BALL  1.4.1
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BALL::GAFFTypeProcessor Class Reference

#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>

Inheritance diagram for BALL::GAFFTypeProcessor:
BALL::UnaryProcessor< Composite > BALL::UnaryFunctor< Composite, Processor::Result >

List of all members.

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< StringgetTypeNames () const

Public Attributes

Options options

Protected Member Functions

std::vector< TypeDefinitiongetCarbonTypes_ ()
std::vector< TypeDefinitiongetHydrogenTypes_ ()
std::vector< TypeDefinitiongetNitrogenTypes_ ()
std::vector< TypeDefinitiongetOxygenTypes_ ()
std::vector< TypeDefinitiongetSulfurTypes_ ()
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_
Moleculecurrent_molecule_

Detailed Description

Definition at line 37 of file GAFFTypeProcessor.h.


Constructor & Destructor Documentation


Member Function Documentation

Helper for precomputeBondProperties.

Helper for precomputeAtomProperties.

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.

virtual Processor::Result BALL::GAFFTypeProcessor::operator() ( Composite ) [virtual]

operator ()

Reimplemented from BALL::UnaryProcessor< Composite >.

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

Store connectivity, number of attached H-atoms and number of attached N,O,F,Cl and Br-atoms for every atom in molecule

compute aromaticity, ring memberships, GAFF bond typization, ...


Member Data Documentation

std::map<Position, std::vector<TypeDefinition> > BALL::GAFFTypeProcessor::atom_types_ [protected]

Definition at line 137 of file GAFFTypeProcessor.h.

Definition at line 134 of file GAFFTypeProcessor.h.

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.

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