39 #ifndef CCP4SRS_MONOMER_H
40 #define CCP4SRS_MONOMER_H
42 #include "mmdb2/mmdb_mmcif_.h"
43 #include "mmdb2/mmdb_math_graph.h"
69 inline mmdb::cpstr
ID () {
return monID; }
84 inline PAtom
atom (
int n ) {
return atoms .at(n); }
85 inline PBond
bond (
int n ) {
return bonds .at(n); }
117 int atom_no ( mmdb::cpstr aname );
118 int get_bound (
int atomNo, mmdb::cpstr elem,
int serNo );
120 int get_bound ( mmdb::cpstr aname,
int n );
142 mmdb::ivector anmatch );
155 mmdb::math::PGraph
getGraph (
int *retCode );
158 mmdb::ivector & leavingAtom,
159 mmdb::ivector & bondedAtom );
164 mmdb::pstr error_desc = NULL );
169 void merge ( PMonomer monomer );
195 mmdb::pstr error_desc );
197 mmdb::pstr error_desc );
199 virtual void write_mem ( PMemIO memIO,
int version );
200 virtual bool read_mem ( PMemIO memIO,
int version,
207 #endif // CCP4SRS_MONOMER_H
Container< Angle > angles
Definition: ccp4srs_monomer.h:180
void add(PChiCenter chicenter)
Definition: ccp4srs_monomer.h:101
void getLeavingAtoms(int &nLeavingAtoms, mmdb::ivector &leavingAtom, mmdb::ivector &bondedAtom)
Definition: ccp4srs_monomer.cpp:102
int readFromCIF(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc=NULL)
Definition: ccp4srs_monomer.cpp:544
Smiles * getACDLabs()
Definition: ccp4srs_monomer.h:112
mmdb::cpstr chem_name()
Definition: ccp4srs_monomer.cpp:87
Container< Torsion > torsions
Definition: ccp4srs_monomer.h:181
PAtom atom(int n)
Definition: ccp4srs_monomer.h:84
mmdb::ResName oldMonID
Definition: ccp4srs_monomer.h:174
void readMonIDFromCIF(mmdb::mmcif::PLoop loop)
Definition: ccp4srs_monomer.cpp:524
void add(PTree stree)
Definition: ccp4srs_monomer.h:98
Definition: ccp4srs_entry.h:48
Definition: ccp4srs_entry.h:53
Definition: ccp4srs_tree.h:48
PChiCenter chicenter(int n)
Definition: ccp4srs_monomer.h:91
mmdb::cpstr ID()
Definition: ccp4srs_monomer.h:69
mmdb::pstr monFormula
Definition: ccp4srs_monomer.h:177
PPlane plane(int n)
Definition: ccp4srs_monomer.h:87
int get_bound(int atomNo, mmdb::cpstr elem, int serNo)
Definition: ccp4srs_monomer.cpp:237
virtual int type()
Definition: ccp4srs_monomer.h:65
CCP4SRS_RC addHydrogens(mmdb::PResidue R)
Definition: ccp4srs_monomer.cpp:310
Definition: ccp4srs_monomer.h:59
Smiles ACDLabs
Definition: ccp4srs_monomer.h:185
void merge(PMonomer monomer)
Definition: ccp4srs_monomer.cpp:1068
void getAtomNameMatch(mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch)
Definition: ccp4srs_monomer.cpp:464
mmdb::cpstr chem_type()
Definition: ccp4srs_monomer.cpp:92
int n_angles()
Definition: ccp4srs_monomer.h:79
Container< Bond > bonds
Definition: ccp4srs_monomer.h:179
CCP4SRS_RC
Definition: ccp4srs_types.h:55
void check_ccp4_coordinates()
Definition: ccp4srs_monomer.cpp:1167
void add(PTorsion torsion)
Definition: ccp4srs_monomer.h:99
mmdb::math::PGraph getGraph(int *retCode)
Definition: ccp4srs_monomer.cpp:1001
Definition: ccp4srs_smiles.h:51
void add(PPlane plane)
Definition: ccp4srs_monomer.h:97
virtual void write_mem(PMemIO memIO, int version)
Definition: ccp4srs_monomer.cpp:949
Container< Angle > * get_angles()
Definition: ccp4srs_monomer.h:106
mmdb::pstr monType
Definition: ccp4srs_monomer.h:176
Smiles * getInChI()
Definition: ccp4srs_monomer.h:115
mmdb::cpstr chem_formula()
Definition: ccp4srs_monomer.cpp:97
PBond bond(int n)
Definition: ccp4srs_monomer.h:85
Container< Atom > atoms
Definition: ccp4srs_monomer.h:178
int n_torsions()
Definition: ccp4srs_monomer.h:80
int n_planes()
Definition: ccp4srs_monomer.h:82
Container< ChiCenter > * get_chicenters()
Definition: ccp4srs_monomer.h:108
int n_bonds()
Definition: ccp4srs_monomer.h:78
mmdb::ResName monID
Definition: ccp4srs_monomer.h:173
void setOldID(mmdb::cpstr oldID)
Definition: ccp4srs_monomer.cpp:83
int atom_no(mmdb::cpstr aname)
Definition: ccp4srs_monomer.cpp:223
void copy(PTree tree, mmdb::ivector anmatch=NULL)
Definition: ccp4srs_tree.cpp:172
int n_atoms()
Definition: ccp4srs_monomer.h:77
void add(PAngle angle)
Definition: ccp4srs_monomer.h:96
Container< Plane > planes
Definition: ccp4srs_monomer.h:183
int readFromCIF_ccp4(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)
Definition: ccp4srs_monomer.cpp:693
Container< Bond > * get_bonds()
Definition: ccp4srs_monomer.h:105
void Init()
Definition: ccp4srs_monomer.cpp:57
void reset()
Definition: ccp4srs_monomer.cpp:65
Container< Torsion > * get_torsions()
Definition: ccp4srs_monomer.h:107
int readFromCIF_rcsb(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)
Definition: ccp4srs_monomer.cpp:552
Smiles * getCACTVS()
Definition: ccp4srs_monomer.h:113
Definition: ccp4srs_angle.cpp:42
Tree * get_tree()
Definition: ccp4srs_monomer.h:110
Tree struct_tree
Definition: ccp4srs_monomer.h:184
Definition: ccp4srs_container.h:48
mmdb::cpstr oldID()
Definition: ccp4srs_monomer.h:70
int n_chicenters()
Definition: ccp4srs_monomer.h:81
Smiles CACTVS
Definition: ccp4srs_monomer.h:186
void add(PAtom atom)
Definition: ccp4srs_monomer.h:94
void add(PBond bond)
Definition: ccp4srs_monomer.h:95
~Monomer()
Definition: ccp4srs_monomer.cpp:53
mmdb::mmcif::PData makeCIF()
Definition: ccp4srs_monomer.cpp:903
Container< Atom > * get_atoms()
Definition: ccp4srs_monomer.h:104
PTorsion torsion(int n)
Definition: ccp4srs_monomer.h:89
mmdb::pstr monName
Definition: ccp4srs_monomer.h:175
virtual bool read_mem(PMemIO memIO, int version, bool *Ok=NULL)
Definition: ccp4srs_monomer.cpp:968
PTree tree()
Definition: ccp4srs_monomer.h:88
Container< ChiCenter > chicenters
Definition: ccp4srs_monomer.h:182
Container< Plane > * get_planes()
Definition: ccp4srs_monomer.h:109
Smiles * getOpenEye()
Definition: ccp4srs_monomer.h:114
PAngle angle(int n)
Definition: ccp4srs_monomer.h:86
Monomer()
Definition: ccp4srs_monomer.cpp:49
Smiles InChI
Definition: ccp4srs_monomer.h:188
Smiles OpenEye
Definition: ccp4srs_monomer.h:187