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

#include <ccp4srs_atom.h>

Public Member Functions

 Atom ()
 
virtual ~Atom ()
 
mmdb::cpstr id ()
 
mmdb::cpstr name ()
 
mmdb::cpstr rcsb_name ()
 
mmdb::cpstr old_name ()
 
mmdb::cpstr element ()
 
mmdb::cpstr energy_type ()
 
mmdb::realtype x ()
 
mmdb::realtype y ()
 
mmdb::realtype z ()
 
mmdb::realtype x_rcsb_cartn ()
 
mmdb::realtype y_rcsb_cartn ()
 
mmdb::realtype z_rcsb_cartn ()
 
mmdb::realtype x_rcsb_ideal ()
 
mmdb::realtype y_rcsb_ideal ()
 
mmdb::realtype z_rcsb_ideal ()
 
mmdb::realtype x_ccp4_mlib ()
 
mmdb::realtype y_ccp4_mlib ()
 
mmdb::realtype z_ccp4_mlib ()
 
mmdb::realtype charge ()
 
mmdb::realtype weight ()
 
mmdb::realtype vdw_radius ()
 
mmdb::realtype vdwh_radius ()
 
mmdb::realtype ion_radius ()
 
int valency ()
 
int sp ()
 
char rcsb_chirality () const
 
char ccp4_chirality () const
 
char chirality () const
 
char leaving () const
 
bool isLeaving () const
 
char hb_type () const
 
bool ccp4_coordinates () const
 
mmdb::cpstr name_pdb (mmdb::pstr aname)
 
mmdb::cpstr rcsb_name_pdb (mmdb::pstr aname)
 
mmdb::cpstr old_name_pdb (mmdb::pstr aname)
 
mmdb::cpstr element_pdb (mmdb::pstr elem)
 
void set_energy_type (mmdb::cpstr etype)
 
void set_old_name (mmdb::cpstr name)
 
void set_rcsb_chirality (char c)
 
void set_chirality (char c)
 
void set_hb_type (char h)
 
void set_ccp4_coordinates (bool on)
 
void set_vdw_radius (mmdb::realtype r)
 
void set_vdwh_radius (mmdb::realtype r)
 
void set_ion_radius (mmdb::realtype r)
 
void set_valency (int v)
 
void set_sp (int s)
 
void makeAtom (mmdb::RPAtom a)
 
mmdb::PAtom makeAtom ()
 
int readFromCIF_ccp4 (mmdb::mmcif::PLoop mmCIFLoop, int atomNo)
 
int readFromCIF_rcsb (mmdb::mmcif::PLoop mmCIFLoop, int atomNo)
 
int readFromCIF (mmdb::mmcif::PStruct mmCIFStruct)
 
void writeToCIF (mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID)
 
void copy (PAtom atom)
 
void merge (PAtom atom)
 
void write_mem (PMemIO memIO, int version)
 
bool read_mem (PMemIO memIO, int version, bool *Ok=NULL)
 

Static Public Member Functions

static void makeCIFTags (mmdb::mmcif::PLoop mmCIFLoop)
 

Protected Member Functions

void Init ()
 

Protected Attributes

mmdb::AtomName atomName
 atom name More...
 
mmdb::AtomName rcsbAtomName
 alternative atom name More...
 
mmdb::AtomName oldAtomName
 old atom name More...
 
mmdb::Element chemElement
 chemical element name More...
 
mmdb::EnergyType energyType
 energy type More...
 
mmdb::realtype ccp4_mlib_x
 ccp4 monomer library More...
 
mmdb::realtype ccp4_mlib_y
 
mmdb::realtype ccp4_mlib_z
 cartesian More...
 
mmdb::realtype rcsb_cartn_x
 coordinates More...
 
mmdb::realtype rcsb_cartn_y
 
mmdb::realtype rcsb_cartn_z
 cartesian coordinates More...
 
mmdb::realtype rcsb_ideal_x
 coordinates More...
 
mmdb::realtype rcsb_ideal_y
 
mmdb::realtype rcsb_ideal_z
 idealised More...
 
mmdb::realtype atomCharge
 coordinates More...
 
mmdb::realtype atomWeight
 atomic weight (in a.u.) More...
 
mmdb::realtype vdwRadius
 Van-Der-Waals radius. More...
 
mmdb::realtype vdwhRadius
 Van-Der-Waals radius with hydrogen. More...
 
mmdb::realtype ionRadius
 ion radius More...
 
int atomValency
 valency More...
 
int atomSP
 sp-hybridization More...
 
char property [5]
 

Constructor & Destructor Documentation

ccp4srs::Atom::Atom ( )
ccp4srs::Atom::~Atom ( )
virtual

Member Function Documentation

char ccp4srs::Atom::ccp4_chirality ( ) const
inline
bool ccp4srs::Atom::ccp4_coordinates ( ) const
inline
mmdb::realtype ccp4srs::Atom::charge ( )
inline
char ccp4srs::Atom::chirality ( ) const
void ccp4srs::Atom::copy ( PAtom  atom)
mmdb::cpstr ccp4srs::Atom::element ( )
inline
mmdb::cpstr ccp4srs::Atom::element_pdb ( mmdb::pstr  elem)
mmdb::cpstr ccp4srs::Atom::energy_type ( )
inline
char ccp4srs::Atom::hb_type ( ) const
inline
mmdb::cpstr ccp4srs::Atom::id ( )
inline
void ccp4srs::Atom::Init ( )
protected

[0]: RCSB chirality : 'R', 'S' or 'N' [1]: MLib chirality : 'R', 'S' or 'N' [2]: leaving atom: 'Y' or 'N' [3]: hydrogen bond type: 'D' donor 'A' acceptor 'B' both 'H' hydrogen candidate 'N' neither [4]: ccp4 coordinates: 'Y' - x,y,z return ccp4_mlib_* 'N' - x,y,z return rcsb_cartn_*

mmdb::realtype ccp4srs::Atom::ion_radius ( )
inline
bool ccp4srs::Atom::isLeaving ( ) const
inline
char ccp4srs::Atom::leaving ( ) const
inline
void ccp4srs::Atom::makeAtom ( mmdb::RPAtom  a)
mmdb::PAtom ccp4srs::Atom::makeAtom ( )
void ccp4srs::Atom::makeCIFTags ( mmdb::mmcif::PLoop  mmCIFLoop)
static
void ccp4srs::Atom::merge ( PAtom  atom)
mmdb::cpstr ccp4srs::Atom::name ( )
inline
mmdb::cpstr ccp4srs::Atom::name_pdb ( mmdb::pstr  aname)
mmdb::cpstr ccp4srs::Atom::old_name ( )
inline
mmdb::cpstr ccp4srs::Atom::old_name_pdb ( mmdb::pstr  aname)
char ccp4srs::Atom::rcsb_chirality ( ) const
inline
mmdb::cpstr ccp4srs::Atom::rcsb_name ( )
inline
mmdb::cpstr ccp4srs::Atom::rcsb_name_pdb ( mmdb::pstr  aname)
bool ccp4srs::Atom::read_mem ( PMemIO  memIO,
int  version,
bool *  Ok = NULL 
)
int ccp4srs::Atom::readFromCIF ( mmdb::mmcif::PStruct  mmCIFStruct)
int ccp4srs::Atom::readFromCIF_ccp4 ( mmdb::mmcif::PLoop  mmCIFLoop,
int  atomNo 
)
int ccp4srs::Atom::readFromCIF_rcsb ( mmdb::mmcif::PLoop  mmCIFLoop,
int  atomNo 
)
void ccp4srs::Atom::set_ccp4_coordinates ( bool  on)
void ccp4srs::Atom::set_chirality ( char  c)
inline
void ccp4srs::Atom::set_energy_type ( mmdb::cpstr  etype)
void ccp4srs::Atom::set_hb_type ( char  h)
inline
void ccp4srs::Atom::set_ion_radius ( mmdb::realtype  r)
inline
void ccp4srs::Atom::set_old_name ( mmdb::cpstr  name)
void ccp4srs::Atom::set_rcsb_chirality ( char  c)
inline
void ccp4srs::Atom::set_sp ( int  s)
inline
void ccp4srs::Atom::set_valency ( int  v)
inline
void ccp4srs::Atom::set_vdw_radius ( mmdb::realtype  r)
inline
void ccp4srs::Atom::set_vdwh_radius ( mmdb::realtype  r)
inline
int ccp4srs::Atom::sp ( )
inline
int ccp4srs::Atom::valency ( )
inline
mmdb::realtype ccp4srs::Atom::vdw_radius ( )
inline
mmdb::realtype ccp4srs::Atom::vdwh_radius ( )
inline
mmdb::realtype ccp4srs::Atom::weight ( )
inline
void ccp4srs::Atom::write_mem ( PMemIO  memIO,
int  version 
)
void ccp4srs::Atom::writeToCIF ( mmdb::mmcif::PLoop  mmCIFLoop,
mmdb::cpstr  monID 
)
mmdb::realtype ccp4srs::Atom::x ( )
mmdb::realtype ccp4srs::Atom::x_ccp4_mlib ( )
inline
mmdb::realtype ccp4srs::Atom::x_rcsb_cartn ( )
inline
mmdb::realtype ccp4srs::Atom::x_rcsb_ideal ( )
inline
mmdb::realtype ccp4srs::Atom::y ( )
mmdb::realtype ccp4srs::Atom::y_ccp4_mlib ( )
inline
mmdb::realtype ccp4srs::Atom::y_rcsb_cartn ( )
inline
mmdb::realtype ccp4srs::Atom::y_rcsb_ideal ( )
inline
mmdb::realtype ccp4srs::Atom::z ( )
mmdb::realtype ccp4srs::Atom::z_ccp4_mlib ( )
inline
mmdb::realtype ccp4srs::Atom::z_rcsb_cartn ( )
inline
mmdb::realtype ccp4srs::Atom::z_rcsb_ideal ( )
inline

Member Data Documentation

mmdb::realtype ccp4srs::Atom::atomCharge
protected

coordinates

partial charge

mmdb::AtomName ccp4srs::Atom::atomName
protected

atom name

int ccp4srs::Atom::atomSP
protected

sp-hybridization

int ccp4srs::Atom::atomValency
protected

valency

mmdb::realtype ccp4srs::Atom::atomWeight
protected

atomic weight (in a.u.)

mmdb::realtype ccp4srs::Atom::ccp4_mlib_x
protected

ccp4 monomer library

mmdb::realtype ccp4srs::Atom::ccp4_mlib_y
protected
mmdb::realtype ccp4srs::Atom::ccp4_mlib_z
protected

cartesian

mmdb::Element ccp4srs::Atom::chemElement
protected

chemical element name

mmdb::EnergyType ccp4srs::Atom::energyType
protected

energy type

mmdb::realtype ccp4srs::Atom::ionRadius
protected

ion radius

mmdb::AtomName ccp4srs::Atom::oldAtomName
protected

old atom name

char ccp4srs::Atom::property[5]
protected

property vector:

mmdb::realtype ccp4srs::Atom::rcsb_cartn_x
protected

coordinates

pdb

mmdb::realtype ccp4srs::Atom::rcsb_cartn_y
protected
mmdb::realtype ccp4srs::Atom::rcsb_cartn_z
protected

cartesian coordinates

mmdb::realtype ccp4srs::Atom::rcsb_ideal_x
protected

coordinates

rcsb

mmdb::realtype ccp4srs::Atom::rcsb_ideal_y
protected
mmdb::realtype ccp4srs::Atom::rcsb_ideal_z
protected

idealised

mmdb::AtomName ccp4srs::Atom::rcsbAtomName
protected

alternative atom name

mmdb::realtype ccp4srs::Atom::vdwhRadius
protected

Van-Der-Waals radius with hydrogen.

mmdb::realtype ccp4srs::Atom::vdwRadius
protected

Van-Der-Waals radius.


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