Charged atom types - #1206

Merged

mliu49 merged 28 commits into

masterfrom

chargedAT

Feb 2, 2018

Commits on Feb 1, 2018

Allow database-test to make sample atoms using nitrogen atomTypes
alongd
committed
d700475
Added a raise DatabaseError to thermo.py
alongd
committed
cdffa14

Commits on Feb 2, 2018

Update lone pairs as first step in molecule.updateAtomType()

nyee
authored and
alongd
committed
dd8e281
Change makeSampleAtom to work with new charge attribute on atomtypes

nyee
authored and
alongd
committed
cd935f2
Change makeSampleMolecule to work with new charge attribute on atomtypes
alongd
committed
5a4a38a
Added the charge attribute to atomTypes
alongd
committed
25c3de8
Implementation of new charged C/N/O/S atomtypes
alongd
committed
8dd7a31
Added new atomTypeTests
alongd
committed
96811b8
Updated atomtypes through the testing_database

nyee
authored and
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4c49870
Updated atomTypes throughout the code

nyee
authored and
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189e2ff
Modified atomtypedatabase.py according to new atomTypes
alongd
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93a3d73
Don't saturate lonePairs on carbon monoxide in solvation

nyee
authored and
alongd
committed
13bacf4
Update isomer in PDep exploration
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committed
41f630b
Added sulfur and nitrogen libraries to documentation
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9b60a5d
Added atomTypes to documentation
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f570240
Refactor Molecule.saturate() to saturateRadical

nyee
authored and
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committed
b7cc911
Add saturateUnfilledValence method to Molecule

nyee
authored and
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committed
27db908
Saturate submols with H in heuristic thermo method for polyrings

nyee
authored and
alongd
committed
ffb38a4
Fixes to thermoTest for new updateLonePair addition in updateAtomtype

nyee
authored and
alongd
committed
bb63824
Reorder updateCharge() and updateAtomTypes() in molecule.py
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8d4757d
Added known SMILES to generator.py
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f66346d
Formating fixes to pass codevac

nyee
authored and
alongd
committed
ea8b2e2
Fix charged polyrings formed in thermoTests
alongd
committed
2b6ff10
Avoid generating carbenes in findAllDelocalizationPathsN5dd_N5ts
alongd
committed
5f117a1
Removed hard-coded exception for carbonMonoxide in group.py
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7e08a24
Deleted species containing O2sn atomType
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committed
ccee9eb
Updated atomTypes throughout the repository
alongd
committed
2a27920
Added N and S atoms to reaction.pairs determination by similarity
alongd
committed
4e17060

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Charged atom types - #1206

Charged atom types#1206
mliu49 merged 28 commits into
masterfrom
chargedAT

Commits on Feb 1, 2018

Allow database-test to make sample atoms using nitrogen atomTypes

Added a raise DatabaseError to thermo.py

Commits on Feb 2, 2018

Update lone pairs as first step in molecule.updateAtomType()

Change makeSampleAtom to work with new charge attribute on atomtypes

Change makeSampleMolecule to work with new charge attribute on atomtypes

Added the charge attribute to atomTypes

Implementation of new charged C/N/O/S atomtypes

Added new atomTypeTests

Updated atomtypes through the testing_database

Updated atomTypes throughout the code

Modified atomtypedatabase.py according to new atomTypes

Don't saturate lonePairs on carbon monoxide in solvation

Update isomer in PDep exploration

Added sulfur and nitrogen libraries to documentation

Added atomTypes to documentation

Refactor Molecule.saturate() to saturateRadical

Add saturateUnfilledValence method to Molecule

Saturate submols with H in heuristic thermo method for polyrings

Fixes to thermoTest for new updateLonePair addition in updateAtomtype

Reorder updateCharge() and updateAtomTypes() in molecule.py

Added known SMILES to generator.py

Formating fixes to pass codevac

Fix charged polyrings formed in thermoTests

Avoid generating carbenes in findAllDelocalizationPathsN5dd_N5ts

Removed hard-coded exception for carbonMonoxide in group.py

Deleted species containing O2sn atomType

Updated atomTypes throughout the repository

Added N and S atoms to reaction.pairs determination by similarity