#include <ccp4srs_monomer.h>
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| Monomer () |
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| ~Monomer () |
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virtual int | type () |
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void | reset () |
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mmdb::cpstr | ID () |
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mmdb::cpstr | oldID () |
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void | setOldID (mmdb::cpstr oldID) |
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mmdb::cpstr | chem_name () |
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mmdb::cpstr | chem_type () |
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mmdb::cpstr | chem_formula () |
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int | n_atoms () |
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int | n_bonds () |
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int | n_angles () |
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int | n_torsions () |
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int | n_chicenters () |
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int | n_planes () |
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PAtom | atom (int n) |
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PBond | bond (int n) |
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PAngle | angle (int n) |
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PPlane | plane (int n) |
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PTree | tree () |
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PTorsion | torsion (int n) |
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PChiCenter | chicenter (int n) |
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void | add (PAtom atom) |
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void | add (PBond bond) |
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void | add (PAngle angle) |
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void | add (PPlane plane) |
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void | add (PTree stree) |
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void | add (PTorsion torsion) |
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void | add (PChiCenter chicenter) |
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Container< Atom > * | get_atoms () |
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Container< Bond > * | get_bonds () |
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Container< Angle > * | get_angles () |
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Container< Torsion > * | get_torsions () |
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Container< ChiCenter > * | get_chicenters () |
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Container< Plane > * | get_planes () |
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Tree * | get_tree () |
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Smiles * | getACDLabs () |
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Smiles * | getCACTVS () |
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Smiles * | getOpenEye () |
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Smiles * | getInChI () |
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int | atom_no (mmdb::cpstr aname) |
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int | get_bound (int atomNo, mmdb::cpstr elem, int serNo) |
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int | get_bound (int atomNo, int n) |
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int | get_bound (mmdb::cpstr aname, int n) |
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CCP4SRS_RC | addHydrogens (mmdb::PResidue R) |
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void | getAtomNameMatch (mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch) |
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void | getAtomNameMatch (Container< Atom > *A, mmdb::ivector anmatch) |
| Matches atoms in given container with atoms in the monomer by atom names. More...
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mmdb::math::PGraph | getGraph (int *retCode) |
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void | getLeavingAtoms (int &nLeavingAtoms, mmdb::ivector &leavingAtom, mmdb::ivector &bondedAtom) |
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int | readFromCIF (mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc=NULL) |
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mmdb::mmcif::PData | makeCIF () |
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void | merge (PMonomer monomer) |
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void | check_ccp4_coordinates () |
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| Entry () |
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virtual | ~Entry () |
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int | write (mmdb::io::RFile f, int version, PMemIO memIO=NULL) |
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int | read (mmdb::io::RFile f, int version, PMemIO memIO=NULL) |
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ccp4srs::Monomer::Monomer |
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ccp4srs::Monomer::~Monomer |
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void ccp4srs::Monomer::add |
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PAtom |
atom | ) |
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inline |
void ccp4srs::Monomer::add |
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PBond |
bond | ) |
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inline |
void ccp4srs::Monomer::add |
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PAngle |
angle | ) |
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inline |
void ccp4srs::Monomer::add |
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PPlane |
plane | ) |
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inline |
void ccp4srs::Monomer::add |
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PTree |
stree | ) |
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inline |
void ccp4srs::Monomer::add |
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PTorsion |
torsion | ) |
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inline |
void ccp4srs::Monomer::add |
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PChiCenter |
chicenter | ) |
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inline |
CCP4SRS_RC ccp4srs::Monomer::addHydrogens |
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mmdb::PResidue |
R | ) |
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PAngle ccp4srs::Monomer::angle |
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int |
n | ) |
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inline |
PAtom ccp4srs::Monomer::atom |
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int |
n | ) |
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inline |
int ccp4srs::Monomer::atom_no |
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mmdb::cpstr |
aname | ) |
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PBond ccp4srs::Monomer::bond |
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int |
n | ) |
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inline |
void ccp4srs::Monomer::check_ccp4_coordinates |
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mmdb::cpstr ccp4srs::Monomer::chem_formula |
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mmdb::cpstr ccp4srs::Monomer::chem_name |
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mmdb::cpstr ccp4srs::Monomer::chem_type |
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PChiCenter ccp4srs::Monomer::chicenter |
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int |
n | ) |
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inline |
int ccp4srs::Monomer::get_bound |
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int |
atomNo, |
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mmdb::cpstr |
elem, |
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int |
serNo |
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) |
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int ccp4srs::Monomer::get_bound |
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int |
atomNo, |
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int |
n |
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) |
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int ccp4srs::Monomer::get_bound |
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mmdb::cpstr |
aname, |
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int |
n |
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) |
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Tree* ccp4srs::Monomer::get_tree |
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inline |
Smiles* ccp4srs::Monomer::getACDLabs |
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inline |
void ccp4srs::Monomer::getAtomNameMatch |
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mmdb::PPAtom |
A, |
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int |
nat, |
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mmdb::pstr |
altLoc, |
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mmdb::ivector |
anmatch |
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) |
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void ccp4srs::Monomer::getAtomNameMatch |
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Container< Atom > * |
A, |
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mmdb::ivector |
anmatch |
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) |
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Matches atoms in given container with atoms in the monomer by atom names.
- Parameters
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[in] | A | pointer to atom container |
[out] | anmatch | allocated 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
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Smiles* ccp4srs::Monomer::getCACTVS |
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inline |
mmdb::math::PGraph ccp4srs::Monomer::getGraph |
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int * |
retCode | ) |
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Smiles* ccp4srs::Monomer::getInChI |
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inline |
void ccp4srs::Monomer::getLeavingAtoms |
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int & |
nLeavingAtoms, |
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mmdb::ivector & |
leavingAtom, |
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mmdb::ivector & |
bondedAtom |
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) |
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Smiles* ccp4srs::Monomer::getOpenEye |
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inline |
mmdb::cpstr ccp4srs::Monomer::ID |
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inline |
void ccp4srs::Monomer::Init |
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protected |
mmdb::mmcif::PData ccp4srs::Monomer::makeCIF |
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void ccp4srs::Monomer::merge |
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PMonomer |
monomer | ) |
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int ccp4srs::Monomer::n_angles |
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inline |
int ccp4srs::Monomer::n_atoms |
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inline |
int ccp4srs::Monomer::n_bonds |
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inline |
int ccp4srs::Monomer::n_chicenters |
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inline |
int ccp4srs::Monomer::n_planes |
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inline |
int ccp4srs::Monomer::n_torsions |
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inline |
mmdb::cpstr ccp4srs::Monomer::oldID |
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inline |
PPlane ccp4srs::Monomer::plane |
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int |
n | ) |
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inline |
bool ccp4srs::Monomer::read_mem |
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PMemIO |
memIO, |
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int |
version, |
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bool * |
Ok = NULL |
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) |
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protectedvirtual |
int ccp4srs::Monomer::readFromCIF |
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mmdb::mmcif::PData |
mmCIFData, |
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mmdb::pstr |
error_desc = NULL |
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) |
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int ccp4srs::Monomer::readFromCIF_ccp4 |
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mmdb::mmcif::PData |
mmCIFData, |
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mmdb::pstr |
error_desc |
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) |
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protected |
int ccp4srs::Monomer::readFromCIF_rcsb |
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mmdb::mmcif::PData |
mmCIFData, |
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mmdb::pstr |
error_desc |
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) |
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protected |
void ccp4srs::Monomer::readMonIDFromCIF |
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mmdb::mmcif::PLoop |
loop | ) |
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protected |
void ccp4srs::Monomer::readMonIDFromCIF |
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mmdb::mmcif::PStruct |
mmCIFStruct | ) |
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protected |
void ccp4srs::Monomer::reset |
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void ccp4srs::Monomer::setOldID |
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mmdb::cpstr |
oldID | ) |
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PTorsion ccp4srs::Monomer::torsion |
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int |
n | ) |
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inline |
PTree ccp4srs::Monomer::tree |
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inline |
virtual int ccp4srs::Monomer::type |
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inlinevirtual |
void ccp4srs::Monomer::write_mem |
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PMemIO |
memIO, |
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int |
version |
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) |
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protectedvirtual |
Smiles ccp4srs::Monomer::ACDLabs |
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protected |
Smiles ccp4srs::Monomer::CACTVS |
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protected |
Smiles ccp4srs::Monomer::InChI |
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protected |
mmdb::pstr ccp4srs::Monomer::monFormula |
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protected |
mmdb::ResName ccp4srs::Monomer::monID |
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protected |
mmdb::pstr ccp4srs::Monomer::monName |
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protected |
mmdb::pstr ccp4srs::Monomer::monType |
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protected |
mmdb::ResName ccp4srs::Monomer::oldMonID |
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protected |
Smiles ccp4srs::Monomer::OpenEye |
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protected |
Tree ccp4srs::Monomer::struct_tree |
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protected |
The documentation for this class was generated from the following files: