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;
104 void parseAtomtypeTableFile_()
105 throw(Exception::FileNotFound);
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);
static const bool 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
Nested class definitions.
std::vector< TypeDefinition > getSulfurTypes_()
static const String GAFF_ATOMTYPE_POSTPROCESSING
switch cleanup of GAFF types (cc=>cd, ...) on or off
std::vector< TypeDefinition > getHydrogenTypes_()
String chemical_environment
String electron_withdrawal_atoms
String attached_hydrogens
std::vector< TypeDefinition > getCarbonTypes_()
-*- Mode: C++; tab-width: 2; -*-
std::vector< TypeDefinition > getOxygenTypes_()
std::vector< TypeDefinition > getNitrogenTypes_()
static const String ATOMTYPE_FILENAME
path to the file containing the atom type definitions