Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Friends

mmdb::Atom Class Reference

#include <mmdb_atom.h>

Inheritance diagram for mmdb::Atom:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 Atom ()
 Atom (PResidue res)
 Atom (io::RPStream Object)
 ~Atom ()
void SetResidue (PResidue res)
void PDBASCIIDump (io::RFile f)
void MakeCIF (mmcif::PData CIF)
int AddBond (PAtom bond_atom, int bond_order, int nAdd_bonds=1)
int GetNBonds ()
void GetBonds (RPAtomBond atomBond, int &nAtomBonds)
void FreeBonds ()
void GetBonds (RPAtomBondI atomBondI, int &nAtomBonds)
void GetBonds (PAtomBondI atomBondI, int &nAtomBonds, int maxlength)
ERROR_CODE ConvertPDBATOM (int ix, cpstr S)
ERROR_CODE ConvertPDBSIGATM (int ix, cpstr S)
ERROR_CODE ConvertPDBANISOU (int ix, cpstr S)
ERROR_CODE ConvertPDBSIGUIJ (int ix, cpstr S)
ERROR_CODE ConvertPDBTER (int ix, cpstr S)
ERROR_CODE ConvertPDBHETATM (int ix, cpstr S)
ERROR_CODE GetCIF (int ix, mmcif::PLoop Loop, mmcif::PLoop LoopAnis)
bool RestoreElementName ()
bool MakePDBAtomName ()
void SetAtomName (int ix, int sN, const AtomName aName, const AltLoc aLoc, const SegID sID, const Element eName)
void SetAtomName (const AtomName atomName)
void SetElementName (const Element elName)
void SetCharge (cpstr chrg)
void SetCharge (realtype chrg)
void SetAtomIndex (int ix)
void MakeTer ()
void SetCoordinates (realtype xx, realtype yy, realtype zz, realtype occ, realtype tFac)
int GetModelNum ()
pstr GetChainID ()
pstr GetLabelAsymID ()
pstr GetResName ()
pstr GetLabelCompID ()
int GetAASimilarity (const ResName resName)
int GetAASimilarity (PAtom A)
realtype GetAAHydropathy ()
realtype GetOccupancy ()
int GetSeqNum ()
int GetLabelSeqID ()
int GetLabelEntityID ()
pstr GetInsCode ()
int GetSSEType ()
pstr GetAtomName ()
pstr GetElementName ()
pstr GetAtomCharge (pstr chrg)
void GetChainCalphas (PPAtom &Calphas, int &nCalphas, cpstr altLoc="")
bool isTer ()
bool isMetal ()
bool isSolvent ()
bool isInSelection (int selHnd)
bool isNTerminus ()
bool isCTerminus ()
void CalAtomStatistics (RAtomStat AS)
realtype GetDist2 (PAtom a)
realtype GetDist2 (PAtom a, mat44 &tm)
realtype GetDist2 (PAtom a, mat33 &r, vect3 &t)
realtype GetDist2 (realtype ax, realtype ay, realtype az)
realtype GetCosine (PAtom a1, PAtom a2)
PResidue GetResidue ()
PChain GetChain ()
PModel GetModel ()
int GetResidueNo ()
void * GetCoordHierarchy ()
pstr GetAtomID (pstr AtomID)
pstr GetAtomIDfmt (pstr AtomID)
int CheckID (const AtomName aname, const Element elname=NULL, const AltLoc aloc=pstr(""))
int CheckIDS (cpstr ID)
void Transform (mat33 &tm, vect3 &v)
void Transform (mat44 &tm)
void TransformCopy (mat44 &tm, realtype &xx, realtype &yy, realtype &zz)
void TransformSet (mat44 &tm, realtype xx, realtype yy, realtype zz)
int PutUDData (int UDDhandle, int iudd)
int PutUDData (int UDDhandle, realtype rudd)
int PutUDData (int UDDhandle, cpstr sudd)
int GetUDData (int UDDhandle, int &iudd)
int GetUDData (int UDDhandle, realtype &rudd)
int GetUDData (int UDDhandle, pstr sudd, int maxLen)
int GetUDData (int UDDhandle, pstr &sudd)
int GetIndex ()
virtual void Copy (PAtom atom)
void SetShortBinary ()
void write (io::RFile f)
void read (io::RFile f)

Public Attributes

int serNum
 serial number
AtomName name
 atom name (ALIGNED)
AtomName label_atom_id
 assigned atom name (not aligned)
AltLoc altLoc
 alternative location indicator ("" for none)
SegID segID
 segment identifier
Element element
 element symbol (ALIGNED TO RIGHT)
EnergyType energyType
 energy type (without spaces)
PResidue residue
 reference to residue
realtype x
realtype y
realtype z
 orthogonal coordinates in angstroms
realtype occupancy
 occupancy
realtype tempFactor
 temperature factor
realtype charge
 charge on the atom
realtype sigX
realtype sigY
realtype sigZ
 standard deviations of the coords
realtype sigOcc
 standard deviation of occupancy
realtype sigTemp
 standard deviation of temp.
realtype u11
realtype u22
realtype u33
 anisotropic temperature
realtype u12
realtype u13
realtype u23
realtype su11
 factors
realtype su22
realtype su33
 standard deviations of
realtype su12
realtype su13
realtype su23
bool Het
 anisotropic temperature factors
bool Ter
 chain terminator
word WhatIsSet

Protected Member Functions

void InitAtom ()
void FreeMemory ()
void StandardPDBOut (cpstr Record, pstr S)
void GetData (cpstr S)
ERROR_CODE CheckData (cpstr S)
void GetStat (realtype v, realtype &v_min, realtype &v_max, realtype &v_m, realtype &v_m2)
void _setBonds (PPAtom A)

Protected Attributes

int index
int nBonds
PAtomBond Bond

Friends

class Residue
class Model
class Root
class CoorManager
class SelManager

Constructor & Destructor Documentation

mmdb::Atom::Atom (  )

0x0001 atomic coordinates 0x0002 occupancy 0x0004 temperature factor 0x0010 coordinate standard deviations 0x0020 deviation of occupancy 0x0040 deviation of temperature factor 0x0100 anisotropic temperature factors 0x1000 anis. temp. fact-s st-d deviations

mmdb::Atom::Atom ( PResidue  res )
mmdb::Atom::Atom ( io::RPStream  Object )
mmdb::Atom::~Atom (  )

Member Function Documentation

void mmdb::Atom::_setBonds ( PPAtom  A ) [protected]
int mmdb::Atom::AddBond ( PAtom  bond_atom,
int  bond_order,
int  nAdd_bonds = 1 
)
void mmdb::Atom::CalAtomStatistics ( RAtomStat  AS )
ERROR_CODE mmdb::Atom::CheckData ( cpstr  S ) [protected]
int mmdb::Atom::CheckID ( const AtomName  aname,
const Element  elname = NULL,
const AltLoc  aloc = pstr("") 
)
int mmdb::Atom::CheckIDS ( cpstr  ID )
ERROR_CODE mmdb::Atom::ConvertPDBANISOU ( int  ix,
cpstr  S 
)
ERROR_CODE mmdb::Atom::ConvertPDBATOM ( int  ix,
cpstr  S 
)
ERROR_CODE mmdb::Atom::ConvertPDBHETATM ( int  ix,
cpstr  S 
)
ERROR_CODE mmdb::Atom::ConvertPDBSIGATM ( int  ix,
cpstr  S 
)
ERROR_CODE mmdb::Atom::ConvertPDBSIGUIJ ( int  ix,
cpstr  S 
)
ERROR_CODE mmdb::Atom::ConvertPDBTER ( int  ix,
cpstr  S 
)
void mmdb::Atom::Copy ( PAtom  atom ) [virtual]
void mmdb::Atom::FreeBonds (  )
void mmdb::Atom::FreeMemory (  ) [protected]
realtype mmdb::Atom::GetAAHydropathy (  )
int mmdb::Atom::GetAASimilarity ( const ResName  resName )
int mmdb::Atom::GetAASimilarity ( PAtom  A )
pstr mmdb::Atom::GetAtomCharge ( pstr  chrg )
pstr mmdb::Atom::GetAtomID ( pstr  AtomID )
pstr mmdb::Atom::GetAtomIDfmt ( pstr  AtomID )
pstr mmdb::Atom::GetAtomName (  ) [inline]
void mmdb::Atom::GetBonds ( PAtomBondI  atomBondI,
int &  nAtomBonds,
int  maxlength 
)
void mmdb::Atom::GetBonds ( RPAtomBondI  atomBondI,
int &  nAtomBonds 
)
void mmdb::Atom::GetBonds ( RPAtomBond  atomBond,
int &  nAtomBonds 
)
PChain mmdb::Atom::GetChain (  )
void mmdb::Atom::GetChainCalphas ( PPAtom &  Calphas,
int &  nCalphas,
cpstr  altLoc = "" 
)
pstr mmdb::Atom::GetChainID (  )
ERROR_CODE mmdb::Atom::GetCIF ( int  ix,
mmcif::PLoop  Loop,
mmcif::PLoop  LoopAnis 
)
void * mmdb::Atom::GetCoordHierarchy (  )
realtype mmdb::Atom::GetCosine ( PAtom  a1,
PAtom  a2 
)
void mmdb::Atom::GetData ( cpstr  S ) [protected]
realtype mmdb::Atom::GetDist2 ( PAtom  a )
realtype mmdb::Atom::GetDist2 ( PAtom  a,
mat44 &  tm 
)
realtype mmdb::Atom::GetDist2 ( PAtom  a,
mat33 &  r,
vect3 &  t 
)
realtype mmdb::Atom::GetDist2 ( realtype  ax,
realtype  ay,
realtype  az 
)
pstr mmdb::Atom::GetElementName (  ) [inline]
int mmdb::Atom::GetIndex (  ) [inline]
pstr mmdb::Atom::GetInsCode (  )
pstr mmdb::Atom::GetLabelAsymID (  )
pstr mmdb::Atom::GetLabelCompID (  )
int mmdb::Atom::GetLabelEntityID (  )
int mmdb::Atom::GetLabelSeqID (  )
PModel mmdb::Atom::GetModel (  )
int mmdb::Atom::GetModelNum (  )
int mmdb::Atom::GetNBonds (  )
realtype mmdb::Atom::GetOccupancy (  )
PResidue mmdb::Atom::GetResidue (  )
int mmdb::Atom::GetResidueNo (  )
pstr mmdb::Atom::GetResName (  )
int mmdb::Atom::GetSeqNum (  )
int mmdb::Atom::GetSSEType (  )
void mmdb::Atom::GetStat ( realtype  v,
realtype &  v_min,
realtype &  v_max,
realtype &  v_m,
realtype &  v_m2 
) [protected]
int mmdb::Atom::GetUDData ( int  UDDhandle,
realtype &  rudd 
)
int mmdb::Atom::GetUDData ( int  UDDhandle,
pstr  sudd,
int  maxLen 
)
int mmdb::Atom::GetUDData ( int  UDDhandle,
int &  iudd 
)
int mmdb::Atom::GetUDData ( int  UDDhandle,
pstr &  sudd 
)
void mmdb::Atom::InitAtom (  ) [protected]
bool mmdb::Atom::isCTerminus (  )
bool mmdb::Atom::isInSelection ( int  selHnd )
bool mmdb::Atom::isMetal (  )
bool mmdb::Atom::isNTerminus (  )
bool mmdb::Atom::isSolvent (  )
bool mmdb::Atom::isTer (  ) [inline]
void mmdb::Atom::MakeCIF ( mmcif::PData  CIF )
bool mmdb::Atom::MakePDBAtomName (  )
void mmdb::Atom::MakeTer (  )
void mmdb::Atom::PDBASCIIDump ( io::RFile  f )
int mmdb::Atom::PutUDData ( int  UDDhandle,
cpstr  sudd 
)
int mmdb::Atom::PutUDData ( int  UDDhandle,
int  iudd 
)
int mmdb::Atom::PutUDData ( int  UDDhandle,
realtype  rudd 
)
void mmdb::Atom::read ( io::RFile  f )

Reimplemented from mmdb::UDData.

bool mmdb::Atom::RestoreElementName (  )
void mmdb::Atom::SetAtomIndex ( int  ix )
void mmdb::Atom::SetAtomName ( int  ix,
int  sN,
const AtomName  aName,
const AltLoc  aLoc,
const SegID  sID,
const Element  eName 
)
void mmdb::Atom::SetAtomName ( const AtomName  atomName )
void mmdb::Atom::SetCharge ( realtype  chrg )
void mmdb::Atom::SetCharge ( cpstr  chrg )
void mmdb::Atom::SetCoordinates ( realtype  xx,
realtype  yy,
realtype  zz,
realtype  occ,
realtype  tFac 
)
void mmdb::Atom::SetElementName ( const Element  elName )
void mmdb::Atom::SetResidue ( PResidue  res )
void mmdb::Atom::SetShortBinary (  )
void mmdb::Atom::StandardPDBOut ( cpstr  Record,
pstr  S 
) [protected]
void mmdb::Atom::Transform ( mat44 &  tm )
void mmdb::Atom::Transform ( mat33 &  tm,
vect3 &  v 
)
void mmdb::Atom::TransformCopy ( mat44 &  tm,
realtype &  xx,
realtype &  yy,
realtype &  zz 
)
void mmdb::Atom::TransformSet ( mat44 &  tm,
realtype  xx,
realtype  yy,
realtype  zz 
)
void mmdb::Atom::write ( io::RFile  f )

Reimplemented from mmdb::UDData.

Friends And Related Function Documentation

friend class CoorManager [friend]
friend class Model [friend]
friend class Residue [friend]
friend class Root [friend]
friend class SelManager [friend]

Reimplemented from mmdb::UDData.

Member Data Documentation

AltLoc mmdb::Atom::altLoc

alternative location indicator ("" for none)

PAtomBond mmdb::Atom::Bond [protected]
realtype mmdb::Atom::charge

charge on the atom

Element mmdb::Atom::element

element symbol (ALIGNED TO RIGHT)

EnergyType mmdb::Atom::energyType

energy type (without spaces)

bool mmdb::Atom::Het

anisotropic temperature factors

indicator of het atom

int mmdb::Atom::index [protected]
AtomName mmdb::Atom::label_atom_id

assigned atom name (not aligned)

AtomName mmdb::Atom::name

atom name (ALIGNED)

int mmdb::Atom::nBonds [protected]
realtype mmdb::Atom::occupancy

occupancy

PResidue mmdb::Atom::residue

reference to residue

SegID mmdb::Atom::segID

segment identifier

int mmdb::Atom::serNum

serial number

realtype mmdb::Atom::sigOcc

standard deviation of occupancy

realtype mmdb::Atom::sigTemp

standard deviation of temp.

factor

realtype mmdb::Atom::sigX
realtype mmdb::Atom::sigY
realtype mmdb::Atom::sigZ

standard deviations of the coords

realtype mmdb::Atom::su11

factors

realtype mmdb::Atom::su12
realtype mmdb::Atom::su13
realtype mmdb::Atom::su22
realtype mmdb::Atom::su23
realtype mmdb::Atom::su33

standard deviations of

realtype mmdb::Atom::tempFactor

temperature factor

bool mmdb::Atom::Ter

chain terminator

realtype mmdb::Atom::u11
realtype mmdb::Atom::u12
realtype mmdb::Atom::u13
realtype mmdb::Atom::u22
realtype mmdb::Atom::u23
realtype mmdb::Atom::u33

anisotropic temperature

word mmdb::Atom::WhatIsSet

mask field

realtype mmdb::Atom::x
realtype mmdb::Atom::y
realtype mmdb::Atom::z

orthogonal coordinates in angstroms

The documentation for this class was generated from the following files:
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Generated on Tue Nov 19 2013 12:37:24 for MMDB Coordinate Library by  doxygen 1.7.2