Charged atom types#1206

Merged

mliu49 merged 28 commits intomasterfrom

chargedAT

Feb 2, 2018

Commits on Feb 1, 2018

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

Commits on Feb 2, 2018

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

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

nyee
authored and
alongd
committed
Change makeSampleMolecule to work with new charge attribute on atomtypes
alongd
committed
Added the charge attribute to atomTypes
alongd
committed
Implementation of new charged C/N/O/S atomtypes
alongd
committed
Added new atomTypeTests
alongd
committed
Updated atomtypes through the testing_database

nyee
authored and
alongd
committed
Updated atomTypes throughout the code

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

nyee
authored and
alongd
committed
Update isomer in PDep exploration
alongd
committed
Added sulfur and nitrogen libraries to documentation
alongd
committed
Added atomTypes to documentation
alongd
committed
Refactor Molecule.saturate() to saturateRadical

nyee
authored and
alongd
committed
Add saturateUnfilledValence method to Molecule

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

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

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

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Charged atom types#1206

Charged atom types#1206
mliu49 merged 28 commits intomasterfrom
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

Charged atom types#1206mliu49 merged 28 commits intomasterReactionMechanismGenerator/RMG-Py:masterfrom chargedATReactionMechanismGenerator/RMG-Py:chargedATCopy head branch name to clipboard

Commits

Commits on Feb 1, 2018

Commits on Feb 2, 2018

Charged atom types#1206
mliu49 merged 28 commits intomasterfrom
chargedAT