| 1 |
gezelter |
1182 |
#include "PDBReader.hpp" |
| 2 |
|
|
|
| 3 |
|
|
PDBReader::PDBReader(void) { |
| 4 |
|
|
} |
| 5 |
|
|
|
| 6 |
|
|
PDBReader::~PDBReader(void) { |
| 7 |
|
|
gzclose(PDBfile); |
| 8 |
|
|
} |
| 9 |
|
|
|
| 10 |
|
|
|
| 11 |
|
|
void PDBReader::setPDBfile(const char *fname) { |
| 12 |
|
|
PDBfile = gzopen(fname, "r"); |
| 13 |
|
|
if (PDBfile == Z_NULL) { |
| 14 |
|
|
printf("Could not open PDB file %s\n", fname); |
| 15 |
|
|
exit(-1); |
| 16 |
|
|
} |
| 17 |
|
|
} |
| 18 |
|
|
|
| 19 |
|
|
vector<VDWAtom*> PDBReader::getAtomList() { |
| 20 |
|
|
|
| 21 |
|
|
char numstr[9]; |
| 22 |
|
|
char resIDstr[6]; |
| 23 |
|
|
char buf[150]; |
| 24 |
|
|
double pos[3]; |
| 25 |
|
|
char aType[4]; |
| 26 |
|
|
char resName[3]; |
| 27 |
|
|
int id, resID, ta; |
| 28 |
|
|
VDWAtom* atom; |
| 29 |
|
|
|
| 30 |
|
|
ta = getTotAtoms(); |
| 31 |
|
|
theAtoms.reserve(ta); |
| 32 |
|
|
|
| 33 |
|
|
gzrewind(PDBfile); |
| 34 |
|
|
|
| 35 |
|
|
while (!gzeof(PDBfile)) { |
| 36 |
|
|
gzgets(PDBfile, buf, 150); |
| 37 |
|
|
if (!strcmp(buf, "END") || |
| 38 |
|
|
!strncmp(buf, "END ", 4) || |
| 39 |
|
|
!strncmp(buf, "TER ", 4) || |
| 40 |
|
|
!strncmp(buf, "ENDMDL", 6)) break; |
| 41 |
|
|
if (!strncmp(buf, "ATOM ", 6) || !strncmp(buf, "HETATM", 6)) { |
| 42 |
|
|
|
| 43 |
|
|
atom = new VDWAtom(); |
| 44 |
|
|
|
| 45 |
|
|
memset(numstr, 0, 9 * sizeof(char)); |
| 46 |
|
|
strncpy(numstr, buf + 30, 8); |
| 47 |
|
|
pos[0] = atof(numstr); |
| 48 |
|
|
|
| 49 |
|
|
memset(numstr, 0, 9 * sizeof(char)); |
| 50 |
|
|
strncpy(numstr, buf + 38, 8); |
| 51 |
|
|
pos[1] = atof(numstr); |
| 52 |
|
|
|
| 53 |
|
|
memset(numstr, 0, 9 * sizeof(char)); |
| 54 |
|
|
strncpy(numstr, buf + 46, 8); |
| 55 |
|
|
pos[2] = atof(numstr); |
| 56 |
|
|
|
| 57 |
|
|
atom->setPos(pos); |
| 58 |
|
|
|
| 59 |
|
|
memset(aType, 0, 4 * sizeof(char)); |
| 60 |
|
|
strncpy(aType, buf + 12, 3); |
| 61 |
|
|
printf("string in aType = %s\n", aType); |
| 62 |
|
|
atom->setType(aType); |
| 63 |
|
|
|
| 64 |
|
|
memset(resName, 0, 3 * sizeof(char)); |
| 65 |
|
|
strncpy(resName, buf + 17, 2); |
| 66 |
|
|
atom->setResName(resName); |
| 67 |
|
|
|
| 68 |
|
|
memset(resIDstr, 0, 6 * sizeof(char)); |
| 69 |
|
|
strncpy(resIDstr, buf + 22, 4); |
| 70 |
|
|
resID = atoi(resIDstr); |
| 71 |
|
|
atom->setResID(resID); |
| 72 |
|
|
|
| 73 |
|
|
theAtoms.push_back(atom); |
| 74 |
|
|
|
| 75 |
|
|
printf("%s\t%lf\t%lf\t%lf\n", atom->getType(), pos[0], pos[1], pos[2]); |
| 76 |
|
|
|
| 77 |
|
|
} |
| 78 |
|
|
} // while |
| 79 |
|
|
return theAtoms; |
| 80 |
|
|
} |
| 81 |
|
|
|
| 82 |
|
|
unsigned int PDBReader::getTotAtoms(void) { |
| 83 |
|
|
char buf[150]; |
| 84 |
|
|
unsigned int ta = 0; |
| 85 |
|
|
gzrewind(PDBfile); |
| 86 |
|
|
while (!gzeof(PDBfile)) { |
| 87 |
|
|
gzgets(PDBfile,buf,150); |
| 88 |
|
|
if (!strcmp(buf, "END") || |
| 89 |
|
|
!strncmp(buf, "END ", 4) || |
| 90 |
|
|
!strncmp(buf, "TER ", 4) || |
| 91 |
|
|
!strncmp(buf, "ENDMDL", 6)) break; |
| 92 |
|
|
if (!strncmp(buf, "ATOM ", 6) || !strncmp(buf, "HETATM", 6)) |
| 93 |
|
|
ta++; |
| 94 |
|
|
} |
| 95 |
|
|
return ta; |
| 96 |
|
|
} |
