "1": [7, 12, 15, 17, 18, 19, 21, 22, 24, 26, 28, 51, 62, 65, 68, 82, 85, 95, 105, 118, 132, 134, 141, 142, 159, 160, 167, 169, 171, 173, 175, 176, 182, 183, 185, 187, 190, 191, 193, 200, 204, 209, 212, 222, 224, 233, 235, 237, 238, 239, 240, 245, 246, 247, 252, 253, 254, 255, 256], "perform": [7, 13, 15, 21, 42, 51, 63, 84, 95, 104, 134, 168, 170, 171, 178, 182, 188, 202, 207, 212, 235, 237, 239, 246, 256], "deep": [7, 230, 237], "greater": 7, "unnam": [7, 12, 17, 19, 28, 41, 61, 63, 64, 65, 66, 68, 69, 78, 85, 92, 95, 100, 104, 105, 116, 121, 122, 123, 127, 128, 134, 137, 138, 139, 140, 142, 157], "typedef": [7, 11, 12, 13, 16, 17, 21, 28, 33, 43, 44, 48, 61, 78, 85, 90, 91, 95, 140], "value_typ": [7, 44, 117, 134, 142, 159, 160], "compat": [7, 78, 178, 207], "allocator_typ": [7, 44, 159, 160], "const_refer": [7, 44, 159, 160], "const_point": [7, 44, 159, 160], "iter": [7, 13, 43, 44, 159, 160], "const_iter": [7, 43, 44, 159, 160], "reverse_iter": [7, 44, 159, 160], "const_reverse_iter": [7, 44, 159, 160], "difference_typ": [7, 44, 159, 160], "size_typ": [7, 44, 142, 159, 160], "intern": [7, 13, 39, 51, 61, 63, 65, 66, 78, 89, 139, 142, 159, 160, 167, 169, 172, 236], "arrayrefcontain": [7, 159, 160], "valuetyp": [7, 8, 9, 10, 13, 44, 159, 160], "inlin": [7, 8, 9, 10, 11, 15, 16, 18, 19, 20, 22, 24, 25, 27, 28, 33, 34, 37, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 68, 69, 70, 75, 77, 79, 80, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 97, 100, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139, 140, 142, 144, 145, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 158], "explicit": [7, 13, 25, 26, 32, 35, 38, 40, 41, 44, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 75, 77, 79, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 104, 122, 126, 127, 128, 133, 143], "size_t": [7, 12, 26, 28, 35, 43, 44, 51, 81, 95, 115, 116, 120, 124, 126, 127, 128, 134, 136, 140], "n": [7, 15, 19, 24, 26, 27, 37, 44, 126, 128, 173, 189, 190, 215], "valu": [7, 8, 9, 15, 18, 19, 21, 22, 24, 25, 27, 28, 33, 37, 38, 42, 43, 44, 48, 49, 51, 61, 65, 67, 77, 78, 81, 84, 85, 86, 92, 96, 98, 104, 117, 118, 121, 126, 128, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 159, 160, 167, 169, 170, 172, 173, 175, 207, 246], "inputiter": [7, 44], "last": [7, 22, 44, 62, 68, 82, 92, 206, 241], "note": [7, 24, 28, 62, 82, 118, 128, 134, 142, 166, 169, 173, 175, 176, 183, 185, 186, 187, 190, 198, 202, 204, 237, 239, 246, 249, 250, 256], "detachwithcopi": [7, 159, 160], "explicitli": [7, 166], "implicitli": 7, "ensur": [7, 21, 28, 62, 66, 82, 85, 95, 123, 132, 173, 207, 237, 240, 245], "retriev": [7, 15, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 82, 106, 109, 110, 111, 112, 113, 114], "underli": [7, 18, 64, 83, 90, 91], "constdata": [7, 159, 160], "max_siz": [7, 159, 160], "capac": [7, 159, 160], "reserv": [7, 13, 27, 159, 160, 178], "sz": 7, "resiz": [7, 20, 51, 89, 104, 123, 159, 160, 165], "rbegin": [7, 159, 160], "rend": [7, 159, 160], "front": [7, 159, 160], "assign": [7, 26, 27, 28, 32, 40, 85, 95, 159, 160, 167, 235, 243, 244], "val": 7, "push_back": [7, 159, 160], "v": [7, 39, 41, 42, 43, 127, 128, 134, 176, 178, 193, 237, 245, 247, 254], "pop_back": [7, 159, 160], "eras": [7, 159, 160], "idx": [7, 67, 79], "othert": 7, "swap": [7, 26, 41, 79, 115, 116, 120, 121, 127, 128, 136, 139, 140, 159, 160, 164, 165], "swapandpop": [7, 159, 160], "index": [7, 11, 12, 13, 16, 17, 19, 20, 22, 24, 26, 28, 33, 37, 62, 67, 79, 82, 85, 86, 90, 91, 93, 94, 95, 98, 115, 117, 120, 124, 126, 127, 128, 131, 133, 134, 136, 142, 159, 160, 163, 164, 165, 171, 173, 176, 190, 245], "delet": [7, 49, 51, 69, 95, 104, 124, 126, 133, 157, 168, 182, 200, 205, 211, 221, 241, 243, 245, 249], "valid": [7, 15, 24, 25, 27, 37, 38, 48, 62, 68, 82, 85, 90, 91, 95, 104, 123, 128, 129, 133, 159, 160, 172, 173, 176, 237, 245], "pop": [7, 170, 188, 194, 196, 197, 207, 208, 210, 211, 230], "preserv": [7, 21, 26, 51, 95, 187], "protect": [7, 8, 13, 15, 18, 22, 28, 32, 33, 40, 48, 67, 79, 84, 88, 89, 92, 95, 96, 104, 121, 124, 126, 129, 133, 134, 139, 158, 178], "attribut": [7, 8, 13, 15, 18, 22, 28, 33, 61, 62, 68, 82, 84, 92, 95, 96, 116, 117, 121, 124, 126, 127, 128, 129, 133, 134, 139, 158, 173, 175, 179], "arrai": [8, 13, 18, 20, 21, 22, 26, 27, 28, 39, 51, 62, 82, 84, 85, 95, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 159, 160, 167, 169, 172, 173, 176], "store": [8, 18, 20, 23, 24, 25, 28, 37, 38, 39, 42, 51, 62, 63, 64, 79, 80, 82, 95, 115, 116, 117, 118, 121, 127, 136, 142, 208, 245], "figur": [8, 73, 213, 251], "subclass": [8, 10, 15, 28, 45, 48, 66, 121, 126, 127, 128, 129, 131, 139, 141, 145], "coordinateset": [8, 159, 160], "istyp": [8, 159, 160], "match": [8, 23, 28, 39, 49, 62, 65, 67, 68, 78, 79, 80, 82, 117, 168, 173, 231, 237], "placehold": [8, 9, 63, 159, 160], "m_content": [8, 9, 159, 160], "m_data": [8, 18, 22, 28, 159, 160], "holder": [8, 10, 159, 160, 178], "type_info": [8, 9, 10], "clone": [8, 9, 10, 15, 24, 37, 159, 160], "atomtempl": [11, 93, 159, 160], "repres": [11, 12, 16, 17, 18, 21, 23, 26, 28, 33, 39, 42, 49, 63, 64, 66, 67, 83, 95, 121, 131, 161, 171, 198, 233, 235], "moleculeclass": [11, 16], "atomtyp": [11, 17, 28, 32, 40, 85, 90, 95, 159, 160, 164], "m": [11, 12, 16, 17, 24, 35, 37, 41, 64, 77, 90, 91, 93, 94, 95, 178, 187, 190], "molecule_t": [12, 17, 90, 91], "setatomicnumb": [12, 28, 95, 159, 160, 164], "unsign": [12, 14, 15, 17, 21, 22, 23, 24, 27, 28, 37, 39, 42, 44, 61, 65, 68, 84, 85, 95, 100, 105, 107, 127, 128, 134, 139, 140, 141, 142, 159, 160], "num": [12, 24, 28, 95, 171], "proton": [12, 72, 230, 246, 253], "atom": [12, 13, 15, 17, 19, 21, 23, 24, 28, 32, 33, 37, 39, 40, 62, 74, 81, 82, 85, 90, 95, 96, 107, 131, 138, 159, 160, 161, 164, 165, 169, 170, 171, 173, 180, 181, 182, 183, 185, 188, 197, 199, 200, 203, 205, 209, 210, 211, 212, 213, 217, 218, 219, 220, 221, 223, 224, 225, 226, 227, 228, 230, 232, 233, 235, 240, 241, 243, 244, 245, 248, 254, 256], "atomicnumb": [12, 23, 28, 85, 95, 159, 160, 164], "setposition2d": [12, 159, 160], "vector2": [12, 28, 95], "po": [12, 22, 28, 84, 95, 119, 135], "2d": [12, 28, 211, 240], "Not": 12, "current": [12, 13, 17, 26, 27, 28, 48, 51, 55, 61, 63, 64, 65, 68, 74, 75, 84, 87, 89, 95, 100, 103, 105, 115, 116, 118, 120, 121, 122, 123, 127, 128, 129, 132, 133, 134, 136, 139, 141, 166, 168, 185, 198, 208, 210, 211, 212, 223, 235, 236, 248], "moleculetyp": [12, 17, 90, 91, 159, 160, 164], "compil": [12, 133, 134, 159, 165, 237], "position2d": [12, 159, 160], "setposition3d": [12, 159, 160], "vector3": [12, 21, 22, 25, 28, 38, 39, 41, 81, 85, 95], "3d": [12, 22, 28, 95, 104, 118, 127, 128, 134, 161, 169, 171, 192, 202, 211, 235, 244], "position3d": [12, 28, 85, 95, 159, 160], "sethybrid": [12, 28, 95, 159, 160, 164], "atomhybrid": [12, 28, 95], "hyb": [12, 28, 95], "hybrid": [12, 28, 95, 159, 160, 164, 248, 253], "coordin": [12, 19, 20, 21, 24, 28, 39, 41, 62, 82, 95, 107, 116, 118, 123, 134, 137, 138, 142, 159, 160, 162, 182, 183, 186, 187, 205, 240, 241, 245], "setformalcharg": [12, 28, 95, 159, 160, 164], "sign": [12, 28, 95, 134, 237, 243], "charg": [12, 28, 62, 82, 95, 173, 174, 175, 207, 215, 230, 235, 241, 243, 244, 245, 246, 256], "formal": [12, 28, 95, 243, 245], "formalcharg": [12, 28, 95, 159, 160, 164], "setcolor": [12, 27, 28, 33, 95, 127, 128, 131, 159, 160, 164, 165], "vector3ub": [12, 28, 33, 95, 115, 119, 120, 127, 128, 130, 131, 134, 135, 136, 140, 144], "color": [12, 18, 23, 27, 28, 33, 62, 82, 95, 115, 120, 127, 128, 131, 132, 136, 140, 142, 157, 159, 160, 164, 165, 173, 174, 176, 180, 185, 198, 199, 207, 209, 230, 235, 240, 241, 243, 244, 245], "setlay": [12, 28, 95, 159, 160, 164], "layer": [12, 28, 85, 95, 159, 160, 164, 241, 242, 243, 244, 245], "invalid": [12, 17, 28, 39, 48, 68, 85, 90, 91, 95, 131, 159, 165, 241], "object": [12, 13, 17, 18, 24, 27, 28, 42, 43, 49, 51, 61, 62, 63, 64, 67, 68, 72, 75, 78, 82, 83, 84, 85, 90, 91, 95, 100, 103, 104, 105, 107, 115, 116, 117, 118, 120, 121, 123, 124, 127, 128, 131, 134, 136, 141, 145, 158, 164, 167, 168, 169, 172, 173, 197, 213, 240], "increment": [12, 17], "self": [12, 17, 244], "check": [12, 15, 17, 21, 25, 27, 28, 38, 39, 48, 62, 68, 75, 82, 85, 92, 95, 104, 123, 126, 170, 171, 175, 176, 200, 211, 213, 218, 220, 221, 225, 240, 244, 245, 250, 251, 256], "postfix": [12, 17], "decrement": [12, 17], "setselect": [12, 159, 160], "select": [12, 28, 65, 68, 78, 85, 89, 95, 159, 160, 164, 176, 180, 181, 182, 185, 188, 189, 190, 191, 192, 193, 194, 196, 198, 199, 200, 201, 202, 205, 208, 209, 211, 213, 214, 215, 217, 219, 220, 221, 222, 223, 224, 228, 230, 231, 232, 240, 241, 242, 243, 244, 245, 246], "setforcevector": [12, 28, 95, 159, 160, 164], "forc": [12, 28, 85, 95, 139, 161, 174, 175, 190, 199, 209, 213, 215, 216, 232, 237, 245, 250, 252, 253, 254, 256], "forcevector": [12, 28, 95, 159, 160, 164], "setlabel": [12, 28, 95, 159, 160, 164], "outputtyp": 13, "interfac": [13, 14, 23, 39, 61, 62, 64, 75, 82, 83, 84, 92, 96, 100, 141, 161, 168, 170, 171, 173, 180, 202, 204, 207, 214, 218, 244, 245], "list": [13, 21, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 66, 67, 68, 75, 78, 79, 102, 104, 106, 109, 110, 111, 112, 113, 114, 124, 126, 167, 168, 169, 170, 171, 173, 175, 178, 207, 208, 237, 240, 244, 253], "identifi": [13, 15, 23, 28, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 68, 82, 85, 90, 91, 101, 106, 109, 110, 111, 112, 113, 114, 115, 119, 120, 121, 123, 124, 131, 134, 135, 136, 142, 159, 162, 164, 165, 173], "mol": [13, 14, 19, 21, 22, 25, 32, 33, 38, 39, 40, 56, 58, 61, 62, 63, 64, 69, 71, 75, 82, 95, 100, 167, 168, 169, 171, 207, 249, 254], "nullptr": [13, 25, 28, 32, 35, 38, 40, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 75, 77, 78, 79, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 121, 122, 124, 126, 129, 143, 157, 241], "setmolecul": [13, 15, 19, 35, 63, 64, 69, 75, 100, 104, 157, 159, 160, 163, 164, 177], "obtain": [13, 28, 31, 36, 67, 81, 85, 90, 91, 95, 128, 171], "lookup": [13, 49, 244], "been": [13, 28, 49, 51, 66, 68, 75, 95, 96, 132, 134, 171, 178, 185, 188, 197, 198, 200, 207, 208, 211, 215, 218, 221, 224, 230, 231, 232, 235, 237], "previous": [13, 207, 208, 211, 224], "cach": [13, 51, 62, 66, 82, 92, 175, 244, 245], "There": [13, 62, 81, 82, 173, 191, 192, 193, 203, 211, 226, 236, 237], "correspond": [13, 15, 24, 28, 61, 62, 82, 95, 173, 175, 176, 178, 182, 214, 218, 246], "reset": [13, 48, 51, 62, 82, 90, 91, 92, 96, 104, 118, 123, 157, 159, 160, 163, 164, 185, 209, 219, 223, 224, 225, 240, 241], "typer": 13, "state": [13, 48, 51, 61, 62, 65, 68, 82, 90, 91, 95, 96, 125, 158, 176, 178, 241], "m_type": [13, 133, 159, 160, 165], "initi": [13, 23, 24, 26, 37, 62, 65, 68, 78, 82, 84, 85, 95, 104, 123, 159, 160, 164, 165, 175, 176, 200, 202, 205, 221, 225, 228, 229, 240, 242, 243, 244, 245], "setup": [13, 61, 169, 209, 214, 243], "prior": [13, 61, 178], "enough": [13, 51], "room": 13, "determin": [13, 32, 40, 49, 51, 61, 62, 82, 117, 125, 175, 187, 188, 190, 207, 220, 224, 229, 230, 245], "m_molecul": [13, 15, 95, 159, 160, 164], "popul": [13, 15, 21, 25, 51, 95], "spglib": [14, 39, 95, 183, 240], "short": [14, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 92, 95, 106, 109, 110, 111, 112, 113, 114, 142, 159, 160], "gethallnumb": [14, 159, 160], "carttol": [14, 39, 95], "1e": [14, 39, 95], "hall": [14, 39, 95], "crystal": [14, 39, 41, 180, 184, 188, 198, 205, 207, 209, 235, 241, 245], "unit": [14, 19, 21, 23, 28, 39, 41, 62, 82, 95, 173, 176, 180, 181, 184, 187, 188, 190, 193, 209, 211, 241, 245, 251], "cell": [14, 19, 21, 28, 39, 41, 95, 173, 180, 181, 184, 185, 188, 190, 193, 209, 211, 241, 245, 251], "exist": [14, 22, 26, 28, 43, 51, 65, 67, 85, 95, 102, 126, 134, 168, 172, 173, 218, 233, 241], "algorithm": [14, 21, 84, 95, 186, 207, 212], "fail": [14, 42, 51, 62, 65, 66, 82, 95, 127, 128, 169, 173, 178], "succe": 14, "handl": [14, 21, 48, 49, 63, 68, 75, 78, 88, 89, 92, 100, 104, 117, 133, 142, 159, 162, 163, 164, 165, 167, 168, 169, 172, 235, 240, 245], "cartesian": [14, 19, 21, 24, 37, 39, 41, 95, 169, 173, 182, 183, 186, 187, 198, 209], "toler": [14, 28, 39, 95, 183, 186, 244], "reducetoprimit": [14, 159, 160], "reduc": [14, 21, 39, 95, 178, 180, 184], "primit": [14, 24, 37, 95, 96, 115, 119, 120, 121, 123, 124, 132, 135, 136, 159, 165, 180, 184], "unless": [14, 18, 178], "miss": [14, 233, 241, 244], "conventionalizecel": [14, 95, 159, 160, 164], "refin": [14, 215], "convention": [14, 95], "symmetr": [14, 95, 159, 160, 187, 235], "basi": [15, 24, 25, 28, 37, 38, 62, 82, 107, 108, 173, 178, 207, 245], "gaussianset": [15, 25, 37, 38, 108, 159, 160], "slaterset": [15, 159, 160], "capabl": [15, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95, 106, 109, 110, 111, 112, 113, 114, 115, 136, 172, 173, 205, 208, 215], "calcul": [15, 24, 25, 27, 28, 37, 38, 62, 63, 64, 68, 82, 84, 105, 118, 141, 163, 173, 181, 182, 183, 185, 188, 190, 209, 214, 215, 224, 229, 230, 232, 235, 244, 246, 256], "electrontyp": [15, 24, 25, 37, 159, 160], "electron": [15, 23, 24, 25, 28, 38, 207, 229, 230, 244], "pair": [15, 24, 25, 26, 27, 28, 34, 37, 62, 82, 85, 95, 116, 159, 160, 173, 175, 176, 207, 229, 235, 244], "alpha": [15, 24, 25, 41, 140, 142, 159, 160, 165, 169, 240, 244], "beta": [15, 24, 25, 41, 159, 160, 169, 233], "cannot": [15, 21, 29, 30, 49, 51, 68, 156, 178, 235], "enumer": [15, 19, 21, 22, 24, 33, 37, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 96, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 171], "destructor": [15, 24, 27, 37, 51, 84], "setelectroncount": [15, 159, 160], "electroncount": [15, 159, 160], "molecule_": 15, "get": [15, 22, 24, 28, 39, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 84, 85, 87, 90, 91, 95, 102, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 157, 158, 161, 167, 169, 171, 180, 236, 237, 240, 253], "belong": [15, 67, 85, 90, 91], "setnam": [15, 22, 27, 159, 160], "settheorynam": [15, 159, 160], "theorynam": [15, 159, 160], "molecularorbitalcount": [15, 24, 37, 159, 160], "molecular": [15, 24, 25, 28, 37, 38, 62, 82, 104, 161, 166, 167, 168, 169, 170, 171, 173, 180, 192, 194, 195, 198, 202, 209, 211, 213, 216, 218, 227, 229, 233, 235, 236, 244, 245, 248, 253], "orbit": [15, 24, 25, 37, 38, 107, 159, 160, 161, 180, 198, 209, 227, 235, 241, 252, 255], "homo": [15, 159, 160], "given": [15, 22, 23, 24, 26, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 67, 78, 83, 85, 95, 104, 106, 109, 110, 111, 112, 113, 114, 167, 170], "mo": [15, 22, 24, 25, 37, 159, 160, 245], "lumo": [15, 159, 160], "m_electron": [15, 159, 160], "total": [15, 28, 61, 245], "close": [15, 48, 51, 64, 70, 159, 162, 178, 209, 213, 230, 231, 241, 243, 244, 251], "shell": [15, 24, 37, 107, 159, 162], "doubli": 15, "occupi": [15, 51], "hold": [15, 84, 107, 171, 192, 196, 202, 203, 218], "possibli": 15, "bond": [15, 17, 28, 33, 62, 81, 82, 85, 91, 95, 131, 159, 160, 161, 164, 165, 171, 173, 180, 182, 188, 190, 199, 200, 203, 205, 207, 211, 212, 215, 218, 221, 222, 223, 224, 226, 229, 242, 243, 244, 245, 250, 251, 252, 253, 254, 255, 256], "read": [15, 28, 36, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 75, 78, 82, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 171, 173, 175, 178, 195, 205, 229, 240, 241, 242, 243, 245], "output": [15, 19, 21, 24, 29, 30, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 68, 82, 92, 106, 107, 109, 110, 111, 112, 113, 114, 156, 162, 163, 167, 168, 169, 172, 173, 206, 213, 215, 229, 231, 232, 244, 245], "necessarili": 15, "m_name": [15, 22, 159, 160], "usual": [15, 171, 237], "standard": [15, 62, 70, 82, 90, 91, 92, 95, 117, 134, 158, 166, 167, 168, 169, 171, 172, 173, 178, 198, 208, 241, 245], "m_theorynam": [15, 159, 160], "theori": [15, 62, 82, 173, 178, 199, 209, 245, 248], "bondtempl": [16, 94, 159, 160], "bondtyp": [16, 28, 85, 91, 95, 159, 160, 164], "atom1": [17, 28, 85, 95, 159, 160], "atom2": [17, 28, 85, 95, 159, 160], "setord": [17, 159, 160], "o": [17, 92, 118, 126, 136, 158, 167, 200, 206, 215, 221, 237, 256], "getotheratom": [17, 159, 160], "represent": [18, 21, 41, 62, 82, 134, 172, 173, 178, 198, 206], "rgb": [18, 62, 82, 140, 173], "three": [18, 23, 24, 37, 127, 128, 142, 198, 203, 205, 224, 226], "float": [18, 22, 27, 42, 84, 115, 118, 119, 120, 121, 123, 124, 125, 127, 130, 132, 134, 135, 136, 138, 139, 140, 142, 144, 159, 160, 167, 169, 171, 244], "rang": [18, 21, 62, 82, 124, 126, 128, 134, 140, 142, 167, 169, 173, 176, 207, 235, 244], "intens": [18, 28, 244], "red": [18, 140, 142, 159, 160, 165, 198, 217, 230, 235], "green": [18, 140, 142, 159, 160, 165, 198, 217], "memori": [18, 24, 51, 95, 134, 243], "3": [18, 27, 62, 82, 84, 127, 128, 134, 140, 142, 159, 160, 167, 169, 176, 182, 186, 190, 200, 209, 212, 213, 222, 237, 240, 246, 247, 253, 254, 255], "pass": [18, 22, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 68, 75, 82, 83, 84, 92, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 122, 134, 166, 168, 173, 241, 244], "directli": [18, 49, 67, 167, 178, 189, 191, 195, 229], "opengl": [18, 123, 132, 161, 237, 243, 244, 245], "conveni": [18, 28, 43, 48, 49, 51, 66, 67, 85, 161, 205, 210, 245], "written": [18, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 82, 84, 106, 109, 110, 111, 112, 113, 114, 168, 173, 176, 178, 230], "emphasi": 18, "effici": [18, 210, 241], "layout": [18, 65, 87], "black": [18, 132, 200, 203, 221, 225, 226], "integ": [18, 22, 27, 142, 173], "255": [18, 62, 82, 134, 140, 173], "expect": [18, 23, 24, 27, 62, 82, 84, 103, 168, 169, 173, 178, 237, 245], "align": [19, 21, 132, 140, 173, 180, 181, 182, 185, 190, 191, 209, 222, 245], "see": [19, 28, 51, 62, 64, 78, 82, 85, 95, 105, 134, 142, 161, 168, 172, 173, 183, 186, 187, 190, 191, 207, 229], "setspecif": [19, 159, 160], "detail": [19, 21, 48, 51, 61, 62, 64, 65, 72, 82, 161, 167, 168, 169, 170, 172, 173, 207], "distanceunit": [19, 159, 160], "distanc": [19, 39, 41, 118, 138, 159, 160, 165, 181, 182, 207, 213, 224, 244, 245, 251], "angstrom": [19, 21, 41, 159, 160, 190, 205, 213], "bohr": [19, 159, 160, 190, 205], "setdistanceunit": [19, 159, 160], "spec": 19, "inform": [19, 24, 28, 39, 62, 82, 95, 104, 123, 134, 168, 173, 175, 178, 187, 197, 198, 203, 205, 207, 209, 210, 213, 215, 218, 223, 236, 243], "z": [19, 22, 28, 169, 173, 181, 185, 190, 191, 198, 205, 207, 211, 217, 219, 240], "6": [19, 21, 27, 62, 74, 82, 84, 123, 158, 159, 160, 167, 169, 171, 173, 190, 213, 222, 237, 245, 248, 254], "carbon": [19, 23, 28, 74, 170, 171, 173, 175, 180, 185, 201, 205, 220, 221, 225, 253, 254, 255], "l": [19, 119, 178, 237], "c1": [19, 245], "gamess": [19, 107, 173, 207, 244, 245], "lattic": [19, 21, 41, 95, 173, 186, 187], "requir": [19, 24, 49, 62, 65, 82, 123, 142, 158, 167, 168, 171, 172, 173, 175, 178, 214, 231, 233, 254], "A": [19, 21, 24, 26, 28, 31, 36, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 70, 75, 78, 79, 81, 82, 85, 86, 87, 90, 91, 92, 95, 96, 98, 99, 100, 102, 104, 106, 109, 110, 111, 112, 113, 114, 115, 122, 124, 126, 132, 133, 134, 136, 142, 161, 168, 173, 176, 178, 179, 182, 188, 189, 191, 193, 194, 196, 200, 203, 205, 207, 211, 212, 220, 221, 225, 230, 231, 235, 237], "liter": [19, 62, 82, 173], "optim": [19, 28, 62, 82, 169, 173, 176, 180, 182, 190, 200, 209, 215, 221, 235, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 254, 255, 256], "flag": [19, 21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 78, 82, 86, 98, 106, 109, 110, 111, 112, 113, 114, 140, 159, 163, 164, 168, 170, 173], "_": [19, 173], "__szxyz110": [19, 173], "replac": [19, 28, 79, 95, 168, 170, 171, 173, 178, 205, 237, 241], "text": [19, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 79, 80, 95, 105, 106, 109, 110, 111, 112, 113, 114, 122, 123, 130, 137, 138, 139, 140, 141, 144, 159, 165, 167, 169, 170, 172, 173, 178, 182, 192, 193, 205, 206, 245], "126214": [19, 173], "765886": [19, 173], "000000": [19, 173], "819345": [19, 173], "564955": [19, 173], "598383": [19, 173], "795127": [19, 173], "310706": [19, 173], "370165": [19, 173], "16": [19, 84, 173, 241], "285330": [19, 173], "757144": [19, 173], "130424": [19, 173], "185837": [19, 173], "548377": [19, 173], "375303": [19, 173], "033768": [19, 173], "794407": [19, 173], "396173": [19, 173], "450760": [19, 173], "generatecoordinateblock": [19, 159, 160], "arrayset": [20, 159, 160], "concret": 20, "_size": 20, "_index": 20, "collect": [21, 61, 62, 64, 65, 82, 104, 115, 120, 121, 124, 132, 136, 161, 171, 173, 178], "common": [21, 48, 62, 82, 121, 124, 126, 129, 145, 167, 168, 173, 179, 196, 207, 215, 235], "crystallograph": [21, 183], "option": [21, 48, 49, 51, 61, 63, 64, 65, 68, 72, 73, 75, 83, 92, 95, 100, 115, 134, 136, 140, 142, 159, 160, 162, 163, 164, 166, 167, 169, 170, 171, 172, 176, 182, 185, 190, 207, 209, 216, 217, 218, 230, 235, 241], "bitwis": [21, 49, 65, 140], "variou": [21, 24, 37, 62, 82, 168, 173, 197, 198, 207, 208, 210, 230, 232, 235, 236, 237, 243], "none": [21, 22, 24, 28, 39, 48, 49, 61, 78, 102, 126, 133, 134, 159, 160, 162, 163, 165, 209, 243], "transformatom": [21, 95, 159, 160], "transform": [21, 39, 95, 118, 143, 178], "along": [21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 72, 73, 95, 106, 109, 110, 111, 112, 113, 114, 161, 167, 169, 172, 185, 190, 202], "wrapatomstounitcel": [21, 159, 160], "adjust": [21, 41, 81, 95, 159, 164, 187, 197, 198, 200, 205, 207, 211, 213, 218, 219, 221, 222, 223, 231, 232, 240, 245, 248], "fraction": [21, 39, 41, 95, 187, 205], "success": [21, 24, 25, 27, 28, 31, 36, 37, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 68, 69, 82, 85, 95, 106, 109, 110, 111, 112, 113, 114, 134, 159, 164, 169], "rotatetostandardorient": [21, 159, 160], "opt": [21, 61, 95, 142, 170, 171], "rotat": [21, 95, 118, 140, 159, 165, 180, 181, 185, 189, 202, 212, 217, 220, 223, 225, 235, 240, 245, 251], "axi": [21, 28, 118, 120, 132, 181, 182, 185, 190, 211, 217], "xy": [21, 37, 159, 160, 181, 185, 190], "plane": [21, 28, 118, 137, 181, 185, 190, 211, 215, 220], "trig": 21, "sinc": [21, 51, 167, 169, 171, 175, 176, 183, 186, 189, 193, 228, 235, 251], "fragil": 21, "neg": [21, 81, 235], "angl": [21, 41, 118, 200, 207, 211, 213, 221, 222, 224, 243, 244, 245, 255, 256], "found": [21, 28, 39, 43, 49, 62, 67, 78, 79, 80, 82, 84, 85, 124, 126, 161, 170, 173, 198, 203, 205, 206, 207, 210, 226, 228, 231, 236, 237, 240, 241, 242, 243, 244], "http": [21, 51, 84, 172, 175, 178, 190, 193, 194, 207, 237, 240, 241, 243, 244], "xtalopt": [21, 166], "openmolecul": 21, "net": [21, 198, 246], "misc": 21, "rotatetostdorient": 21, "pdf": 21, "setvolum": [21, 159, 160], "real": [21, 41, 42, 169, 245], "newvolum": [21, 95], "isotrop": 21, "scale": [21, 95, 118, 159, 165, 180, 184, 219, 225, 244], "volum": [21, 41, 95, 157, 159, 160, 180, 184, 186], "cubic": [21, 41], "failur": [21, 24, 25, 28, 31, 36, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 95, 106, 109, 110, 111, 112, 113, 114, 134, 178, 242], "nigglireduc": [21, 159, 160], "niggli": [21, 95, 186], "reduct": [21, 95, 186], "produc": [21, 64, 122, 172, 178, 190], "canon": 21, "strive": 21, "gross": 21, "kunstlev": 21, "rw": 21, "sauter": 21, "nk": 21, "adam": 21, "pd": 21, "numer": [21, 62, 82, 115, 134, 136, 167, 168, 169, 173, 240], "stabl": [21, 27, 159, 160], "comput": [21, 118, 167, 202, 204, 207, 211, 218, 235, 236], "acta": 21, "crystallographica": 21, "foundat": 21, "crystallographi": [21, 181, 188, 193], "2003": 21, "60": 21, "modifi": [21, 27, 28, 49, 64, 81, 85, 95, 104, 118, 157, 159, 164, 168, 170, 171, 178, 188, 202, 209, 228, 235, 236], "extend": [21, 161, 174, 236, 240, 248], "isnigglireduc": [21, 159, 160], "alreadi": [21, 39, 66, 85, 95, 107, 172, 188, 200, 214, 221, 245], "gruber": 21, "cryst": 21, "1973": 21, "29": 21, "4": [21, 84, 105, 128, 140, 141, 159, 160, 166, 169, 179, 181, 186, 190, 212, 218, 222, 235, 247, 248, 254], "433": 21, "440": [21, 240], "buildsupercel": [21, 95, 159, 160, 164], "supercel": [21, 95, 180, 181, 184, 186], "expand": [21, 65, 68, 187, 188, 211], "upon": [21, 95, 126, 178], "zero": [21, 23, 28, 62, 79, 82, 95, 118, 169, 173, 176, 219, 245], "setcellmatrix": [21, 41, 159, 160], "matrix3": [21, 41, 95], "newcellcolmatrix": 21, "ignor": [21, 28, 62, 82, 95, 96, 104, 142, 159, 164, 173, 175, 209, 213, 237, 244], "fractionalcoordin": [21, 159, 160], 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"class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md2"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md16"]], "Short Free-Form Text Parameters": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md3"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md17"], [176, "short-free-form-text-parameters"]], "Existing files": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md4"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md18"], [176, "existing-files"]], "Clamped Integer Values": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md5"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md19"]], "Boolean Parameters": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md6"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md20"], [176, "boolean-parameters"]], "Special Parameters": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md7"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md21"], [173, "special-parameters"]], "Syntax Highlighting": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md8"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md22"], [173, "syntax-highlighting"]], "Requesting Full Structure of Current Molecule": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md9"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md23"], [173, "requesting-full-structure-of-current-molecule"]], "Handling User Selections: \u2013generate-input": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md10"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md24"]], "Automatic Generation of Geometry": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md11"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md25"], [173, "automatic-generation-of-geometry"]], "Error Handling": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md12"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md26"], [173, "error-handling"]], "Debugging": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md13"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md27"], [173, "debugging"], [168, "debugging"]], "Class Avogadro::Io::MMTFFormat": [[54, "class-avogadro-io-mmtfformat"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[69, "class-avogadro-qtgui-backgroundfileformat"]], "Class Avogadro::Io::OutcarFormat": [[56, "class-avogadro-io-outcarformat"]], "Class Avogadro::Io::XyzFormat": [[60, "class-avogadro-io-xyzformat"]], "Class Avogadro::QtGui::ElementTranslator": [[74, "class-avogadro-qtgui-elementtranslator"]], "Class Avogadro::Io::PoscarFormat": [[58, "class-avogadro-io-poscarformat"]], "Class Avogadro::MoleQueue::MoleQueueDialog": [[65, "class-avogadro-molequeue-molequeuedialog"]], "Hydrogen Clusters": [[251, "hydrogen-clusters"]], "Task": [[251, "task"], [250, "task"], [252, "task"], [255, "task"], [256, "task"], [254, "task"], [247, "task"], [248, "task"]], "Solution": [[251, "solution"], [252, "solution"], [255, "solution"], [256, "solution"], [254, "solution"], [246, "solution"], [249, "solution"]], "Issues": [[251, "issues"]], "See also": [[251, "see-also"], [250, "see-also"], [252, "see-also"], [255, "see-also"], [256, "see-also"], [254, "see-also"], [247, "see-also"], [248, "see-also"]], "Sources": [[251, "sources"], [252, "sources"], [256, "sources"]], "HCN dipole": [[250, "hcn-dipole"]], "Hydrogen Molecule": [[252, "hydrogen-molecule"]], "Teach": [[253, "teach"]], "Organic Hybridization": [[255, "organic-hybridization"]], "Further reading": [[255, "further-reading"], [254, "further-reading"], [246, "further-reading"], [248, "further-reading"]], "Water": [[256, "water"]], "Markovnikov\u2019s Rule": [[254, "markovnikovs-rule"]], "Class Avogadro::QtGui::PersistentAtom": [[90, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::MoleculeModel": [[86, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::FileBrowseWidget": [[77, "class-avogadro-qtgui-filebrowsewidget"]], "Class Avogadro::QtGui::GenericHighlighter": [[79, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::MeshGenerator": [[84, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::PeriodicTableScene": [[88, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::ScenePluginModel": [[98, "class-avogadro-qtgui-scenepluginmodel"]], "Class Avogadro::QtGui::FileFormatDialog": [[78, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::PythonScript": [[92, "class-avogadro-qtgui-pythonscript"]], "Class Avogadro::QtGui::ScriptLoader": [[99, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::QtGui::InterfaceScript": [[82, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::MultiViewWidget": [[87, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::HydrogenTools": [[81, "class-avogadro-qtgui-hydrogentools"]], "Class Avogadro::QtGui::ScenePlugin": [[96, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::QtGui::RWMolecule": [[95, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::ScenePluginFactory": [[97, "class-avogadro-qtgui-scenepluginfactory"]], "Class Avogadro::QtGui::PeriodicTableView": [[89, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::PersistentBond": [[91, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::RWAtom": [[93, "class-avogadro-qtgui-rwatom"]], "Class Avogadro::QtGui::ExtensionPlugin": [[75, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[76, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::InterfaceWidget": [[83, "class-avogadro-qtgui-interfacewidget"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[80, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::Molecule": [[85, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::RWBond": [[94, "class-avogadro-qtgui-rwbond"]], "Optimizing Geometry": [[216, "optimizing-geometry"]], "Optimization": [[216, null]], "Getting Started": [[201, "getting-started"], [201, null]], "Geometry Constraints": [[213, "geometry-constraints"]], "Constraints": [[213, "constraints"], [207, "constraints"]], "Example": [[213, "example"]], "Optimizations": [[213, "optimizations"]], "Example cont.": [[213, "example-cont"]], "Extension Menu": [[207, "extension-menu"]], "Animation": [[207, "animation"]], "Optimize Geometry": [[207, "optimize-geometry"]], "Molecular Mechanics": [[207, "molecular-mechanics"]], "Setup Force Field\u2026": [[207, "setup-force-field"]], "Calculate Energy": [[207, "calculate-energy"]], "Conformer Search": [[207, "conformer-search"]], "Ignore Selection": [[207, "ignore-selection"]], "Fix Selected Atoms": [[207, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[207, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[207, "general-how-to-for-plugins"]], "Running Gaussian": [[207, "running-gaussian"]], "Molecular Orbitals": [[207, "molecular-orbitals"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[207, "qtaim-quantum-theory-of-atoms-in-molecules"], [198, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Spectra\u2026": [[207, "spectra"]], "Create Surfaces\u2026": [[207, "create-surfaces"]], "Auto-Rotate Tool": [[219, "auto-rotate-tool"]], "Align Tool": [[217, "align-tool"]], "Drawing Molecules": [[200, "drawing-molecules"]], "Creating Carbon Dioxide": [[200, "creating-carbon-dioxide"]], "Enabling additional force fields": [[214, "enabling-additional-force-fields"]], "Creating an avogadro conda environment": [[214, "creating-an-avogadro-conda-environment"]], "Setting the Python path": [[214, "setting-the-python-path"]], "Menus": [[209, "menus"], [209, null]], "Introduction": [[202, "introduction"]], "Opening a File": [[202, "opening-a-file"]], "Navigation": [[202, "navigation"]], "Manipulate Tool": [[223, "manipulate-tool"]], "Bond-Centric Manipulate Tool": [[220, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[220, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[220, "adjusting-bonds-and-torsion-angles"]], "User Guide": [[204, "user-guide"]], "Avogadro: Molecular Editor and Visualization": [[204, "avogadro-molecular-editor-and-visualization"], [179, "avogadro-molecular-editor-and-visualization"]], "Avogadro 2": [[204, "avogadro-2"]], "Making Selections": [[203, "making-selections"]], "Build Menu": [[205, "build-menu"]], "Cartesian Editor\u2026": [[205, "cartesian-editor"]], "1. Sort by\u2026": [[205, "sort-by"]], "2. Unit of Measure": [[205, "unit-of-measure"]], "3. Editing & Modifying Data": [[205, "editing-modifying-data"]], "Change H to Methyl": [[205, "change-h-to-methyl"]], "Add Hydrogens": [[205, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[205, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[205, "remove-hydrogens"]], "Insert": [[205, "insert"]], "Invert Chirality": [[205, "invert-chirality"]], "Super Cell Builder\u2026": [[205, "super-cell-builder"]], "Nanotube Builder\u2026": [[205, "nanotube-builder"]], "Edit Menu": [[206, "edit-menu"]], "Undo": [[206, "undo"]], "Redo": [[206, "redo"]], "Cut": [[206, "cut"]], "Copy": [[206, "copy"]], "Copy As": [[206, "copy-as"]], "Paste": [[206, "paste"]], "Clear": [[206, "clear"]], "Select All": [[206, "select-all"], [210, "select-all"]], "Select None": [[206, "select-none"], [210, "select-none"]], "Tools": [[222, "tools"], [222, null]], "File Menu": [[208, "file-menu"]], "New": [[208, "new"]], "Open": [[208, "open"]], "Open Recent": [[208, "open-recent"]], "Close": [[208, "close"]], "Save": [[208, "save"]], "Save As\u2026": [[208, "save-as"]], "Revert to Saved": [[208, "revert-to-saved"]], "Import": [[208, "import"]], "Export": [[208, "export"]], "Introduction to Molecular Mechanics": [[215, "introduction-to-molecular-mechanics"]], "UFF": [[215, "uff"]], "MMFF94(s)": [[215, "mmff94-s"]], "GAFF": [[215, "gaff"]], "Finding Conformers of Molecules": [[212, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[212, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[212, "optimize-the-geometry"]], "Change the force field options": [[212, "change-the-force-field-options"]], "Set the conformer search options": [[212, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[212, "pick-a-search-method-and-start-the-search"]], "Select Menu": [[210, "select-menu"]], "Invert Selection": [[210, "invert-selection"]], "Select SMARTS\u2026": [[210, "select-smarts"]], "Select by Element\u2026": [[210, "select-by-element"]], "Select by Residue\u2026": [[210, "select-by-residue"]], "Select Solvent": [[210, "select-solvent"]], "Add Name Selection\u2026": [[210, "add-name-selection"]], "Measure Tool": [[224, "measure-tool"]], "Draw Tool": [[221, "draw-tool"]], "1. Creating a Molecule": [[221, "creating-a-molecule"]], "2.": [[221, "id1"]], "3.": [[221, "id2"]], "4.": [[221, "id3"]], "5.": [[221, "id4"]], "6.": [[221, "id5"]], "7.": [[221, "id6"]], "8.": [[221, "id7"]], "9.": [[221, "id8"]], "Auto-Optimize Tool": [[218, "auto-optimize-tool"]], "Force Fields & Algorithms": [[218, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[218, "fixing-ignoring-selections"]], "View Menu": [[211, "view-menu"]], "New View": [[211, "new-view"]], "Duplicate View": [[211, "duplicate-view"]], "Detach View": [[211, "detach-view"]], "Close View": [[211, "close-view"]], "Center": [[211, "center"]], "Align View to Axes": [[211, "align-view-to-axes"]], "Full Screen": [[211, "full-screen"]], "Reset Display Types": [[211, "reset-display-types"]], "Set Background Color\u2026": [[211, "set-background-color"]], "Projection": [[211, "projection"]], "Display Axes": [[211, "display-axes"]], "Debug Information": [[211, "debug-information"]], "Use Quick Render": [[211, "use-quick-render"]], "All Molecules in File\u2026": [[211, "all-molecules-in-file"]], "Crystal View Options\u2026": [[211, "crystal-view-options"]], "Properties": [[211, "properties"]], "Class Avogadro::Core::Variant": [[42, "class-avogadro-core-variant"]], "Class Avogadro::Core::GaussianSetTools": [[25, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[44, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Core::SlaterSet": [[37, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::Molecule": [[28, "class-avogadro-core-molecule"]], "Class Avogadro::Io::CmlFormat": [[46, "class-avogadro-io-cmlformat"]], "Class Avogadro::Core::SpaceGroups": [[39, "class-avogadro-core-spacegroups"]], "Class Avogadro::Io::CjsonFormat": [[45, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Core::MoleculeDeserializer": [[29, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::VariantMap": [[43, "class-avogadro-core-variantmap"]], "Class Avogadro::Io::DcdFormat": [[47, "class-avogadro-io-dcdformat"]], "Class Avogadro::Core::NameAtomTyper": [[32, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::RingPerceiver": [[35, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::ResidueData": [[34, "class-avogadro-core-residuedata"]], "Class Avogadro::Io::FileFormat": [[48, "class-avogadro-io-fileformat"]], "Class Avogadro::Core::SharedMutex": [[36, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::Residue": [[33, "class-avogadro-core-residue"]], "Class Avogadro::Core::UnitCell": [[41, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::Graph": [[26, "class-avogadro-core-graph"]], "Class Avogadro::Core::SlaterSetTools": [[38, "class-avogadro-core-slatersettools"]], "Class Avogadro::Io::FileFormatManager": [[49, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::Core::MoleculeSerializer": [[30, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::Mutex": [[31, "class-avogadro-core-mutex"]], "Class Avogadro::Core::SymbolAtomTyper": [[40, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::Mesh": [[27, "class-avogadro-core-mesh"]], "Install": [[238, "install"], [236, "install"]], "Release Notes v1.97.0": [[244, "release-notes-v1-97-0"]], "Highlights (tldr)": [[244, "highlights-tldr"], [245, "highlights-tldr"]], "\u2728 Features": [[244, "features"], [245, "features"], [243, "features"], [242, "features"], [241, "features"]], "\ud83d\udc1b Bug Fixes": [[244, "bug-fixes"], [245, "bug-fixes"], [243, "bug-fixes"], [242, "bug-fixes"], [240, "bug-fixes"], [241, "bug-fixes"]], "\ud83d\ude80 Performance Improvements": [[244, "performance-improvements"], [245, "performance-improvements"]], "\ud83e\uddf0 Maintenance": [[244, "maintenance"], [245, "maintenance"], [243, "maintenance"], [242, "maintenance"], [240, "maintenance"], [241, "maintenance"]], "\ud83d\udcda Translations": [[244, "translations"], [245, "translations"], [243, "translations"], [242, "translations"], [241, "translations"]], "Navigate Tool": [[225, "navigate-tool"]], "Viewing Vibrations": [[232, "viewing-vibrations"]], "Acid-Base Properties of Amino Acids": [[246, "acid-base-properties-of-amino-acids"]], "Tasks": [[246, "tasks"], [249, "tasks"]], "Using QTAIM (Atoms in Molecules) Analysis": [[229, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[229, "start-with-a-wfn-file"]], "Release Notes v1.98.0": [[245, "release-notes-v1-98-0"]], "What\u2019s New in Avogadro 2": [[233, "whats-new-in-avogadro-2"]], "Release Notes v1.96.0": [[243, "release-notes-v1-96-0"]], "Changes": [[243, "changes"], [241, "changes"]], "\ud83d\ude80 Performance Fixes": [[243, "performance-fixes"]], "Selection Tool": [[226, "selection-tool"]], "Major New Features": [[235, "major-new-features"]], "Speed and Stability": [[235, "speed-and-stability"]], "Rendering": [[235, "rendering"]], "New real-time shadows and depth effects": [[235, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[235, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[235, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[235, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[235, "layers"]], "Symmetry Properties": [[235, "symmetry-properties"]], "Template Tool": [[235, "template-tool"]], "Solvent Accessible and Solvent Excluded Surfaces": [[235, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[235, "flexible-electrostatics-models"]], "New Analysis Tools": [[235, "new-analysis-tools"]], "Python Commands / Plugins": [[235, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[235, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[235, "new-and-updated-interfaces-to-external-programs"]], "Version History": [[239, "version-history"], [239, null]], "Alkene Isomers": [[247, "alkene-isomers"]], "Tutorials": [[227, "tutorials"], [227, null]], "Release Notes v1.95.1": [[242, "release-notes-v1-95-1"]], "Naming a Molecule": [[228, "naming-a-molecule"]], "Viewing Electrostatic Potential Maps": [[230, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[230, "changing-surface-settings"]], "Building Source Code": [[237, "building-source-code"]], "Cloning Repositories": [[237, "cloning-repositories"]], "Updating": [[237, "updating"]], "Prerequisites": [[237, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[237, "debian-based-distribution-or-ubuntu"]], "Building": [[237, "building"]], "Finding Qt, Windows Generators": [[237, "finding-qt-windows-generators"]], "Normal Development": [[237, "normal-development"]], "Build Tree Layout": [[237, "build-tree-layout"]], "Running Executables": [[237, "running-executables"]], "Building Packages": [[237, "building-packages"]], "Release Notes v1.94.0": [[240, "release-notes-v1-94-0"]], "Features": [[240, "features"], [236, "features"]], "\ud83d\udc0d Python Improvements": [[240, "python-improvements"]], "Basic VSEPR": [[248, "basic-vsepr"]], "Interface Changes": [[234, "interface-changes"]], "Resources": [[236, "resources"]], "Connecting with the Avogadro community": [[236, "connecting-with-the-avogadro-community"]], "Viewing Molecular Orbitals": [[231, "viewing-molecular-orbitals"]], "Configure": [[231, "configure"]], "1,3-diaxial interactions": [[249, "diaxial-interactions"]], "Release Notes v1.95.0": [[241, "release-notes-v1-95-0"]], "Building a Supercell": [[188, "building-a-supercell"]], "Creating a Surface": [[188, "creating-a-surface"]], "Building a Peptide": [[189, "building-a-peptide"]], "Different Display Styles": [[198, "different-display-styles"]], "Locating Display Types": [[198, "locating-display-types"]], "Axes": [[198, "axes"]], "Ball and Stick": [[198, "ball-and-stick"]], "Cartoon": [[198, "cartoon"]], "Dipole": [[198, "dipole"]], "Force": [[198, "force"]], "Hydrogen Bond": [[198, "hydrogen-bond"]], "Label": [[198, "label"]], "Polygon": [[198, "polygon"]], "Ribbon": [[198, "ribbon"]], "Ring": [[198, "ring"]], "Stick": [[198, "stick"]], "Surfaces": [[198, "surfaces"]], "Van der Waals Spheres": [[198, "van-der-waals-spheres"]], "Wireframe": [[198, "wireframe"]], "Perceiving Crystall Symmetry": [[183, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[183, "open-a-crystal-file"]], "Building DNA or RNA": [[191, "building-dna-or-rna"]], "VTK Classes": [[177, "vtk-classes"]], "Table of contents": [[180, "table-of-contents"]], "Scaling Crystal Cell Volume": [[187, "scaling-crystal-cell-volume"]], "Building a Polymer Unit Cell": [[182, "building-a-polymer-unit-cell"]], "Making a Crystal Surface Slab": [[181, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[181, "import-the-appropriate-crystal-structure"]], "Importing Molecules by Name": [[194, "importing-molecules-by-name"]], "Display Types": [[199, "display-types"], [199, null]], "Installing Script Plugins": [[175, "installing-script-plugins"]], "Directories": [[175, "directories"]], "Plugin Packages and Repositories": [[175, "plugin-packages-and-repositories"]], "Adding to the Plugin Directory": [[175, "adding-to-the-plugin-directory"]], "Importing from the Protein Data Bank (PDB)": [[193, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[193, "importing-directly"]], "Reading a Downloaded PDB file": [[193, "reading-a-downloaded-pdb-file"]], "Building Materials": [[184, "building-materials"], [184, null]], "Reducing Crystals to a Primitive Unit Cell": [[186, "reducing-crystals-to-a-primitive-unit-cell"]], "Building Molecule-Surface Interactions": [[185, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[185, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[185, "new-window-create-our-molecule"]], "Building with SMILES": [[192, "building-with-smiles"]], "Script Interfaces": [[176, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[176, "fixed-string-lists-pop-up-menus"]], "Integer Values": [[176, "integer-values"]], "Floating-point values": [[176, "floating-point-values"]], "Insert Molecular Fragments": [[196, "insert-molecular-fragments"]], "Building Molecules": [[195, "building-molecules"], [195, null]], "License": [[178, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[178, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[178, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[178, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[178, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[178, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[178, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[178, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[178, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[178, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[178, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[178, "section-8-interpretation"]], "Building Carbon Nanotubes": [[190, "building-carbon-nanotubes"]], "Coloring Part of a Molecules": [[197, "coloring-part-of-a-molecules"]], "Hemoglobin": [[197, "hemoglobin"]], "Select by Residue": [[197, "select-by-residue"]], "Select by Element": [[197, "select-by-element"]], "Class Avogadro::Rendering::Scene": [[132, "class-avogadro-rendering-scene"]], "Class Avogadro::Rendering::Sphere": [[135, "class-avogadro-rendering-sphere"]], "Class Avogadro::Rendering::POVRayVisitor": [[130, "class-avogadro-rendering-povrayvisitor"]], "Class Avogadro::Rendering::SphereGeometry": [[136, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::TypeTraits": [[147, "class-avogadro-typetraits"]], "Class Avogadro::Rendering::VRMLVisitor": [[144, "class-avogadro-rendering-vrmlvisitor"]], "Class Avogadro::Rendering::TextLabel3D": [[138, "class-avogadro-rendering-textlabel3d"]], "Class Avogadro::Rendering::LineStripGeometry": [[127, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::Rendering::ShaderProgram": [[134, "class-avogadro-rendering-shaderprogram"]], "Class Avogadro::Rendering::VolumeGeometry": [[146, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::Rendering::Visitor": [[145, "class-avogadro-rendering-visitor"]], "Class Avogadro::Rendering::TextLabel2D": [[137, "class-avogadro-rendering-textlabel2d"]], "Class Avogadro::Rendering::MeshGeometry": [[128, "class-avogadro-rendering-meshgeometry"]], "Class Avogadro::Rendering::TextLabelBase": [[139, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::Rendering::TextRenderStrategy": [[141, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::Rendering::GeometryVisitor": [[125, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::Primitive": [[131, "class-avogadro-rendering-primitive"]], "Class Avogadro::Rendering::Texture2D": [[142, "class-avogadro-rendering-texture2d"]], "Class Avogadro::Rendering::TransformNode": [[143, "class-avogadro-rendering-transformnode"]], "Class Avogadro::TypeTraits< char >": [[148, "class-avogadro-typetraits-char"]], "Class Avogadro::Rendering::Node": [[129, "class-avogadro-rendering-node"]], "Class Avogadro::Rendering::Shader": [[133, "class-avogadro-rendering-shader"]], "Class Avogadro::Rendering::GroupNode": [[126, "class-avogadro-rendering-groupnode"]], "Class Avogadro::Rendering::TextProperties": [[140, "class-avogadro-rendering-textproperties"]], "Class Avogadro::TypeTraits< double >": [[149, "class-avogadro-typetraits-double"]], "MoleQueue Classes": [[163, "molequeue-classes"]], "Class vtkAvogadroActor": [[158, "class-vtkavogadroactor"]], "Class Avogadro::TypeTraits< short >": [[152, "class-avogadro-typetraits-short"]], "Class Avogadro::TypeTraits< unsigned short >": [[155, "class-avogadro-typetraits-unsigned-short"]], "Class Avogadro::VTK::vtkGLWidget": [[157, "class-avogadro-vtk-vtkglwidget"]], "Avogadro Remote Procedure Call (RPC)": [[166, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[166, "rpc-protocol"]], "Methods": [[166, "methods"]], "File Formats": [[172, "file-formats"]], "Identify the Format with --metadata": [[172, "identify-the-format-with-metadata"]], "Reading a format with --read": [[172, "reading-a-format-with-read"]], "Writing a format with --write": [[172, "writing-a-format-with-write"]], "Input Generators": [[173, "input-generators"]], "Specifying parameters with --print-options": [[173, "specifying-parameters-with-print-options"]], "Handling User Selections: --generate-input": [[173, "handling-user-selections-generate-input"]], "Coordinate Blocks": [[173, "coordinate-blocks"]], "IO Classes": [[162, "io-classes"]], "Class Avogadro::TypeTraits< unsigned int >": [[154, "class-avogadro-typetraits-unsigned-int"]], "Class Avogadro::VTK::VtkPlot": [[156, "class-avogadro-vtk-vtkplot"]], "Class Avogadro::TypeTraits< float >": [[150, "class-avogadro-typetraits-float"]], "Energy / Force Fields": [[169, "energy-force-fields"]], "Identify the Script with --metadata": [[169, "identify-the-script-with-metadata"], [167, "identify-the-script-with-metadata"]], "Calculating Energies and Gradients": [[169, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[169, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[169, "lattice-vectors-and-fractional-coordinates"]], "Rendering Classes": [[165, "rendering-classes"]], "Class Avogadro::TypeTraits< unsigned char >": [[153, "class-avogadro-typetraits-unsigned-char"]], "Charges / Electrostatics": [[167, "charges-electrostatics"]], "Calculating Atomic Partial Charges with --charge": [[167, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials with --potential": [[167, "generating-electrostatic-potentials-with-potential"]], "Example Plugin Script - Part 2": [[171, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[171, "providing-input-to-run-command"]], "runCommand() Function": [[171, "runcommand-function"]], "Operation Function": [[171, "operation-function"]], "Retrieving necessary components": [[171, "retrieving-necessary-components"]], "Support for Selection": [[171, "support-for-selection"]], "Sample Input and Output": [[171, "sample-input-and-output"]], "Example Plugin Script - Part 1": [[170, "example-plugin-script-part-1"]], "The Main function:": [[170, "the-main-function"]], "Input Arguments": [[170, "input-arguments"]], "getOptions() Function": [[170, "getoptions-function"]], "Develop": [[161, "develop"]], "Script Plugins": [[161, "script-plugins"], [174, "script-plugins"]], "External Scripting": [[161, "external-scripting"]], "Libraries": [[161, "libraries"]], "Main Classes": [[161, "main-classes"]], "Command Scripts": [[168, "command-scripts"]], "Specifying UI options with \u2013print-options": [[168, "specifying-ui-options-with-print-options"]], "Returning Data": [[168, "returning-data"]], "Returning Data in a Specific File Format": [[168, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[168, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[168, "bonding-new-atoms"]], "Selected Atoms": [[168, "selected-atoms"]], "QtGui Classes": [[164, "qtgui-classes"]], "Core Classes": [[160, "core-classes"]], "Class Avogadro::TypeTraits< int >": [[151, "class-avogadro-typetraits-int"]], "Class List": [[159, "class-list"]], "Class Avogadro::QuantumIO::NWChemLog": [[114, "class-avogadro-quantumio-nwchemlog"]], "Class Avogadro::QtOpenGL::GLWidget": [[104, "class-avogadro-qtopengl-glwidget"]], "Class Avogadro::QtGui::ViewFactory": [[102, "class-avogadro-qtgui-viewfactory"]], "Class Avogadro::QuantumIO::GaussianFchk": [[110, "class-avogadro-quantumio-gaussianfchk"]], "Class Avogadro::QtGui::ToolPlugin": [[100, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[107, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::Rendering::GLRenderVisitor": [[122, "class-avogadro-rendering-glrendervisitor"]], "Class Avogadro::Rendering::GLRenderer": [[123, "class-avogadro-rendering-glrenderer"]], "Class Avogadro::QuantumIO::GaussianCube": [[109, "class-avogadro-quantumio-gaussiancube"]], "Class 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"avogadro::typetraits::[anonymous]::enumvalue (c++ enumerator)": [[153, "_CPPv4N8Avogadro10TypeTraitsIhEUt1_29EnumValueE"]], "avogadro::typetraits::name (c++ function)": [[153, "_CPPv4N8Avogadro10TypeTraitsIhE4nameEv"]], "avogadro::typetraits (c++ class)": [[154, "_CPPv4IEN8Avogadro10TypeTraitsIjEE"]], "avogadro::typetraits::[anonymous] (c++ enum)": [[154, "_CPPv4N8Avogadro10TypeTraitsIjEUt1_6E"]], "avogadro::typetraits::[anonymous]::enumvalue (c++ enumerator)": [[154, "_CPPv4N8Avogadro10TypeTraitsIjEUt1_69EnumValueE"]], "avogadro::typetraits::name (c++ function)": [[154, "_CPPv4N8Avogadro10TypeTraitsIjE4nameEv"]], "avogadro::typetraits (c++ class)": [[155, "_CPPv4IEN8Avogadro10TypeTraitsItEE"]], "avogadro::typetraits::[anonymous] (c++ enum)": [[155, "_CPPv4N8Avogadro10TypeTraitsItEUt1_4E"]], "avogadro::typetraits::[anonymous]::enumvalue (c++ enumerator)": [[155, "_CPPv4N8Avogadro10TypeTraitsItEUt1_49EnumValueE"]], "avogadro::typetraits::name (c++ function)": [[155, "_CPPv4N8Avogadro10TypeTraitsItE4nameEv"]], "avogadro::vtk::vtkglwidget (c++ class)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidgetE"]], "avogadro::vtk::vtkglwidget::clearscene (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget10clearSceneEv"]], "avogadro::vtk::vtkglwidget::cube (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget4cubeEv"]], "avogadro::vtk::vtkglwidget::cubevolume (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget10cubeVolumeEPN4Core4CubeE"]], "avogadro::vtk::vtkglwidget::imagedata (c++ function)": [[157, "_CPPv4NK8Avogadro3VTK11vtkGLWidget9imageDataEv"]], "avogadro::vtk::vtkglwidget::imagedataupdated (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget16imageDataUpdatedEv"]], "avogadro::vtk::vtkglwidget::lut (c++ function)": [[157, "_CPPv4NK8Avogadro3VTK11vtkGLWidget3lutEv"]], "avogadro::vtk::vtkglwidget::molecule (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget8moleculeEv"], [157, "_CPPv4NK8Avogadro3VTK11vtkGLWidget8moleculeEv"]], "avogadro::vtk::vtkglwidget::opacityfunction (c++ function)": [[157, "_CPPv4NK8Avogadro3VTK11vtkGLWidget15opacityFunctionEv"]], "avogadro::vtk::vtkglwidget::renderisosurface (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget16renderIsosurfaceEb"]], "avogadro::vtk::vtkglwidget::rendervolume (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget12renderVolumeEb"]], "avogadro::vtk::vtkglwidget::renderer (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget8rendererEv"]], "avogadro::vtk::vtkglwidget::resetcamera (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget11resetCameraEv"]], "avogadro::vtk::vtkglwidget::resetgeometry (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget13resetGeometryEv"]], "avogadro::vtk::vtkglwidget::scenemodel (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget10sceneModelEv"], [157, "_CPPv4NK8Avogadro3VTK11vtkGLWidget10sceneModelEv"]], "avogadro::vtk::vtkglwidget::setcube (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget7setCubeEPN4Core4CubeE"]], "avogadro::vtk::vtkglwidget::setisovalue (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget11setIsoValueEd"]], "avogadro::vtk::vtkglwidget::setmolecule (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget11setMoleculeEPN5QtGui8MoleculeE"]], "avogadro::vtk::vtkglwidget::setopacity (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget10setOpacityEd"]], "avogadro::vtk::vtkglwidget::updatescene (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget11updateSceneEv"]], "avogadro::vtk::vtkglwidget::vtkglwidget (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidget11vtkGLWidgetEP7QWidgetN2Qt11WindowFlagsE"]], "avogadro::vtk::vtkglwidget::~vtkglwidget (c++ function)": [[157, "_CPPv4N8Avogadro3VTK11vtkGLWidgetD0Ev"]], "vtkavogadroactor (c++ class)": [[158, "_CPPv416vtkAvogadroActor"]], "vtkavogadroactor::getbounds (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor9GetBoundsEv"]], "vtkavogadroactor::getscene (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor8GetSceneEv"]], "vtkavogadroactor::hastranslucentpolygonalgeometry (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor31HasTranslucentPolygonalGeometryEv"]], "vtkavogadroactor::new (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor3NewEv"]], "vtkavogadroactor::renderopaquegeometry (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor20RenderOpaqueGeometryEP11vtkViewport"]], "vtkavogadroactor::rendertranslucentpolygonalgeometry (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor34RenderTranslucentPolygonalGeometryEP11vtkViewport"]], "vtkavogadroactor::m_bounds (c++ member)": [[158, "_CPPv4N16vtkAvogadroActor8m_boundsE"]], "vtkavogadroactor::m_initialized (c++ member)": [[158, "_CPPv4N16vtkAvogadroActor13m_initializedE"]], "vtkavogadroactor::m_scene (c++ member)": [[158, "_CPPv4N16vtkAvogadroActor7m_sceneE"]], "vtkavogadroactor::setscene (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor8setSceneEPN8Avogadro9Rendering5SceneE"]], "vtkavogadroactor::vtkavogadroactor (c++ function)": [[158, "_CPPv4N16vtkAvogadroActor16vtkAvogadroActorEv"]], "vtkavogadroactor::~vtkavogadroactor (c++ function)": [[158, "_CPPv4N16vtkAvogadroActorD0Ev"]]}}) \ No newline at end of file diff --git a/teach/acid_base.html b/teach/acid_base.html new file mode 100644 index 00000000..10cf0bb2 --- /dev/null +++ b/teach/acid_base.html @@ -0,0 +1,670 @@ + + + + + + + + + + + Acid-Base Properties of Amino Acids — Avogadro 1.98.1 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Acid-Base Properties of Amino Acids#

    +

    Investigate the pH-dependent protonation of amino acids.

    +
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    Tasks#

    +
      +
    1. Create and optimize the geometry of a glycine molecule (H2NCH2COOH). Open the “Build” menu and select “Add Hydrogens for pH…”. Choose different values of pH (1, 2, 3, …, 13) and note the effect of pH shift on the electrical charge of glycine.

    2. +
    3. In a new View, create a (glutamic acid - lysine) dipeptide using the “Build” menu, then “Insert”, then “Peptides…”. Set the pH to 3 and calculate the corresponding electrical charge of the dipeptide. Do the same for pH 7 and pH 13.

    4. +
    +

    When performing a paper electrophoresis at these pHs, in which direction will the dipeptide move (towards the anode or cathode)?

    +
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    +

    Solution#

    +
      +
    1. Glycine electrical charge according to pH shift:

      +
        +
      • pH < 5: NH3+-CH2-COO-H+; net charge = +1.

      • +
      • 5 ≤ pH < 10: NH3+-CH2-COO-; net charge = 0.

      • +
      • 10 ≤ pH ≤ 13: NH2-CH2-COO-; net charge = -1.

      • +
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    2. +
    3. Glu-Lys dipeptide:

    4. +
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    pH

    Net charge

    +1

    -1

    -2

    Electrophoresis

    → cathode (-)

    → anode (+)

    →→ anode (+)

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    Further reading#

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    + + + + + + + + \ No newline at end of file diff --git a/teach/alkene_isomers.html b/teach/alkene_isomers.html new file mode 100644 index 00000000..8e0c369c --- /dev/null +++ b/teach/alkene_isomers.html @@ -0,0 +1,643 @@ + + + + + + + + + + + Alkene Isomers — Avogadro 1.98.1 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Alkene Isomers#

    +

    Investigate the stability of alkene isomers due to steric interactions.

    +
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    Task#

    +

    Build and optimize the geometry of isomeric alkenes and compare their relative energies to confirm empirical rules for evaluating alkene stability: Zaitsef’s rule, cis- vs trans-, isolate vs conjugated dienes.

    +

    Examples:

    +
      +
    • Compare: 1-hexene, 2-hexene (cis and trans), 2-methyl-2-pentene, 2,3-dimethyl-2-butene.

    • +
    • Compare: 1,4-pentadiene and 1,3-pentadiene.

    • +
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    See also#

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    Markovnikov’s Rule

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    Basic VSEPR#

    +

    Investigate molecular geometries using VSEPR rules.

    +
    +

    Task#

    +

    Build and optimize the geometry of simple molecules to illustrate VSEPR theory.

    +
      +
    • For organic-type molecules, use the MMFF94 forcefield.

    • +
    +

    Examples: methane, water, ammonia, etc.

    +
      +
    • For octahedral-based geometries, use the UFF forcefield which is optimized for all elements.

    • +
    +

    Examples: SF6, IF5, XeF4, etc.

    +
      +
    • Try even 7, 8, or 9 atoms around a central metal - how do the VSEPR rules extend beyond octahedral molecules?

    • +
    +
    +
    +

    See also#

    +

    Organic Hybridization

    +
    +
    +

    Further reading#

    +

    VSEPR theory (wikipedia)

    +
    +

    Warning

    +

    Geometries derived from the trigonal bipyramidal geometry are not currently reliable.

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    Tip

    +

    When using the Draw tool, you may wish to uncheck the “Adjust Hydrogens” box.

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    1,3-diaxial interactions#

    +

    Investigate steric interactions in cyclohexane derivatives.

    +
    +

    Tasks#

    +
      +
    1. Create and optimize the geometry of a cyclohexane molecule.

    2. +
    3. Add methyl substituents to the 1 and 3 positions in a diequatorial arrangement, optimize the geometry and note the energy.

    4. +
    5. Delete the diequatorial substituents to return to cyclohexane, and optimize the geometry again.

    6. +
    7. Place methyl substituents in 1,3-diaxial positions, optimize the geometry and note the movement of the groups and the energy.

    8. +
    +
    +
    +

    Solution#

    + + + + + + + + + + + + + + + + + + + + +

    Molecule

    Cyclohexane

    Diequatorial

    Diaxial

    Energy

    30 kJ/mol

    40 kJ/mol

    98 kJ/mol

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    HCN dipole#

    +

    Investigate polar intermolecular interactions using HCN.

    +
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    Task#

    +

    Create two molecules of HCN, run a force field geometry optimization. Check the orientation of the molecules, note the energy of interaction. Find primary dipoles, compare length of interatomic and intermolecular bonds.

    +
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    See also#

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    Water

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    Hydrogen Clusters#

    +

    Investigate the intermolecular interactions of solid hydrogen.

    +
    +

    Task#

    +

    Create 7 molecules of hydrogen. Optimize the geometry using the UFF forcefield and correct figure until all molecules are standing in a flat hexagonal order. Check the energy of interaction and distance between molecules.

    +
    +
    +

    Solution#

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    Cell parameters

    a

    b

    c

    α

    β

    γ

    Webelements

    470 pm

    470 pm

    340 pm

    90.0°

    90.0°

    120.0°

    UFF

    486-496 pm

    486-496 pm

    324 pm

    90.0°

    90.0°

    120.0°

    +
      +
    • Space group: P63/mmc (Space group number: 194).

    • +
    • Structure: hcp (hexagonal close-packed).

    • +
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    +
    +

    Issues#

    +

    Melting of this cluster is poorly controllable.

    +

    Cluster is a bit deformed, with long optimization some molecules tend to rotate and stand skew to neighbours.

    +

    Since UFF does not properly include quantum mechanical effects and hydrogen bonding, the configuration and size of the unit cell are somewhat different than the experimental configuration.

    +
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    +

    See also#

    +

    Hydrogen Molecule

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    Sources#

    +

    Webelements data on hydrogen clusters

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    Hydrogen Molecule#

    +

    Investigate the hydrogen molecule and its bond length using different force fields.

    +
    +

    Task#

    +
      +
    • Create the H2 molecule using the drawing tool.

    • +
    • Optimize the geometry with a variety of force fields and tabulate the resulting bond lengths.

    • +
    • Enable display of its orbitals (?)

    • +
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    Solution#

    +

    + + + + + + + + + + + + + + + + + + + + +

    Force field

    Bond length (Å)

    GAFF

    1.10

    Ghemical

    1.01

    MMFF

    Error

    UFF

    0.71

    +

    An accurate bond length (see sources) for the molecule is 0.074 nm, so the UFF force field should be used.

    +
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    +

    See also#

    +

    Hydrogen Clusters

    +
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    Sources#

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    Hyperphysics data on the hydrogen molecule

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    Warning

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    This section is in the process of being migrated from the original Avogadro documentation. Some instructions and screenshots may be out of date.

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    Avogadro is intended not only for molecular modeling research, but also for educational use. This category is intended to help educators around the world find lessons and tips for using Avogadro 2 in teaching chemistry. If you have an exercise or article that you would like to list here, please get in touch via Avogadro Discussion.

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    1,3-diaxial interactions

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    Investigate steric interactions in cyclohexane derivatives.

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    Alkene Isomers

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    Investigate the stability of alkene isomers due to steric interactions.

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    Basic VSEPR

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    Investigate molecular geometries using VSEPR rules.

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    HCN dipole

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    Investigate polar intermolecular interactions using HCN.

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    Hydrogen Clusters

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    Investigate the intermolecular interactions of solid hydrogen.

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    Hydrogen Molecule

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    Investigate the hydrogen molecule and its bond length using different force fields.

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    Markovnikov’s Rule

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    Investigate the stability of reactions using Markovnikov’s rule.

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    Organic Hybridization

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    Illustrate the geometry and bond lengths in sp3, sp2 and sp hybridized carbons.

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    Water

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    Investigate the geometry of water and hydrogen bonding between molecules.

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    Acid-Base Properties of Amino Acids

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    Investigate the pH-dependent protonation of amino acids.

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    Markovnikov’s Rule#

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    Investigate the stability of reactions using Markovnikov’s rule.

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    Task#

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    Build a propene molecule and optimize its geometry. Compare the relative energy of bromine-hydrogen substitution at either the 1-carbon or 2-carbon of the carbon-carbon double bond. Which of these two bromopropane compounds will be the major product of a propene bromination reaction?

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    Solution#

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    Results of relative energies expressed in kJ/mol (need confirmation in literature).

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    Force field

    Intermediate primary carbocation (1’)

    Intermediate secondary carbocation (2’)

    1-bromopropane (1)

    2-bromopropane (2)

    Ghemical

    -2.24

    -2.06

    -2.39

    -1.87

    MMFF94

    -9.88

    -3.84

    -8.96

    +2.70

    UFF

    +4.05

    +3.63

    +4.15

    +4.86

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    UFF data is considered in this case, the secondary carbocation intermediate requires less energy (2’) than the primary carbocation intermediate (1’) (resp. 3.6 vs 4 kJ/mol). So compound (2) will be the major form. This is called the Markovnikov’s rule: “the major product of the addition of HX (where X is some atom more electronegative than H, the bromine in our case) to an alkene (here the propene) has the hydrogen atom in the less substituted position and X in the more substituted position”. Mechanisms which avoid the carbocation intermediate such as the presence of dialkyl peroxides will reverse the reaction result and compound (1) becomes the major product (Anti-Markovnikov rule).

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    See also#

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    Alkene Isomers

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    Further reading#

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    Markovnikov’s rule (wikipedia)

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    Organic Hybridization#

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    Illustrate the geometry and bond lengths in sp3, sp2 and sp hybridized carbons.

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    Task#

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    For each of ethane, ethylene and ethyne, build the molecule and optimize the geometry. Use the measurement tool to examine bond lengths and bond angles.

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    Solution#

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    Results using the MMFF94 forcefield:

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    • sp3 - ethane bond angle: 110°; C-C bond length: 1.5 Å.

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    • sp2 - ethylene bond angle: 121°; C-C bond length: 1.336 Å.

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    • sp - ethyne bond angle: 180°; C-C bond length: 1.200 Å.

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    See also#

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    Basic VSEPR

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    Further reading#

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    Orbital hybridization (wikipedia)

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    Water#

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    Investigate the geometry of water and hydrogen bonding between molecules.

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    Task#

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    Create a water molecule and optimize its geometry. Use the measurement tool to check the bond lengths and angle.

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    Add another water molecule and use the same force field to optimize the geometry of the resulting dimer. Check the bond lengths in both molecules, and the angles between the bonds. Check how the molecules are oriented to each other. Calculate the energy of interaction, pay attention to the role of hydrogen bonds. Measure the deformation of bonds.

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    Force field

    Bond length (Å)

    Angle (°)

    GAFF

    1.10

    102.8

    Ghemical

    0.95

    109.5

    MMFF94

    0.97

    104.0

    UFF

    0.96

    104.5

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    Wikipedia gives an experimental O-H bond length of 95.84 pm, and a H-O-H bond angle of 104.45°, so both MMFF94 and UFF perform reasonably.

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    Note that there is a significant electrostatic interaction between the positively charged hydrogen atom and the oxygen on neighboring molecules.

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    Warning

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    Only the MMFF94 force field includes hydrogen bonding terms, so two water molecules may not attract each other using the other force fields.

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    See also#

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    HCN dipole

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    Sources#

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    Wikipedia page on the properties of water

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