#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>
Definition at line 37 of file GAFFTypeProcessor.h.
BALL::GAFFTypeProcessor::GAFFTypeProcessor |
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BALL::GAFFTypeProcessor::GAFFTypeProcessor |
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const Options & |
new_options | ) |
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virtual BALL::GAFFTypeProcessor::~GAFFTypeProcessor |
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virtual |
void BALL::GAFFTypeProcessor::annotateAliphaticAndAromaticRingAtoms_ |
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void BALL::GAFFTypeProcessor::annotateBondTypes_ |
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Helper for precomputeBondProperties.
void BALL::GAFFTypeProcessor::annotatePlanarRingAtoms_ |
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void BALL::GAFFTypeProcessor::annotateRingSizes_ |
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Helper for precomputeAtomProperties.
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.
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getCarbonTypes_ |
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inlineprotected |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getHydrogenTypes_ |
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inlineprotected |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getNitrogenTypes_ |
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inlineprotected |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getOxygenTypes_ |
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inlineprotected |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getSulfurTypes_ |
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std::set<String> BALL::GAFFTypeProcessor::getTypeNames |
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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.
bool BALL::GAFFTypeProcessor::planarAtom_ |
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const Atom & |
atom | ) |
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void BALL::GAFFTypeProcessor::postProcessAtomTypes_ |
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Molecule * |
molecule | ) |
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Postprocessing and cleanup for GAFF types
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
void BALL::GAFFTypeProcessor::precomputeBondProperties_ |
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Molecule * |
molecule | ) |
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compute aromaticity, ring memberships, GAFF bond typization, ...
Molecule* BALL::GAFFTypeProcessor::current_molecule_ |
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Options BALL::GAFFTypeProcessor::options |
std::vector<std::vector<Atom*> > BALL::GAFFTypeProcessor::sssr_ |
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