PDBAtom Class Reference

#include <PDBData.h>

Inheritance diagram for PDBAtom:

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 Types inherited from PDBData
enum	PDBType {   HEADER, OBSLTE, COMPND, SOURCE,   EXPDTA, AUTHOR, REVDAT, SPRSDE,   JRNL, REMARK, SEQRES, FTNOTE,   HET, FORMUL, HELIX, SHEET,   TURN, SSBOND, SITE, CRYST1,   ORIGX, SCALE, MTRIX, TVECT,   MODEL, ATOM, HETATM, SIGATM,   ANISOU, SIGUIJ, TER, ENDMDL,   CONECT, MASTER, END, UNKNOWN }
enum	PDBFormatStyle { COLUMNS, FIELDS }

Public Member Functions
	PDBAtom (void)
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)
Public Member Functions inherited from PDBData
	PDBData (PDBType newtype)
virtual	~PDBData (void)
PDBType	type (void)

Static Public Attributes
static const int	default_serial = -1
static const int	default_residueseq = -1
static const BigReal	default_coor = 9999.000
static const BigReal	default_occupancy = 1.00
static const BigReal	default_temperaturefactor = 0.00
static const int	no_footnote = 0
Static Public Attributes inherited from PDBData
static const char *	PDBNames [UNKNOWN+1]

Protected Types
enum	PDBPossibleAtoms { USE_ATOM = ATOM, USE_HETATM = HETATM }

Protected Member Functions
	PDBAtom (const char *data, PDBPossibleAtoms whichatom)

Additional Inherited Members
Static Protected Member Functions inherited from PDBData
static void	scan (const char *data, int len, int start, int size, int *ans, int defalt)
static void	scan (const char *data, int len, int start, int size, BigReal *ans, BigReal defalt)
static void	scan (const char *data, int len, int start, int size, char *ans)
static void	field (const char *data, int fld, char *result)
static void	sprintcol (char *s, int start, int len, const char *val)
static void	sprintcol (char *s, int start, int len, int val)
	*** provide a simple way to print to a specific column More...
static void	sprintcol (char *s, int start, int len, int prec, BigReal val)

Detailed Description

Definition at line 134 of file PDBData.h.

Member Enumeration Documentation

Length

enum PDBAtom::Length

Enumerator
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.

                {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};

PDBPossibleAtoms

enum PDBAtom::PDBPossibleAtoms

protected

Enumerator
USE_ATOM
USE_HETATM

Definition at line 181 of file PDBData.h.

{USE_ATOM = ATOM, USE_HETATM = HETATM};

Start

enum PDBAtom::Start

Enumerator
STYPE
SSERIAL
SNAME
SALT
SRESNAME
SCHAIN
SRESSEQ
SINSERT
SX
SY
SZ
SOCC
STEMPF
SFOOT
SSEGNAME
SELEMENT

Definition at line 138 of file PDBData.h.

               {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};

Constructor & Destructor Documentation

PDBAtom() [1/2]

PDBAtom::PDBAtom ( const char *  data, PDBPossibleAtoms  whichatom  )

protected

Definition at line 203 of file PDBData.C.

References parse().

        : PDBData( atomclass==USE_HETATM ? PDBData::HETATM : PDBData::ATOM)
{
 parse(data);
};

PDBAtom() [2/2]

PDBAtom::PDBAtom

(

void

)

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().

                      : PDBData( PDBData:: ATOM)
{
  serialnumber(default_serial);
  name("");
  alternatelocation("");
  residuename("");
  chain("");
  residueseq(default_residueseq);
  insertioncode("");
  xcoor(default_coor);
  ycoor(default_coor);
  zcoor(default_coor);
  occupancy(default_occupancy);
  temperaturefactor(default_temperaturefactor);
  footnote(no_footnote);
  segmentname("");
  element("");
}

~PDBAtom()

PDBAtom::~PDBAtom ( void  )

virtual

Definition at line 230 of file PDBData.C.

                       {
}

Member Function Documentation

alternatelocation() [1/2]

const char * PDBAtom::alternatelocation

(

void

)

Definition at line 392 of file PDBData.C.

Referenced by PDB::PDB(), and PDBAtom().

{ return myalternatelocation; }

alternatelocation() [2/2]

void PDBAtom::alternatelocation

(

const char *

newalternatelocation

)

Definition at line 394 of file PDBData.C.

References LALT.

{ strncpy(myalternatelocation, newalternatelocation, LALT);
  myalternatelocation[LALT]=0;}

chain() [1/2]

const char * PDBAtom::chain

(

void

)

Definition at line 405 of file PDBData.C.

Referenced by PDBAtom().

{ return mychain; }

chain() [2/2]

void PDBAtom::chain

(

const char *

newchain

)

Definition at line 407 of file PDBData.C.

References LCHAIN.

{ strncpy(mychain, newchain, LCHAIN); mychain[LCHAIN]=0;}

coordinates() [1/2]

const BigReal * PDBAtom::coordinates

(

void

)

Definition at line 438 of file PDBData.C.

Referenced by PDB::PDB().

{ return mycoor; }

coordinates() [2/2]

void PDBAtom::coordinates

(

const BigReal *

newcoordinates

)

Definition at line 440 of file PDBData.C.

{ for (int i=0; i<3; i++) mycoor[i] = newcoordinates[i]; }

element() [1/2]

const char * PDBAtom::element

(

void

)

Definition at line 470 of file PDBData.C.

Referenced by PDBAtom(), and Molecule::prepare_qm().

{ return myelement; }

element() [2/2]

void PDBAtom::element

(

const char *

newelement

)

Definition at line 472 of file PDBData.C.

References LELEMENT.

{ strncpy(myelement, newelement, LELEMENT); myelement[LELEMENT]=0;}

footnote() [1/2]

int PDBAtom::footnote

(

void

)

Definition at line 456 of file PDBData.C.

Referenced by PDBAtom().

{ return myfootnote; }

footnote() [2/2]

void PDBAtom::footnote

(

int

newfootnote

)

Definition at line 458 of file PDBData.C.

{ myfootnote = newfootnote; }

insertioncode() [1/2]

const char * PDBAtom::insertioncode

(

void

)

Definition at line 417 of file PDBData.C.

Referenced by PDBAtom().

{ return myinsertioncode; }

insertioncode() [2/2]

void PDBAtom::insertioncode

(

const char *

newinsertioncode

)

Definition at line 419 of file PDBData.C.

References LINSERT.

{ strncpy(myinsertioncode, newinsertioncode, LINSERT); 
  myinsertioncode[LINSERT]=0;}

name() [1/2]

const char * PDBAtom::name

(

void

)

Definition at line 386 of file PDBData.C.

Referenced by PDB::PDB(), and PDBAtom().

{ return myname; }

name() [2/2]

void PDBAtom::name

(

const char *

newname

)

Definition at line 388 of file PDBData.C.

References LNAME.

{ strncpy(myname, newname, LNAME); myname[LNAME]=0; }

occupancy() [1/2]

BigReal PDBAtom::occupancy

(

void

)

Definition at line 444 of file PDBData.C.

Referenced by PDB::PDB(), PDBAtom(), and Molecule::prepare_qm().

{ return myoccupancy ;}

occupancy() [2/2]

void PDBAtom::occupancy

(

BigReal

newoccupancy

)

Definition at line 446 of file PDBData.C.

{ myoccupancy = newoccupancy; }

parse()

void PDBAtom::parse

(

const char *

s

)

Definition at line 193 of file PDBData.C.

References PDBData::field().

Referenced by PDBAtom().

{
 char tempstr[100];
 field(data, 1, tempstr);  // get info about field #1 (the first one)
 if (tempstr[0] == '#')  {
   parse_field_data(data);
 } else {
   parse_column_data(data);
 } 
}

residuename() [1/2]

const char * PDBAtom::residuename

(

void

)

Definition at line 399 of file PDBData.C.

Referenced by PDB::PDB(), PDBAtom(), and Molecule::prepare_qm().

{ return myresiduename; }

residuename() [2/2]

void PDBAtom::residuename

(

const char *

newresiduename

)

Definition at line 401 of file PDBData.C.

References LRESNAME.

{ strncpy(myresiduename, newresiduename, LRESNAME); myresiduename[LRESNAME]=0;}

residueseq() [1/2]

int PDBAtom::residueseq

(

void

)

Definition at line 411 of file PDBData.C.

Referenced by Molecule::build_go_arrays(), PDB::PDB(), PDBAtom(), and Molecule::prepare_qm().

{ return myresidueseq; }

residueseq() [2/2]

void PDBAtom::residueseq

(

int

newresidueseq

)

Definition at line 413 of file PDBData.C.

{ myresidueseq = newresidueseq; }

segmentname() [1/2]

const char * PDBAtom::segmentname

(

void

)

Definition at line 464 of file PDBData.C.

Referenced by PDBAtom(), and Molecule::prepare_qm().

{ return mysegmentname; }

segmentname() [2/2]

void PDBAtom::segmentname

(

const char *

newsegmentname

)

Definition at line 466 of file PDBData.C.

References LSEGNAME.

{ strncpy(mysegmentname, newsegmentname, LSEGNAME); mysegmentname[LSEGNAME]=0;}

serialnumber() [1/2]

int PDBAtom::serialnumber

(

void

)

Definition at line 380 of file PDBData.C.

Referenced by PDB::PDB(), and PDBAtom().

{ return myserialnumber; }

serialnumber() [2/2]

void PDBAtom::serialnumber

(

int

newserialnumber

)

Definition at line 382 of file PDBData.C.

{ myserialnumber = newserialnumber; }

sprint()

void PDBAtom::sprint ( char *  s, PDBFormatStyle  usestyle = COLUMNS  )

virtual

Reimplemented from PDBData.

Definition at line 615 of file PDBData.C.

References PDBData::COLUMNS.

Referenced by PDB::write().

{
 if (usestyle == PDBData::COLUMNS)
   sprint_columns( outstr);
 else
   sprint_fields( outstr);
}

temperaturefactor() [1/2]

BigReal PDBAtom::temperaturefactor

(

void

)

Definition at line 450 of file PDBData.C.

Referenced by PDB::PDB(), PDBAtom(), and Molecule::prepare_qm().

{ return mytemperaturefactor; }

temperaturefactor() [2/2]

void PDBAtom::temperaturefactor

(

BigReal

newtemperaturefactor

)

Definition at line 452 of file PDBData.C.

{ mytemperaturefactor = newtemperaturefactor; }

xcoor() [1/2]

BigReal PDBAtom::xcoor

(

void

)

Definition at line 425 of file PDBData.C.

Referenced by Molecule::build_go_arrays(), PDB::find_extremes(), PDBAtom(), and PDB::set_all_positions().

{ return mycoor[0]; }

xcoor() [2/2]

void PDBAtom::xcoor

(

BigReal

newxcoor

)

Definition at line 427 of file PDBData.C.

{ mycoor[0] = newxcoor; }

ycoor() [1/2]

BigReal PDBAtom::ycoor

(

void

)

Definition at line 429 of file PDBData.C.

Referenced by Molecule::build_go_arrays(), PDB::find_extremes(), and PDBAtom().

{ return mycoor[1]; }

ycoor() [2/2]

void PDBAtom::ycoor

(

BigReal

newycoor

)

Definition at line 431 of file PDBData.C.

{ mycoor[1] = newycoor; }

zcoor() [1/2]

BigReal PDBAtom::zcoor

(

void

)

Definition at line 433 of file PDBData.C.

Referenced by Molecule::build_go_arrays(), PDB::find_extremes(), and PDBAtom().

{ return mycoor[2]; }

zcoor() [2/2]

void PDBAtom::zcoor

(

BigReal

newzcoor

)

Definition at line 435 of file PDBData.C.

{ mycoor[2] = newzcoor; }

Member Data Documentation

default_coor

const BigReal PDBAtom::default_coor = 9999.000

static

Definition at line 155 of file PDBData.h.

Referenced by PDBAtom().

default_occupancy

const BigReal PDBAtom::default_occupancy = 1.00

static

Definition at line 156 of file PDBData.h.

Referenced by PDB::PDB(), and PDBAtom().

default_residueseq

const int PDBAtom::default_residueseq = -1

static

Definition at line 154 of file PDBData.h.

Referenced by PDBAtom().

default_serial

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 153 of file PDBData.h.

Referenced by PDBAtom().

default_temperaturefactor

const BigReal PDBAtom::default_temperaturefactor = 0.00

static

Definition at line 157 of file PDBData.h.

Referenced by PDB::PDB(), and PDBAtom().

no_footnote

const int PDBAtom::no_footnote = 0

static

Definition at line 158 of file PDBData.h.

Referenced by PDBAtom().

---

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

• PDBData.h
• PDBData.C