PDBData Class Reference

#include <PDBData.h>

Inheritance diagram for PDBData:

Public Types
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
	PDBData (PDBType newtype)
virtual	~PDBData (void)
PDBType	type (void)
virtual void	sprint (char *s, PDBFormatStyle usestyle=COLUMNS)

Static Public Attributes
static const char *	PDBNames [UNKNOWN+1]

Static Protected Member Functions
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

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 33 of file PDBData.h.

Member Enumeration Documentation

enum PDBData::PDBFormatStyle

Enumerator
COLUMNS
FIELDS

Definition at line 48 of file PDBData.h.

{ COLUMNS, FIELDS };  // used to specify if the

enum PDBData::PDBType

Enumerator
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

Definition at line 42 of file PDBData.h.

                {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};

Constructor & Destructor Documentation

PDBData::PDBData ( PDBType  newtype )

inline

Definition at line 90 of file PDBData.h.

                              {
       mytype = newtype;
     }

virtual PDBData::~PDBData ( void  )

inlinevirtual

Definition at line 93 of file PDBData.h.

                             {
     }

Member Function Documentation

void PDBData::field ( const char *  data, int  fld, char *  result  )

staticprotected

Definition at line 133 of file PDBData.C.

References FALSE, and TRUE.

Referenced by PDBAtom::parse().

{
  int i;

  Bool onword = FALSE;
  if (fld<=0)  {     // ask a stupid question, get a stupid answer
    result[0]='#';
    result[1]=0;
    return;
  }
  for (i=0; data[i]; i++)
    if (!onword && data[i] != ' ' && data[i] != '\t')  {  // if I found a field
       onword = TRUE;     // mark that I'm on it
       if (--fld <= 0)    // am I done?
         break;
    } else {
      if (onword && (data[i] == ' ' || data[i] == '\t')) { // left a field
        onword = FALSE;   // mark that I left
      }
    }
  if (fld>0) {  // oh no, didn't find the field!
     result[0] = '#';
     result[1] = 0;
     return;
  }
  
  int cpy=0;  // copy the field to the output
  while (data[i] != ' ' && data[i] != '\t' && data[i])
     result[cpy++] = data[i++];
  result[cpy] = 0;  // terminate and I'm done
}

void PDBData::scan ( const char *  data, int  len, int  start, int  size, int *  ans, int  defalt  )

staticprotected

Definition at line 53 of file PDBData.C.

{
  char tempbuffer[200];       // temp. string buffer
  if (length < start) {       // check if the string is long enough
    *ans = defalt;                   // return the default
    return;
  }
  if (size>199)                      // make sure I won't overflow my array
    size=199;
  strncpy(tempbuffer, data + start-1, size);  // convert the string to an int
  tempbuffer[size]= 0;
  int flg=0;
  for (int i=strlen(tempbuffer)-1; i>=0; i--) { // see if this is a blank string
    if (tempbuffer[i]>' ') {
       flg = 1;
       break;
    }
  }
  if (flg != 1) {  // then it was a blank string
    *ans = defalt;
  } else {
  *ans = atoi(tempbuffer);
  }
}

void PDBData::scan ( const char *  data, int  len, int  start, int  size, BigReal *  ans, BigReal  defalt  )

staticprotected

Definition at line 97 of file PDBData.C.

{
  char tempbuffer[200];
  if (length < start) {               // check if the string is long enough
   *ans = defalt;                     // return the default
   return;
  }
  if (size>199)                       // make sure I won't overflow my array
    size=199;
  strncpy(tempbuffer, data + start - 1, size);// convert the string to a BigReal
  tempbuffer[size]= 0;
  int flg=0;
  for (int i=strlen(tempbuffer)-1; i>=0; i--) { // see if this is a blank string
    if (tempbuffer[i]>' ') {
       flg = 1;
       break;
    }
  }
  if (flg != 1) {  // then it was a blank string
    *ans = defalt;
  } else {
    *ans = atof(tempbuffer);  // WARNING : ASSUMES BigReal <= double!!!
  }
}

void PDBData::scan ( const char *  data, int  len, int  start, int  size, char *  ans  )

staticprotected

Definition at line 81 of file PDBData.C.

{
  if (length < start) {             // check if the string is long enough
   ans[0] = 0;
   return;
  }
  strncpy(ans, data + start - 1, size);
  ans[size]=0;
                      //  fix up leading and trailing spaces
  int i,j;
  for (i=0,j=0; ans[i]; i++)  //   all this does is strip out _all_ the
    if (ans[i]!=' ' && ans[i]!='\t')   //   spaces -- this is important because I
      ans[j++]=ans[i];  // check that a string is empty by looking to see if 
  ans[j]=0;   // [0] == 0 instead of checking to see if all the elements are spaces
}

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

inlinevirtual

Reimplemented in PDBAtom, and PDBUnknown.

Definition at line 99 of file PDBData.h.

References COLUMNS.

                                                                      {
       if (usestyle == COLUMNS)     // get rid of warning
         strcpy(s, "REMARK     (undefined remark - this is a bug)");
        else
         strcpy(s, "REMARK     (undefined remark - this is a bug)");
     }

void PDBData::sprintcol ( char *  s, int  start, int  len, const char *  val  )

staticprotected

Definition at line 183 of file PDBData.C.

Referenced by sprintcol().

{
 s+=start-1;
 while (len-- >0 && *val)  // copy string up to end of string or len
  *s++ = *val++;
}

void PDBData::sprintcol ( char *  s, int  start, int  len, int  val  )

staticprotected

*** provide a simple way to print to a specific column

Definition at line 169 of file PDBData.C.

References sprintcol().

{
 char temps[100];
 sprintf(temps, "%*d", len, val);  // convert the int to a string
 sprintcol( s, start, len, temps); // copy to the output string
}

void PDBData::sprintcol ( char *  s, int  start, int  len, int  prec, BigReal  val  )

staticprotected

Definition at line 176 of file PDBData.C.

References sprintcol().

{
 char temps[100];
 sprintf(temps, "%*.*f", len, prec, val);
 sprintcol( s, start, len, temps); // copy to the output string
}

PDBType PDBData::type ( void  )

inline

Definition at line 95 of file PDBData.h.

                         {
       return mytype;
     }

Member Data Documentation

const char * PDBData::PDBNames

static

Initial value:

= {
       "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"}

Definition at line 52 of file PDBData.h.

Referenced by new_PDBData().

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

• PDBData.h
• PDBData.C