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[DO NOT MERGE] Pre-generate residue templates #492

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[DO NOT MERGE] Pre-generate residue templates #492

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d90ac7a
polymer engine works, point mutation engineminor changes
zhang-ivy Sep 26, 2018
a6ca053
fix point mutation engine, still have oemol res warnings
zhang-ivy Oct 3, 2018
5cb8e31
Merge remote-tracking branch 'origin/master' into protein_mutations_ivy
zhang-ivy Oct 3, 2018
be3b200
fix chain id problem, compute state key base class problem, and const…
zhang-ivy Oct 4, 2018
2638a02
finish PointMutationEngine, started stereochem
zhang-ivy Oct 9, 2018
01d7ffe
update stereochem, getting NaNs for logP_work and logP_energy
zhang-ivy Oct 18, 2018
a00cb9b
add print statements to debug NaNs
zhang-ivy Oct 22, 2018
b1f9770
Merge branch 'master' into protein_mutations_ivy
zhang-ivy Oct 22, 2018
1945230
move print statements in oemol from residue
zhang-ivy Oct 23, 2018
5d0ee5c
modify and unmodify FFAllAngleGeometryEngine.write_proposal_pdb
zhang-ivy Oct 23, 2018
ee71cdc
fix geometry.py for linux
zhang-ivy Oct 24, 2018
d6e513e
add print statement in choose mutant
zhang-ivy Oct 24, 2018
c676319
try to make geomtery match 10/09 commit
zhang-ivy Oct 24, 2018
d9c7c7f
add print statements in determine extra torsions/angles
zhang-ivy Oct 25, 2018
d42954c
fix topology_index, clean up a bit
zhang-ivy Oct 25, 2018
b8067fc
add .modified to new_topology, more clean up
zhang-ivy Oct 25, 2018
b1b4c76
more clean up
zhang-ivy Oct 30, 2018
f67dc45
merge with master
zhang-ivy Oct 30, 2018
b84a880
update generateOEMolFromResidue, replace openmoltools calls with call…
zhang-ivy Oct 31, 2018
a13c41b
fix topology smiles mismatch, use update openmoltools functions, work…
zhang-ivy Nov 5, 2018
9ff8ed9
include test_ivy.py
zhang-ivy Nov 5, 2018
ab7b6df
skip header of clinical-kinase-inhibitors.csv in KinaseInhibitorsTest…
zhang-ivy Nov 5, 2018
e8ea4f0
reset head and merge with master
zhang-ivy Nov 5, 2018
941cda7
fix atom.stereo missing in determine_extra_torsions
zhang-ivy Nov 6, 2018
2df557b
handle atom and bond stereochemistry in determine extra torsions
zhang-ivy Nov 7, 2018
5eb6595
add atom and bond stereo to determine_extra_torsions, changed test sy…
zhang-ivy Nov 9, 2018
12640ea
use generateForcefieldFromMolecules
zhang-ivy Nov 12, 2018
9668220
prep for merge with commit from experiment-harness
zhang-ivy Nov 9, 2018
cd1bf5e
Remove chargeProd*=0
pgrinaway Nov 11, 2018
3a62f15
merged with experiment-harness
zhang-ivy Nov 12, 2018
3240b3a
generate residue templates on the fly, fix stereo by passing current …
zhang-ivy Nov 14, 2018
9d55c38
remove extra files
zhang-ivy Nov 14, 2018
a8983e2
remove more files
zhang-ivy Nov 14, 2018
352512f
clean up some comments
zhang-ivy Nov 14, 2018
de77680
load ffxml instead of pre-generating templates
zhang-ivy Nov 14, 2018
8a5462e
added changes from protein_mutations_ivy for passing state key throug…
zhang-ivy Nov 14, 2018
5730185
use metadata['smiles']
zhang-ivy Nov 14, 2018
d696c25
use protein_mutations_ivy metadata['smiles'] changes
zhang-ivy Nov 14, 2018
248d921
fix HybridTopologyFactory's create_topology and switch to GeometrySys…
zhang-ivy Nov 15, 2018
cde1809
use protein_mutation_ivy's fixHybridTopologyFactory's create_topology
zhang-ivy Nov 21, 2018
a2f2e4c
make sure clinical-kinase-inhibitors files are correct
zhang-ivy Nov 21, 2018
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24 changes: 1 addition & 23 deletions perses/data/clinical-kinase-inhibitors.csv
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Original file line number Diff line number Diff line change
@@ -1,26 +1,4 @@
Imatinib,C5=C(C1=CN=CC=C1)N=C(NC2=C(C=CC(=C2)NC(C3=CC=C(C=C3)CN4CCN(CC4)C)=O)C)N=C5
Dasatinib,C1=C(SC(=N1)NC2=CC(=NC(=N2)C)N3CCN(CC3)CCO)C(=O)NC4=C(C=CC=C4Cl)C
Nilotinib,Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)C(=O)Nc4cc(cc(c4)n5cc(nc5)C)C(F)(F)F
Bosutinib,C1=C(C(=CC2=C1C(=C(C=N2)C#N)NC3=C(C=C(C(=C3)OC)Cl)Cl)OCCCN4CCN(CC4)C)OC
Ponatinib,Cc1ccc(cc1C#Cc2cnc3n2nccc3)C(=O)Nc4ccc(c(c4)C(F)(F)F)CN5CCN(CC5)C
Gefitinib,COc1cc2c(cc1OCCCN3CCOCC3)c(ncn2)Nc4ccc(c(c4)Cl)F
Erlotinib,COCCOc1cc2c(cc1OCCOC)ncnc2Nc3cccc(c3)C#C
Afatinib,CN(C)C/C=C/C(=O)NC1=C(C=C2C(=C1)C(=NC=N2)NC3=CC(=C(C=C3)F)Cl)O[C@H]4CCOC4
Lapatinib,CS(=O)(=O)CCNCc1ccc(o1)c2ccc3c(c2)c(ncn3)Nc4ccc(c(c4)Cl)OCc5cccc(c5)F
Sorafenib,CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl
Sunitinib,CCN(CC)CCNC(=O)c1c(c([nH]c1C)/C=C\2/c3cc(ccc3NC2=O)F)C
Vandetanib,CN1CCC(CC1)COc2cc3c(cc2OC)c(ncn3)Nc4ccc(cc4F)Br
Axitinib,CNC(=O)c1ccccc1Sc2ccc3c(c2)[nH]nc3/C=C/c4ccccn4
Regorafenib,CNC(=O)C1=NC=CC(=C1)OC2=CC(=C(C=C2)NC(=O)NC3=CC(=C(C=C3)Cl)C(F)(F)F)F
Crizotinib,C[C@H](C1=C(C=CC(=C1Cl)F)Cl)OC2=C(N=CC(=C2)C3=CN(N=C3)C4CCNCC4)N
Ceritinib,Cc1cc(c(cc1C2CCNCC2)OC(C)C)Nc3ncc(c(n3)Nc4ccccc4S(=O)(=O)C(C)C)Cl
Vemurafenib,CCCS(=O)(=O)Nc1ccc(c(c1F)C(=O)c2c[nH]c3c2cc(cn3)c4ccc(cc4)Cl)F
Dabrafenib,CC(C)(C)c1nc(c(s1)c2ccnc(n2)N)c3cccc(c3F)NS(=O)(=O)c4c(cccc4F)F
Ruxolitinib,c1c[nH]c2c1c(ncn2)c3cnn(c3)[C@H](CC#N)C4CCCC4
Tofacitinib,C[C@@H]1CCN(C[C@@H]1N(C)C2=NC=NC3=C2C=CN3)C(=O)CC#N
Cabozantinib,COc1cc2c(ccnc2cc1OC)Oc3ccc(cc3)NC(=O)C4(CC4)C(=O)Nc5ccc(cc5)F
Ibrutinib,C=CC(=O)N1CCC[C@H](C1)n2c3c(c(n2)c4ccc(cc4)Oc5ccccc5)c(ncn3)N
Trametinib,CC1=C2C(=C(N(C1=O)C)NC3=C(C=C(C=C3)I)F)C(=O)N(C(=O)N2C4=CC=CC(=C4)NC(=O)C)C5CC5
Idelalisib,CC[C@@H](C1=NC2=C(C(=CC=C2)F)C(=O)N1C3=CC=CC=C3)NC4=C5C(=NC=N5)N=CN4
Lenvatinib,COC1=CC2=NC=CC(=C2C=C1C(=O)N)OC3=CC(=C(C=C3)NC(=O)NC4CC4)Cl
Palbociclib,Cc1c2cnc(nc2n(c(=O)c1C(=O)C)C3CCCC3)Nc4ccc(cn4)N5CCNCC5
Bosutinib,C1=C(C(=CC2=C1C(=C(C=N2)C#N)NC3=C(C=C(C(=C3)OC)Cl)Cl)OCCCN4CCN(CC4)C)OC
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