5 #ifndef BALL_MOLMEC_AMBER_GAFFTYPEPROCESSOR_H 6 #define BALL_MOLMEC_AMBER_GAFFTYPEPROCESSOR_H 8 #ifndef BALL_CONCEPT_COMPOSITE_H 12 #ifndef BALL_CONCEPT_PROCESSOR_H 16 #ifndef BALL_MOLMEC_AMBER_GAFFCESPARSER_H 20 #ifndef BALL_DATATYPE_OPTIONS_H 24 #ifndef BALL_COMMON_EXCEPTION_H 28 #ifndef BALL_KERNEL_MOLECULE_H 82 GAFFTypeProcessor(
const Options& new_options);
83 virtual ~GAFFTypeProcessor();
86 std::set<String> getTypeNames()
const;
105 void parseAtomtypeTableFile_();
108 void precomputeBondProperties_(
Molecule* molecule);
113 void precomputeAtomProperties_(
Molecule* molecule);
116 void annotateBondTypes_();
119 void annotateRingSizes_();
120 void annotateAliphaticAndAromaticRingAtoms_();
121 void annotatePlanarRingAtoms_();
122 bool planarAtom_(
const Atom& atom);
126 bool assignAtomtype_(
Atom& atom);
130 void postProcessAtomTypes_(
Molecule* molecule);
140 std::vector<std::vector<Atom*> >
sssr_;
std::map< Position, std::vector< TypeDefinition > > atom_types_
std::vector< std::vector< Atom * > > sssr_
static const String ATOMTYPE_FILENAME
path to the file containing the atom type definitions
String chemical_environment
String electron_withdrawal_atoms
std::vector< TypeDefinition > getNitrogenTypes_()
Molecule * current_molecule_
String attached_hydrogens
StringHashMap< GAFFCESParser * > ces_parsers_
std::vector< TypeDefinition > getSulfurTypes_()
std::vector< TypeDefinition > getOxygenTypes_()
Nested class definitions.
std::vector< TypeDefinition > getHydrogenTypes_()
static const String ATOMTYPE_FILENAME
path to the file containing the atom type definitions
std::vector< TypeDefinition > getCarbonTypes_()
static const bool GAFF_ATOMTYPE_POSTPROCESSING
switch cleanup of GAFF types (cc=>cd, ...) on or off
static const String GAFF_ATOMTYPE_POSTPROCESSING
switch cleanup of GAFF types (cc=>cd, ...) on or off