ccp4srs  Version 1.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
ccp4srs::Chem Class Reference

#include <ccp4srs_chem.h>

Inheritance diagram for ccp4srs::Chem:
Inheritance graph
[legend]

Public Member Functions

 Chem ()
 
 ~Chem ()
 
CCP4SRS_RC getEnergyTypes (mmdb::PResidue R, mmdb::io::PFile structFile)
 
CCP4SRS_RC getEnergyTypes (mmdb::PPResidue R, int nRes, mmdb::io::PFile structFile)
 
CCP4SRS_RC getEnergyTypes (mmdb::PChain chain, mmdb::io::PFile structFile)
 
CCP4SRS_RC getEnergyTypes (mmdb::PModel model, mmdb::io::PFile structFile)
 
CCP4SRS_RC getEnergyTypes (mmdb::PManager MMDB, mmdb::io::PFile structFile)
 
CCP4SRS_RC addHydrogens (mmdb::PResidue R, mmdb::io::PFile structFile)
 
CCP4SRS_RC addHydrogens (mmdb::PChain chain, mmdb::io::PFile structFile)
 
CCP4SRS_RC addHydrogens (mmdb::PModel model, mmdb::io::PFile structFile)
 
CCP4SRS_RC addHydrogens (mmdb::PManager MMDB, mmdb::io::PFile structFile)
 
CCP4SRS_RC makeBonds (mmdb::PResidue R, mmdb::pstr altLoc, mmdb::io::PFile structFile, PDASelHnds selHandles, bool ignoreNegSigOcc)
 
CCP4SRS_RC CalcHBonds (mmdb::PPResidue Res1, int nres1, mmdb::PPResidue Res2, int nres2, RPAtomPair HBond, int &nHBonds, RPAtomPair SBridge, int &nSBridges, mmdb::io::PFile structFile=NULL, mmdb::pstr altLoc=NULL, bool ignoreNegSigOcc=false)
 
- Public Member Functions inherited from ccp4srs::Base
 Base ()
 Constructor. More...
 
 ~Base ()
 Destructor. More...
 
int loadIndex (mmdb::cpstr srsPath)
 
int loadStructure (mmdb::cpstr entryID)
 
PIndex getIndex (mmdb::cpstr entryID)
 
PIndex getIndex (int n)
 
int unloadStructure (mmdb::cpstr entryID)
 
mmdb::pstr getPath (mmdb::pstr &S, mmdb::cpstr FName)
 
mmdb::io::PFile getStructFile ()
 
mmdb::io::PFile getGraphFile ()
 
int n_entries ()
 
int getEntryNo (mmdb::cpstr entryID)
 
PMonomer getMonomer (mmdb::cpstr entryID)
 
PMonomer getMonomer (int entryNo, mmdb::io::PFile structFile)
 
PMonomer getMonomer (mmdb::cpstr entryID, mmdb::io::PFile structFile)
 
int getNofAtoms (mmdb::cpstr entryID)
 Returns the number of atoms in the references monomer. More...
 
int getNofAtoms (int entryNo)
 Returns the number of atoms in the references monomer. More...
 
int getNofAtoms (int entryNo, int &nNonHAtoms, int &nHAtoms)
 Returns number of non-hydrogen and hydrogen atoms for referenced structure. More...
 
int getAtNames (int entryNo, mmdb::PAtomName AtName, int &nAtoms, int &nH)
 Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer. More...
 
int getAtNames (mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &nAtoms, int &nH)
 Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer. More...
 
int getAtoms (mmdb::cpstr entryID, int &nNonHAtoms, mmdb::PAtomName NonHAtName, int &nHAtoms, mmdb::PAtomName HAtName, mmdb::ivector Hconnect, mmdb::ivector Elem, mmdb::ivector Chiral)
 Retrieves various atom properties for referenced structure. More...
 
int getBonds (mmdb::cpstr entryID, mmdb::ivector nBonds, mmdb::imatrix bondPair, int &nAtoms, int maxNAtoms, int maxNBonds)
 Retrieves bonds for referenced structure. More...
 
int getHetInfo (mmdb::cpstr entryID, mmdb::pstr Formula, mmdb::pstr Hname, mmdb::pstr Hsynonym, mmdb::pstr Hcharge, mmdb::PAtomName &ClinkAtom, mmdb::PElement &ClinkEle, mmdb::PAtomName &SlinkAtom, mmdb::PElement &SlinkEle, int &nLeavingAtoms)
 
int getGraph (mmdb::io::PFile graphFile, mmdb::math::RPGraph G)
 
int getGraph (mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)
 
int getGraph (mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)
 
int getGraph (int entryNo, mmdb::math::RPGraph G, int Hflag)
 
int getGraph (mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)
 

Protected Member Functions

void init_chem ()
 
- Protected Member Functions inherited from ccp4srs::Base
void init_base ()
 
void freeMemory ()
 

Protected Attributes

mmdb::realtype minDAdist
 
mmdb::realtype maxSBdist
 
mmdb::realtype maxDAdist
 
mmdb::realtype maxHAdist2
 
mmdb::realtype maxDHAcos
 
mmdb::realtype maxHAAcos
 
mmdb::realtype maxDAAcos
 
mmdb::realtype maxDDAcos
 
- Protected Attributes inherited from ccp4srs::Base
MemIO memIO
 
PPIndex index
 
mmdb::pstr srsDir
 
int srsVersion
 
int nEntries
 

Constructor & Destructor Documentation

ccp4srs::Chem::Chem ( )
ccp4srs::Chem::~Chem ( )

Member Function Documentation

CCP4SRS_RC ccp4srs::Chem::addHydrogens ( mmdb::PResidue  R,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::addHydrogens ( mmdb::PChain  chain,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::addHydrogens ( mmdb::PModel  model,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::addHydrogens ( mmdb::PManager  MMDB,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::CalcHBonds ( mmdb::PPResidue  Res1,
int  nres1,
mmdb::PPResidue  Res2,
int  nres2,
RPAtomPair  HBond,
int &  nHBonds,
RPAtomPair  SBridge,
int &  nSBridges,
mmdb::io::PFile  structFile = NULL,
mmdb::pstr  altLoc = NULL,
bool  ignoreNegSigOcc = false 
)
CCP4SRS_RC ccp4srs::Chem::getEnergyTypes ( mmdb::PResidue  R,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::getEnergyTypes ( mmdb::PPResidue  R,
int  nRes,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::getEnergyTypes ( mmdb::PChain  chain,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::getEnergyTypes ( mmdb::PModel  model,
mmdb::io::PFile  structFile 
)
CCP4SRS_RC ccp4srs::Chem::getEnergyTypes ( mmdb::PManager  MMDB,
mmdb::io::PFile  structFile 
)
void ccp4srs::Chem::init_chem ( )
protected
CCP4SRS_RC ccp4srs::Chem::makeBonds ( mmdb::PResidue  R,
mmdb::pstr  altLoc,
mmdb::io::PFile  structFile,
PDASelHnds  selHandles,
bool  ignoreNegSigOcc 
)

Member Data Documentation

mmdb::realtype ccp4srs::Chem::maxDAAcos
protected
mmdb::realtype ccp4srs::Chem::maxDAdist
protected
mmdb::realtype ccp4srs::Chem::maxDDAcos
protected
mmdb::realtype ccp4srs::Chem::maxDHAcos
protected
mmdb::realtype ccp4srs::Chem::maxHAAcos
protected
mmdb::realtype ccp4srs::Chem::maxHAdist2
protected
mmdb::realtype ccp4srs::Chem::maxSBdist
protected
mmdb::realtype ccp4srs::Chem::minDAdist
protected

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