ccp4srs
Version 1.0.0
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#include <ccp4srs_base.h>
Public Member Functions | |
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_base () |
void | freeMemory () |
Protected Attributes | |
MemIO | memIO |
PPIndex | index |
mmdb::pstr | srsDir |
int | srsVersion |
int | nEntries |
ccp4srs::Base::Base | ( | ) |
Constructor.
ccp4srs::Base::~Base | ( | ) |
Destructor.
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int ccp4srs::Base::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.
[in] | entryNo | entry number (0...n_entries()-1) |
[out] | AtName | array of atom names, prealocated with sufficient length |
[out] | nAtoms | total number of atoms |
[out] | nH | number of hydrogens |
int ccp4srs::Base::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.
[in] | structFile | pre-open SRS structure file |
[in] | entryNo | entry number (0...n_entries()-1) |
[out] | AtName | array of atom names, prealocated with sufficient length |
[out] | nAtoms | total number of atoms |
[out] | nH | number of hydrogens |
int ccp4srs::Base::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.
[in] | entryID | monomer's cif id |
[out] | nNonHAtoms | number of non-hydrogen atoms |
[out] | nNonHAtomName | non-hydrogen atom names |
[out] | nHAtoms | number of hydrogen atoms |
[out] | nNonHAtomName | hydrogen atom names |
[out] | Hconnect | connectivity to non-hydrogen atoms: hydrogen HAtName[i] is connected to non-hydrogen NonHAtom[Hconnect[i]], if Hconnect[i]>=0. |
[out] | Elem | element IDs |
[out] | Chiral | chirality IDs |
int ccp4srs::Base::getBonds | ( | mmdb::cpstr | entryID, |
mmdb::ivector | nBonds, | ||
mmdb::imatrix | bondPair, | ||
int & | nAtoms, | ||
int | maxNAtoms, | ||
int | maxNBonds | ||
) |
Retrieves bonds for referenced structure.
[in] | entryID | monomer's cif id |
[out] | nBonds | number of bonds for ith atom |
[out] | bondPair | bonded atoms: bondPair[i][j] (0<=i<nAtoms, 0<=j<=nBonds[i]) gives the number of atom connected to ith atom; only pairs i<j are returned |
[in] | maxNAtoms | length of nBonds[] and bondPairs[] |
[in] | maxNBonds | length of bondPairs[][] |
int ccp4srs::Base::getEntryNo | ( | mmdb::cpstr | entryID | ) |
int ccp4srs::Base::getGraph | ( | mmdb::io::PFile | graphFile, |
mmdb::math::RPGraph | G | ||
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int ccp4srs::Base::getGraph | ( | mmdb::io::PFile | graphFile, |
int | entryNo, | ||
mmdb::math::RPGraph | G, | ||
int | Hflag | ||
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int ccp4srs::Base::getGraph | ( | mmdb::io::PFile | graphFile, |
mmdb::math::RPGraph | G, | ||
int | Hflag | ||
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int ccp4srs::Base::getGraph | ( | int | entryNo, |
mmdb::math::RPGraph | G, | ||
int | Hflag | ||
) |
int ccp4srs::Base::getGraph | ( | mmdb::cpstr | entryID, |
mmdb::math::RPGraph | G, | ||
int | Hflag | ||
) |
mmdb::io::PFile ccp4srs::Base::getGraphFile | ( | ) |
int ccp4srs::Base::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 | ||
) |
PIndex ccp4srs::Base::getIndex | ( | mmdb::cpstr | entryID | ) |
PIndex ccp4srs::Base::getIndex | ( | int | n | ) |
PMonomer ccp4srs::Base::getMonomer | ( | mmdb::cpstr | entryID | ) |
PMonomer ccp4srs::Base::getMonomer | ( | int | entryNo, |
mmdb::io::PFile | structFile | ||
) |
PMonomer ccp4srs::Base::getMonomer | ( | mmdb::cpstr | entryID, |
mmdb::io::PFile | structFile | ||
) |
int ccp4srs::Base::getNofAtoms | ( | mmdb::cpstr | entryID | ) |
Returns the number of atoms in the references monomer.
int ccp4srs::Base::getNofAtoms | ( | int | entryNo | ) |
Returns the number of atoms in the references monomer.
[in] | entryNo | entry number (0...n_entries()-1) |
int ccp4srs::Base::getNofAtoms | ( | int | entryNo, |
int & | nNonHAtoms, | ||
int & | nHAtoms | ||
) |
Returns number of non-hydrogen and hydrogen atoms for referenced structure.
[in] | entryNo | entry number (0...n_entries()-1) |
[out] | nNonHAtoms | number of non-hydrogen atoms |
[out] | nHAtoms | number of hydrogen atoms |
mmdb::pstr ccp4srs::Base::getPath | ( | mmdb::pstr & | S, |
mmdb::cpstr | FName | ||
) |
mmdb::io::PFile ccp4srs::Base::getStructFile | ( | ) |
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int ccp4srs::Base::loadIndex | ( | mmdb::cpstr | srsPath | ) |
int ccp4srs::Base::loadStructure | ( | mmdb::cpstr | entryID | ) |
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int ccp4srs::Base::unloadStructure | ( | mmdb::cpstr | entryID | ) |
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