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#include "PDBReader.hpp" |
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|
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PDBReader::PDBReader(void) { |
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} |
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|
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PDBReader::~PDBReader(void) { |
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gzclose(PDBfile); |
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} |
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|
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|
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void PDBReader::setPDBfile(const char *fname) { |
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PDBfile = gzopen(fname, "r"); |
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if (PDBfile == Z_NULL) { |
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printf("Could not open PDB file %s\n", fname); |
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exit(-1); |
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} |
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} |
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|
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vector<VDWAtom*> PDBReader::getAtomList() { |
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|
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char numstr[9]; |
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char resIDstr[6]; |
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char buf[150]; |
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double pos[3]; |
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char aType[5]; |
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char aBase[2]; |
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char resName[3]; |
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int id, resID, ta; |
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VDWAtom* atom; |
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|
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ta = getTotAtoms(); |
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theAtoms.reserve(ta); |
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|
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gzrewind(PDBfile); |
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|
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while (!gzeof(PDBfile)) { |
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gzgets(PDBfile, buf, 150); |
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if (!strcmp(buf, "END") || |
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!strncmp(buf, "END ", 4) || |
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!strncmp(buf, "TER ", 4) || |
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!strncmp(buf, "ENDMDL", 6)) break; |
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if (!strncmp(buf, "ATOM ", 6) || !strncmp(buf, "HETATM", 6)) { |
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|
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atom = new VDWAtom(); |
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|
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memset(numstr, 0, 9 * sizeof(char)); |
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strncpy(numstr, buf + 30, 8); |
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pos[0] = atof(numstr); |
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|
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memset(numstr, 0, 9 * sizeof(char)); |
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strncpy(numstr, buf + 38, 8); |
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pos[1] = atof(numstr); |
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|
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memset(numstr, 0, 9 * sizeof(char)); |
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strncpy(numstr, buf + 46, 8); |
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pos[2] = atof(numstr); |
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|
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atom->setPos(pos); |
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|
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memset(aType, 0, 5 * sizeof(char)); |
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strncpy(aType, buf + 12, 4); |
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memset(aBase, 0, 2 * sizeof(char)); |
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strncpy(aBase, buf + 13, 1); |
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|
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atom->setType(TrimSpaces(aType)); |
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atom->setBase(TrimSpaces(aBase)); |
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|
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memset(resName, 0, 3 * sizeof(char)); |
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strncpy(resName, buf + 17, 2); |
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atom->setResName(resName); |
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|
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memset(resIDstr, 0, 6 * sizeof(char)); |
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strncpy(resIDstr, buf + 22, 4); |
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resID = atoi(resIDstr); |
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atom->setResID(resID); |
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|
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theAtoms.push_back(atom); |
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|
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} |
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} // while |
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return theAtoms; |
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} |
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|
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unsigned int PDBReader::getTotAtoms(void) { |
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char buf[150]; |
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unsigned int ta = 0; |
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gzrewind(PDBfile); |
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while (!gzeof(PDBfile)) { |
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gzgets(PDBfile,buf,150); |
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if (!strcmp(buf, "END") || |
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!strncmp(buf, "END ", 4) || |
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!strncmp(buf, "TER ", 4) || |
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!strncmp(buf, "ENDMDL", 6)) break; |
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if (!strncmp(buf, "ATOM ", 6) || !strncmp(buf, "HETATM", 6)) |
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ta++; |
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} |
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return ta; |
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} |
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|
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/** |
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* Removes left and right spaces from a string |
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* |
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* @param str String to trim |
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* |
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* @return char* to the trimed string |
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*/ |
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char * PDBReader::TrimSpaces(char *str) { |
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size_t len; |
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char *right, *left; |
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|
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/* Trim whitespace from left side */ |
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for (left = str; isspace(*left); left++); |
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|
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/* Trim whitespace from right side */ |
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if ((len = strlen(left))) |
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{ |
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right = left + (len - 1); |
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|
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while (isspace(*right)) |
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{ |
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*right = '\0'; |
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right--; |
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} |
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} |
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|
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/* Only do the str copy if their was spaces to the left */ |
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if (left != str) |
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strcpy(str, left); |
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|
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return (str); |
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} |
