PDBAtom Class Reference

#include <PDBData.h>

Inheritance diagram for PDBAtom:

List of all members.


Public Types
enum	Start { STYPE = 1, SSERIAL = 7, SNAME = 13, SALT = 17, SRESNAME = 18, SCHAIN = 22, SRESSEQ = 23, SINSERT = 27, SX = 31, SY = 39, SZ = 47, SOCC = 55, STEMPF = 61, SFOOT = 68, SSEGNAME = 73, SELEMENT = 77 }
enum	Length { LTYPE = 6, LSERIAL = 5, LNAME = 4, LALT = 1, LRESNAME = 4, LCHAIN = 1, LRESSEQ = 4, LINSERT = 1, LCOOR = 8, LCOORPREC = 3, LOCC = 6, LOCCPREC = 2, LTEMPF = 6, LTEMPFPREC = 2, LFOOT = 3, LSEGNAME = 4, LELEMENT = 2 }
Public Member Functions
virtual	~PDBAtom (void)
void	parse (const char *s)
void	sprint (char *s, PDBFormatStyle usestyle=COLUMNS)
int	serialnumber (void)
void	serialnumber (int newserialnumber)
const char *	name (void)
void	name (const char *newname)
const char *	alternatelocation (void)
void	alternatelocation (const char *newalternatelocation)
const char *	residuename (void)
void	residuename (const char *newresiduename)
const char *	chain (void)
void	chain (const char *newchain)
int	residueseq (void)
void	residueseq (int newresidueseq)
const char *	insertioncode (void)
void	insertioncode (const char *newinsertioncode)
BigReal	xcoor (void)
void	xcoor (BigReal newxcoor)
BigReal	ycoor (void)
void	ycoor (BigReal newycoor)
BigReal	zcoor (void)
void	zcoor (BigReal newzcoor)
const BigReal *	coordinates (void)
void	coordinates (const BigReal *newcoordinates)
BigReal	occupancy (void)
void	occupancy (BigReal newoccupancy)
BigReal	temperaturefactor (void)
void	temperaturefactor (BigReal newtemperaturefactor)
int	footnote (void)
void	footnote (int newfootnote)
const char *	segmentname (void)
void	segmentname (const char *newsegmentname)
const char *	element (void)
void	element (const char *newelement)
Static Public Attributes
const int	default_serial = -1
const int	default_residueseq = -1
const BigReal	default_coor = 9999.000
const BigReal	default_occupancy = 1.00
const BigReal	default_temperaturefactor = 0.00
const int	no_footnote = 0
Protected Types
enum	PDBPossibleAtoms { USE_ATOM = ATOM, USE_HETATM = HETATM }
Protected Member Functions
	PDBAtom (const char *data, PDBPossibleAtoms whichatom)
	PDBAtom (void)

Member Enumeration Documentation

enum PDBAtom::Length

Enumeration values:

LTYPE

LSERIAL

LNAME

LALT

LRESNAME

LCHAIN

LRESSEQ

LINSERT

LCOOR

LCOORPREC

LOCC

LOCCPREC

LTEMPF

LTEMPFPREC

LFOOT

LSEGNAME

LELEMENT

Definition at line 147 of file PDBData.h.
00147 {LTYPE=6, LSERIAL=5, LNAME=4, LALT=1, LRESNAME=4, LCHAIN=1, 00148 LRESSEQ=4, LINSERT=1, LCOOR=8, 00149 LCOORPREC=3, LOCC=6, LOCCPREC=2, LTEMPF=6, 00150 LTEMPFPREC=2, LFOOT=3, LSEGNAME=4, LELEMENT=2};

enum PDBAtom::PDBPossibleAtoms [protected]

Enumeration values:

USE_ATOM

USE_HETATM

Definition at line 181 of file PDBData.h.
00181 {USE_ATOM = ATOM, USE_HETATM = HETATM};

enum PDBAtom::Start

Enumeration values:

STYPE

SSERIAL

SNAME

SALT

SRESNAME

SCHAIN

SRESSEQ

SINSERT

SX

SY

SZ

SOCC

STEMPF

SFOOT

SSEGNAME

SELEMENT

Definition at line 138 of file PDBData.h.
00138 {STYPE=1,SSERIAL=7, SNAME=13, SALT=17, SRESNAME=18, SCHAIN=22, 00139 SRESSEQ=23, SINSERT=27, SX=31, SY=39, SZ=47, 00140 SOCC=55, STEMPF=61, SFOOT=68, SSEGNAME=73, SELEMENT=77};

Constructor & Destructor Documentation

PDBAtom::PDBAtom ( const char * data,

PDBPossibleAtoms whichatom

) [protected]

Definition at line 203 of file PDBData.C.
References parse().
00204 : PDBData( atomclass==USE_HETATM ? PDBData::HETATM : PDBData::ATOM) 00205 { 00206 parse(data); 00207 };

PDBAtom::PDBAtom ( void ) [protected]

Definition at line 210 of file PDBData.C.
References alternatelocation(), chain(), default_coor, default_occupancy, default_residueseq, default_serial, default_temperaturefactor, element(), footnote(), insertioncode(), name(), no_footnote, occupancy(), residuename(), residueseq(), segmentname(), serialnumber(), temperaturefactor(), xcoor(), ycoor(), and zcoor().
00210 : PDBData( PDBData:: ATOM) 00211 { 00212 serialnumber(default_serial); 00213 name(""); 00214 alternatelocation(""); 00215 residuename(""); 00216 chain(""); 00217 residueseq(default_residueseq); 00218 insertioncode(""); 00219 xcoor(default_coor); 00220 ycoor(default_coor); 00221 zcoor(default_coor); 00222 occupancy(default_occupancy); 00223 temperaturefactor(default_temperaturefactor); 00224 footnote(no_footnote); 00225 segmentname(""); 00226 element(""); 00227 }

PDBAtom::~PDBAtom ( void ) [virtual]

Definition at line 230 of file PDBData.C.
00230 { 00231 }

Member Function Documentation

void PDBAtom::alternatelocation ( const char * newalternatelocation )

Definition at line 394 of file PDBData.C.
References LALT.
00395 { strncpy(myalternatelocation, newalternatelocation, LALT); 00396 myalternatelocation[LALT]=0;}

const char * PDBAtom::alternatelocation ( void )

Definition at line 392 of file PDBData.C.
Referenced by PDBAtom().
00393 { return myalternatelocation; }

void PDBAtom::chain ( const char * newchain )

Definition at line 407 of file PDBData.C.
References LCHAIN.
00408 { strncpy(mychain, newchain, LCHAIN); mychain[LCHAIN]=0;}

const char * PDBAtom::chain ( void )

Definition at line 405 of file PDBData.C.
Referenced by PDBAtom().
00406 { return mychain; }

void PDBAtom::coordinates ( const BigReal * newcoordinates )

Definition at line 440 of file PDBData.C.
00441 { for (int i=0; i<3; i++) mycoor[i] = newcoordinates[i]; }

const BigReal * PDBAtom::coordinates ( void )

Definition at line 438 of file PDBData.C.
References BigReal.
Referenced by PDB::PDB().
00439 { return mycoor; }

void PDBAtom::element ( const char * newelement )

Definition at line 472 of file PDBData.C.
References LELEMENT.
00473 { strncpy(myelement, newelement, LELEMENT); myelement[LELEMENT]=0;}

const char * PDBAtom::element ( void )

Definition at line 470 of file PDBData.C.
Referenced by PDBAtom().
00471 { return myelement; }

void PDBAtom::footnote ( int newfootnote )

Definition at line 458 of file PDBData.C.
00459 { myfootnote = newfootnote; }

int PDBAtom::footnote ( void )

Definition at line 456 of file PDBData.C.
Referenced by PDBAtom().
00457 { return myfootnote; }

void PDBAtom::insertioncode ( const char * newinsertioncode )

Definition at line 419 of file PDBData.C.
References LINSERT.
00420 { strncpy(myinsertioncode, newinsertioncode, LINSERT); 00421 myinsertioncode[LINSERT]=0;}

const char * PDBAtom::insertioncode ( void )

Definition at line 417 of file PDBData.C.
Referenced by PDBAtom().
00418 { return myinsertioncode; }

void PDBAtom::name ( const char * newname )

Definition at line 388 of file PDBData.C.
References LNAME.
00389 { strncpy(myname, newname, LNAME); myname[LNAME]=0; }

const char * PDBAtom::name ( void )

Definition at line 386 of file PDBData.C.
Referenced by PDB::PDB(), and PDBAtom().
00387 { return myname; }

void PDBAtom::occupancy ( BigReal newoccupancy )

Definition at line 446 of file PDBData.C.
00447 { myoccupancy = newoccupancy; }

BigReal PDBAtom::occupancy ( void )

Definition at line 444 of file PDBData.C.
References BigReal.
Referenced by Molecule::build_constant_forces(), PDB::PDB(), and PDBAtom().
00445 { return myoccupancy ;}

void PDBAtom::parse ( const char * s )

Definition at line 193 of file PDBData.C.
References PDBData::field().
Referenced by PDBAtom().
00194 { 00195 char tempstr[100]; 00196 field(data, 1, tempstr); // get info about field #1 (the first one) 00197 if (tempstr[0] == '#') { 00198 parse_field_data(data); 00199 } else { 00200 parse_column_data(data); 00201 } 00202 }

void PDBAtom::residuename ( const char * newresiduename )

Definition at line 401 of file PDBData.C.
References LRESNAME.
00402 { strncpy(myresiduename, newresiduename, LRESNAME); myresiduename[LRESNAME]=0;}

const char * PDBAtom::residuename ( void )

Definition at line 399 of file PDBData.C.
Referenced by PDB::PDB(), and PDBAtom().
00400 { return myresiduename; }

void PDBAtom::residueseq ( int newresidueseq )

Definition at line 413 of file PDBData.C.
00414 { myresidueseq = newresidueseq; }

int PDBAtom::residueseq ( void )

Definition at line 411 of file PDBData.C.
Referenced by PDB::PDB(), and PDBAtom().
00412 { return myresidueseq; }

void PDBAtom::segmentname ( const char * newsegmentname )

Definition at line 466 of file PDBData.C.
References LSEGNAME.
00467 { strncpy(mysegmentname, newsegmentname, LSEGNAME); mysegmentname[LSEGNAME]=0;}

const char * PDBAtom::segmentname ( void )

Definition at line 464 of file PDBData.C.
Referenced by PDBAtom().
00465 { return mysegmentname; }

void PDBAtom::serialnumber ( int newserialnumber )

Definition at line 382 of file PDBData.C.
00383 { myserialnumber = newserialnumber; }

int PDBAtom::serialnumber ( void )

Definition at line 380 of file PDBData.C.
Referenced by PDB::PDB(), and PDBAtom().
00381 { return myserialnumber; }

void PDBAtom::sprint ( char * s,

PDBFormatStyle usestyle = COLUMNS

) [virtual]

Reimplemented from PDBData.
Definition at line 615 of file PDBData.C.
Referenced by PDB::write().
00616 { 00617 if (usestyle == PDBData::COLUMNS) 00618 sprint_columns( outstr); 00619 else 00620 sprint_fields( outstr); 00621 }

void PDBAtom::temperaturefactor ( BigReal newtemperaturefactor )

Definition at line 452 of file PDBData.C.
00453 { mytemperaturefactor = newtemperaturefactor; }

BigReal PDBAtom::temperaturefactor ( void )

Definition at line 450 of file PDBData.C.
References BigReal.
Referenced by PDB::PDB(), and PDBAtom().
00451 { return mytemperaturefactor; }

void PDBAtom::xcoor ( BigReal newxcoor )

Definition at line 427 of file PDBData.C.
00428 { mycoor[0] = newxcoor; }

BigReal PDBAtom::xcoor ( void )

Definition at line 425 of file PDBData.C.
References BigReal.
Referenced by Molecule::build_constant_forces(), PDB::find_extremes(), and PDBAtom().
00426 { return mycoor[0]; }

void PDBAtom::ycoor ( BigReal newycoor )

Definition at line 431 of file PDBData.C.
00432 { mycoor[1] = newycoor; }

BigReal PDBAtom::ycoor ( void )

Definition at line 429 of file PDBData.C.
References BigReal.
Referenced by Molecule::build_constant_forces(), PDB::find_extremes(), and PDBAtom().
00430 { return mycoor[1]; }

void PDBAtom::zcoor ( BigReal newzcoor )

Definition at line 435 of file PDBData.C.
00436 { mycoor[2] = newzcoor; }

BigReal PDBAtom::zcoor ( void )

Definition at line 433 of file PDBData.C.
References BigReal.
Referenced by Molecule::build_constant_forces(), PDB::find_extremes(), and PDBAtom().
00434 { return mycoor[2]; }

Member Data Documentation

const BigReal PDBAtom::default_coor = 9999.000 [static]

Definition at line 28 of file PDBData.C.
Referenced by PDBAtom().

const BigReal PDBAtom::default_occupancy = 1.00 [static]

Definition at line 29 of file PDBData.C.
Referenced by PDBAtom().

const int PDBAtom::default_residueseq = -1 [static]

Definition at line 27 of file PDBData.C.
Referenced by PDBAtom().

const int PDBAtom::default_serial = -1 [static]

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.
Definition at line 26 of file PDBData.C.
Referenced by PDBAtom().

const BigReal PDBAtom::default_temperaturefactor = 0.00 [static]

Definition at line 30 of file PDBData.C.
Referenced by PDBAtom().

const int PDBAtom::no_footnote = 0 [static]

Definition at line 31 of file PDBData.C.
Referenced by PDBAtom().

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

Generated on Thu Jul 24 04:07:45 2008 for NAMD by

1.3.9.1

PDBAtom Class Reference

Public Types

Public Member Functions

Static Public Attributes

Protected Types

Protected Member Functions

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation