trunk/SHAPES/PDBReader.cpp

#include "PDBReader.hpp"

PDBReader::PDBReader(void) {
}

PDBReader::~PDBReader(void) {
  fclose(PDBfile);
}


void PDBReader::setPDBfileName(const char *fname) {
  PDBfile = fopen(fname, "r");
  if (PDBfile == NULL) { 
    printf("Could not open PDB file %s\n", fname);
    exit(-1);
  } else 
    setPDBfile(PDBfile);
}

void PDBReader::setPDBfile(FILE* myFile) {
  PDBfile = myFile;
}

vector<VDWAtom*> PDBReader::getAtomList() {

  char numstr[9];
  char resIDstr[6];
  char buf[150];
  double pos[3];
  char aType[5];
  char aBase[2];
  char resName[3];
  int id, resID, ta;
  VDWAtom* atom;

  ta = getTotAtoms();
  theAtoms.reserve(ta);

  rewind(PDBfile);

  while (!feof(PDBfile)) {
    fgets( buf, 150, PDBfile);
    if (!strcmp(buf, "END") || 
        !strncmp(buf, "END ", 4) || 
        !strncmp(buf, "TER ", 4) || 
        !strncmp(buf, "ENDMDL", 6)) break;
    if (!strncmp(buf, "ATOM  ", 6) || !strncmp(buf, "HETATM", 6)) {
      
      atom = new VDWAtom();

      memset(numstr, 0, 9 * sizeof(char));
      strncpy(numstr, buf + 30, 8);
      pos[0] = atof(numstr);

      memset(numstr, 0, 9 * sizeof(char));
      strncpy(numstr, buf + 38, 8);
      pos[1] = atof(numstr);

      memset(numstr, 0, 9 * sizeof(char));
      strncpy(numstr, buf + 46, 8);
      pos[2] = atof(numstr);

      atom->setPos(pos);

      memset(aType, 0, 5 * sizeof(char));
      strncpy(aType, buf + 12, 4);
      memset(aBase, 0, 2 * sizeof(char));
      strncpy(aBase, buf + 13, 1);

      atom->setType(TrimSpaces(aType));
      atom->setBase(TrimSpaces(aBase));
      
      memset(resName, 0, 3 * sizeof(char));
      strncpy(resName, buf + 17, 2);
      atom->setResName(resName);

      memset(resIDstr, 0, 6 * sizeof(char));
      strncpy(resIDstr, buf + 22, 4);
      resID = atoi(resIDstr);
      atom->setResID(resID);
      
      theAtoms.push_back(atom);

    }
  } // while
  return theAtoms;
}

unsigned int PDBReader::getTotAtoms(void) {
  char buf[150];
  unsigned int ta = 0;
  rewind(PDBfile);
  while (!feof(PDBfile)) {
    fgets(buf,150,PDBfile);
    if (!strcmp(buf, "END") ||
        !strncmp(buf, "END ", 4) ||
        !strncmp(buf, "TER ", 4) ||
        !strncmp(buf, "ENDMDL", 6)) break;
    if (!strncmp(buf, "ATOM  ", 6) || !strncmp(buf, "HETATM", 6))
      ta++;
  }
  return ta;
}

/**
 * Removes left and right spaces from a string
 *
 * @param str  String to trim
 *
 * @return  char* to the trimed string
 */
char * PDBReader::TrimSpaces(char *str) {
  size_t len;
  char *right, *left;
  
  /* Trim whitespace from left side */
  for (left = str; isspace(*left); left++);
  
  /* Trim whitespace from right side */
  if ((len = strlen(left)))
    {
      right = left + (len - 1);
      
      while (isspace(*right))
        {
          *right = '\0';
          right--;
        }
    }
  
  /* Only do the str copy if their was spaces to the left */
  if (left != str)
    strcpy(str, left);
  
  return (str);
}
Revision:	1360
Committed:	Tue Jul 20 20:02:15 2004 UTC (21 years, 3 months ago) by gezelter
File size:	2927 byte(s)
Log Message:	Changes for CGI and for gengetopts --unamed-opt="PDBFILE"
#	User	Rev	Content
1	gezelter	1240	#include "PDBReader.hpp"
2
3			PDBReader::PDBReader(void) {
4			}
5
6			PDBReader::~PDBReader(void) {
7	gezelter	1360	fclose(PDBfile);
8	gezelter	1240	}
9
10
11	gezelter	1360	void PDBReader::setPDBfileName(const char *fname) {
12			PDBfile = fopen(fname, "r");
13			if (PDBfile == NULL) {
14	gezelter	1240	printf("Could not open PDB file %s\n", fname);
15			exit(-1);
16	gezelter	1360	} else
17			setPDBfile(PDBfile);
18	gezelter	1240	}
19
20	gezelter	1360	void PDBReader::setPDBfile(FILE* myFile) {
21			PDBfile = myFile;
22			}
23
24	gezelter	1240	vector<VDWAtom*> PDBReader::getAtomList() {
25
26			char numstr[9];
27			char resIDstr[6];
28			char buf[150];
29			double pos[3];
30			char aType[5];
31			char aBase[2];
32			char resName[3];
33			int id, resID, ta;
34			VDWAtom* atom;
35
36			ta = getTotAtoms();
37			theAtoms.reserve(ta);
38
39	gezelter	1360	rewind(PDBfile);
40	gezelter	1240
41	gezelter	1360	while (!feof(PDBfile)) {
42			fgets( buf, 150, PDBfile);
43	gezelter	1240	if (!strcmp(buf, "END") \|\|
44			!strncmp(buf, "END ", 4) \|\|
45			!strncmp(buf, "TER ", 4) \|\|
46			!strncmp(buf, "ENDMDL", 6)) break;
47			if (!strncmp(buf, "ATOM ", 6) \|\| !strncmp(buf, "HETATM", 6)) {
48
49			atom = new VDWAtom();
50
51			memset(numstr, 0, 9 * sizeof(char));
52			strncpy(numstr, buf + 30, 8);
53			pos[0] = atof(numstr);
54
55			memset(numstr, 0, 9 * sizeof(char));
56			strncpy(numstr, buf + 38, 8);
57			pos[1] = atof(numstr);
58
59			memset(numstr, 0, 9 * sizeof(char));
60			strncpy(numstr, buf + 46, 8);
61			pos[2] = atof(numstr);
62
63			atom->setPos(pos);
64
65			memset(aType, 0, 5 * sizeof(char));
66			strncpy(aType, buf + 12, 4);
67			memset(aBase, 0, 2 * sizeof(char));
68			strncpy(aBase, buf + 13, 1);
69
70			atom->setType(TrimSpaces(aType));
71			atom->setBase(TrimSpaces(aBase));
72
73			memset(resName, 0, 3 * sizeof(char));
74			strncpy(resName, buf + 17, 2);
75			atom->setResName(resName);
76
77			memset(resIDstr, 0, 6 * sizeof(char));
78			strncpy(resIDstr, buf + 22, 4);
79			resID = atoi(resIDstr);
80			atom->setResID(resID);
81
82			theAtoms.push_back(atom);
83
84			}
85			} // while
86			return theAtoms;
87			}
88
89			unsigned int PDBReader::getTotAtoms(void) {
90			char buf[150];
91			unsigned int ta = 0;
92	gezelter	1360	rewind(PDBfile);
93			while (!feof(PDBfile)) {
94			fgets(buf,150,PDBfile);
95	gezelter	1240	if (!strcmp(buf, "END") \|\|
96			!strncmp(buf, "END ", 4) \|\|
97			!strncmp(buf, "TER ", 4) \|\|
98			!strncmp(buf, "ENDMDL", 6)) break;
99			if (!strncmp(buf, "ATOM ", 6) \|\| !strncmp(buf, "HETATM", 6))
100			ta++;
101			}
102			return ta;
103			}
104
105			/**
106			* Removes left and right spaces from a string
107			*
108			* @param str String to trim
109			*
110			* @return char* to the trimed string
111			*/
112			char * PDBReader::TrimSpaces(char *str) {
113			size_t len;
114			char right, left;
115
116			/* Trim whitespace from left side */
117			for (left = str; isspace(*left); left++);
118
119			/* Trim whitespace from right side */
120			if ((len = strlen(left)))
121			{
122			right = left + (len - 1);
123
124			while (isspace(*right))
125			{
126			*right = '\0';
127			right--;
128			}
129			}
130
131			/* Only do the str copy if their was spaces to the left */
132			if (left != str)
133			strcpy(str, left);
134
135			return (str);
136			}