test case progression

[BrandeisPatrick]

high priority

• test_advanced_example_1

pass

• test_boxgen_naphthalene_water

pass

• test_boxgen (custom solvent)

working on adding .prep file

---

low priority

• test_example_4 (resp needs gaussian to test)

I will not prioritize this test since I only need bcc so far

• test_clustergen

clustergen not refactored yet
not priority

• test_autosolvate

package, module issue.
not priority

• test_multicomponent

multicomponent not refactored
not priority

[BrandeisPatrick]

about test_boxgen (custom solvent)

description

solvate naphthalene_neutral in acetonitrile

my question

1. why .frcmod file is provided but .mol2 file is not provided?
2. what is .prep file for?

[BrandeisPatrick]

PDB Issue

when directly import PDB, residue name in .pdb file could be different than the molecule.residue_name define in object.

• we should either check .pdb residue name before importing pdb
  or we should automate the setting of molecule.residue_name

[BrandeisPatrick]

property Issue

box.closeness = 2 will cause issue
box.closeness has to be a float (ex. box.closeness = 2.0)

• use @Property @name.setter to solve this issue, converting 2 to 2.0

[BrandeisPatrick]

review edit_system_pdb() in tools

• improve this method's definition, and where it is referenced

[BrandeisPatrick]

prep file Issue

• add .prep attribute to molecule object

• I needs to figure out when .prep is needed
  if we try to create custom solvent with only .pdb file, is .prep file needed

• what is .prep file's function

• is following appropriate?
  if mol.prep != None:
  doc.write('{:<20} {:<20} \n'.format('loadamberprep', mol.prep))

needs review

[BrandeisPatrick]

lib file issue

• figure out if .lib file starts with residue name or mol name

[BrandeisPatrick]

Default Value

• why these are default value
• these default value should be in common.py

box.duplicate_solute_num = 1
box.duplicate_solvent_num = 1680
box.closeness = 2.0
box.cubesize = 56