// // with Modifications by J. Michael Word, Duke University // // Copyright (c) 1989, 1992 The Regents of the University of California. // All rights reserved. // // Redistribution and use in source and binary forms are permitted // provided that the above copyright notice and this paragraph are // duplicated in all such forms and that any documentation, // advertising materials, and other materials related to such // distribution and use acknowledge that the software was developed // by the University of California, San Francisco. The name of the // University may not be used to endorse or promote products derived // from this software without specific prior written permission. // THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR // IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED // WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. // // subroutine for reading PDB format files // # include "pdb++.h" #ifdef OLD_STD_HDRS #include #else #include using std::memset; #endif # ifndef NULL # define NULL 0 # endif # ifndef HASSSCANFEXTERN extern "C" int sscanf(const char *, const char *, ...); # endif // // for each pdb record type there is a format reading in the // record values and for printing them out. // // The actual format of a line written, is the print format // followed by blank padding to 72 characters, followed by // 8 characters of file and line information. // static char const * const pdbRecordFormat[PDB::NUM_TYPES] = { #include "read_format.i" }; static char const * const pdbrun5[PDB::NUM_USER] = { #include "pdbrun5_read.i" }; static char const * const pdbrun6[PDB::NUM_USER] = { #include "pdbrun6_read.i" }; #include PDB::PDB(const char *buf) { initialize_everything(); // char dummy='\0'; // rmi added for 3 character resname // removed when 2 character chains were added const char *fmt; Sheet *sh; Residue *sha0, *sha1; // convert pdb record to C structure memset(&rType, 0, sizeof(RecordType)); memset(&unknown, 0, sizeof(Unknown)); rType = getType(buf); if (rType < USER_PDBRUN) fmt = pdbRecordFormat[rType]; else if (pdbrunInputVersion < 6) fmt = pdbrun5[rType - USER_PDBRUN]; else fmt = pdbrun6[rType - USER_PDBRUN]; switch (rType) { default: case UNKNOWN: unknown: rType = UNKNOWN; // in case of goto fmt = pdbRecordFormat[rType]; (void) ::sprintf(unknown.junk, fmt, buf); break; case AGGRGT: if (0 > sscanf(buf, fmt, &aggrgt.serialNum, &aggrgt.numComponents, &aggrgt.cmpontSerialNums[0], &aggrgt.cmpontSerialNums[1], &aggrgt.cmpontSerialNums[2], &aggrgt.cmpontSerialNums[3], &aggrgt.cmpontSerialNums[4], &aggrgt.cmpontSerialNums[5], &aggrgt.cmpontSerialNums[6], &aggrgt.cmpontSerialNums[7], &aggrgt.cmpontSerialNums[8], &aggrgt.cmpontSerialNums[9], &aggrgt.cmpontSerialNums[10], &aggrgt.cmpontSerialNums[11], &aggrgt.cmpontSerialNums[12], &aggrgt.cmpontSerialNums[13],endOfLineInfo)) goto unknown; break; case AGRDES: case CMPDES: case FTNOTE: case MTXDES: case REMARK: case SYMDES: if (0 > sscanf(buf, fmt, &agrdes.num, agrdes.text,endOfLineInfo)) goto unknown; break; case ANISOU: case SIGUIJ: if (0 > sscanf(buf, fmt, &anisou.serialNum, anisou.name, &anisou.altLoc, anisou.residue.name, &anisou.residue.chainId, &anisou.residue.seqNum, &anisou.residue.insertCode, &anisou.u[0], &anisou.u[1], &anisou.u[2], &anisou.u[3], &anisou.u[4], &anisou.u[5], anisou.segID, anisou.element, anisou.charge, anisou.annotation)) // *annotaton* is non-standard goto unknown; break; case ATOM: case HETATM: case SIGATM: if (0 > sscanf(buf, fmt, &atom.serialNum, atom.name, &atom.altLoc, atom.residue.name, &atom.residue.chainId, &atom.residue.seqNum, &atom.residue.insertCode, &atom.xyz[0], &atom.xyz[1], &atom.xyz[2], &atom.occupancy, &atom.tempFactor, atom.segID, atom.element, atom.charge, atom.annotation)) // *annotaton* is non-standard goto unknown; break; case AUTHOR: case COMPND: case EXPDTA: case JRNL: case SOURCE: if (0 > sscanf(buf, fmt, &author.continuation, author.data,endOfLineInfo)) goto unknown; break; case CONECT: if (0 > sscanf(buf, fmt, &conect.serialNum, &conect.covalent[0], &conect.covalent[1], &conect.covalent[2], &conect.covalent[3], &conect.bonds[0].hydrogen[0], &conect.bonds[0].hydrogen[1], &conect.bonds[0].salt, &conect.bonds[1].hydrogen[0], &conect.bonds[1].hydrogen[1], &conect.bonds[1].salt,endOfLineInfo)) goto unknown; break; case CMPONT: if (0 > sscanf(buf, fmt, &cmpont.seqNum, cmpont.residues[0].name, &cmpont.residues[0].chainId, &cmpont.residues[0].seqNum, &cmpont.residues[0].insertCode, cmpont.residues[1].name, &cmpont.residues[1].chainId, &cmpont.residues[1].seqNum, &cmpont.residues[1].insertCode,endOfLineInfo)) goto unknown; break; case CRYST1: if (0 > sscanf(buf, fmt, &cryst1.a, &cryst1.b, &cryst1.c, &cryst1.alpha, &cryst1.beta, &cryst1.gamma, cryst1.spaceGrp, &cryst1.z,endOfLineInfo)) goto unknown; break; case END: case ENDMDL: sscanf(buf, fmt, endOfLineInfo); break; case FORMUL: if (0 > sscanf(buf, fmt, &formul.component, formul.hetId, &formul.continuation, &formul.exclude, formul.formula,endOfLineInfo)) goto unknown; break; case HEADER: if (0 > sscanf(buf, fmt, header.classification, header.timestamp, &header.type, header.id,endOfLineInfo)) goto unknown; break; case HELIX: if (0 > sscanf(buf, fmt, &helix.serialNum, helix.id, helix.residues[0].name, &helix.residues[0].chainId, &helix.residues[0].seqNum, &helix.residues[0].insertCode, helix.residues[1].name, &helix.residues[1].chainId, &helix.residues[1].seqNum, &helix.residues[1].insertCode, &helix.type, helix.comment,endOfLineInfo)) goto unknown; break; case HET: if (0 > sscanf(buf, fmt, het.hetGrp.name, &het.hetGrp.chainId, &het.hetGrp.seqNum, &het.hetGrp.insertCode, &het.numAtoms, het.text,endOfLineInfo)) goto unknown; break; case MASTER: if (0 > sscanf(buf, fmt, &master.numRemark, &master.numFtnote, &master.numHet, &master.numHelix, &master.numSheet, &master.numTurn, &master.numSite, &master.numTransform, &master.numCoordinate, &master.numTer, &master.numConect, &master.numSeqres,endOfLineInfo)) goto unknown; break; case MODEL: if (0 > sscanf(buf, fmt, &model.num,endOfLineInfo)) goto unknown; break; case MTRIX: if (0 > sscanf(buf, fmt, &mtrix.rowNum, &mtrix.serialNum, &mtrix.m1, &mtrix.m2, &mtrix.m3, &mtrix.v, &mtrix.given,endOfLineInfo)) goto unknown; break; case OBSLTE: if (0 > sscanf(buf, fmt, &obslte.continuation, obslte.timestamp, obslte.oldId, obslte.idMap[0], obslte.idMap[1], obslte.idMap[2], obslte.idMap[3], obslte.idMap[4], obslte.idMap[2], obslte.idMap[6], obslte.idMap[7],endOfLineInfo)) goto unknown; break; case ORIGX: if (0 > sscanf(buf, fmt, &origx.rowNum, &origx.o1, &origx.o2, &origx.o3, &origx.t,endOfLineInfo)) goto unknown; break; case REVDAT: if (0 > sscanf(buf, fmt, &revdat.modification, &revdat.continuation, revdat.timestamp, revdat.id, &revdat.modType, revdat.corrections,endOfLineInfo)) goto unknown; break; case SCALE: if (0 > sscanf(buf, fmt, &scale.rowNum, &scale.s1, &scale.s2, &scale.s3, &scale.u,endOfLineInfo)) goto unknown; break; case SEQRES: if (0 > sscanf(buf, fmt, &seqres.serialNum, &seqres.chainId, &seqres.count, seqres.names[0], seqres.names[1], seqres.names[2], seqres.names[3], seqres.names[4], seqres.names[5], seqres.names[6], seqres.names[7], seqres.names[8], seqres.names[9], seqres.names[10], seqres.names[11], seqres.names[12],endOfLineInfo)) goto unknown; break; case SHEET: sh = &sheet; sha0 = &sh->atoms[0].residue; sha1 = &sh->atoms[1].residue; if (0 > sscanf(buf, fmt, &sh->strandNum, sh->id, &sh->count, sh->residues[0].name, &sh->residues[0].chainId, &sh->residues[0].seqNum, &sh->residues[0].insertCode, sh->residues[1].name, &sh->residues[1].chainId, &sh->residues[1].seqNum, &sh->residues[1].insertCode, &sh->sense, sh->atoms[0].name, sha0->name, &sha0->chainId, &sha0->seqNum, &sha0->insertCode, sh->atoms[1].name, sha1->name, &sha1->chainId, &sha1->seqNum, &sha1->insertCode,endOfLineInfo)) goto unknown; break; case SITE: if (0 > sscanf(buf, fmt, &site.seqNum, site.id, &site.count, site.residues[0].name, &site.residues[0].chainId, &site.residues[0].seqNum, &site.residues[0].insertCode, site.residues[1].name, &site.residues[1].chainId, &site.residues[1].seqNum, &site.residues[1].insertCode, site.residues[2].name, &site.residues[2].chainId, &site.residues[2].seqNum, &site.residues[2].insertCode, site.residues[3].name, &site.residues[3].chainId, &site.residues[3].seqNum, &site.residues[3].insertCode,endOfLineInfo)) goto unknown; break; case SPRSDE: if (0 > sscanf(buf, fmt, &sprsde.continuation, sprsde.timestamp, sprsde.id, sprsde.supersede[0], sprsde.supersede[1], sprsde.supersede[2], sprsde.supersede[3], sprsde.supersede[4], sprsde.supersede[5], sprsde.supersede[6], sprsde.supersede[7],endOfLineInfo)) goto unknown; break; case SSBOND: if (0 > sscanf(buf, fmt, &ssbond.seqNum, ssbond.residues[0].name, &ssbond.residues[0].chainId, &ssbond.residues[0].seqNum, &ssbond.residues[0].insertCode, ssbond.residues[1].name, &ssbond.residues[1].chainId, &ssbond.residues[1].seqNum, &ssbond.residues[1].insertCode, ssbond.comment,endOfLineInfo)) goto unknown; break; case SYMOP: if (0 > sscanf(buf, fmt, &symop.rowNum, &symop.serialNum, &symop.s1, &symop.s2, &symop.s3, &symop.t,endOfLineInfo)) goto unknown; break; case TER: if (0 > sscanf(buf, fmt, &ter.serialNum, ter.residue.name, &ter.residue.chainId, &ter.residue.seqNum, &ter.residue.insertCode,endOfLineInfo)) goto unknown; break; case TRNSFM: if (0 > sscanf(buf, fmt, &trnsfm.resultSerialNum, &trnsfm.applySerialNum, &trnsfm.sourceSerialNum,endOfLineInfo)) goto unknown; break; case TURN: if (0 > sscanf(buf, fmt, &turn.seqNum, turn.id, turn.residues[0].name, &turn.residues[0].chainId, &turn.residues[0].seqNum, &turn.residues[0].insertCode, turn.residues[1].name, &turn.residues[1].chainId, &turn.residues[1].seqNum, &turn.residues[1].insertCode, turn.comment,endOfLineInfo)) goto unknown; break; case TVECT: if (0 > sscanf(buf, fmt, &tvect.serialNum, &tvect.t1, &tvect.t2, &tvect.t3, tvect.comment,endOfLineInfo)) goto unknown; break; user: rType = USER; fmt = pdbRecordFormat[rType]; case USER: if (0 > sscanf(buf, fmt, user.subtype, user.text,endOfLineInfo)) goto unknown; break; case USER_PDBRUN: if (0 > sscanf(buf, fmt, &userPdbrun.version)) goto user; pdbrunInputVersion = userPdbrun.version; break; case USER_EYEPOS: if (0 > sscanf(buf, fmt, &userEyePos.xyz[0], &userEyePos.xyz[1], &userEyePos.xyz[2])) goto user; break; case USER_ATPOS: if (0 > sscanf(buf, fmt, &userAtPos.xyz[0], &userAtPos.xyz[1], &userAtPos.xyz[2])) goto user; break; case USER_WINDOW: if (0 > sscanf(buf, fmt, &userWindow.left, &userWindow.right, &userWindow.bottom, &userWindow.top, &userWindow.hither, &userWindow.yon)) goto user; break; case USER_FOCUS: if (0 > sscanf(buf, fmt, &userFocus.focus)) goto user; break; case USER_VIEWPORT: if (0 > sscanf(buf, fmt, &userViewport.xmin, &userViewport.xmax, &userViewport.ymin, &userViewport.ymax)) goto user; break; case USER_BGCOLOR: if (pdbrunInputVersion < 6) { if (0 > ::sscanf(buf, fmt, &userBgColor.rgb[0], &userBgColor.rgb[1], &userBgColor.rgb[2])) goto user; } else if (0 > sscanf(buf, fmt, &userBgColor.rgb[0], &userBgColor.rgb[1], &userBgColor.rgb[2])) goto user; break; case USER_ANGLE: if (pdbrunInputVersion < 6) { if (0 > sscanf(buf, fmt, &userAngle.which, &userAngle.atom0, &userAngle.atom1, &userAngle.atom2, &userAngle.atom3, &userAngle.angle)) goto user; } else if (0 > sscanf(buf, fmt, &userAngle.atom0, &userAngle.atom1, &userAngle.atom2, &userAngle.atom3, &userAngle.angle)) goto user; break; case USER_DISTANCE: if (pdbrunInputVersion < 6) { if (0 > sscanf(buf, fmt, &userDistance.which, &userDistance.atom0, &userDistance.atom1, &userDistance.distance)) goto user; } else if (0 > sscanf(buf, fmt, &userDistance.atom0, &userDistance.atom1, &userDistance.distance)) goto user; break; case USER_FILE: if (pdbrunInputVersion < 6) { if (0 > sscanf(buf, fmt, userFile.filename)) goto user; } else if (0 > sscanf(buf, fmt, &userFile.model, userFile.filename)) goto user; break; case USER_MARKNAME: if (pdbrunInputVersion < 6 || 0 > sscanf(buf, fmt, userMarkname.markname)) goto user; break; case USER_MARK: if (pdbrunInputVersion < 6 || 0 > sscanf(buf, fmt, userMark.markname)) goto user; break; case USER_CNAME: if (pdbrunInputVersion < 6) { if (0 > ::sscanf(buf, fmt, userCName.name, &userCName.rgb[0], &userCName.rgb[1], &userCName.rgb[2])) goto user; } else if (0 > sscanf(buf, fmt, &userCName.rgb[0], &userCName.rgb[1], &userCName.rgb[2], userCName.name)) goto user; break; case USER_COLOR: if (pdbrunInputVersion < 6) { if (0 > ::sscanf(buf, fmt, userColor.spec, &userColor.rgb[0], &userColor.rgb[1], &userColor.rgb[2])) goto user; } else if (0 > sscanf(buf, fmt, &userColor.rgb[0], &userColor.rgb[1], &userColor.rgb[2], userColor.spec)) goto user; break; case USER_RADIUS: if (0 > sscanf(buf, fmt, &userRadius.radius)) goto user; break; case USER_OBJECT: if (pdbrunInputVersion < 6) { if (0 > sscanf(buf, fmt, &userObject.model)) goto user; } break; case USER_ENDOBJ: if (pdbrunInputVersion < 6) { if (0 > sscanf(buf, fmt, &userEndObj.model)) goto user; } break; case USER_CHAIN: if (pdbrunInputVersion < 6) { if (0 > ::sscanf(buf, fmt, &userChain.atom0, &userChain.atom1)) goto user; } else if (0 > sscanf(buf, fmt, &userChain.atom0, &userChain.atom1)) goto user; break; case USER_GFX_BEGIN: if (pdbrunInputVersion < 6 || 0 > sscanf(buf, fmt, userGfxBegin.unknown)) goto user; userGfxBegin.primitive = getGfxType(userGfxBegin.unknown); break; case USER_GFX_END: if (pdbrunInputVersion < 6) goto user; break; case USER_GFX_COLOR: if (pdbrunInputVersion < 6) { if (0 > ::sscanf(buf, fmt, userGfxColor.spec, &userGfxColor.rgb[0], &userGfxColor.rgb[1], &userGfxColor.rgb[2])) goto user; } else if (0 > sscanf(buf, fmt, &userGfxColor.rgb[0], &userGfxColor.rgb[1], &userGfxColor.rgb[2], userGfxColor.spec)) goto user; break; case USER_GFX_NORMAL: if (pdbrunInputVersion < 6 || 0 > sscanf(buf, fmt, &userGfxNormal.xyz[0], &userGfxNormal.xyz[1], &userGfxNormal.xyz[2])) goto user; break; case USER_GFX_VERTEX: if (pdbrunInputVersion < 6 || 0 > sscanf(buf, fmt, &userGfxVertex.xyz[0], &userGfxVertex.xyz[1], &userGfxVertex.xyz[2])) goto user; break; case USER_GFX_FONT: if (pdbrunInputVersion < 6) { if (0 > ::sscanf(buf, fmt, userGfxFont.name, &userGfxFont.size)) goto user; } else if (0 > sscanf(buf, fmt, &userGfxFont.size, userGfxFont.name)) goto user; break; case USER_GFX_TEXTPOS: if (pdbrunInputVersion < 6 || 0 > sscanf(buf, fmt, &userGfxTextPos.xyz[0], &userGfxTextPos.xyz[1], &userGfxTextPos.xyz[2])) goto user; break; case USER_GFX_LABEL: if (pdbrunInputVersion < 6) { if (0 > ::sscanf(buf, fmt, &userGfxLabel.xyz[0], &userGfxLabel.xyz[1], &userGfxLabel.xyz[2], userGfxLabel.text)) goto user; } else if (0 > sscanf(buf, fmt, userGfxLabel.text)) goto user; // TODO: process text? break; case USER_GFX_MOVE: if (pdbrunInputVersion >= 6 || 0 > sscanf(buf, fmt, &userGfxMove.xyz[0], &userGfxMove.xyz[1], &userGfxMove.xyz[2])) goto user; break; case USER_GFX_DRAW: if (pdbrunInputVersion >= 6 || 0 > sscanf(buf, fmt, &userGfxDraw.xyz[0], &userGfxDraw.xyz[1], &userGfxDraw.xyz[2])) goto user; break; case USER_GFX_MARKER: if (pdbrunInputVersion >= 6 || 0 > sscanf(buf, fmt, &userGfxMarker.xyz[0], &userGfxMarker.xyz[1], &userGfxMarker.xyz[2])) goto user; break; case USER_GFX_POINT: if (pdbrunInputVersion >= 6 || 0 > sscanf(buf, fmt, &userGfxPoint.xyz[0], &userGfxPoint.xyz[1], &userGfxPoint.xyz[2])) goto user; break; } }