/* pdbmodule.c - PDB parser/accelorator for mmLib * */ #include "Python.h" #include #define MAX_LINE 82 static PyObject *PDBModuleErr = NULL; typedef enum { PDB_FIELD_TYPE_STRING, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_TYPE_FLOAT_4, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_TYPE_FLOAT_6 } PDBFieldType; typedef enum { PDB_FIELD_RJUST, PDB_FIELD_LJUST } PDBFieldAlign; struct PDBFieldDef { char *name; int istart; int iend; PDBFieldType type; PDBFieldAlign align; }; static struct PDBFieldDef keywds_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"keywds", 11, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef seqres_fields[] = { {"serNum", 9, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"chainID", 12, 12, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"numRes", 14, 17, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"resName1", 20, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName2", 24, 26, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName3", 28, 30, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName4", 32, 34, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName5", 36, 38, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName6", 40, 42, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName7", 44, 46, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName8", 48, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName9", 52, 54, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName10", 56, 58, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName11", 60, 62, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName12", 64, 66, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName13", 68, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef link_fields[] = { {"name1", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"altLoc1", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName1", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID1", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq1", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode1", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"name2", 43, 46, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"altLoc2", 47, 47, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName2", 48, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID2", 52, 52, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq2", 53, 56, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode2", 57, 57, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym1", 60, 65, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym2", 67, 72, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef origx1_fields[] = { {"o[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"o[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"o[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"t[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, }; static struct PDBFieldDef endmdl_fields[] = { {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, }; static struct PDBFieldDef hetsyn_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"hetID", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"hetSynonyms", 16, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef sigatm_fields[] = { {"serial", 7, 11, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"name", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"altLoc", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sigX", 31, 38, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"sigY", 39, 46, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"sigZ", 47, 54, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"sigOccupancy",55, 60, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, {"sigTempFactor",61, 66, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, {"segID", 73, 76, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"element", 77, 78, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"charge", 79, 80, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef mtrix2_fields[] = { {"serial", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"s[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"v[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {"iGiven", 60, 60, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef mtrix3_fields[] = { {"serial", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"s[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"v[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {"iGiven", 60, 60, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef helix_fields[] = { {"serNum", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"helixID", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initResName", 16, 18, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initChainID", 20, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initSeqNum", 22, 25, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"initICode", 26, 26, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endResName", 28, 30, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endChainID", 32, 32, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endSeqNum", 34, 37, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"endICode", 38, 38, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"helixClass", 39, 40, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"comment", 41, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"length", 72, 76, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef mtrix1_fields[] = { {"serial", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"s[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"v[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {"iGiven", 60, 60, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef turn_fields[] = { {"seq", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"turnID", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initResName", 16, 18, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initChainID", 20, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initSeqNum", 21, 24, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"initICode", 25, 25, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endResName", 27, 29, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endChainID", 31, 31, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endSeqNum", 32, 35, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"endICode", 36, 36, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"comment", 41, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef anisou_fields[] = { {"serial", 7, 11, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"name", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"altLoc", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"u[0][0]", 29, 35, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"u[1][1]", 36, 42, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"u[2][2]", 43, 49, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"u[0][1]", 50, 56, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"u[0][2]", 57, 63, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"u[1][2]", 64, 70, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"segID", 73, 76, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"element", 77, 78, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"charge", 79, 80, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef title_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"title", 11, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef sltbrg_fields[] = { {"name1", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"altLoc1", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName1", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID1", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq1", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode1", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"name2", 43, 46, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"altLoc2", 47, 47, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName2", 48, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID2", 52, 52, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq2", 53, 56, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode2", 57, 57, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym1", 60, 65, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym2", 67, 72, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef remark_fields[] = { {"remarkNum", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"text", 12, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef end_fields[] = { {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef sheet_fields[] = { {"strand", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"sheetID", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"numStrands", 15, 16, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"initResName", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initChainID", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"initSeqNum", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"initICode", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endResName", 29, 31, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endChainID", 33, 33, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"endSeqNum", 34, 37, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"endICode", 38, 38, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sense", 39, 40, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"curAtom", 42, 45, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"curResName", 46, 48, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"curChainID", 50, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"curResSeq", 51, 54, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"curICode", 55, 55, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"prevAtom", 57, 60, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"prevResName", 61, 63, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"prevChainID", 65, 65, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"prevResSeq", 66, 69, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"prevICode", 70, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef scale2_fields[] = { {"s[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"u[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, }; static struct PDBFieldDef author_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"authorList", 11, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef cryst1_fields[] = { {"a", 7, 15, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"b", 16, 24, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"c", 25, 33, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"alpha", 34, 40, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"beta", 41, 47, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"gamma", 48, 54, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"sgroup", 56, 66, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"z", 67, 70, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef siguij_fields[] = { {"serial", 7, 11, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"name", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"altLoc", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sig[1][1]", 29, 35, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"sig[2][2]", 36, 42, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"sig[3][3]", 43, 49, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"sig[1][2]", 50, 56, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"sig[1][3]", 57, 63, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"sig[2][3]", 64, 70, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"segID", 73, 76, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"element", 77, 78, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"charge", 79, 80, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef cryst3_fields[] = { {"a", 7, 15, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"b", 16, 24, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"c", 25, 33, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"alpha", 34, 40, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"beta", 41, 47, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"gamma", 48, 54, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"sgroup", 56, 66, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"z", 67, 70, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef cryst2_fields[] = { {"a", 7, 15, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"b", 16, 24, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"c", 25, 33, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"alpha", 34, 40, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"beta", 41, 47, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"gamma", 48, 54, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"sgroup", 56, 66, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"z", 67, 70, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef cispep_fields[] = { {"serial", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"resName1", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID1", 16, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqNum1", 18, 21, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode1", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName2", 26, 28, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID2", 30, 30, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqNum2", 32, 35, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode2", 36, 36, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"modNum", 44, 46, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"measure", 54, 59, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, }; static struct PDBFieldDef atom_fields[] = { {"serial", 7, 11, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"name", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"altLoc", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"x", 31, 38, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"y", 39, 46, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"z", 47, 54, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"occupancy", 55, 60, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, {"tempFactor", 61, 66, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, {"segID", 73, 76, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"element", 77, 78, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"charge", 79, 80, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef origx3_fields[] = { {"o[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"o[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"o[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"t[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, }; static struct PDBFieldDef origx2_fields[] = { {"o[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"o[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"o[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"t[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, }; static struct PDBFieldDef modres_fields[] = { {"idCode", 8, 11, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName", 13, 15, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqNum", 19, 22, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 23, 23, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"stdRes", 25, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"comment", 30, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef source_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"srcName", 11, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef formul_fields[] = { {"compNum", 9, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"hetID", 13, 15, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"continuation",17, 18, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"asterisk", 19, 19, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"text", 20, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef master_fields[] = { {"numRemark", 11, 15, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"O", 16, 20, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numHet", 21, 25, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numHelix", 26, 30, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numSheet", 31, 35, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numTurn", 36, 40, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numSite", 41, 45, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numXForm", 46, 50, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numCoord", 51, 55, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numTer", 56, 60, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numConect", 61, 65, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"numSeq", 66, 70, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef caveat_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"idCode", 12, 15, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"comment", 20, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef het_fields[] = { {"hetID", 8, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 13, 13, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqNum", 14, 17, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 18, 18, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"numHetAtoms", 21, 25, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"text", 31, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef compnd_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"compound", 11, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef model_fields[] = { {"serial", 11, 14, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef revdat_fields[] = { {"modNum", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"continuation",11, 12, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"modDate", 14, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"modID", 24, 28, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"modType", 32, 32, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"record1", 40, 45, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"record2", 47, 52, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"record3", 54, 59, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"record4", 61, 66, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef ssbond_fields[] = { {"serNum", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"resName1", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID1", 16, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqNum1", 18, 21, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode1", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName2", 26, 28, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID2", 30, 30, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqNum2", 32, 35, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode2", 36, 36, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym1", 60, 65, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym2", 67, 72, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef obslte_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"repDate", 12, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"idCode", 22, 25, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode1", 32, 35, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode2", 37, 40, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode3", 42, 45, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode4", 47, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode5", 52, 55, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode6", 57, 60, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode7", 62, 65, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"rIdCode8", 67, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef conect_fields[] = { {"serial", 7, 11, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialBond1", 12, 16, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialBond2", 17, 21, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialBond3", 22, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialBond4", 27, 31, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialHydBond1",32, 36, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialHydBond2",37, 41, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialSaltBond1",42, 46, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialHydBond3",47, 51, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialHydBond4",52, 56, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"serialSaltBond2",57, 61, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, }; static struct PDBFieldDef jrnl_fields[] = { {"text", 13, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef hetnam_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"hetID", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"text", 16, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef sprsde_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sprsdeDate", 12, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"idCode", 22, 25, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode1", 32, 35, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode2", 37, 40, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode3", 42, 45, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode4", 47, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode5", 52, 55, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode6", 57, 60, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode7", 62, 65, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sIdCode8", 67, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef header_fields[] = { {"classification",11, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"depDate", 51, 59, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"idCode", 63, 66, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef site_fields[] = { {"seqNum", 8, 10, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"siteID", 12, 14, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"numRes", 16, 17, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"resName1", 19, 21, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID1", 23, 23, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seq1", 24, 27, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode1", 28, 28, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName2", 30, 32, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID2", 34, 34, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seq2", 35, 38, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode2", 39, 39, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName3", 41, 43, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID3", 45, 45, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seq3", 46, 49, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode3", 50, 50, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName4", 52, 54, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID4", 56, 56, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seq4", 57, 60, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode4", 61, 61, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef scale1_fields[] = { {"s[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"u[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, }; static struct PDBFieldDef hydbnd_fields[] = { {"name1", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"altLoc1", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName1", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID1", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq1", 23, 27, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode1", 28, 28, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"nameH", 30, 33, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"altLocH", 34, 34, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainH", 36, 36, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeqH", 37, 41, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCodeH", 42, 42, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"name2", 44, 47, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"altLoc2", 48, 48, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName2", 49, 51, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID2", 53, 53, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq2", 54, 58, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode2", 59, 59, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym1", 60, 65, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"sym2", 67, 72, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef ter_fields[] = { {"serial", 7, 11, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"resName", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef dbref_fields[] = { {"idCode", 8, 11, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chain_ID", 13, 13, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqBegin", 15, 18, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"insertBegin", 19, 19, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqEnd", 21, 24, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"insertEnd", 25, 25, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"database", 27, 32, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"dbAccession", 34, 41, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"dbIdCode", 43, 54, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"dbseqBegin", 56, 60, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"idbnsBeg", 61, 61, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"dbseqEnd", 63, 67, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"dbinsEnd", 68, 68, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef expdta_fields[] = { {"continuation", 9, 10, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"technique", 11, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBFieldDef scale3_fields[] = { {"s[n][1]", 11, 20, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][2]", 21, 30, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"s[n][3]", 31, 40, PDB_FIELD_TYPE_FLOAT_6, PDB_FIELD_LJUST}, {"u[n]", 46, 55, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_FLOAT_5, PDB_FIELD_LJUST}, }; static struct PDBFieldDef hetatm_fields[] = { {"serial", 7, 11, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"name", 13, 16, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"altLoc", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName", 18, 20, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 22, 22, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resSeq", 23, 26, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 27, 27, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"x", 31, 38, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"y", 39, 46, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"z", 47, 54, PDB_FIELD_TYPE_FLOAT_3, PDB_FIELD_LJUST}, {"occupancy", 55, 60, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, {"tempFactor", 61, 66, PDB_FIELD_TYPE_FLOAT_2, PDB_FIELD_LJUST}, {"segID", 73, 76, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"element", 77, 78, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"charge", 79, 80, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, }; static struct PDBFieldDef seqadv_fields[] = { {"idCode", 8, 11, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"resName", 13, 15, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"chainID", 17, 17, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"seqNum", 19, 22, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"iCode", 23, 23, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"database", 25, 28, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"dbIDCode", 30, 38, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {"dbRes", 40, 42, PDB_FIELD_TYPE_STRING, PDB_FIELD_LJUST}, {"dbSeq", 44, 48, PDB_FIELD_TYPE_INTEGER, PDB_FIELD_LJUST}, {"convlict", 40, 70, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, {NULL, 0, 0, PDB_FIELD_TYPE_STRING, PDB_FIELD_RJUST}, }; static struct PDBRecordDef { char *name; struct PDBFieldDef *fields; } pdb_record_defs[] = { {"ATOM ", atom_fields}, {"ANISOU", anisou_fields}, {"REMARK", remark_fields}, {"KEYWDS", keywds_fields}, {"SEQRES", seqres_fields}, {"LINK ", link_fields}, {"ORIGX1", origx1_fields}, {"ENDMDL", endmdl_fields}, {"HETSYN", hetsyn_fields}, {"SIGATM", sigatm_fields}, {"MTRIX2", mtrix2_fields}, {"MTRIX3", mtrix3_fields}, {"HELIX ", helix_fields}, {"MTRIX1", mtrix1_fields}, {"TURN ", turn_fields}, {"TITLE ", title_fields}, {"SLTBRG", sltbrg_fields}, {"END ", end_fields}, {"SHEET ", sheet_fields}, {"SCALE2", scale2_fields}, {"AUTHOR", author_fields}, {"CRYST1", cryst1_fields}, {"SIGUIJ", siguij_fields}, {"CRYST3", cryst3_fields}, {"CRYST2", cryst2_fields}, {"CISPEP", cispep_fields}, {"ORIGX3", origx3_fields}, {"ORIGX2", origx2_fields}, {"MODRES", modres_fields}, {"SOURCE", source_fields}, {"FORMUL", formul_fields}, {"MASTER", master_fields}, {"CAVEAT", caveat_fields}, {"HET ", het_fields}, {"COMPND", compnd_fields}, {"MODEL ", model_fields}, {"REVDAT", revdat_fields}, {"SSBOND", ssbond_fields}, {"OBSLTE", obslte_fields}, {"CONECT", conect_fields}, {"JRNL ", jrnl_fields}, {"HETNAM", hetnam_fields}, {"SPRSDE", sprsde_fields}, {"HEADER", header_fields}, {"SITE ", site_fields}, {"SCALE1", scale1_fields}, {"HYDBND", hydbnd_fields}, {"TER ", ter_fields}, {"DBREF ", dbref_fields}, {"EXPDTA", expdta_fields}, {"SCALE3", scale3_fields}, {"HETATM", hetatm_fields}, {"SEQADV", seqadv_fields}, {NULL, NULL} }; static PyObject * pdb_read(PyObject *self, PyObject *args) { int i; int n; int irec; int ifie; int ibuf; char *pdb_path; char in_buff[MAX_LINE]; char field[MAX_LINE]; FILE *pdb_fil; PyObject *py_pdb_list = NULL; PyObject *py_rec_dict = NULL; PyObject *py_strx = NULL; PyObject *py_intx = NULL; PyObject *py_floatx = NULL; if (!PyArg_ParseTuple(args, "s", &pdb_path)) return NULL; /* open input/output files */ if ((pdb_fil = fopen(pdb_path, "r")) == NULL) { Py_INCREF(Py_None); return Py_None; } py_pdb_list = PyList_New(0); while (fgets(in_buff, MAX_LINE, pdb_fil) != NULL) { /* strip newlines */ ibuf = strnlen(in_buff, MAX_LINE) - 1; while (in_buff[ibuf] == '\n' && ibuf >= 0) { in_buff[ibuf] = '\0'; ibuf--; } if (ibuf < 0) { continue; } if (ibuf < 5) { n = ibuf + 1; } else { n = 6; } /* find the index in */ for (irec = 0; pdb_record_defs[irec].name != NULL; irec++) { if (strncmp(pdb_record_defs[irec].name, in_buff, n) == 0) { break; } } if (pdb_record_defs[irec].name == NULL) { continue; } /* create the new python dictionary for this record */ py_rec_dict = PyDict_New(); PyList_Append(py_pdb_list, py_rec_dict); /* set the record name */ py_strx = PyString_FromString(pdb_record_defs[irec].name); PyDict_SetItemString(py_rec_dict, "RECORD", py_strx); Py_XDECREF(py_strx); for (ifie = 0; pdb_record_defs[irec].fields[ifie].name != NULL; ifie++) { /* beginning index of the field */ i = pdb_record_defs[irec].fields[ifie].istart - 1; /* length of the field */ n = pdb_record_defs[irec].fields[ifie].iend - i; /* stop reading at the end of the buffer */ if (i > ibuf) { break; } /* reduce the length of the field if the field definition * extends beyond the end of the in_buff */ if (i+n-1 > ibuf) { n = ibuf - i + 1; } switch (pdb_record_defs[irec].fields[ifie].type) { case PDB_FIELD_TYPE_STRING: strncpy(field, &in_buff[i], n); field[n] = '\0'; /* strip right hand whitespace */ i = strnlen(field, MAX_LINE) - 1; while (field[i] == ' ' && i >= 0) { field[i] = '\0'; i--; } /* no blanks */ if (i >= 0) { py_strx = PyString_FromString(field); PyDict_SetItemString( py_rec_dict, pdb_record_defs[irec].fields[ifie].name, py_strx); Py_XDECREF(py_strx); } break; case PDB_FIELD_TYPE_INTEGER: strncpy(field, &in_buff[i], n); field[n] = '\0'; py_intx = PyInt_FromString(field, NULL, 10); if (py_intx != NULL) { PyDict_SetItemString( py_rec_dict, pdb_record_defs[irec].fields[ifie].name, py_intx); Py_XDECREF(py_intx); } else { PyErr_Clear(); } break; case PDB_FIELD_TYPE_FLOAT_2: case PDB_FIELD_TYPE_FLOAT_3: case PDB_FIELD_TYPE_FLOAT_4: case PDB_FIELD_TYPE_FLOAT_5: case PDB_FIELD_TYPE_FLOAT_6: py_strx = PyString_FromStringAndSize(&in_buff[i], n); py_floatx = PyFloat_FromString(py_strx, NULL); Py_XDECREF(py_strx); if (py_floatx != NULL) { PyDict_SetItemString( py_rec_dict, pdb_record_defs[irec].fields[ifie].name, py_floatx); Py_XDECREF(py_floatx); } else { PyErr_Clear(); } break; } /* switch */ } /* for (fields) */ Py_XDECREF(py_rec_dict); } /* while (records) */ /* close file */ fclose(pdb_fil); return py_pdb_list; } static PyMethodDef PDBModuleMethods[] = { {"read", pdb_read, METH_VARARGS, "Reads a PDB file and returns a list."}, {NULL, NULL, 0, NULL} }; DL_EXPORT(void) initpdbmodule(void) { PyObject *m; m = Py_InitModule("pdbmodule", PDBModuleMethods); PDBModuleErr = PyErr_NewException("pdbmodule.error", NULL, NULL); Py_INCREF(PDBModuleErr); PyModule_AddObject(m, "error", PDBModuleErr); }