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MTKpp::complex Class Reference

complex More...

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

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List of all members.

Public Member Functions

 complex (collection *pCollection, bool bLigOnly)
 complex Constructor
virtual ~complex ()
 complex Destructor.
int getNumAtoms ()
 Get number of atoms.
int getNumResidues ()
 Get number of residues.
int getNumRecAtoms ()
 Get number of atoms in the receptor.
int getNumRecResidues ()
 Get number of residues in the receptor.
int getNumLigAtoms ()
 Get number of atoms in the ligand.
int getNumLigResidues ()
 Get number of residues in the ligand.
int getAtomsMatrixSize ()
 Get size of the atom interactions matrix.
int getResMatrixSize ()
 Get size of the residue interactions matrix.
bool getLigOnly ()
 Only store the interactions involing ligand atoms.
int getRecRecAtoms ()
 Get the number of receptor-receptor atom interactions.
int getRecRecResidues ()
 Get the number or receptor-receptor residue interactions.
int getRecFlags (int recFlags[])
 Get receptor flags arrary.
int getLigFlags (int ligFlags[])
 Get ligand flags arrary.
bool isAtomLig (int a)
 Is the atom in a ligand?
int getAtomIndex (int a)
 Get new index for atom.
bool isResLig (int r)
 Is the residue in a ligand?
int getResIndex (int r)
 Get new index for residue.
int setCoreFragment (std::string coreFrag)
 Set the core fragment in the ligand.
void addMapping (std::string m1, std::string m2)
 Set the mapping.
std::string getMapping (std::string m1)
 Get residue mapping.
std::string getResNameID (int i)
 Get residue name and id.
std::vector< std::vector< int > > getResidues ()
 Set residue vectors.
std::vector< int > getLigandFragments ()
 Get ligand fragments.
std::vector< submolecule * > getReceptorSubMols ()
 Get receptor residues.
std::vector< submolecule * > getLigandSubMols ()
 Get ligand residues.
bool isChain (int c, int a)
 Is the atom in a chain?

Protected Types

typedef std::map< std::string,
std::string >::iterator 
stringMapIterator
 string map iterator

Protected Member Functions

void setup ()
 Define receptor, ligand, and solvent molecules.

Protected Attributes

collectionpCollection
 Name of complex.
int nAtoms
 Total number of atoms.
int nRecAtoms
 Number of atoms in receptor.
int nLigAtoms
 Number of atoms in ligand.
int atomMatrixSize
 Size of atom matrices.
int nResidues
 Total Number of residues.
int nRecResidues
 Number of residues in receptor.
int nLigResidues
 Number of residues in ligand.
int resMatrixSize
 Size of residue matrices.
bool bLigOnly
 Do only lig-lig and rec-lig interactions.
int nRecRecAtoms
 Number of rec-rec atom interactions.
int nRecRecResidues
 Number of rec-rec residue interactions.
int * rec
 receptor atoms
int * lig
 ligand atoms
int * cof
 cofactor atoms
int * sol
 solvent atoms
int * recSol
 receptor and solvent atoms
int * atomIndices
 receptor and solvent atom indices
int * resRec
 receptor residues
int * resLig
 ligand residues
int * resSol
 solvent residues
int * resRecSol
 receptor and solvent residues
int * resIndices
 receptor and solvent residue indices
int chainCounter
 chain counter
int * chain
 chain indices
std::vector< submolecule * > receptor
 Vector of receptor residues.
moleculepLigand
 ligand molecule
std::vector< submolecule * > ligand
 Vector of ligand fragments.
std::vector< submolecule * > cofactor
 Vector of cofactor fragments.
std::vector< submolecule * > solvent
 Vector of solvent residues.
std::vector< std::vector< int > > residues
 Vector of atom indices.
std::vector< int > ligandIndices
 Indices pointing to ligand fragments in the residues vector.
std::vector< std::string > residueNAMEIDs
 vector of residue names and ids
std::map< std::string,
std::string > 
residueMap
 Map of residue names and ids.
std::vector< std::string > cofactors
 cofactor names

Friends

class collection

Detailed Description

complex

Author:
Martin Peters

Member Typedef Documentation

typedef std::map<std::string, std::string>::iterator MTKpp::complex::stringMapIterator [protected]

string map iterator


Constructor & Destructor Documentation

MTKpp::complex::complex ( collection pCollection,
bool  bLigOnly 
)

complex Constructor

Parameters:
pCollectioncollection pointer
bLigOnlyOnly consider ligand-ligand interactions

References atomIndices, bLigOnly, chain, chainCounter, cof, cofactors, lig, pCollection, pLigand, rec, recSol, resIndices, resLig, resRec, resRecSol, resSol, setup(), and sol.

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

complex Destructor.

References atomIndices, chain, lig, rec, recSol, resIndices, resLig, resRec, resRecSol, resSol, and sol.


Member Function Documentation

int MTKpp::complex::getNumAtoms ( )

Get number of atoms.

References nAtoms.

int MTKpp::complex::getNumResidues ( )

Get number of residues.

References nResidues.

int MTKpp::complex::getNumRecAtoms ( )

Get number of atoms in the receptor.

References nRecAtoms.

int MTKpp::complex::getNumRecResidues ( )

Get number of residues in the receptor.

References nRecResidues.

int MTKpp::complex::getNumLigAtoms ( )

Get number of atoms in the ligand.

References nLigAtoms.

int MTKpp::complex::getNumLigResidues ( )

Get number of residues in the ligand.

References nLigResidues.

int MTKpp::complex::getAtomsMatrixSize ( )

Get size of the atom interactions matrix.

References atomMatrixSize.

int MTKpp::complex::getResMatrixSize ( )

Get size of the residue interactions matrix.

References resMatrixSize.

bool MTKpp::complex::getLigOnly ( )

Only store the interactions involing ligand atoms.

References bLigOnly.

int MTKpp::complex::getRecRecAtoms ( )

Get the number of receptor-receptor atom interactions.

References nRecRecAtoms.

int MTKpp::complex::getRecRecResidues ( )

Get the number or receptor-receptor residue interactions.

References nRecRecResidues.

int MTKpp::complex::getRecFlags ( int  recFlags[])

Get receptor flags arrary.

Parameters:
recFlagsligand flags array

References MTKpp::errorLogger, nAtoms, rec, and MTKpp::errorHandler::throwError().

int MTKpp::complex::getLigFlags ( int  ligFlags[])

Get ligand flags arrary.

Parameters:
ligFlagsligand flags array

References MTKpp::errorLogger, lig, nAtoms, and MTKpp::errorHandler::throwError().

bool MTKpp::complex::isAtomLig ( int  a)

Is the atom in a ligand?

Parameters:
aatom index

References lig, and nAtoms.

int MTKpp::complex::getAtomIndex ( int  a)

Get new index for atom.

Parameters:
aatom index

References atomIndices, and nAtoms.

bool MTKpp::complex::isResLig ( int  r)

Is the residue in a ligand?

Parameters:
rresidue index

References nResidues, and resLig.

int MTKpp::complex::getResIndex ( int  r)

Get new index for residue.

Parameters:
rresidue index

References nResidues, and resIndices.

int MTKpp::complex::setCoreFragment ( std::string  coreFrag)
void MTKpp::complex::addMapping ( std::string  m1,
std::string  m2 
)

Set the mapping.

Parameters:
m1internal code
m2map code
Returns:
success

References residueMap.

Referenced by setCoreFragment().

std::string MTKpp::complex::getMapping ( std::string  m1)

Get residue mapping.

Parameters:
m1internal code
Returns:
map code

References residueMap.

std::string MTKpp::complex::getResNameID ( int  i)

Get residue name and id.

Parameters:
iindex
Returns:
internal code

References residueNAMEIDs.

std::vector< std::vector< int > > MTKpp::complex::getResidues ( )

Set residue vectors.

Returns:
vector of vectors of atom indices

References residues.

std::vector< int > MTKpp::complex::getLigandFragments ( )

Get ligand fragments.

Returns:
vector of ligand fragment indices

References ligandIndices.

std::vector< submolecule * > MTKpp::complex::getReceptorSubMols ( )

Get receptor residues.

Returns:
vector of receptor submolecule

References receptor.

std::vector< submolecule * > MTKpp::complex::getLigandSubMols ( )

Get ligand residues.

Returns:
vector of ligand submolecule

References ligand.

bool MTKpp::complex::isChain ( int  c,
int  a 
)

Is the atom in a chain?

Parameters:
cchain index
aatom index

References chain, and nAtoms.

void MTKpp::complex::setup ( ) [protected]

Friends And Related Function Documentation

friend class collection [friend]

Member Data Documentation

Name of complex.

Referenced by complex(), and setup().

int MTKpp::complex::nAtoms [protected]

Total number of atoms.

Referenced by getAtomIndex(), getLigFlags(), getNumAtoms(), getRecFlags(), isAtomLig(), isChain(), and setup().

int MTKpp::complex::nRecAtoms [protected]

Number of atoms in receptor.

Referenced by getNumRecAtoms(), and setup().

int MTKpp::complex::nLigAtoms [protected]

Number of atoms in ligand.

Referenced by getNumLigAtoms(), and setup().

Size of atom matrices.

Referenced by getAtomsMatrixSize(), and setup().

int MTKpp::complex::nResidues [protected]

Total Number of residues.

Referenced by getNumResidues(), getResIndex(), isResLig(), and setup().

Number of residues in receptor.

Referenced by getNumRecResidues(), and setup().

Number of residues in ligand.

Referenced by getNumLigResidues().

Size of residue matrices.

Referenced by getResMatrixSize(), and setup().

bool MTKpp::complex::bLigOnly [protected]

Do only lig-lig and rec-lig interactions.

Referenced by complex(), getLigOnly(), and setup().

Number of rec-rec atom interactions.

Referenced by getRecRecAtoms(), and setup().

Number of rec-rec residue interactions.

Referenced by getRecRecResidues(), and setup().

int* MTKpp::complex::rec [protected]

receptor atoms

Referenced by complex(), getRecFlags(), setup(), and ~complex().

int* MTKpp::complex::lig [protected]

ligand atoms

Referenced by complex(), getLigFlags(), isAtomLig(), setup(), and ~complex().

int* MTKpp::complex::cof [protected]

cofactor atoms

Referenced by complex(), and setup().

int* MTKpp::complex::sol [protected]

solvent atoms

Referenced by complex(), setup(), and ~complex().

int* MTKpp::complex::recSol [protected]

receptor and solvent atoms

Referenced by complex(), setup(), and ~complex().

int* MTKpp::complex::atomIndices [protected]

receptor and solvent atom indices

Referenced by complex(), getAtomIndex(), setup(), and ~complex().

int* MTKpp::complex::resRec [protected]

receptor residues

Referenced by complex(), setup(), and ~complex().

int* MTKpp::complex::resLig [protected]

ligand residues

Referenced by complex(), isResLig(), setup(), and ~complex().

int* MTKpp::complex::resSol [protected]

solvent residues

Referenced by complex(), setup(), and ~complex().

int* MTKpp::complex::resRecSol [protected]

receptor and solvent residues

Referenced by complex(), setup(), and ~complex().

int* MTKpp::complex::resIndices [protected]

receptor and solvent residue indices

Referenced by complex(), getResIndex(), setup(), and ~complex().

chain counter

Referenced by complex(), and setup().

int* MTKpp::complex::chain [protected]

chain indices

Referenced by complex(), isChain(), setup(), and ~complex().

std::vector<submolecule*> MTKpp::complex::receptor [protected]

Vector of receptor residues.

Referenced by getReceptorSubMols(), setCoreFragment(), and setup().

ligand molecule

Referenced by complex(), setCoreFragment(), and setup().

std::vector<submolecule*> MTKpp::complex::ligand [protected]

Vector of ligand fragments.

Referenced by getLigandSubMols(), setCoreFragment(), and setup().

std::vector<submolecule*> MTKpp::complex::cofactor [protected]

Vector of cofactor fragments.

Referenced by setup().

std::vector<submolecule*> MTKpp::complex::solvent [protected]

Vector of solvent residues.

Referenced by setCoreFragment(), and setup().

std::vector<std::vector<int> > MTKpp::complex::residues [protected]

Vector of atom indices.

Referenced by getResidues(), and setCoreFragment().

std::vector<int> MTKpp::complex::ligandIndices [protected]

Indices pointing to ligand fragments in the residues vector.

Referenced by getLigandFragments(), and setCoreFragment().

std::vector<std::string> MTKpp::complex::residueNAMEIDs [protected]

vector of residue names and ids

Referenced by getResNameID(), and setCoreFragment().

std::map<std::string, std::string> MTKpp::complex::residueMap [protected]

Map of residue names and ids.

Referenced by addMapping(), and getMapping().

std::vector<std::string> MTKpp::complex::cofactors [protected]

cofactor names

Referenced by complex(), and setup().


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

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