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
140 std::vector<std::vector<Atom*> >
sssr_;
GAFFTypeProcessor(const Options &new_options)
std::vector< std::vector< Atom * > > sssr_
StringHashMap< GAFFCESParser * > ces_parsers_
Molecule * current_molecule_
virtual ~GAFFTypeProcessor()
void precomputeAtomProperties_(Molecule *molecule)
void annotateBondTypes_()
Helper for precomputeBondProperties.
bool planarAtom_(const Atom &atom)
std::vector< TypeDefinition > getCarbonTypes_()
void annotateRingSizes_()
Helper for precomputeAtomProperties.
void precomputeBondProperties_(Molecule *molecule)
compute aromaticity, ring memberships, GAFF bond typization, ...
void annotateAliphaticAndAromaticRingAtoms_()
void annotatePlanarRingAtoms_()
std::vector< TypeDefinition > getOxygenTypes_()
void postProcessAtomTypes_(Molecule *molecule)
std::vector< TypeDefinition > getHydrogenTypes_()
std::map< Position, std::vector< TypeDefinition > > atom_types_
std::vector< TypeDefinition > getNitrogenTypes_()
std::set< String > getTypeNames() const
bool assignAtomtype_(Atom &atom)
std::vector< TypeDefinition > getSulfurTypes_()
void parseAtomtypeTableFile_()
Nested class definitions.
String attached_hydrogens
String electron_withdrawal_atoms
String chemical_environment
static const String ATOMTYPE_FILENAME
path to the file containing the atom type definitions
static const String GAFF_ATOMTYPE_POSTPROCESSING
switch cleanup of GAFF types (cc=>cd, ...) on or off
static const String ATOMTYPE_FILENAME
path to the file containing the atom type definitions
static const bool GAFF_ATOMTYPE_POSTPROCESSING
switch cleanup of GAFF types (cc=>cd, ...) on or off