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

#include <ccp4srs_monomer.h>

Inheritance diagram for ccp4srs::Monomer:
Inheritance graph
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Public Member Functions

 Monomer ()
 
 ~Monomer ()
 
virtual int type ()
 
void reset ()
 
mmdb::cpstr ID ()
 
mmdb::cpstr oldID ()
 
void setOldID (mmdb::cpstr oldID)
 
mmdb::cpstr chem_name ()
 
mmdb::cpstr chem_type ()
 
mmdb::cpstr chem_formula ()
 
int n_atoms ()
 
int n_bonds ()
 
int n_angles ()
 
int n_torsions ()
 
int n_chicenters ()
 
int n_planes ()
 
PAtom atom (int n)
 
PBond bond (int n)
 
PAngle angle (int n)
 
PPlane plane (int n)
 
PTree tree ()
 
PTorsion torsion (int n)
 
PChiCenter chicenter (int n)
 
void add (PAtom atom)
 
void add (PBond bond)
 
void add (PAngle angle)
 
void add (PPlane plane)
 
void add (PTree stree)
 
void add (PTorsion torsion)
 
void add (PChiCenter chicenter)
 
Container< Atom > * get_atoms ()
 
Container< Bond > * get_bonds ()
 
Container< Angle > * get_angles ()
 
Container< Torsion > * get_torsions ()
 
Container< ChiCenter > * get_chicenters ()
 
Container< Plane > * get_planes ()
 
Treeget_tree ()
 
SmilesgetACDLabs ()
 
SmilesgetCACTVS ()
 
SmilesgetOpenEye ()
 
SmilesgetInChI ()
 
int atom_no (mmdb::cpstr aname)
 
int get_bound (int atomNo, mmdb::cpstr elem, int serNo)
 
int get_bound (int atomNo, int n)
 
int get_bound (mmdb::cpstr aname, int n)
 
CCP4SRS_RC addHydrogens (mmdb::PResidue R)
 
void getAtomNameMatch (mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch)
 
void getAtomNameMatch (Container< Atom > *A, mmdb::ivector anmatch)
 Matches atoms in given container with atoms in the monomer by atom names. More...
 
mmdb::math::PGraph getGraph (int *retCode)
 
void getLeavingAtoms (int &nLeavingAtoms, mmdb::ivector &leavingAtom, mmdb::ivector &bondedAtom)
 
int readFromCIF (mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc=NULL)
 
mmdb::mmcif::PData makeCIF ()
 
void merge (PMonomer monomer)
 
void check_ccp4_coordinates ()
 
- Public Member Functions inherited from ccp4srs::Entry
 Entry ()
 
virtual ~Entry ()
 
int write (mmdb::io::RFile f, int version, PMemIO memIO=NULL)
 
int read (mmdb::io::RFile f, int version, PMemIO memIO=NULL)
 

Protected Member Functions

void Init ()
 
void readMonIDFromCIF (mmdb::mmcif::PLoop loop)
 
void readMonIDFromCIF (mmdb::mmcif::PStruct mmCIFStruct)
 
int readFromCIF_ccp4 (mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)
 
int readFromCIF_rcsb (mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)
 
virtual void write_mem (PMemIO memIO, int version)
 
virtual bool read_mem (PMemIO memIO, int version, bool *Ok=NULL)
 

Protected Attributes

mmdb::ResName monID
 
mmdb::ResName oldMonID
 
mmdb::pstr monName
 
mmdb::pstr monType
 
mmdb::pstr monFormula
 
Container< Atomatoms
 
Container< Bondbonds
 
Container< Angleangles
 
Container< Torsiontorsions
 
Container< ChiCenterchicenters
 
Container< Planeplanes
 
Tree struct_tree
 
Smiles ACDLabs
 
Smiles CACTVS
 
Smiles OpenEye
 
Smiles InChI
 

Additional Inherited Members

- Public Types inherited from ccp4srs::Entry
enum  { None, Monomer, Link }
 

Constructor & Destructor Documentation

ccp4srs::Monomer::Monomer ( )
ccp4srs::Monomer::~Monomer ( )

Member Function Documentation

void ccp4srs::Monomer::add ( PAtom  atom)
inline
void ccp4srs::Monomer::add ( PBond  bond)
inline
void ccp4srs::Monomer::add ( PAngle  angle)
inline
void ccp4srs::Monomer::add ( PPlane  plane)
inline
void ccp4srs::Monomer::add ( PTree  stree)
inline
void ccp4srs::Monomer::add ( PTorsion  torsion)
inline
void ccp4srs::Monomer::add ( PChiCenter  chicenter)
inline
CCP4SRS_RC ccp4srs::Monomer::addHydrogens ( mmdb::PResidue  R)
PAngle ccp4srs::Monomer::angle ( int  n)
inline
PAtom ccp4srs::Monomer::atom ( int  n)
inline
int ccp4srs::Monomer::atom_no ( mmdb::cpstr  aname)
PBond ccp4srs::Monomer::bond ( int  n)
inline
void ccp4srs::Monomer::check_ccp4_coordinates ( )
mmdb::cpstr ccp4srs::Monomer::chem_formula ( )
mmdb::cpstr ccp4srs::Monomer::chem_name ( )
mmdb::cpstr ccp4srs::Monomer::chem_type ( )
PChiCenter ccp4srs::Monomer::chicenter ( int  n)
inline
Container<Angle>* ccp4srs::Monomer::get_angles ( )
inline
Container<Atom>* ccp4srs::Monomer::get_atoms ( )
inline
Container<Bond>* ccp4srs::Monomer::get_bonds ( )
inline
int ccp4srs::Monomer::get_bound ( int  atomNo,
mmdb::cpstr  elem,
int  serNo 
)
int ccp4srs::Monomer::get_bound ( int  atomNo,
int  n 
)
int ccp4srs::Monomer::get_bound ( mmdb::cpstr  aname,
int  n 
)
Container<ChiCenter>* ccp4srs::Monomer::get_chicenters ( )
inline
Container<Plane>* ccp4srs::Monomer::get_planes ( )
inline
Container<Torsion>* ccp4srs::Monomer::get_torsions ( )
inline
Tree* ccp4srs::Monomer::get_tree ( )
inline
Smiles* ccp4srs::Monomer::getACDLabs ( )
inline
void ccp4srs::Monomer::getAtomNameMatch ( mmdb::PPAtom  A,
int  nat,
mmdb::pstr  altLoc,
mmdb::ivector  anmatch 
)
void ccp4srs::Monomer::getAtomNameMatch ( Container< Atom > *  A,
mmdb::ivector  anmatch 
)

Matches atoms in given container with atoms in the monomer by atom names.

Parameters
[in]Apointer to atom container
[out]anmatchallocated integer vector [0..A->numberOf()-1], where the match will be returned:
  • anmatch[i]>=0 : atom A->at(i) matches anmathch[i]-th atom in the monomer
  • anmatch[i]<0 : atom A->at(i) does not have a name match in the monomer
Smiles* ccp4srs::Monomer::getCACTVS ( )
inline
mmdb::math::PGraph ccp4srs::Monomer::getGraph ( int *  retCode)
Smiles* ccp4srs::Monomer::getInChI ( )
inline
void ccp4srs::Monomer::getLeavingAtoms ( int &  nLeavingAtoms,
mmdb::ivector &  leavingAtom,
mmdb::ivector &  bondedAtom 
)
Smiles* ccp4srs::Monomer::getOpenEye ( )
inline
mmdb::cpstr ccp4srs::Monomer::ID ( )
inline
void ccp4srs::Monomer::Init ( )
protected
mmdb::mmcif::PData ccp4srs::Monomer::makeCIF ( )
void ccp4srs::Monomer::merge ( PMonomer  monomer)
int ccp4srs::Monomer::n_angles ( )
inline
int ccp4srs::Monomer::n_atoms ( )
inline
int ccp4srs::Monomer::n_bonds ( )
inline
int ccp4srs::Monomer::n_chicenters ( )
inline
int ccp4srs::Monomer::n_planes ( )
inline
int ccp4srs::Monomer::n_torsions ( )
inline
mmdb::cpstr ccp4srs::Monomer::oldID ( )
inline
PPlane ccp4srs::Monomer::plane ( int  n)
inline
bool ccp4srs::Monomer::read_mem ( PMemIO  memIO,
int  version,
bool *  Ok = NULL 
)
protectedvirtual

Reimplemented from ccp4srs::Entry.

int ccp4srs::Monomer::readFromCIF ( mmdb::mmcif::PData  mmCIFData,
mmdb::pstr  error_desc = NULL 
)
int ccp4srs::Monomer::readFromCIF_ccp4 ( mmdb::mmcif::PData  mmCIFData,
mmdb::pstr  error_desc 
)
protected
int ccp4srs::Monomer::readFromCIF_rcsb ( mmdb::mmcif::PData  mmCIFData,
mmdb::pstr  error_desc 
)
protected
void ccp4srs::Monomer::readMonIDFromCIF ( mmdb::mmcif::PLoop  loop)
protected
void ccp4srs::Monomer::readMonIDFromCIF ( mmdb::mmcif::PStruct  mmCIFStruct)
protected
void ccp4srs::Monomer::reset ( )
void ccp4srs::Monomer::setOldID ( mmdb::cpstr  oldID)
PTorsion ccp4srs::Monomer::torsion ( int  n)
inline
PTree ccp4srs::Monomer::tree ( )
inline
virtual int ccp4srs::Monomer::type ( )
inlinevirtual

Reimplemented from ccp4srs::Entry.

void ccp4srs::Monomer::write_mem ( PMemIO  memIO,
int  version 
)
protectedvirtual

Reimplemented from ccp4srs::Entry.

Member Data Documentation

Smiles ccp4srs::Monomer::ACDLabs
protected
Container<Angle> ccp4srs::Monomer::angles
protected
Container<Atom> ccp4srs::Monomer::atoms
protected
Container<Bond> ccp4srs::Monomer::bonds
protected
Smiles ccp4srs::Monomer::CACTVS
protected
Container<ChiCenter> ccp4srs::Monomer::chicenters
protected
Smiles ccp4srs::Monomer::InChI
protected
mmdb::pstr ccp4srs::Monomer::monFormula
protected
mmdb::ResName ccp4srs::Monomer::monID
protected
mmdb::pstr ccp4srs::Monomer::monName
protected
mmdb::pstr ccp4srs::Monomer::monType
protected
mmdb::ResName ccp4srs::Monomer::oldMonID
protected
Smiles ccp4srs::Monomer::OpenEye
protected
Container<Plane> ccp4srs::Monomer::planes
protected
Tree ccp4srs::Monomer::struct_tree
protected
Container<Torsion> ccp4srs::Monomer::torsions
protected

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