BALL
1.4.1
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#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>
Classes | |
struct | Default |
struct | Option |
struct | TypeDefinition |
Nested class definitions. More... | |
Public Member Functions | |
GAFFTypeProcessor () | |
GAFFTypeProcessor (const Options &new_options) | |
virtual | ~GAFFTypeProcessor () |
virtual Processor::Result | operator() (Composite &composite) |
std::set< String > | getTypeNames () const |
Public Attributes | |
Options | options |
Protected Member Functions | |
std::vector< TypeDefinition > | getCarbonTypes_ () |
std::vector< TypeDefinition > | getHydrogenTypes_ () |
std::vector< TypeDefinition > | getNitrogenTypes_ () |
std::vector< TypeDefinition > | getOxygenTypes_ () |
std::vector< TypeDefinition > | getSulfurTypes_ () |
void | parseAtomtypeTableFile_ () throw (Exception::FileNotFound) |
void | precomputeBondProperties_ (Molecule *molecule) |
compute aromaticity, ring memberships, GAFF bond typization, ... | |
void | precomputeAtomProperties_ (Molecule *molecule) |
void | annotateBondTypes_ () |
Helper for precomputeBondProperties. | |
void | annotateRingSizes_ () |
Helper for precomputeAtomProperties. | |
void | annotateAliphaticAndAromaticRingAtoms_ () |
void | annotatePlanarRingAtoms_ () |
bool | planarAtom_ (const Atom &atom) |
bool | assignAtomtype_ (Atom &atom) |
void | postProcessAtomTypes_ (Molecule *molecule) |
Protected Attributes | |
StringHashMap< GAFFCESParser * > | ces_parsers_ |
std::map< Position, std::vector< TypeDefinition > > | atom_types_ |
std::vector< std::vector< Atom * > > | sssr_ |
Molecule * | current_molecule_ |
Definition at line 37 of file GAFFTypeProcessor.h.
BALL::GAFFTypeProcessor::GAFFTypeProcessor | ( | const Options & | new_options | ) |
virtual BALL::GAFFTypeProcessor::~GAFFTypeProcessor | ( | ) | [virtual] |
void BALL::GAFFTypeProcessor::annotateAliphaticAndAromaticRingAtoms_ | ( | ) | [protected] |
void BALL::GAFFTypeProcessor::annotateBondTypes_ | ( | ) | [protected] |
Helper for precomputeBondProperties.
void BALL::GAFFTypeProcessor::annotatePlanarRingAtoms_ | ( | ) | [protected] |
void BALL::GAFFTypeProcessor::annotateRingSizes_ | ( | ) | [protected] |
Helper for precomputeAtomProperties.
bool BALL::GAFFTypeProcessor::assignAtomtype_ | ( | Atom & | atom | ) | [protected] |
Check the atom against each possible atom type and try to assign one.
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getCarbonTypes_ | ( | ) | [inline, protected] |
Definition at line 92 of file GAFFTypeProcessor.h.
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getHydrogenTypes_ | ( | ) | [inline, protected] |
Definition at line 93 of file GAFFTypeProcessor.h.
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getNitrogenTypes_ | ( | ) | [inline, protected] |
Definition at line 94 of file GAFFTypeProcessor.h.
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getOxygenTypes_ | ( | ) | [inline, protected] |
Definition at line 95 of file GAFFTypeProcessor.h.
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getSulfurTypes_ | ( | ) | [inline, protected] |
Definition at line 96 of file GAFFTypeProcessor.h.
std::set<String> BALL::GAFFTypeProcessor::getTypeNames | ( | ) | const |
virtual Processor::Result BALL::GAFFTypeProcessor::operator() | ( | Composite & | ) | [virtual] |
operator ()
Reimplemented from BALL::UnaryProcessor< Composite >.
void BALL::GAFFTypeProcessor::parseAtomtypeTableFile_ | ( | ) | throw (Exception::FileNotFound) [protected] |
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_ | ( | const Atom & | atom | ) | [protected] |
void BALL::GAFFTypeProcessor::postProcessAtomTypes_ | ( | Molecule * | molecule | ) | [protected] |
Postprocessing and cleanup for GAFF types
void BALL::GAFFTypeProcessor::precomputeAtomProperties_ | ( | Molecule * | molecule | ) | [protected] |
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_ | ( | Molecule * | molecule | ) | [protected] |
compute aromaticity, ring memberships, GAFF bond typization, ...
std::map<Position, std::vector<TypeDefinition> > BALL::GAFFTypeProcessor::atom_types_ [protected] |
Definition at line 137 of file GAFFTypeProcessor.h.
StringHashMap<GAFFCESParser*> BALL::GAFFTypeProcessor::ces_parsers_ [protected] |
Definition at line 134 of file GAFFTypeProcessor.h.
Molecule* BALL::GAFFTypeProcessor::current_molecule_ [protected] |
Definition at line 143 of file GAFFTypeProcessor.h.
Definition at line 88 of file GAFFTypeProcessor.h.
std::vector<std::vector<Atom*> > BALL::GAFFTypeProcessor::sssr_ [protected] |
Definition at line 140 of file GAFFTypeProcessor.h.