#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>
Definition at line 37 of file GAFFTypeProcessor.h.
◆ GAFFTypeProcessor() [1/2]
BALL::GAFFTypeProcessor::GAFFTypeProcessor |
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◆ GAFFTypeProcessor() [2/2]
BALL::GAFFTypeProcessor::GAFFTypeProcessor |
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const Options & |
new_options | ) |
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◆ ~GAFFTypeProcessor()
virtual BALL::GAFFTypeProcessor::~GAFFTypeProcessor |
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◆ annotateAliphaticAndAromaticRingAtoms_()
void BALL::GAFFTypeProcessor::annotateAliphaticAndAromaticRingAtoms_ |
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◆ annotateBondTypes_()
void BALL::GAFFTypeProcessor::annotateBondTypes_ |
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Helper for precomputeBondProperties.
◆ annotatePlanarRingAtoms_()
void BALL::GAFFTypeProcessor::annotatePlanarRingAtoms_ |
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◆ annotateRingSizes_()
void BALL::GAFFTypeProcessor::annotateRingSizes_ |
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Helper for precomputeAtomProperties.
◆ assignAtomtype_()
bool BALL::GAFFTypeProcessor::assignAtomtype_ |
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Atom & |
atom | ) |
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Check the atom against each possible atom type and try to assign one.
◆ getCarbonTypes_()
std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getCarbonTypes_ |
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◆ getHydrogenTypes_()
std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getHydrogenTypes_ |
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◆ getNitrogenTypes_()
std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getNitrogenTypes_ |
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◆ getOxygenTypes_()
std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getOxygenTypes_ |
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◆ getSulfurTypes_()
std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getSulfurTypes_ |
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◆ getTypeNames()
std::set< String > BALL::GAFFTypeProcessor::getTypeNames |
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◆ operator()()
◆ parseAtomtypeTableFile_()
void BALL::GAFFTypeProcessor::parseAtomtypeTableFile_ |
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Read file with table of atomtypes and push atomtypes and their TypeDefinition in corresponding vector and store a GAFFCESParser for every CESstring. The path to the atom type file is taken from the value of the option ATOMTYPE_FILENAME.
- Exceptions
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◆ planarAtom_()
bool BALL::GAFFTypeProcessor::planarAtom_ |
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const Atom & |
atom | ) |
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◆ postProcessAtomTypes_()
void BALL::GAFFTypeProcessor::postProcessAtomTypes_ |
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Molecule * |
molecule | ) |
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Postprocessing and cleanup for GAFF types
◆ precomputeAtomProperties_()
void BALL::GAFFTypeProcessor::precomputeAtomProperties_ |
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Molecule * |
molecule | ) |
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Store connectivity, number of attached H-atoms and number of attached N,O,F,Cl and Br-atoms for every atom in molecule
◆ precomputeBondProperties_()
void BALL::GAFFTypeProcessor::precomputeBondProperties_ |
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Molecule * |
molecule | ) |
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compute aromaticity, ring memberships, GAFF bond typization, ...
◆ atom_types_
◆ ces_parsers_
◆ current_molecule_
Molecule* BALL::GAFFTypeProcessor::current_molecule_ |
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◆ options
Options BALL::GAFFTypeProcessor::options |
◆ sssr_
std::vector<std::vector<Atom*> > BALL::GAFFTypeProcessor::sssr_ |
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