MTK++ Latest version: 0.2.0

Public Member Functions | Public Attributes | Protected Types | Protected Member Functions | Protected Attributes | Friends
MTKpp::collection Class Reference

Container for molecules. More...

#include <mtkpp/src/Molecule/collection.h>

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List of all members.

Public Member Functions

 collection ()
 Collection Constructor.
virtual ~collection ()
 Collection Destructor.
void setName (std::string name)
 Set collection name.
std::string getName ()
 Get collection name.
virtual moleculeaddMolecule ()
 Add Molecule to Collection.
void delMolecule (molecule *pMol)
 Delete Molecule from Collection.
void delAllMolecules ()
 Delete all Molecules from Collection.
void clear ()
 Clears Collection.
moleculegetMolecule ()
 Get last added Molecule from list of molecules.
moleculegetMolecule (int id)
 Get Molecule from list of molecules based on id.
moleculegetMolecule (std::string name)
 Get Molecule from list of molecules based on name.
moleculegetLastAddedMolecule ()
 Get last added Molecule from list of molecules.
virtual std::vector< molecule * > getMoleculeList ()
 Get list of molecules.
atomgetAtom (int number, bool atomIndex=true, bool fileId=false, bool atomColIndex=false)
 Get atom.
virtual std::vector< atom * > getAtomList ()
 Get list of atoms.
int getNumberMolecules ()
 Get number of molecules.
int getNumberSubMolecules ()
 Get number of submolecules.
int getNumAtoms ()
 Get number of atoms in collection.
int getNumBonds ()
 Get number of bonds in collection.
int getBonds (int bonds[])
 Get bond list.
int getBondParams (double bondParams[])
 Get bond parameters.
int getNumBondsWithH ()
 Get number of bonds that contain a Hydrogen.
int getNumBondsWithOutH ()
 Get number of bonds that do not contain a Hydrogen.
int getNumUniqueBondTypes ()
 Get number of unique bond types used.
int getNumAngles ()
 Get number of angles in collection.
int getAngles (int angles[])
 Get angle list.
int getAngleParams (double angleParams[])
 Get angle parameters.
int getNumAnglesWithH ()
 Get number of angles that contain a Hydrogen.
int getNumAnglesWithOutH ()
 Get number of angles that do not contain a Hydrogen.
int getNumUniqueAngleTypes ()
 Get number of unique angle types used.
int getNumTorsions ()
 Get number of torsions in collection.
int getNumMMTorsions ()
 Get number of MM torsions in collection.
int getMMTorsions (int torsions[], double torsionParams[])
 Get torsion atom indices and parameters.
int getNumImpropers ()
 Get number of impropers in collection.
int getNumMMImpropers ()
 Get number of MM impropers in collection.
int getMMImpropers (int impropers[], double improperParams[])
 Get improper atom indices and parameters.
int getNumDihedralsWithH ()
 Get number of dihedrals that contain a Hydrogen.
int getNumDihedralsWithOutH ()
 Get number of dihedrals that do not contain a Hydrogen.
int getNumUniqueDihedralTypes ()
 Get number of unique dihedral types used.
int getCoordinates (double coords[])
 Get all atomic coordinates.
int setCoordinates (double coords[])
 Set all atomic coordinates.
virtual void addStdLibrary ()
 Add standard library to the collection.
virtual stdLibrarygetStdLibrary ()
 Get Standard Library.
void addAtomTyper ()
 Add atom typer object to the collection.
atomTypergetAtomTyper ()
 Get atom typer object.
void addParameters ()
 Add mm parameters object to the collection.
parametersgetParameters ()
 Get mm parameters object.
int getNumMMnonBondedPairs (double cutoff)
 Get number of MM non bonded interactions.
int getMMnonBondedPairs (int nonBonded[], int nonBondedPtrs[], double nonBondedParams[], int nonBonded14Ptrs[], double cutoff)
 Get MM non bonded pairs.
int getMMCharges (double charges[])
 Get all atomic charges.
int getAtomSymbols (char symbols[])
 Get all atomic symbols.
int getAtomNames (char names[])
 Get all atomic names.
int getAtomMasses (double masses[])
 Get all atomic masses.
int getNumUniqueAtomTypes ()
 Get number of unique atom types used.
std::vector< std::string > getUniqueAtomTypes ()
 Get number of unique atom types used.
std::vector< bondParam * > getUniqueBondTypes ()
 Get number of unique bond types used.
std::vector< angleParam * > getUniqueAngleTypes ()
 Get number of unique angle types used.
std::vector< torsionParam * > getUniqueTorsionTypes ()
 Get number of unique torsion types used.
std::vector< improperParam * > getUniqueImproperTypes ()
 Get number of unique improper types used.
int getAtomTypes (int a[])
 Get numeric atom types.
int getAtomTypes (char a[])
 Get numeric atom types.
int getLJParams (double r6[], double r12[])
 Get L-J Params.
int getNumExcludedAtoms ()
 Get number of excluded atoms per atom.
int getNumExcludedAtoms (int e[])
 Get number of excluded atoms per atom.
int getExcludedAtoms (int e[])
 Get excluded atom list.
int getNumExcluded14Atoms ()
 Get number of excluded atoms per atom.
int getNumExcluded14Atoms (int e[])
 Get number of excluded atoms per atom.
int getExcluded14Atoms (int e[])
 Get excluded atom list.
int getResidueNames (char resNames[])
 Get all residue names.
int getResiduePointers (int resPointers[])
 Get all residue pointers.
void setAtomIndex (const int &n)
 Set atom index.
int getAtomIndex ()
 Get atom index.
void setSubMoleculeIndex (const int &n)
 Set submolecule index.
int getSubMoleculeIndex ()
 Get submolecule index.
virtual int getFormalCharge ()
 Get total formal charge.
int getNumNeighbors (atom *pAt, double d)
 Get number of nonbonded neighbors within a certain distance.
int getNumHeavyNeighbors (atom *pAt, double d)
 Get number of heavy atom nonbonded neighbors within a certain distance.
int largestResidueSize ()
 Get number of atoms in the largest residue.
void renumber ()
 Renumber entire collection.
bool hasMetal ()
 Determine if the collection contains metal atoms.
void findMetals ()
 Finds and stores a vector of all metal atoms.
void determineMetalEnvironments ()
 Determines the coordination sphere of the metal atoms.
void assignMetalPartners ()
 Determine if metal centers share ligating residues.
void assignMetalParameters ()
 Assign parameters to metal centers.
std::vector< metalCenter * > getMetalCenters ()
 Determines the coordination sphere of the metal atoms.

Public Attributes

elementspElements
 elements object pointer
moleculepMolecule
 molecule pointer
submoleculepSubMolecule
 submolecule pointer

Protected Types

typedef std::vector< molecule * >
::iterator 
moleculeIterator
 molecule iterator
typedef std::vector
< submolecule * >::iterator 
sMolIterator
 submolecule iterator
typedef std::vector< atom * >
::iterator 
AtomIterator
 atom iterator
typedef std::map< int, Bond * >
::iterator 
BondMapIterator
 Bond map iterator.
typedef std::map< ULONG_KIND,
Angle * >::iterator 
AngleMapIterator
 Angle map iterator.
typedef std::map< ULONG_KIND,
Torsion * >::iterator 
TorsionMapIterator
 Torsion map iterator.
typedef std::map< int,
Improper * >::iterator 
ImproperMapIterator
 Improper map iterator.
typedef std::vector
< metalCenter * >::iterator 
MetalCenterIterator
 Metal Center map iterator.
typedef std::vector
< metalGroup * >::iterator 
MetalGroupIterator
 Metal Group map iterator.
typedef std::vector< unsigned
int >::iterator 
intVectorIterator
 int vector iterator
typedef std::vector
< std::string >::iterator 
stringVectorIterator
 string vector iterator
typedef std::map< std::string,
double >::iterator 
strDbMapIterator
 string:double map iterator
typedef std::map< std::string,
int >::iterator 
strIntMapIterator
 string:int map iterator
typedef std::map< std::string,
std::string >::iterator 
strStrMapIterator
 string:string map iterator

Protected Member Functions

void findMatchings (int pos, int nBondedAtoms, int matchMatrix[], std::vector< int > &match, std::vector< std::vector< int > > &matchings)
 Determine matchings for metal centers.
void updateMatchMatrix (int iPos, int jPos, int nBondedAtoms, int matchMatrix[])
 Determine if the fragment is a subgraph of the molecule.
void refineMatchMatrix (int nBondedAtoms, int matchMatrix[], bool &mismatch)

Protected Attributes

std::vector< molecule * > itsMoleculeList
 molecule list
std::string itsName
 collection name
int itsAtomIndex
 atom index
int itsSubMoleculeIndex
 submolecule index
stdLibrarypStdLibrary
 standard library pointer
parameterspParameters
 parameters pointer
atomTyperpAtomTyper
 atomTyper pointer
bondParampBondParam
 Bond parameter pointer.
angleParampAngleParam
 Angle parameter pointer.
torsionParampTorsionParam
 Torsion parameter pointer.
improperParampImproperParam
 Improper parameter pointer.
hBondParampHBondParam
 H Bond Param.
LJ612Param * pLJ612Param
 LJ 6-12 Param.
LJ612SEpLJ612SE
 LJ 6-12 Sigma and Epsilon.
BondpBond
 Bond pointer.
AnglepAngle
 Angle pointer.
TorsionpTorsion
 Torsion pointer.
ImproperpImproper
 Improper pointer.
std::vector< std::string > atomTypesUsed
 Atom Types used.
std::vector< bondParam * > uniqueBondParams
 Bond Types used.
std::vector< angleParam * > uniqueAngleParams
 Angle Types used.
std::vector< torsionParam * > uniqueTorsionParams
 Torsion Types used.
std::vector< improperParam * > uniqueImproperParams
 Improper Types used.
std::vector< std::string > availableMetals
 Available metal ions.
std::map< std::string, double > metalDonorDists
 Metal donor bond distances.
std::vector< atom * > itsMetalAtoms
 Metal atoms.
std::vector< metalCenter * > itsMetalCenters
 Metal coordinations.
std::vector< metalGroup * > itsMetalGroups
 Metal groups.

Friends

class molecule

Detailed Description

Container for molecules.


Member Typedef Documentation

typedef std::vector<molecule*>::iterator MTKpp::collection::moleculeIterator [protected]

molecule iterator

typedef std::vector<submolecule*>::iterator MTKpp::collection::sMolIterator [protected]

submolecule iterator

typedef std::vector<atom*>::iterator MTKpp::collection::AtomIterator [protected]

atom iterator

typedef std::map<int, Bond*>::iterator MTKpp::collection::BondMapIterator [protected]

Bond map iterator.

typedef std::map<ULONG_KIND, Angle*>::iterator MTKpp::collection::AngleMapIterator [protected]

Angle map iterator.

typedef std::map<ULONG_KIND, Torsion*>::iterator MTKpp::collection::TorsionMapIterator [protected]

Torsion map iterator.

typedef std::map<int, Improper*>::iterator MTKpp::collection::ImproperMapIterator [protected]

Improper map iterator.

typedef std::vector<metalCenter*>::iterator MTKpp::collection::MetalCenterIterator [protected]

Metal Center map iterator.

typedef std::vector<metalGroup*>::iterator MTKpp::collection::MetalGroupIterator [protected]

Metal Group map iterator.

typedef std::vector<unsigned int>::iterator MTKpp::collection::intVectorIterator [protected]

int vector iterator

typedef std::vector<std::string>::iterator MTKpp::collection::stringVectorIterator [protected]

string vector iterator

typedef std::map<std::string, double>::iterator MTKpp::collection::strDbMapIterator [protected]

string:double map iterator

typedef std::map<std::string, int>::iterator MTKpp::collection::strIntMapIterator [protected]

string:int map iterator

typedef std::map<std::string, std::string>::iterator MTKpp::collection::strStrMapIterator [protected]

string:string map iterator


Constructor & Destructor Documentation

MTKpp::collection::collection ( )
MTKpp::collection::~collection ( ) [virtual]

Collection Destructor.

References itsMoleculeList, pAtomTyper, pElements, and pMolecule.


Member Function Documentation

void MTKpp::collection::setName ( std::string  name)

Set collection name.

Parameters:
namecollection name

References itsName.

Referenced by main().

std::string MTKpp::collection::getName ( )
molecule * MTKpp::collection::addMolecule ( ) [virtual]
void MTKpp::collection::delMolecule ( molecule pMol)

Delete Molecule from Collection.

Parameters:
pMolmolecule pointer

References itsMoleculeList.

Referenced by assignMetalParameters(), and main().

void MTKpp::collection::delAllMolecules ( )

Delete all Molecules from Collection.

References itsAtomIndex, itsMoleculeList, pMolecule, and pSubMolecule.

Referenced by clear(), and main().

void MTKpp::collection::clear ( )

Clears Collection.

References delAllMolecules(), itsMetalAtoms, itsMetalCenters, and itsMetalGroups.

Referenced by main().

molecule * MTKpp::collection::getMolecule ( )

Get last added Molecule from list of molecules.

Returns:
molecule pointer

References itsMoleculeList.

Referenced by main(), MTKpp::selection::parse(), MTKpp::gaussianParser::Write(), MTKpp::molParser::Write(), and MTKpp::zmatParser::Write().

molecule * MTKpp::collection::getMolecule ( int  id)

Get Molecule from list of molecules based on id.

Parameters:
idmolecule id
Returns:
molecule pointer
See also:
getMoleculeList()

References MTKpp::molecule::getMolId(), itsMoleculeList, and pMolecule.

molecule * MTKpp::collection::getMolecule ( std::string  name)

Get Molecule from list of molecules based on name.

Parameters:
namemolecule name
Returns:
molecule pointer
See also:
getMoleculeList()

References MTKpp::molecule::getName(), itsMoleculeList, and pMolecule.

molecule * MTKpp::collection::getLastAddedMolecule ( )

Get last added Molecule from list of molecules.

Returns:
molecule pointer

References itsMoleculeList.

Referenced by main().

std::vector< molecule * > MTKpp::collection::getMoleculeList ( ) [virtual]
atom * MTKpp::collection::getAtom ( int  number,
bool  atomIndex = true,
bool  fileId = false,
bool  atomColIndex = false 
)

Get atom.

Parameters:
numberinteger value
atomIndexreturn atom based on index (default)
fileIdreturn atom based on file id
atomColIndexatom collection index
Returns:
atom pointer

References MTKpp::submolecule::getAtomList(), MTKpp::atom::getColIndex(), MTKpp::atom::getFileID(), MTKpp::atom::getIndex(), MTKpp::molecule::getName(), MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, pMolecule, and pSubMolecule.

Referenced by assignMetalParameters().

std::vector< atom * > MTKpp::collection::getAtomList ( ) [virtual]
int MTKpp::collection::getNumberMolecules ( )
int MTKpp::collection::getNumberSubMolecules ( )

Get number of submolecules.

Returns:
number of submolecules in the collection

References MTKpp::molecule::getNumSubMolecules(), itsMoleculeList, and pMolecule.

Referenced by main(), and MTKpp::complex::setup().

int MTKpp::collection::getNumAtoms ( )

Get number of atoms in collection.

Returns:
number of atoms in the collection

References MTKpp::molecule::getNumAtoms(), itsMoleculeList, and pMolecule.

Referenced by main(), and MTKpp::complex::setup().

int MTKpp::collection::getNumBonds ( )

Get number of bonds in collection.

Returns:
number of bonds in the collection

References itsMetalCenters, itsMoleculeList, MTKpp::molecule::numBonds(), and pMolecule.

Referenced by determineMetalEnvironments(), and main().

int MTKpp::collection::getBonds ( int  bonds[])

Get bond list.

Parameters:
bondsarray of atom indices

References MTKpp::Bond::atom1, MTKpp::Bond::atom2, MTKpp::molecule::getBondMap(), MTKpp::atom::getColIndex(), itsMetalAtoms, itsMetalCenters, itsMoleculeList, pBond, and pMolecule.

Referenced by main().

int MTKpp::collection::getBondParams ( double  bondParams[])
int MTKpp::collection::getNumBondsWithH ( )
int MTKpp::collection::getNumBondsWithOutH ( )
int MTKpp::collection::getNumUniqueBondTypes ( )
int MTKpp::collection::getNumAngles ( )

Get number of angles in collection.

Returns:
number of angles in the collection

References itsMetalCenters, itsMoleculeList, MTKpp::molecule::numAngles(), and pMolecule.

Referenced by main().

int MTKpp::collection::getAngles ( int  angles[])

Get angle list.

Parameters:
anglesarray of atom indices

References MTKpp::Angle::atom1, MTKpp::Angle::atom2, MTKpp::Angle::atom3, MTKpp::molecule::getAngleMap(), MTKpp::atom::getColIndex(), itsMoleculeList, pAngle, and pMolecule.

Referenced by main().

int MTKpp::collection::getAngleParams ( double  angleParams[])
int MTKpp::collection::getNumAnglesWithH ( )
int MTKpp::collection::getNumAnglesWithOutH ( )
int MTKpp::collection::getNumUniqueAngleTypes ( )
int MTKpp::collection::getNumTorsions ( )

Get number of torsions in collection.

Returns:
number of torsions in the collection

References itsMoleculeList, MTKpp::molecule::numTorsions(), and pMolecule.

int MTKpp::collection::getNumMMTorsions ( )
int MTKpp::collection::getMMTorsions ( int  torsions[],
double  torsionParams[] 
)
int MTKpp::collection::getNumImpropers ( )

Get number of impropers in collection.

Returns:
number of impropers in the collection

References itsMoleculeList, MTKpp::molecule::numImpropers(), and pMolecule.

int MTKpp::collection::getNumMMImpropers ( )
int MTKpp::collection::getMMImpropers ( int  impropers[],
double  improperParams[] 
)
int MTKpp::collection::getNumDihedralsWithH ( )
int MTKpp::collection::getNumDihedralsWithOutH ( )
int MTKpp::collection::getNumUniqueDihedralTypes ( )
int MTKpp::collection::getCoordinates ( double  coords[])

Get all atomic coordinates.

Parameters:
coordsarray of coordinates

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

Referenced by main().

int MTKpp::collection::setCoordinates ( double  coords[])

Set all atomic coordinates.

Parameters:
coordsarray of coordinates

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

Referenced by main().

void MTKpp::collection::addStdLibrary ( ) [virtual]

Add standard library to the collection.

References MTKpp::stdLibrary::getInstance(), and pStdLibrary.

Referenced by main().

stdLibrary * MTKpp::collection::getStdLibrary ( ) [virtual]
void MTKpp::collection::addAtomTyper ( )

Add atom typer object to the collection.

References pAtomTyper.

atomTyper * MTKpp::collection::getAtomTyper ( )

Get atom typer object.

References pAtomTyper.

void MTKpp::collection::addParameters ( )

Add mm parameters object to the collection.

References MTKpp::parameters::getInstance(), pElements, and pParameters.

Referenced by main().

parameters * MTKpp::collection::getParameters ( )
int MTKpp::collection::getNumMMnonBondedPairs ( double  cutoff)
int MTKpp::collection::getMMnonBondedPairs ( int  nonBonded[],
int  nonBondedPtrs[],
double  nonBondedParams[],
int  nonBonded14Ptrs[],
double  cutoff 
)
int MTKpp::collection::getMMCharges ( double  charges[])

Get all atomic charges.

Parameters:
chargesarray of charges
Returns:
success

References MTKpp::E2KCAL, MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

Referenced by main().

int MTKpp::collection::getAtomSymbols ( char  symbols[])

Get all atomic symbols.

Parameters:
symbolschar array of symbols
Returns:
success

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

Referenced by main().

int MTKpp::collection::getAtomNames ( char  names[])

Get all atomic names.

Parameters:
nameschar array of names
Returns:
success

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

int MTKpp::collection::getAtomMasses ( double  masses[])

Get all atomic masses.

Parameters:
masseschar array of masses
Returns:
success

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, MTKpp::element::mass, and pMolecule.

int MTKpp::collection::getNumUniqueAtomTypes ( )

Get number of unique atom types used.

Returns:
number of unique atom types used

References atomTypesUsed, MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, pMolecule, and MTKpp::stdAtom::type.

Referenced by main(), and MTKpp::amberParser::Write().

std::vector< std::string > MTKpp::collection::getUniqueAtomTypes ( )

Get number of unique atom types used.

Returns:
number of unique atom types used

References atomTypesUsed.

Referenced by MTKpp::amberParser::Write().

std::vector< bondParam * > MTKpp::collection::getUniqueBondTypes ( )

Get number of unique bond types used.

Returns:
number of unique bond types used

References uniqueBondParams.

Referenced by MTKpp::amberParser::Write().

std::vector< angleParam * > MTKpp::collection::getUniqueAngleTypes ( )

Get number of unique angle types used.

Returns:
number of unique angle types used

References uniqueAngleParams.

Referenced by MTKpp::amberParser::Write().

std::vector< torsionParam * > MTKpp::collection::getUniqueTorsionTypes ( )

Get number of unique torsion types used.

Returns:
number of unique torsion types used

References uniqueTorsionParams.

Referenced by MTKpp::amberParser::Write().

std::vector< improperParam * > MTKpp::collection::getUniqueImproperTypes ( )

Get number of unique improper types used.

Returns:
number of unique improper types used

References uniqueImproperParams.

Referenced by MTKpp::amberParser::Write().

int MTKpp::collection::getAtomTypes ( int  a[])

Get numeric atom types.

Parameters:
aatom types array
Returns:
success

References atomTypesUsed, MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, pMolecule, and MTKpp::stdAtom::type.

Referenced by main().

int MTKpp::collection::getAtomTypes ( char  a[])

Get numeric atom types.

Parameters:
aatom types array
Returns:
success

References atomTypesUsed, MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, pMolecule, and MTKpp::stdAtom::type.

int MTKpp::collection::getLJParams ( double  r6[],
double  r12[] 
)

Get L-J Params.

Parameters:
r6L-J R6 array
r12L-J R12 array
Returns:
success

References atomTypesUsed, MTKpp::LJ612SE::epsilon, MTKpp::errorLogger, MTKpp::parameters::getLJ612SE(), pLJ612SE, pParameters, MTKpp::LJ612SE::sigma, and MTKpp::errorHandler::throwError().

Referenced by main().

int MTKpp::collection::getNumExcludedAtoms ( )
int MTKpp::collection::getNumExcludedAtoms ( int  e[])

Get number of excluded atoms per atom.

Parameters:
eexcluded atom list
Returns:
success

References MTKpp::errorLogger, getAtomList(), MTKpp::atom::has13BondedAtom(), MTKpp::atom::has14BondedAtom(), MTKpp::atom::hasBondedAtom(), and MTKpp::errorHandler::throwError().

int MTKpp::collection::getExcludedAtoms ( int  e[])

Get excluded atom list.

Parameters:
eexcluded atom list
Returns:
success

References getAtomList(), MTKpp::atom::getColIndex(), MTKpp::atom::has13BondedAtom(), MTKpp::atom::has14BondedAtom(), and MTKpp::atom::hasBondedAtom().

Referenced by main().

int MTKpp::collection::getNumExcluded14Atoms ( )

Get number of excluded atoms per atom.

Returns:
success

References MTKpp::errorLogger, getAtomList(), MTKpp::atom::has13BondedAtom(), MTKpp::atom::has14BondedAtom(), and MTKpp::errorHandler::throwError().

Referenced by main().

int MTKpp::collection::getNumExcluded14Atoms ( int  e[])

Get number of excluded atoms per atom.

Parameters:
eexcluded atom list
Returns:
success

References MTKpp::errorLogger, getAtomList(), MTKpp::atom::has13BondedAtom(), MTKpp::atom::has14BondedAtom(), and MTKpp::errorHandler::throwError().

int MTKpp::collection::getExcluded14Atoms ( int  e[])

Get excluded atom list.

Parameters:
eexcluded atom list
Returns:
success

References getAtomList(), MTKpp::atom::getColIndex(), MTKpp::atom::has13BondedAtom(), and MTKpp::atom::has14BondedAtom().

Referenced by main().

int MTKpp::collection::getResidueNames ( char  resNames[])

Get all residue names.

Parameters:
resNameschar array of residue names
Returns:
success

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

int MTKpp::collection::getResiduePointers ( int  resPointers[])

Get all residue pointers.

Parameters:
resPointersint array of residue pointers
Returns:
success

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

void MTKpp::collection::setAtomIndex ( const int &  n)

Set atom index.

Parameters:
natom index

References itsAtomIndex.

Referenced by MTKpp::submolecule::addAtom(), and main().

int MTKpp::collection::getAtomIndex ( )

Get atom index.

Returns:
atom index

References itsAtomIndex.

Referenced by MTKpp::submolecule::addAtom().

void MTKpp::collection::setSubMoleculeIndex ( const int &  n)

Set submolecule index.

Parameters:
nindex

References itsSubMoleculeIndex.

Referenced by MTKpp::molecule::addSubMolecule().

int MTKpp::collection::getSubMoleculeIndex ( )

Get submolecule index.

Returns:
n index

References itsSubMoleculeIndex.

Referenced by MTKpp::molecule::addSubMolecule().

int MTKpp::collection::getFormalCharge ( ) [virtual]
int MTKpp::collection::getNumNeighbors ( atom pAt,
double  d 
)

Get number of nonbonded neighbors within a certain distance.

Parameters:
pAtatom pointer
ddistance
Returns:
number of nonbonded neighbors

References MTKpp::atom::getCoords(), MTKpp::atom::getParent(), MTKpp::molecule::getSubMoleculeList(), MTKpp::atom::has13BondedAtom(), MTKpp::atom::has14BondedAtom(), MTKpp::atom::hasBondedAtom(), itsMoleculeList, and pMolecule.

int MTKpp::collection::getNumHeavyNeighbors ( atom pAt,
double  d 
)

Get number of heavy atom nonbonded neighbors within a certain distance.

Parameters:
pAtatom pointer
ddistance
Returns:
number of nonbonded neighbors

References MTKpp::atom::getCoords(), MTKpp::atom::getParent(), MTKpp::molecule::getSubMoleculeList(), MTKpp::atom::has13BondedAtom(), MTKpp::atom::has14BondedAtom(), MTKpp::atom::hasBondedAtom(), itsMoleculeList, and pMolecule.

Referenced by MTKpp::atomTyper::perceiveCysteines(), and MTKpp::atomTyper::perceiveHistidines().

int MTKpp::collection::largestResidueSize ( )

Get number of atoms in the largest residue.

Returns:
number of atoms in the largest residue

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

Referenced by MTKpp::amberParser::Write().

void MTKpp::collection::renumber ( )

Renumber entire collection.

References MTKpp::molecule::getSubMoleculeList(), itsMoleculeList, and pMolecule.

Referenced by main().

bool MTKpp::collection::hasMetal ( )

Determine if the collection contains metal atoms.

References availableMetals, MTKpp::errorLogger, MTKpp::INFO, itsMoleculeList, and MTKpp::errorHandler::throwError().

Referenced by main().

void MTKpp::collection::findMetals ( )

Finds and stores a vector of all metal atoms.

References availableMetals, MTKpp::errorLogger, getName(), MTKpp::i2s(), MTKpp::INFO, itsMetalAtoms, itsMoleculeList, and MTKpp::errorHandler::throwError().

Referenced by main().

void MTKpp::collection::determineMetalEnvironments ( )
void MTKpp::collection::assignMetalPartners ( )
void MTKpp::collection::assignMetalParameters ( )
std::vector< metalCenter * > MTKpp::collection::getMetalCenters ( )

Determines the coordination sphere of the metal atoms.

References itsMetalCenters.

Referenced by MTKpp::connections::assignAngles(), main(), and MTKpp::amberParser::Write().

void MTKpp::collection::findMatchings ( int  pos,
int  nBondedAtoms,
int  matchMatrix[],
std::vector< int > &  match,
std::vector< std::vector< int > > &  matchings 
) [protected]

Determine matchings for metal centers.

Parameters:
posCurrent atom being considered
nBondedAtomsNumber of atoms
matchMatrixMatch matrix
matchstorage vector
matchingsstorage vector for all matches

References refineMatchMatrix(), and updateMatchMatrix().

void MTKpp::collection::updateMatchMatrix ( int  iPos,
int  jPos,
int  nBondedAtoms,
int  matchMatrix[] 
) [protected]

Determine if the fragment is a subgraph of the molecule.

Parameters:
iPosWhich atom is being considered
jPosWhich atom is being considered
nBondedAtomsNumber of atoms
matchMatrixMatch matrix

Referenced by findMatchings().

void MTKpp::collection::refineMatchMatrix ( int  nBondedAtoms,
int  matchMatrix[],
bool &  mismatch 
) [protected]
Parameters:
nBondedAtomsNumber of atoms
matchMatrixMatch matrix
mismatchWhether or not a mismatch occurs or not in the updated match match, i.e a row that contains all zeros

Referenced by findMatchings().


Friends And Related Function Documentation

friend class molecule [friend]

Referenced by addMolecule().


Member Data Documentation

submolecule pointer

Referenced by delAllMolecules(), and getAtom().

std::vector<molecule*> MTKpp::collection::itsMoleculeList [protected]
std::string MTKpp::collection::itsName [protected]

collection name

Referenced by collection(), getName(), and setName().

atom index

Referenced by collection(), delAllMolecules(), getAtomIndex(), and setAtomIndex().

submolecule index

Referenced by collection(), getSubMoleculeIndex(), and setSubMoleculeIndex().

standard library pointer

Referenced by addStdLibrary(), assignMetalParameters(), collection(), and getStdLibrary().

H Bond Param.

LJ612Param* MTKpp::collection::pLJ612Param [protected]

LJ 6-12 Param.

LJ 6-12 Sigma and Epsilon.

Referenced by getLJParams(), and getMMnonBondedPairs().

std::vector<std::string> MTKpp::collection::atomTypesUsed [protected]

Bond Types used.

Referenced by getNumUniqueBondTypes(), and getUniqueBondTypes().

Angle Types used.

Referenced by getNumUniqueAngleTypes(), and getUniqueAngleTypes().

std::vector<std::string> MTKpp::collection::availableMetals [protected]

Available metal ions.

Referenced by collection(), findMetals(), and hasMetal().

std::map<std::string, double> MTKpp::collection::metalDonorDists [protected]

Metal donor bond distances.

Referenced by collection(), and determineMetalEnvironments().

std::vector<atom*> MTKpp::collection::itsMetalAtoms [protected]
std::vector<metalGroup*> MTKpp::collection::itsMetalGroups [protected]

Metal groups.

Referenced by assignMetalParameters(), assignMetalPartners(), and clear().


The documentation for this class was generated from the following files:

Generated on Fri Dec 23 2011 09:28:56 for MTK++ by Doxygen 1.7.5.1