39 #ifndef CCP4SRS_ATOM_H
40 #define CCP4SRS_ATOM_H
45 #include "mmdb2/mmdb_atom.h"
46 #include "mmdb2/mmdb_mmcif_.h"
47 #include "mmdb2/mmdb_defs.h"
90 inline char leaving ()
const {
return property[2]; }
92 inline char hb_type ()
const {
return property[3]; }
96 mmdb::cpstr
name_pdb ( mmdb::pstr aname );
117 static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
120 int readFromCIF ( mmdb::mmcif::PStruct mmCIFStruct );
121 void writeToCIF ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID );
123 void copy ( PAtom atom );
124 void merge ( PAtom atom );
126 void write_mem ( PMemIO memIO,
int version );
127 bool read_mem ( PMemIO memIO,
int version,
bool * Ok = NULL );
170 mmdb::cpstr Tag,
int row,
185 #endif // CCP4SRS_ATOM_H
mmdb::realtype atomCharge
coordinates
Definition: ccp4srs_atom.h:144
mmdb::realtype ccp4_mlib_x
ccp4 monomer library
Definition: ccp4srs_atom.h:135
void set_vdwh_radius(mmdb::realtype r)
Definition: ccp4srs_atom.h:109
mmdb::realtype y_rcsb_cartn()
Definition: ccp4srs_atom.h:71
mmdb::realtype rcsb_cartn_y
Definition: ccp4srs_atom.h:139
bool isLeaving() const
Definition: ccp4srs_atom.h:91
mmdb::realtype vdw_radius()
Definition: ccp4srs_atom.h:81
static void makeCIFTags(mmdb::mmcif::PLoop mmCIFLoop)
Definition: ccp4srs_atom.cpp:222
bool ccp4_coordinates() const
Definition: ccp4srs_atom.h:93
char hb_type() const
Definition: ccp4srs_atom.h:92
int readFromCIF_rcsb(mmdb::mmcif::PLoop mmCIFLoop, int atomNo)
Definition: ccp4srs_atom.cpp:262
mmdb::realtype weight()
Definition: ccp4srs_atom.h:80
void set_valency(int v)
Definition: ccp4srs_atom.h:111
mmdb::realtype rcsb_cartn_x
coordinates
Definition: ccp4srs_atom.h:138
mmdb::realtype x()
Definition: ccp4srs_atom.cpp:175
char chirality() const
Definition: ccp4srs_atom.cpp:191
void set_ion_radius(mmdb::realtype r)
Definition: ccp4srs_atom.h:110
mmdb::cpstr rcsb_name_pdb(mmdb::pstr aname)
Definition: ccp4srs_atom.cpp:110
void get_atom_from_cif(int &index, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, Container< Atom > &atoms, int &rc)
Definition: ccp4srs_atom.cpp:507
Definition: ccp4srs_atom.h:53
mmdb::PAtom makeAtom()
Definition: ccp4srs_atom.cpp:208
void copy(PAtom atom)
Definition: ccp4srs_atom.cpp:371
mmdb::cpstr old_name_pdb(mmdb::pstr aname)
Definition: ccp4srs_atom.cpp:127
int atomSP
sp-hybridization
Definition: ccp4srs_atom.h:150
mmdb::realtype atomWeight
atomic weight (in a.u.)
Definition: ccp4srs_atom.h:145
void set_sp(int s)
Definition: ccp4srs_atom.h:112
mmdb::cpstr energy_type()
Definition: ccp4srs_atom.h:66
mmdb::cpstr rcsb_name()
Definition: ccp4srs_atom.h:63
mmdb::realtype vdwhRadius
Van-Der-Waals radius with hydrogen.
Definition: ccp4srs_atom.h:147
void set_rcsb_chirality(char c)
Definition: ccp4srs_atom.h:103
void set_chirality(char c)
Definition: ccp4srs_atom.h:104
mmdb::realtype rcsb_ideal_z
idealised
Definition: ccp4srs_atom.h:143
void set_ccp4_coordinates(bool on)
Definition: ccp4srs_atom.cpp:170
int readFromCIF_ccp4(mmdb::mmcif::PLoop mmCIFLoop, int atomNo)
Definition: ccp4srs_atom.cpp:233
bool read_mem(PMemIO memIO, int version, bool *Ok=NULL)
Definition: ccp4srs_atom.cpp:471
void add_atom_to_cif(mmdb::mmcif::PLoop loop, int atom_no, Container< Atom > &atoms)
Definition: ccp4srs_atom.cpp:529
void set_old_name(mmdb::cpstr name)
Definition: ccp4srs_atom.cpp:166
void merge(PAtom atom)
Definition: ccp4srs_atom.cpp:404
mmdb::realtype z_rcsb_cartn()
Definition: ccp4srs_atom.h:72
int valency()
Definition: ccp4srs_atom.h:84
mmdb::Element chemElement
chemical element name
Definition: ccp4srs_atom.h:133
mmdb::realtype y_rcsb_ideal()
Definition: ccp4srs_atom.h:74
mmdb::realtype z()
Definition: ccp4srs_atom.cpp:185
mmdb::realtype z_rcsb_ideal()
Definition: ccp4srs_atom.h:75
mmdb::realtype y_ccp4_mlib()
Definition: ccp4srs_atom.h:77
void write_mem(PMemIO memIO, int version)
Definition: ccp4srs_atom.cpp:445
mmdb::cpstr old_name()
Definition: ccp4srs_atom.h:64
char leaving() const
Definition: ccp4srs_atom.h:90
mmdb::realtype rcsb_cartn_z
cartesian coordinates
Definition: ccp4srs_atom.h:140
mmdb::realtype charge()
Definition: ccp4srs_atom.h:79
mmdb::realtype x_rcsb_ideal()
Definition: ccp4srs_atom.h:73
Definition: ccp4srs_angle.cpp:42
mmdb::realtype ion_radius()
Definition: ccp4srs_atom.h:83
void writeToCIF(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID)
Definition: ccp4srs_atom.cpp:337
mmdb::cpstr element()
Definition: ccp4srs_atom.h:65
mmdb::realtype x_ccp4_mlib()
Definition: ccp4srs_atom.h:76
Definition: ccp4srs_container.h:48
int atomValency
valency
Definition: ccp4srs_atom.h:149
mmdb::AtomName atomName
atom name
Definition: ccp4srs_atom.h:130
mmdb::realtype ionRadius
ion radius
Definition: ccp4srs_atom.h:148
mmdb::realtype vdwh_radius()
Definition: ccp4srs_atom.h:82
int readFromCIF(mmdb::mmcif::PStruct mmCIFStruct)
Definition: ccp4srs_atom.cpp:300
int sp()
Definition: ccp4srs_atom.h:85
mmdb::realtype ccp4_mlib_y
Definition: ccp4srs_atom.h:136
char rcsb_chirality() const
Definition: ccp4srs_atom.h:87
mmdb::realtype z_ccp4_mlib()
Definition: ccp4srs_atom.h:78
mmdb::cpstr name_pdb(mmdb::pstr aname)
Definition: ccp4srs_atom.cpp:93
void Init()
Definition: ccp4srs_atom.cpp:54
mmdb::realtype rcsb_ideal_x
coordinates
Definition: ccp4srs_atom.h:141
mmdb::cpstr name()
Definition: ccp4srs_atom.h:62
mmdb::cpstr id()
Definition: ccp4srs_atom.h:60
char property[5]
Definition: ccp4srs_atom.h:151
void set_energy_type(mmdb::cpstr etype)
Definition: ccp4srs_atom.cpp:162
void set_hb_type(char h)
Definition: ccp4srs_atom.h:105
char ccp4_chirality() const
Definition: ccp4srs_atom.h:88
mmdb::realtype x_rcsb_cartn()
Definition: ccp4srs_atom.h:70
mmdb::cpstr element_pdb(mmdb::pstr elem)
Definition: ccp4srs_atom.cpp:144
mmdb::realtype ccp4_mlib_z
cartesian
Definition: ccp4srs_atom.h:137
mmdb::AtomName oldAtomName
old atom name
Definition: ccp4srs_atom.h:132
Atom()
Definition: ccp4srs_atom.cpp:48
mmdb::AtomName rcsbAtomName
alternative atom name
Definition: ccp4srs_atom.h:131
mmdb::realtype rcsb_ideal_y
Definition: ccp4srs_atom.h:142
mmdb::EnergyType energyType
energy type
Definition: ccp4srs_atom.h:134
void set_vdw_radius(mmdb::realtype r)
Definition: ccp4srs_atom.h:108
mmdb::realtype y()
Definition: ccp4srs_atom.cpp:180
virtual ~Atom()
Definition: ccp4srs_atom.cpp:52
mmdb::realtype vdwRadius
Van-Der-Waals radius.
Definition: ccp4srs_atom.h:146