// // with Modifications by J. Michael Word, Duke University // // Copyright (c) 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" extern "C" { #ifdef OLD_STD_HDRS #include #include #else #include #include using std::islower; using std::toupper; #endif } #if defined(__DECCXX_VER) || defined(_MSC_VER) #define NEEDSTRCASECMP #endif #ifdef NEEDSTRCASECMP int strncasecmp(const char *buf, const char *pat, int sz); int strcasecmp(const char *buf, const char *pat); #endif int PDB::pdbrunInputVersion = PDB::PDBRUNVersion; // just in case int PDB::pdbrunOutputVersion = PDB::PDBRUNVersion; // just in case PDB::GfxType PDB::getGfxType(const char *buf) { switch (buf[0]) { case 'L': case 'l': if (strcasecmp(buf + 1, "INE-LOOP") == 0) return GFX_LINE_LOOP; if (strcasecmp(buf + 1, "INE-STRIP") == 0) return GFX_LINE_STRIP; if (strcasecmp(buf + 1, "INES") == 0) return GFX_LINES; break; case 'M': case 'm': if (strcasecmp(buf + 1, "ARKERS") == 0) return GFX_MARKERS; break; case 'P': case 'p': if (strcasecmp(buf + 1, "OINTS") == 0) return GFX_POINTS; if (strcasecmp(buf + 1, "OLYGON") == 0) return GFX_POLYGON; break; case 'Q': case 'q': if (strcasecmp(buf + 1, "UAD-STRIP") == 0) return GFX_QUAD_STRIP; if (strcasecmp(buf + 1, "UADS") == 0) return GFX_QUADS; break; case 'T': case 't': if (strcasecmp(buf + 1, "RIANGLE-FAN") == 0) return GFX_TRIANGLE_FAN; if (strcasecmp(buf + 1, "RIANGLE-STRIP") == 0) return GFX_TRIANGLE_STRIP; if (strcasecmp(buf + 1, "RIANGLES") == 0) return GFX_TRIANGLES; break; } return GFX_UNKNOWN; } const char * PDB::gfxChars(GfxType gt) { switch (gt) { default: return "UNKNOWN"; case GFX_POINTS: return "POINTS"; case GFX_MARKERS: return "MARKERS"; case GFX_LINES: return "LINES"; case GFX_LINE_STRIP: return "LINE-STRIP"; case GFX_LINE_LOOP: return "LINE-LOOP"; case GFX_TRIANGLES: return "TRIANGLES"; case GFX_TRIANGLE_STRIP: return "TRIANGLE-STRIP"; case GFX_TRIANGLE_FAN: return "TRIANGLE-FAN"; case GFX_QUADS: return "QUADS"; case GFX_QUAD_STRIP: return "QUAD-STRIP"; case GFX_POLYGON: return "POLYGON"; } } static PDB::RecordType pdbrun5Type(const char *buf) { switch (buf[0]) { case 'A': case 'a': if (strncasecmp(buf + 1, "NGLE ", 5) == 0) return PDB::USER_ANGLE; if (strncasecmp(buf + 1, "TPOS ", 5) == 0) return PDB::USER_ATPOS; break; case 'B': case 'b': if (strncasecmp(buf + 1, "GCOLOR ", 7) == 0) return PDB::USER_BGCOLOR; break; case 'C': case 'c': if (strncasecmp(buf + 1, "HAIN ", 5) == 0) return PDB::USER_CHAIN; if (strncasecmp(buf + 1, "NAME ", 5) == 0) return PDB::USER_CNAME; if (strncasecmp(buf + 1, "OLOR ", 5) == 0) return PDB::USER_COLOR; break; case 'D': case 'd': if (strncasecmp(buf + 1, "ISTANCE ", 8) == 0) return PDB::USER_DISTANCE; break; case 'E': case 'e': if (strncasecmp(buf + 1, "NDOBJ ", 6) == 0) return PDB::USER_ENDOBJ; if (strncasecmp(buf + 1, "YEPOS ", 6) == 0) return PDB::USER_EYEPOS; break; case 'F': case 'f': if (strncasecmp(buf + 1, "ILE ", 4) == 0) return PDB::USER_FILE; if (strncasecmp(buf + 1, "OCUS ", 5) == 0) return PDB::USER_FOCUS; break; case 'G': case 'g': if (strncasecmp(buf + 1, "FX ", 3) != 0) break; if (strncasecmp(buf + 4, "COLOR ", 6) == 0) return PDB::USER_GFX_COLOR; if (strncasecmp(buf + 4, "DRAW ", 5) == 0) return PDB::USER_GFX_DRAW; if (strncasecmp(buf + 4, "FONT ", 5) == 0) return PDB::USER_GFX_FONT; if (strncasecmp(buf + 4, "LABEL ", 6) == 0) return PDB::USER_GFX_LABEL; if (strncasecmp(buf + 4, "MARKER ", 7) == 0) return PDB::USER_GFX_MARKER; if (strncasecmp(buf + 4, "MOVE ", 5) == 0) return PDB::USER_GFX_MOVE; if (strncasecmp(buf + 4, "POINT ", 6) == 0) return PDB::USER_GFX_POINT; break; case 'O': case 'o': if (strncasecmp(buf + 1, "BJECT ", 6) == 0) return PDB::USER_OBJECT; break; case 'P': case 'p': if (strncasecmp(buf + 1, "DBRUN ", 6) == 0) return PDB::USER_PDBRUN; break; case 'R': case 'r': if (strncasecmp(buf + 1, "ADIUS ", 6) == 0) return PDB::USER_RADIUS; break; case 'V': case 'v': if (strncasecmp(buf + 1, "IEWPORT ", 8) == 0) return PDB::USER_VIEWPORT; break; case 'W': case 'w': if (strncasecmp(buf + 1, "INDOW ", 6) == 0) return PDB::USER_WINDOW; break; } return PDB::USER; } static PDB::RecordType pdbrun6Type(const char *buf) { switch (buf[0]) { case 'A': case 'a': if (strncasecmp(buf + 1, "NGLE ", 5) == 0) return PDB::USER_ANGLE; if (strncasecmp(buf + 1, "TPOS ", 5) == 0) return PDB::USER_ATPOS; break; case 'B': case 'b': if (strncasecmp(buf + 1, "GCOLOR ", 7) == 0) return PDB::USER_BGCOLOR; break; case 'C': case 'c': if (strncasecmp(buf + 1, "HAIN ", 5) == 0) return PDB::USER_CHAIN; if (strncasecmp(buf + 1, "NAME ", 5) == 0) return PDB::USER_CNAME; if (strncasecmp(buf + 1, "OLOR ", 5) == 0) return PDB::USER_COLOR; break; case 'D': case 'd': if (strncasecmp(buf + 1, "ISTANCE ", 8) == 0) return PDB::USER_DISTANCE; break; case 'E': case 'e': if (strncasecmp(buf + 1, "NDOBJ", 5) == 0 && (buf[6] == '\0' || buf[6] == '\n' || buf[6] == '\r' || buf[6] == ' ')) return PDB::USER_ENDOBJ; if (strncasecmp(buf + 1, "YEPOS ", 6) == 0) return PDB::USER_EYEPOS; break; case 'F': case 'f': if (strncasecmp(buf + 1, "ILE ", 4) == 0) return PDB::USER_FILE; if (strncasecmp(buf + 1, "OCUS ", 5) == 0) return PDB::USER_FOCUS; break; case 'G': case 'g': if (buf[1] != 'F' || buf[2] != 'X' || buf[3] != ' ') break; switch (buf[4]) { case 'B': case 'b': if (strncasecmp(buf + 5, "EGIN ", 5) == 0) return PDB::USER_GFX_BEGIN; break; case 'C': case 'c': if (strncasecmp(buf + 5, "OLOR ", 5) == 0) return PDB::USER_GFX_COLOR; break; case 'E': case 'e': if (buf[5] == 'N' && buf[6] == 'D' && (buf[7] == '\0' || buf[7] == '\n' || buf[7] == '\r' || buf[7] == ' ')) return PDB::USER_GFX_END; break; case 'F': case 'f': if (strncasecmp(buf + 5, "ONT ", 4) == 0) return PDB::USER_GFX_FONT; break; case 'L': case 'l': if (strncasecmp(buf + 5, "ABEL ", 5) == 0) return PDB::USER_GFX_LABEL; break; case 'N': case 'n': if (strncasecmp(buf + 5, "ORMAL ", 6) == 0) return PDB::USER_GFX_NORMAL; break; case 'T': case 't': if (strncasecmp(buf + 5, "EXTPOS ", 7) == 0) return PDB::USER_GFX_TEXTPOS; break; case 'V': case 'v': if (strncasecmp(buf + 5, "ERTEX ", 6) == 0) return PDB::USER_GFX_VERTEX; break; } break; case 'M': case 'm': if (strncasecmp(buf + 1, "ARK ", 4) == 0) return PDB::USER_MARK; if (strncasecmp(buf + 1, "ARKNAME ", 6) == 0) return PDB::USER_MARKNAME; break; case 'O': case 'o': if (strncasecmp(buf + 1, "BJECT", 5) == 0 && (buf[6] == '\0' || buf[6] == '\n' || buf[6] == '\r' || buf[6] == ' ')) return PDB::USER_OBJECT; break; case 'P': case 'p': if (strncasecmp(buf + 1, "DBRUN ", 6) == 0) return PDB::USER_PDBRUN; break; case 'R': case 'r': if (strncasecmp(buf + 1, "ADIUS ", 6) == 0) return PDB::USER_RADIUS; break; case 'V': case 'v': if (strncasecmp(buf + 1, "IEWPORT ", 6) == 0) return PDB::USER_VIEWPORT; break; case 'W': case 'w': if (strncasecmp(buf + 1, "INDOW ", 6) == 0) return PDB::USER_WINDOW; break; } return PDB::USER; } PDB::RecordType PDB::getType(const char *buf) { char rt[4]; // PDB record type int i; for (i = 0; buf[i] != '\0' && buf[i] != '\n' && buf[i] != '\r' && i < 4; i += 1) { if (islower(buf[i])) rt[i] = toupper(buf[i]); else rt[i] = buf[i]; } if (i < 4) for (; i < 4; i += 1) rt[i] = ' '; switch (rt[0]) { case 'A': switch (rt[1]) { case 'G': if (rt[2] == 'R' && rt[3] == 'D') return AGRDES; if (rt[2] == 'G' && rt[3] == 'R') return AGGRGT; break; case 'N': if (rt[2] == 'I' && rt[3] == 'S') return ANISOU; break; case 'T': if (rt[2] == 'O' && rt[3] == 'M') return ATOM; break; case 'U': if (rt[2] == 'T' && rt[3] == 'H') return AUTHOR; break; } break; case 'C': switch (rt[1]) { case 'M': if (rt[2] == 'P' && rt[3] == 'D') return CMPDES; if (rt[2] == 'P' && rt[3] == 'O') return CMPONT; break; case 'O': if (rt[2] == 'M' && rt[3] == 'P') return COMPND; if (rt[2] == 'N' && rt[3] == 'E') return CONECT; break; case 'R': if (rt[2] == 'Y' && rt[3] == 'S') return CRYST1; break; } break; case 'E': switch (rt[1]) { case 'N': if (rt[2] == 'D' && rt[3] == ' ') return END; if (rt[2] == 'D' && rt[3] == 'M') return ENDMDL; break; case 'X': if (rt[2] == 'P' && rt[3] == 'D') return EXPDTA; break; } break; case 'F': switch (rt[1]) { case 'T': if (rt[2] == 'N' && rt[3] == 'O') return FTNOTE; break; case 'O': if (rt[2] == 'R' && rt[3] == 'M') return FORMUL; break; } break; case 'H': if (rt[1] != 'E') break; if (rt[2] == 'T' && rt[3] == 'A') return HETATM; if (rt[2] == 'A' && rt[3] == 'D') return HEADER; if (rt[2] == 'T' && rt[3] == ' ') return HET; if (rt[2] == 'L' && rt[3] == 'I') return HELIX; break; case 'J': if (rt[1] == 'R' && rt[2] == 'N' && rt[3] == 'L') return JRNL; break; case 'M': switch (rt[1]) { case 'A': if (rt[2] == 'S' && rt[3] == 'T') return MASTER; break; case 'O': if (rt[2] == 'D' && rt[3] == 'E') return MODEL; break; case 'T': if (rt[2] == 'R' && rt[3] == 'I') return MTRIX; if (rt[2] == 'X' && rt[3] == 'D') return MTXDES; break; } break; case 'O': switch (rt[1]) { case 'B': if (rt[2] == 'S' && rt[3] == 'L') return OBSLTE; break; case 'R': if (rt[2] == 'I' && rt[3] == 'G') return ORIGX; break; } break; case 'R': if (rt[1] != 'E') break; if (rt[2] == 'M' && rt[3] == 'A') return REMARK; if (rt[2] == 'V' && rt[3] == 'D') return REVDAT; break; case 'S': switch (rt[1]) { case 'C': if (rt[2] == 'A' && rt[3] == 'L') return SCALE; break; case 'E': if (rt[2] == 'Q' && rt[3] == 'R') return SEQRES; break; case 'H': if (rt[2] == 'E' && rt[3] == 'E') return SHEET; break; case 'I': if (rt[2] == 'T' && rt[3] == 'E') return SITE; if (rt[2] == 'G' && rt[3] == 'A') return SIGATM; if (rt[2] == 'G' && rt[3] == 'U') return SIGUIJ; break; case 'O': if (rt[2] == 'U' && rt[3] == 'R') return SOURCE; break; case 'P': if (rt[2] == 'R' && rt[3] == 'S') return SPRSDE; break; case 'S': if (rt[2] == 'B' && rt[3] == 'O') return SSBOND; break; case 'Y': if (rt[2] == 'M' && rt[3] == 'D') return SYMDES; if (rt[2] == 'M' && rt[3] == 'O') return SYMOP; break; } break; case 'T': switch (rt[1]) { case 'E': if (rt[2] == 'R' && rt[3] == ' ') return TER; break; case 'R': if (rt[2] == 'N' && rt[3] == 'S') return TRNSFM; break; case 'U': if (rt[2] == 'R' && rt[3] == 'N') return TURN; break; case 'V': if (rt[2] == 'E' && rt[3] == 'C') return TVECT; break; } break; case 'U': if (rt[1] == 'S' && rt[2] == 'E' && rt[3] == 'R') switch (pdbrunInputVersion) { case 1: case 2: case 3: case 4: case 5: return pdbrun5Type(buf + 6); case 6: return pdbrun6Type(buf + 6); default: if (strncasecmp(buf + 6, "PDBRUN ", 7) == 0) return USER_PDBRUN; return USER; } break; } return UNKNOWN; }