#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>
List of all members.
Classes |
struct | Default |
struct | Option |
struct | TypeDefinition |
| Nested class definitions. More...
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Public Types |
enum | BOND_TYPES {
sb,
SB,
db,
DB,
TB,
DL,
AB
} |
Public Member Functions |
| GAFFTypeProcessor () |
| GAFFTypeProcessor (const Options &new_options) |
virtual | ~GAFFTypeProcessor () |
virtual Processor::Result | operator() (Composite &composite) |
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.
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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_ |
Member Enumeration Documentation
Constructor & Destructor Documentation
BALL::GAFFTypeProcessor::GAFFTypeProcessor |
( |
| ) |
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BALL::GAFFTypeProcessor::GAFFTypeProcessor |
( |
const Options & |
new_options | ) |
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virtual BALL::GAFFTypeProcessor::~GAFFTypeProcessor |
( |
| ) |
[virtual] |
Member Function Documentation
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] |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getHydrogenTypes_ |
( |
| ) |
[inline, protected] |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getNitrogenTypes_ |
( |
| ) |
[inline, protected] |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getOxygenTypes_ |
( |
| ) |
[inline, protected] |
std::vector<TypeDefinition> BALL::GAFFTypeProcessor::getSulfurTypes_ |
( |
| ) |
[inline, 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, ...
Member Data Documentation