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#! /bin/sh
# This is a shell archive, meaning:
# 1. Remove everything above the #! /bin/sh line.
# 2. Save the resulting text in a file.
# 3. Execute the file with /bin/sh (not csh) to create:
# pdb++.3
# Makefile
# pdb++.h
# pdbrun5_read.i
# pdbrun5_write.i
# pdbrun6_read.i
# pdbrun6_write.i
# read_format.i
# write_format.i
# pdb++.cc
# pdb_chars.cc
# pdb_read.cc
# pdb_sprntf.cc
# pdb_sscanf.cc
# pdb_type.cc
# pdbinput.cc
# This archive created: Mon May 22 13:08:52 1995
export PATH; PATH=/bin:/usr/bin:$PATH
echo shar: "extracting 'pdb++.3'" '(8002 characters)'
if test -f 'pdb++.3'
then
echo shar: "will not over-write existing file 'pdb++.3'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb++.3'
X.\" Copyright 1994, U.C.S.F. Computer Graphics Laboratory
X.\" $Id: pdb++.3,v 1.9 94/12/13 15:22:03 gregc Exp $
X.TH PDB++ 3
X.SH NAME
Xpdb++ \- A C++ class for manipulating Brookhaven Protein DataBank records
X.SH SYNOPSIS
X.nf
X#include
X
X\&....
X PDB record;
X
X while (cin >> record) {
X switch (record.type()) {
X case PDB::ATOM:
X cout << record.atom.xyz[0] << ' ' << record.atom.xyz[0]
X << ' ' << record.atom.xyz[0] << endl;
X ....
X break;
X }
X }
X\&....
X.fi
X.SH DESCRIPTION
XThe routines listed above are available in the pdb++ library,
X.IR "-L/usr/local/lib/midas -lpdb++" .
X.PP
XThe
X.B PDB
Xclass provides methods for parsing Brookhaven Protein DataBank (PDB) records
X(lines from a PDB file) into structures
Xand expanding those structures back into PDB records.
XRather than provide access functions for each possible field,
Xthe structure containing the parsed record is publicly available.
XThe field names are listed in the header file.
X.PP
XThe
X.B PDB
Xclass has two enhancements to the Brookhaven Protein DataBank specification:
Xfour character residue names, and the PDBRUN set of scene annotation records.
XFor character residue names work because
Xeverywhere in the specification a three character residue name appears,
Xthere is a blank afterwards.
X.SH "MEMBER CONSTANTS"
X.TP
X.B BufLen
XThe maximum length of a generated PDB record string (including the null byte).
X.TP
X.B PDBRUNVersion
XThe default version of the PDBRUN scene annotation records.
X.PP
XThere are also constants for each known PDB record type
X.RI ( e.g. ,
X.BR ATOM ,
X.BR HETATM ,
X.IR etc. ),
Xand the constant
X.B UNKNOWN
Xfor an unknown PDB record.
X.PP
XThe following constants are for each PDBRUN scene annotation record type:
X.BR USER_PDBRUN ,
X.BR USER_EYEPOS ,
X.BR USER_ATPOS ,
X.BR USER_WINDOW ,
X.BR USER_FOCUS ,
X.BR USER_VIEWPORT ,
X.BR USER_BGCOLOR ,
X.BR USER_ANGLE ,
X.BR USER_DISTANCE ,
X.BR USER_FILE ,
X.BR USER_MARKNAME ,
X.BR USER_MARK ,
X.BR USER_CNAME ,
X.BR USER_COLOR ,
X.BR USER_RADIUS ,
X.BR USER_OBJECT ,
X.BR USER_ENDOBJ ,
X.BR USER_CHAIN ,
X.BR USER_GFX_BEGIN ,
X.BR USER_GFX_END ,
X.BR USER_GFX_COLOR ,
X.BR USER_GFX_NORMAL ,
X.BR USER_GFX_VERTEX ,
X.BR USER_GFX_FONT ,
X.BR USER_GFX_TEXTPOS ,
Xand
X.BR USER_GFX_LABEL .
X.PP
XThe following constants are for the various graphics primitives supported
Xin scenes:
X.BR GFX_UNKNOWN ,
X.BR GFX_POINTS ,
X.BR GFX_MARKERS ,
X.BR GFX_LINES ,
X.BR GFX_LINE_STRIP ,
X.BR GFX_LINE_LOOP ,
X.BR GFX_TRIANGLES ,
X.BR GFX_TRIANGLE_STRIP ,
X.BR GFX_TRIANGLE_FAN ,
X.BR GFX_QUADS ,
X.BR GFX_QUAD_STRIP ,
Xand
X.BR GFX_POLYGON .
X.SH "MEMBER TYPES"
X.TP
Xtypedef char \fBDate\fP[10]
XA text field containing a date, typically \fIday\fP\-\fImonth\fP\-\fIyear\fP,
Xwhere
X.I day
Xis numeric,
X.I month
Xis a three-letter abbreviation,
Xand
X.I year
Xis the last two digits of the year.
X.TP
Xtypedef char \fBAName\fP[5]
XA PDB atom name, \fIe.g.\fP, NO2*.
X.TP
Xtypedef char \fBRName\fP[5]
XResidue name, \fIe.g.\fP, ALA.
X.TP
Xtypedef char \fBPName\fP[5]
XPDB name, \fIe.g.\fP, 9lyz.
X.TP
Xtypedef char \fBId\fP[4]
XGeneric short id field.
X.TP
Xtypedef double \fBReal\fP
XSize of floating point numbers read and written.
X.TP
Xstruct \fBResidue\fP
XA \fBResidue\fP consists of a residue name (\fBname\fP),
Xa chain identifier (\fBchainId\fP), a sequence number (\fBseqNum\fP),
Xand an insertion code (\fBinsertCode\fP).
X.SH "MEMBER FUNCTIONS"
X.LP
X.BR pdb ()
X.br
X.BR pdb "(RecordType t)"
X.br
X.BR pdb "(const char *buf)"
X.RS
XConstructors.
XThe first two above construct a zeroed instance of the given record type
X(default
X.BR UNKNOWN ).
XThe last constructor above fills in all of the fields of the instance
Xfrom the given PDB record text.
X.RE
X.TP
XRecordType \fBtype\fP() const
XReturn the type of PDB instance.
X.TP
Xvoid \fBtype\fP(RecordType t)
XChange the PDB record type of the instance
Xand reinitialize all the fields to default values
X(zero in all cases except for an
X.BR ATOM 's
Xoccupancy which defaults to 1.0).
X.TP
Xconst char *\fBchars\fP() const;
XReturn a string containing the PDB record in textual form.
X.TP
Xstatic int \fBPdbrunInputVersion\fP()
XReturn the current PDBRUN scene annotation version used to parse text records.
X.TP
Xstatic int \fBPdbrunOutputVersion\fP()
XReturn the current PDBRUN scene annotation version used to create text records.
X.TP
Xstatic void \fBPdbrunInputVersion\fP(int v)
XSet the current PDBRUN scene annotation version used to parse text records.
X.TP
Xstatic void \fBPdbrunOutputVersion\fP(int v)
XSet the current PDBRUN scene annotation version used to create text records.
X.TP
Xstatic recordType \fBgetType\fP(const char *buf)
XReturn the PDB record type for the given line of text.
X.TP
Xstatic GfxType \fBgetGfxType\fP(const char *buf)
X.TP
Xstatic const char *\fBgfxChars\fP(GfxType gt)
X.TP
Xstatic int \fBsscanf\fP(const char *, const char *, ...)
XA version of
X.BR sscanf (3)
Xwhose format's behave like \s-2FORTRAN\s0 formats where field widths
Xare sacrosanct.
XIf the input line is short,
Xthen the rest of the fields are initialized to default values.
XAny literal characters in the format must match the input.
XThe format characters are:
Xspace, ignore input character;
X.BR c ,
Xcharacter (array), default to a space;
X.BR d ,
Xinteger, default zero;
X.BR f ,
Xdouble, default zero;
X.BR s ,
Xget a C string, trailing spaces are stripped and it is null terminated,
Xdefault an empty string.
X.B sscanf
Xreturns the number of input fields converted
X(may be less than expected if the input line is short)
Xor \(mi1 if an error is found.
X.TP
Xstatic int \fBsprintf\fP(char *, const char *, ...)
XA version of
X.BR sprintf (3)
Xwhose format's behave like \s-2FORTRAN\s0 formats where field widths
Xare sacrosanct.
XLiteral characters are copied as is.
XIf the text or number to be printed is larger than the given field width,
Xthen the field is filled in with asterisks.
XThe format characters are:
X.BR d ,
Xinteger;
X.BR D ,
Xinteger where zero is written as spaces;
X.BR s ,
Xright-justified string (a negative field width left-justifies);
X.BR c ,
Xcharacter (array), zero characters are converted to spaces;
X.BR f ,
Xfloating point, normal
X.B printf
Xprecisions are used.
X.SH "I/O FUNCTIONS"
X.TP
Xostream &\fBoperator<<\fP(ostream &s, const PDB &p)
XOutput the current PDB record on the given output stream.
X.TP
Xistream &\fBoperator>>\fP(istream &s, PDB &p)
XRead a line from the given input stream and convert to a PDB record.
X.SH "SEE ALSO"
X``Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description,'' Febuary 1992,
XBrookhaven National Laboratory,
Xthe January 1993 Protein Data Bank Quarterly Newsletter,
X``Annotating PDB Files with Scene Information,''
XGregory S. Couch, \fIet. al.\fP, (submitted for publication).
X.SH NOTES
XThe subtype field of USERxx structure tells what the
X.I xx
Xpart was.
XThe rest of the line, up to the card sequence portion, is the text field.
X.PP
XDue to the way Brookhaven encodes their files,
Xatom names often have leading blanks and sometimes have embedded blanks.
XResidue names occasionally have leading blanks too.
XTo be entirely consistent with the PDB format,
Xthe programmer should put those blanks in before using the
X.B chars
Xmember function.
X.SH BUGS
XRoutines are needed to convert to and from PDB typesetting conventions in
X.BR COMPND ,
X.BR SOURCE ,
X.BR AUTHOR ,
Xand
X.B JRNL
Xrecords.
X.SH COPYRIGHT
XCopyright \(co 1994 The Regents of the University of California.
XAll rights reserved.
X.PP
XRedistribution and use in source and binary forms are permitted
Xprovided that the above copyright notice and this paragraph are
Xduplicated in all such forms and that any documentation,
Xadvertising materials, and other materials related to such
Xdistribution and use acknowledge that the software was developed
Xby the University of California, San Francisco. The name of the
XUniversity may not be used to endorse or promote products derived
Xfrom this software without specific prior written permission.
XTHIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
XIMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
XWARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
SHAR_EOF
if test 8002 -ne "`wc -c < 'pdb++.3'`"
then
echo shar: "error transmitting 'pdb++.3'" '(should have been 8002 characters)'
fi
fi
echo shar: "extracting 'Makefile'" '(821 characters)'
if test -f 'Makefile'
then
echo shar: "will not over-write existing file 'Makefile'"
else
sed 's/^ X//' << \SHAR_EOF > 'Makefile'
X#
X# On BSD machines, RANLIB should be 'ranlib'
X#
X# On System V machines, RANLIB should be ':'
X#
XSHELL = /bin/sh
XRANLIB = :
X
XCXX = gcc -felide-constructors
X#CXX = CC
X
X.SUFFIXES: .cc
X
X.cc.o:
X $(CXX) -c $< -o $@
X
XOPT = -O
XDEBUG =
XCFLAGS = $(OPT) $(DEBUG)
XLIBRARY = pdb++
X
XLIBARCH = lib$(LIBRARY).a
XOBJS = pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_chars.o \
X pdb_type.o pdb++.o pdbinput.o
XSRCS = pdb_read.cc pdb_sprntf.cc pdb_sscanf.cc pdb_chars.cc \
X pdb_type.cc pdb++.cc pdbinput.cc
X
Xall: $(LIBARCH)
X
Xinstall: $(LIBARCH)
X install -F /usr/local/lib $(LIBARCH)
X
X$(LIBARCH): $(OBJS)
X @echo "Loading $(LIBARCH) ... "
X @ar cru $(LIBARCH) $(OBJS)
X @$(RANLIB) $(LIBARCH)
X @echo "done"
X
Xclean:; @rm -f $(OBJS)
X
Xspotless:; @rm -f $(OBJS) $(LIBARCH)
X
Xtags: $(HDRS) $(SRCS); @ctags -w $(HDRS) $(SRCS)
SHAR_EOF
if test 821 -ne "`wc -c < 'Makefile'`"
then
echo shar: "error transmitting 'Makefile'" '(should have been 821 characters)'
fi
fi
echo shar: "extracting 'pdb++.h'" '(10596 characters)'
if test -f 'pdb++.h'
then
echo shar: "will not over-write existing file 'pdb++.h'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb++.h'
X//
X// Copyright (c) 1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdb++.h,v 1.14 95/02/28 14:09:49 gregc Exp $
X//
X// Based on Brookhaven National Laboratory Protein Data Bank, Feb 1992
X//
X// C structure declarations
X//
X
X#ifndef PDB_H
X#define PDB_H
X
X#include
X
Xclass PDB {
Xpublic:
X#ifdef PDB_WORKAROUND
X enum { BufLen = 73, PDBRUNVersion = 6 };
X#else
X static const int BufLen = 73; // PDB record length (72 + '\0')
X static const int PDBRUNVersion = 6; // Best version generated
X#endif
X typedef char Date[10];
X typedef char AName[5]; // atom name - NO2*
X typedef char RName[5]; // residue name - ALA
X typedef char PName[5]; // pdb name - 9lyz
X typedef char Id[4]; // generic short id field
X typedef double Real; // size of floating point
X
X struct Residue { // residue info
X RName name;
X char chainId;
X int seqNum;
X char insertCode;
X };
X
X // graphics primitive types
X enum GfxType {
X GFX_UNKNOWN, GFX_POINTS, GFX_MARKERS, GFX_LINES,
X GFX_LINE_STRIP, GFX_LINE_LOOP, GFX_TRIANGLES,
X GFX_TRIANGLE_STRIP, GFX_TRIANGLE_FAN, GFX_QUADS,
X GFX_QUAD_STRIP, GFX_POLYGON
X };
X
X //
X // structures declarations for each record type
X //
X
X struct Unknown {
X char junk[BufLen];
X };
X struct Aggrgt {
X int serialNum;
X int numComponents;
X int cmpontSerialNums[14];
X };
X struct Agrdes {
X int num;
X char text[60];
X };
X struct Anisou {
X int serialNum;
X AName name;
X char altLoc;
X Residue residue;
X int u[6];
X };
X struct Atom {
X int serialNum;
X AName name;
X char altLoc;
X Residue residue;
X Real xyz[3];
X Real occupancy, tempFactor;
X int ftnoteNum;
X };
X struct Author {
X char data[61];
X char continuation;
X };
X typedef Agrdes Cmpdes;
X struct Cmpont {
X int seqNum;
X Residue residues[2];
X };
X typedef Author Compnd;
X struct Conect {
X int serialNum;
X int covalent[4];
X struct {
X int hydrogen[2];
X int salt;
X } bonds[2];
X };
X struct Cryst1 {
X Real a, b, c;
X Real alpha, beta, gamma;
X char spaceGrp[12];
X int z;
X };
X // no structure for END
X // no structure for ENDMDL
X typedef Author Expdta;
X struct Formul {
X int component;
X RName hetId;
X int continuation;
X char exclude; // * to exclude
X char formula[52];
X };
X typedef Agrdes Ftnote;
X struct Header {
X char classification[41];
X Date timestamp;
X PName id;
X char type;
X };
X struct Helix {
X int serialNum;
X Id id;
X Residue residues[2];
X int type;
X char comment[31];
X };
X struct Het {
X Residue hetGrp;
X int numAtoms;
X char text[41];
X };
X typedef Atom Hetatm;
X typedef Author Jrnl;
X struct Master {
X int numRemark;
X int numFtnote;
X int numHet;
X int numHelix;
X int numSheet;
X int numTurn;
X int numSite;
X int numTransform;
X int numCoordinate;
X int numTer;
X int numConect;
X int numSeqres;
X };
X struct Model {
X int num;
X };
X struct Mtrix {
X int rowNum;
X int serialNum;
X Real m1, m2, m3, v;
X int given;
X };
X typedef Agrdes Mtxdes;
X struct Obslte {
X int continuation;
X Date timestamp;
X PName oldId;
X PName idMap[8];
X };
X struct Origx {
X int rowNum;
X Real o1, o2, o3, t;
X };
X typedef Ftnote Remark;
X struct Revdat {
X int modification;
X int continuation;
X Date timestamp;
X char id[8];
X char modType;
X char corrections[31];
X };
X struct Scale {
X int rowNum;
X Real s1, s2, s3, u;
X };
X struct Seqres {
X int serialNum;
X char chainId;
X int count;
X RName names[13];
X };
X struct Sheet {
X int strandNum;
X Id id;
X int count;
X Residue residues[2];
X int sense;
X struct {
X AName name;
X Residue residue;
X } atoms[2];
X };
X typedef Atom Sigatm;
X typedef Anisou Siguij;
X struct Site {
X int seqNum;
X Id id;
X int count;
X Residue residues[4];
X };
X typedef Author Source;
X struct Sprsde {
X int continuation;
X Date timestamp;
X PName id;
X PName supersede[8];
X };
X struct Ssbond {
X int seqNum;
X Residue residues[2];
X char comment[31];
X };
X typedef Agrdes Symdes;
X struct Symop {
X int rowNum;
X int serialNum;
X Real s1, s2, s3, t;
X };
X struct Ter {
X int serialNum;
X Residue residue;
X };
X struct Trnsfm {
X int resultSerialNum;
X int applySerialNum;
X int sourceSerialNum;
X };
X struct Turn {
X int seqNum;
X Id id;
X Residue residues[2];
X char comment[31];
X };
X struct Tvect {
X int serialNum;
X Real t1, t2, t3;
X char comment[31];
X };
X struct User {
X char subtype[3];
X char text[67];
X };
X struct UserPdbrun {
X int version;
X };
X struct UserEyePos {
X Real xyz[3];
X };
X typedef UserEyePos UserAtPos;
X struct UserWindow {
X Real left, right, bottom, top, hither, yon;
X };
X struct UserFocus {
X Real focus;
X };
X struct UserViewport {
X Real xmin, xmax, ymin, ymax;
X };
X struct UserBgColor {
X Real rgb[3];
X };
X struct UserAngle {
X int atom0, atom1, atom2, atom3;
X Real angle;
X int which; // version 5 -- obsolete
X };
X struct UserDistance {
X int atom0, atom1;
X Real distance;
X int which; // version 5 -- obsolete
X };
X struct UserFile {
X char filename[62];
X int model; // not in version 5
X };
X struct UserMarkname { // not in version 5
X char markname[58];
X };
X typedef UserMarkname UserMark; // not in version 5
X struct UserCName {
X Real rgb[3];
X char name[39];
X };
X struct UserColor {
X Real rgb[3];
X char spec[39];
X };
X struct UserRadius {
X Real radius;
X };
X struct UserObject {
X int model; // version 5 -- obsolete
X };
X struct UserEndObj {
X int model; // version 5 -- obsolete
X };
X struct UserChain {
X int atom0, atom1;
X };
X struct UserGfxBegin { // not in version 5
X GfxType primitive;
X char unknown[33];
X };
X // no structure for USER GFX END
X typedef UserColor UserGfxColor;
X struct UserGfxNormal { // not in version 5
X Real xyz[3];
X };
X typedef UserGfxNormal UserGfxVertex;
X struct UserGfxFont {
X int size;
X char name[54];
X };
X struct UserGfxTextPos { // not in version 5
X Real xyz[3];
X };
X struct UserGfxLabel {
X Real xyz[3]; // version 5 -- obsolete
X char text[57]; // 27 in version 5
X };
X struct UserGfxMove { // version 5 -- obsolete
X Real xyz[3];
X };
X typedef UserGfxMove UserGfxDraw; // version 5 -- obsolete
X typedef UserGfxMove UserGfxMarker; // version 5 -- obsolete
X typedef UserGfxMove UserGfxPoint; // version 5 -- obsolete
X
X enum RecordType { UNKNOWN, ANISOU, ATOM, AUTHOR, COMPND, CONECT, CRYST1,
X END, FORMUL, FTNOTE, HEADER, HELIX, HET, HETATM, JRNL, MASTER,
X MTRIX, OBSLTE, ORIGX, REMARK, REVDAT, SCALE, SEQRES, SHEET,
X SIGATM, SIGUIJ, SITE, SOURCE, SPRSDE, SSBOND, TER, TURN, TVECT,
X USER, MODEL, ENDMDL, EXPDTA, SYMDES, SYMOP, MTXDES, CMPDES,
X CMPONT, TRNSFM, AGRDES, AGGRGT,
X USER_PDBRUN, USER_EYEPOS, USER_ATPOS, USER_WINDOW, USER_FOCUS,
X USER_VIEWPORT, USER_BGCOLOR, USER_ANGLE, USER_DISTANCE,
X USER_FILE, USER_MARKNAME, USER_MARK, USER_CNAME, USER_COLOR,
X USER_RADIUS, USER_OBJECT, USER_ENDOBJ, USER_CHAIN,
X USER_GFX_BEGIN, USER_GFX_END, USER_GFX_COLOR, USER_GFX_NORMAL,
X USER_GFX_VERTEX, USER_GFX_FONT, USER_GFX_TEXTPOS,
X USER_GFX_LABEL,
X USER_GFX_MOVE, USER_GFX_DRAW, USER_GFX_MARKER, USER_GFX_POINT
X };
X#ifdef PDB_WORKAROUND
X enum { NUM_TYPES = AGGRGT + 1,
X NUM_USER = USER_GFX_POINT - USER_PDBRUN + 1 };
X#else
X static const int NUM_TYPES = AGGRGT + 1;
X static const int NUM_USER = USER_GFX_POINT - USER_PDBRUN + 1;
X#endif
Xprivate:
X RecordType rType;
X static int pdbrunInputVersion, pdbrunOutputVersion;
X static int byteCmp(const PDB &l, const PDB &r);
Xpublic:
X union {
X Unknown unknown;
X Aggrgt aggrgt;
X Agrdes agrdes;
X Anisou anisou;
X Atom atom;
X Author author;
X Cmpdes cmpdes;
X Cmpont cmpont;
X Compnd compnd;
X Conect conect;
X Cryst1 cryst1;
X // no End structure
X // no Endmdl structure
X Expdta expdta;
X Formul formul;
X Ftnote ftnote;
X Header header;
X Helix helix;
X Het het;
X Hetatm hetatm;
X Jrnl jrnl;
X Master master;
X Model model;
X Mtrix mtrix;
X Mtxdes mtxdes;
X Obslte obslte;
X Origx origx;
X Remark remark;
X Revdat revdat;
X Scale scale;
X Seqres seqres;
X Sheet sheet;
X Sigatm sigatm;
X Siguij siguij;
X Site site;
X Source source;
X Sprsde sprsde;
X Ssbond ssbond;
X Symdes symdes;
X Symop symop;
X Ter ter;
X Trnsfm trnsfm;
X Turn turn;
X Tvect tvect;
X User user;
X UserPdbrun userPdbrun;
X UserEyePos userEyePos;
X UserAtPos userAtPos;
X UserWindow userWindow;
X UserFocus userFocus;
X UserViewport userViewport;
X UserBgColor userBgColor;
X UserAngle userAngle;
X UserDistance userDistance;
X UserFile userFile;
X UserMarkname userMarkname;
X UserMark userMark;
X UserCName userCName;
X UserColor userColor;
X UserRadius userRadius;
X UserObject userObject;
X UserEndObj userEndObj;
X UserChain userChain;
X UserGfxBegin userGfxBegin;
X // no UserGfxEnd structure
X UserGfxColor userGfxColor;
X UserGfxNormal userGfxNormal;
X UserGfxVertex userGfxVertex;
X UserGfxFont userGfxFont;
X UserGfxTextPos userGfxTextPos;
X UserGfxLabel userGfxLabel;
X UserGfxMove userGfxMove;
X UserGfxDraw userGfxDraw;
X UserGfxMarker userGfxMarker;
X UserGfxPoint userGfxPoint;
X };
X
X PDB() { type(UNKNOWN); }
X PDB(RecordType t) { type(t); }
X PDB(const char *buf);
X RecordType type() const { return rType; }
X void type(RecordType t);
X const char *chars() const;
X static int PdbrunInputVersion() { return pdbrunInputVersion; }
X static int PdbrunOutputVersion() { return pdbrunOutputVersion; }
X static void PdbrunInputVersion(int v) { pdbrunInputVersion = v; }
X static void PdbrunOutputVersion(int v) { pdbrunOutputVersion = v; }
X static RecordType
X getType(const char *buf);
X static GfxType getGfxType(const char *buf);
X static const char
X *gfxChars(GfxType gt);
X static int sscanf(const char *, const char *, ...);
X static int sprintf(char *, const char *, ...);
X
X inline bool operator==(const PDB &r) const {
X if (rType != r.rType)
X return 0;
X return byteCmp(*this, r) == 0;
X }
X inline bool operator!=(const PDB &r) const {
X if (rType != r.rType)
X return 1;
X return byteCmp(*this, r) != 0;
X }
X
X friend istream &operator>>(istream &s, PDB &p);
X};
X
Xinline ostream &
Xoperator<<(ostream &s, const PDB &p)
X{
X s << p.chars();
X return s;
X}
X
X# endif // PDB_H
SHAR_EOF
if test 10596 -ne "`wc -c < 'pdb++.h'`"
then
echo shar: "error transmitting 'pdb++.h'" '(should have been 10596 characters)'
fi
fi
echo shar: "extracting 'pdbrun5_read.i'" '(1873 characters)'
if test -f 'pdbrun5_read.i'
then
echo shar: "will not over-write existing file 'pdbrun5_read.i'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdbrun5_read.i'
X/*
X * Copyright (c) 1994 The Regents of the University of California.
X * All rights reserved.
X *
X * Redistribution and use in source and binary forms are permitted
X * provided that the above copyright notice and this paragraph are
X * duplicated in all such forms and that any documentation,
X * advertising materials, and other materials related to such
X * distribution and use acknowledge that the software was developed
X * by the University of California, San Francisco. The name of the
X * University may not be used to endorse or promote products derived
X * from this software without specific prior written permission.
X * THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X * IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X * WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X *
X * $Id: pdbrun5_read.i,v 1.4 1994/11/16 22:09:29 gregc Exp $
X */
X/* PDBRUN */ "%12 %2d",
X/* EYEPOS */ "%12 %9f %9f %9f",
X/* ATPOS */ "%11 %9f %9f %9f",
X/* WINDOW */ "%12 %9f %9f %9f %9f %9f %9f",
X/* FOCUS */ "%11 %9f",
X/* VIEWPORT */ "%14 %9f %9f %9f %9f",
X/* BGCOLOR */ "USER BGCOLOR %lf %lf %lf",
X/* ANGLE */ "%11 %2d %6d %6d %6d %6d %8f",
X/* DISTANCE */ "%14 %2d %6d %6d %8f",
X/* FILE */ "%10 %61s",
X/* MARKNAME */ NULL,
X/* MARK */ NULL,
X/* CNAME */ "USER CNAME %s %lf %lf %lf",
X/* COLOR */ "USER COLOR %s %lf %lf %lf",
X/* RADIUS */ "%12 %7f",
X/* OBJECT */ "%12 %3d",
X/* ENDOBJ */ "%12 %3d",
X/* CHAIN */ "USER CHAIN %d %d",
X/* GFX BEGIN */ NULL,
X/* GFX END */ NULL,
X/* GFX COLOR */ "USER GFX COLOR %s %lf %lf %lf",
X/* GFX NORMAL */ NULL,
X/* GFX VERTEX */ NULL,
X/* GFX FONT */ "USER GFX FONT %s %d",
X/* GFX TEXTPOS */ NULL,
X/* GFX LABEL */ "USER GFX LABEL %lf %lf %lf %26[^\n]",
X/* GFX MOVE */ "%14 %9f %9f %9f",
X/* GFX DRAW */ "%14 %9f %9f %9f",
X/* GFX MARKER */ "%16 %9f %9f %9f",
X/* GFX POINT */ "%15 %9f %9f %9f",
SHAR_EOF
if test 1873 -ne "`wc -c < 'pdbrun5_read.i'`"
then
echo shar: "error transmitting 'pdbrun5_read.i'" '(should have been 1873 characters)'
fi
fi
echo shar: "extracting 'pdbrun5_write.i'" '(1843 characters)'
if test -f 'pdbrun5_write.i'
then
echo shar: "will not over-write existing file 'pdbrun5_write.i'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdbrun5_write.i'
X/*
X * Copyright (c) 1994 The Regents of the University of California.
X * All rights reserved.
X *
X * Redistribution and use in source and binary forms are permitted
X * provided that the above copyright notice and this paragraph are
X * duplicated in all such forms and that any documentation,
X * advertising materials, and other materials related to such
X * distribution and use acknowledge that the software was developed
X * by the University of California, San Francisco. The name of the
X * University may not be used to endorse or promote products derived
X * from this software without specific prior written permission.
X * THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X * IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X * WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X *
X * $Id: pdbrun5_write.i,v 1.2 1994/11/16 22:09:29 gregc Exp $
X */
X"USER PDBRUN %2d",
X"USER EYEPOS %9.3f %9.3f %9.3f",
X"USER ATPOS %9.3f %9.3f %9.3f",
X"USER WINDOW %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f",
X"USER FOCUS %9.3f",
X"USER VIEWPORT %9.3f %9.3f %9.3f %9.3f",
X"USER BGCOLOR %.3f %.3f %.3f",
X"USER ANGLE %2d %6d %6d %6d %6d %8.3f",
X"USER DISTANCE %2d %6d %6d %8.3f",
X"USER FILE %-61s",
XNULL, /* USER MARKNAME */
XNULL, /* USER MARK */
X"USER CNAME %-.38s %.3f %.3f %.3f",
X"USER COLOR %-.38s %5.3f %5.3f %5.3f",
X"USER RADIUS %7.3f",
X"USER OBJECT %3d",
X"USER ENDOBJ %3d",
X"USER CHAIN %d %d",
XNULL, /* USER GFX BEGIN */
XNULL, /* USER GFX END */
X"USER GFX COLOR %-.38s %.3f %.3f %.3f",
XNULL, /* USER GFX NORMAL */
XNULL, /* USER GFX VERTEX */
X"USER GFX FONT %-.53s %d",
XNULL, /* USER GFX TEXTPOS */
X"USER GFX LABEL %9.3f %9.3f %9.3f \"%-.24s\"",
X"USER GFX MOVE %9.3f %9.3f %9.3f",
X"USER GFX DRAW %9.3f %9.3f %9.3f",
X"USER GFX MARKER %9.3f %9.3f %9.3f",
X"USER GFX POINT %9.3f %9.3f %9.3f",
SHAR_EOF
if test 1843 -ne "`wc -c < 'pdbrun5_write.i'`"
then
echo shar: "error transmitting 'pdbrun5_write.i'" '(should have been 1843 characters)'
fi
fi
echo shar: "extracting 'pdbrun6_read.i'" '(1804 characters)'
if test -f 'pdbrun6_read.i'
then
echo shar: "will not over-write existing file 'pdbrun6_read.i'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdbrun6_read.i'
X/*
X * Copyright (c) 1994 The Regents of the University of California.
X * All rights reserved.
X *
X * Redistribution and use in source and binary forms are permitted
X * provided that the above copyright notice and this paragraph are
X * duplicated in all such forms and that any documentation,
X * advertising materials, and other materials related to such
X * distribution and use acknowledge that the software was developed
X * by the University of California, San Francisco. The name of the
X * University may not be used to endorse or promote products derived
X * from this software without specific prior written permission.
X * THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X * IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X * WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X *
X * $Id: pdbrun6_read.i,v 1.3 1995/01/20 01:20:36 gregc Exp $
X */
X/* PDBRUN */ "%12 %2d",
X/* EYEPOS */ "%12 %9f %9f %9f",
X/* ATPOS */ "%11 %9f %9f %9f",
X/* WINDOW */ "%12 %9f %9f %9f %9f %9f %9f",
X/* FOCUS */ "%11 %9f",
X/* VIEWPORT */ "%14 %9f %9f %9f %9f",
X/* BGCOLOR */ "%13 %5f %5f %5f",
X/* ANGLE */ "%11 %6d %6d %6d %6d %9f",
X/* DISTANCE */ "%14 %6d %6d %9f",
X/* FILE */ "%10 %4d %56s",
X/* MARKNAME */ "%14 %57s",
X/* MARK */ "%10 %57s",
X/* CNAME */ "%11 %5f %5f %5f %38s",
X/* COLOR */ "%11 %5f %5f %5f %38s",
X/* RADIUS */ "%12 %7f",
X/* OBJECT */ "%12 ",
X/* ENDOBJ */ "%12 ",
X/* CHAIN */ "%11 %6d %6d",
X/* GFX BEGIN */ "%15 %32s",
X/* GFX END */ "%13 ",
X/* GFX COLOR */ "%15 %5f %5f %5f %38s",
X/* GFX NORMAL */ "%16 %9f %9f %9f",
X/* GFX VERTEX */ "%16 %9f %9f %9f",
X/* GFX FONT */ "%14 %3d %53s",
X/* GFX TEXTPOS */ "%17 %9f %9f %9f",
X/* GFX LABEL */ "%15 %56s",
X/* GFX MOVE */ NULL,
X/* GFX DRAW */ NULL,
X/* GFX MARKER */ NULL,
X/* GFX POINT */ NULL,
SHAR_EOF
if test 1804 -ne "`wc -c < 'pdbrun6_read.i'`"
then
echo shar: "error transmitting 'pdbrun6_read.i'" '(should have been 1804 characters)'
fi
fi
echo shar: "extracting 'pdbrun6_write.i'" '(1787 characters)'
if test -f 'pdbrun6_write.i'
then
echo shar: "will not over-write existing file 'pdbrun6_write.i'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdbrun6_write.i'
X/*
X * Copyright (c) 1994 The Regents of the University of California.
X * All rights reserved.
X *
X * Redistribution and use in source and binary forms are permitted
X * provided that the above copyright notice and this paragraph are
X * duplicated in all such forms and that any documentation,
X * advertising materials, and other materials related to such
X * distribution and use acknowledge that the software was developed
X * by the University of California, San Francisco. The name of the
X * University may not be used to endorse or promote products derived
X * from this software without specific prior written permission.
X * THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X * IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X * WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X *
X * $Id: pdbrun6_write.i,v 1.3 1995/01/20 01:20:36 gregc Exp $
X */
X"USER PDBRUN %2d",
X"USER EYEPOS %9.3f %9.3f %9.3f",
X"USER ATPOS %9.3f %9.3f %9.3f",
X"USER WINDOW %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f",
X"USER FOCUS %9.3f",
X"USER VIEWPORT %9.3f %9.3f %9.3f %9.3f",
X"USER BGCOLOR %5.3f %5.3f %5.3f",
X"USER ANGLE %6d %6d %6d %6d %9.3f",
X"USER DISTANCE %6d %6d %9.3f",
X"USER FILE %4d %-56s",
X"USER MARKNAME %-57s",
X"USER MARK %-57s",
X"USER CNAME %5.3f %5.3f %5.3f %-42s",
X"USER COLOR %5.3f %5.3f %5.3f %-42s",
X"USER RADIUS %7.3f",
X"USER OBJECT",
X"USER ENDOBJ",
X"USER CHAIN %6d %6d",
X"USER GFX BEGIN %-32s",
X"USER GFX END",
X"USER GFX COLOR %5.3f %5.3f %5.3f %s",
X"USER GFX NORMAL %9.3f %9.3f %9.3f",
X"USER GFX VERTEX %9.3f %9.3f %9.3f",
X"USER GFX FONT %3d %-53s",
X"USER GFX TEXTPOS %9.3f %9.3f %9.3f",
X"USER GFX LABEL %-56s",
XNULL, /* USER GFX MOVE */
XNULL, /* USER GFX DRAW */
XNULL, /* USER GFX MARKER */
XNULL, /* USER GFX POINT */
SHAR_EOF
if test 1787 -ne "`wc -c < 'pdbrun6_write.i'`"
then
echo shar: "error transmitting 'pdbrun6_write.i'" '(should have been 1787 characters)'
fi
fi
echo shar: "extracting 'read_format.i'" '(3131 characters)'
if test -f 'read_format.i'
then
echo shar: "will not over-write existing file 'read_format.i'"
else
sed 's/^ X//' << \SHAR_EOF > 'read_format.i'
X/*
X * Copyright (c) 1993 The Regents of the University of California.
X * All rights reserved.
X *
X * Redistribution and use in source and binary forms are permitted
X * provided that the above copyright notice and this paragraph are
X * duplicated in all such forms and that any documentation,
X * advertising materials, and other materials related to such
X * distribution and use acknowledge that the software was developed
X * by the University of California, San Francisco. The name of the
X * University may not be used to endorse or promote products derived
X * from this software without specific prior written permission.
X * THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X * IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X * WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X *
X * $Id: read_format.i,v 1.2 93/04/21 19:55:49 gregc Exp $
X */
X/* UNKNOWN */ NULL,
X/* ANISOU */ "%6 %5d %4s%c%4s%c%4d%c %7d%7d%7d%7d%7d%7d", /* SIGUIJ */
X/* ATOM */ "%6 %5d %4s%c%4s%c%4d%c %8f%8f%8f%6f%6f %3d", /* HETATM, SIGATM */
X/* AUTHOR */ "%9 %c%60s", /* COMPND, EXPDTA, JRNL, SOURCE */
X/* COMPND */ "%9 %c%60s", /* AUTHOR */
X/* CONECT */ "%6 %5d%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d",
X/* CRYST1 */ "%6 %9f%9f%9f%7f%7f%7f %11s%4d",
X/* END */ NULL,
X/* FORMUL */ "%8 %2d %4s%2d%c%51s",
X/* FTNOTE */ "%7 %3d %59s", /* REMARK, SYMDES, MTXDES, CMPDES, AGRDES */
X/* HEADER */ "%10 %40s%9s %c%4s",
X/* HELIX */ "%7 %3d %3s %4s%c %4d%c %4s%c %4d%c%2d%30s",
X/* HET */ "%7 %4s %c%4d%c %5d%5 %40s",
X/* HETATM */ "%6 %5d %4s%c%4s%c%4d%c %8f%8f%8f%6f%6f %3d", /* ATOM */
X/* JRNL */ "%9 %c%60s", /* AUTHOR */
X/* MASTER */ "%10 %5d%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d",
X/* MTRIX */ "%5 %d %3d%10f%10f%10f%5 %10f %2d",
X/* OBSLTE */ "%8 %2d %9s %4s%6 %4s %4s %4s %4s %4s %4s %4s %4s",
X/* ORIGX */ "%5 %d%4 %10f%10f%10f%5 %10f", /* SCALE */
X/* REMARK */ "%7 %3d %59s", /* FTNOTE */
X/* REVDAT */ "%7 %3d%2d %9s %7s %c%7 %31s",
X/* SCALE */ "%5 %d%4 %10f%10f%10f%5 %10f",
X/* SEQRES */ "%6 %4d %c %4d %4s%4s%4s%4s%4s%4s%4s%4s%4s%4s%4s%4s%4s",
X/* SHEET */ "%6 %4d %3s%2d %4s%c%4d%c %4s%c%4d%c%2d %4s%4s%c%4d%c %4s%4s%c%4d%c",
X/* SIGATM */ "%6 %5d %4s%c%4s%c%4d%c %8f%8f%8f%6f%6f %3d", /* ATOM */
X/* SIGUIJ */ "%6 %5d %4s%c%4s%c%4d%c %7d%7d%7d%7d%7d%7d", /* ANISOU */
X/* SITE */ "%7 %3d %3s %2d %4s%c%4d%c %4s%c%4d%c %4s%c%4d%c %4s%c%4d%c",
X/* SOURCE */ "%9 %c%60s", /* AUTHOR */
X/* SPRSDE */ "%8 %2d %9s %4s%6 %4s %4s %4s %4s %4s %4s %4s %4s",
X/* SSBOND */ "%7 %3d %4s%c %4d%c %4s%c %4d%c%4 %30s",
X/* TER */ "%6 %5d%6 %4s%c%4d%c",
X/* TURN */ "%7 %3d %3s %4s%c%4d%c %4s%c%4d%c%4 %30s",
X/* TVECT */ "%7 %3d%10f%10f%10f%30s",
X/* USER */ "%4 %2s%66s",
X/* MODEL */ "%9 %5d",
X/* ENDMDL */ NULL,
X/* EXPDTA */ "%9 %c%60s", /* AUTHOR */
X/* SYMDES */ "%7 %3d %59s", /* FTNOTE */
X/* SYMOP */ "%5 %d %3d%10f%10f%10f%5 %10f",
X/* MTXDES */ "%7 %3d %59s", /* FTNOTE */
X/* CMPDES */ "%7 %3d %59s", /* FTNOTE */
X/* CMPONT */ "%7 %3d %4s%c %4d%c %4s%c %4d%c",
X/* TRNSFM */ "%7 %3d %3d %3d",
X/* AGRDES */ "%7 %3d %59s", /* FTNOTE */
X/* AGGRGT */ "%7 %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d",
SHAR_EOF
if test 3131 -ne "`wc -c < 'read_format.i'`"
then
echo shar: "error transmitting 'read_format.i'" '(should have been 3131 characters)'
fi
fi
echo shar: "extracting 'write_format.i'" '(2897 characters)'
if test -f 'write_format.i'
then
echo shar: "will not over-write existing file 'write_format.i'"
else
sed 's/^ X//' << \SHAR_EOF > 'write_format.i'
X/*
X * Copyright (c) 1993 The Regents of the University of California.
X * All rights reserved.
X *
X * Redistribution and use in source and binary forms are permitted
X * provided that the above copyright notice and this paragraph are
X * duplicated in all such forms and that any documentation,
X * advertising materials, and other materials related to such
X * distribution and use acknowledge that the software was developed
X * by the University of California, San Francisco. The name of the
X * University may not be used to endorse or promote products derived
X * from this software without specific prior written permission.
X * THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X * IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X * WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X *
X * $Id: write_format.i,v 1.3 93/06/24 11:53:47 gregc Exp $
X */
X"UNKNOWN: ??%-6.6s??",
X"ANISOU%5d %-4s%c%-4s%c%4d%c %7d%7d%7d%7d%7d%7d", /* SIGUIJ */
X"ATOM %5d %-4s%c%-4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %3D", /* HETATM, SIGATM */
X"AUTHOR %c%-60s", /* COMPND, EXPDTA, JRNL, SOURCE */
X"COMPND %c%-60s", /* AUTHOR */
X"CONECT%5d%5D%5D%5D%5D%5D%5D%5D%5D%5D%5D",
X"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d",
X"END",
X"FORMUL %2D %-4s%2D%c%-51s",
X"FTNOTE %3D %-59s", /* REMARK */
X"HEADER %-40s%-11s%c%-4s",
X"HELIX %3D %3s %-4s%c %4d%c %-4s%c %4d%c%2D%-30s",
X"HET %-4s %c%4d%c %5d %-40s",
X"HETATM%5d %-4s%c%-4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %3D",
X"JRNL %c%-60s", /* AUTHOR */
X"MASTER %5d%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d",
X"MTRIX%1d %3d%10.6f%10.6f%10.6f %10.5f %2D",
X"OBSLTE %2D %-9s %-10s%-5s%-5s%-5s%-5s%-5s%-5s%-5s%-4s",
X"ORIGX%1d %10.6f%10.6f%10.6f %10.5f", /* SCALE */
X"REMARK %3D %-59s",
X"REVDAT %3D%2D %-9s %-7s %c %-31s",
X"SCALE%1d %10.6f%10.6f%10.6f %10.5f", /* ORIGX */
X"SEQRES%4d %c %4d %-4s%-4s%-4s%-4s%-4s%-4s%-4s%-4s%-4s%-4s%-4s%-4s%-4s",
X"SHEET %4D %3s%2d %-4s%c%4d%c %-4s%c%4d%c%2d %-4s%-4s%c%4D%c %-4s%-4s%c%4D%c",
X"SIGATM%5d %-4s%c%-4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %3D",
X"SIGUIJ%5d %-4s%c%-4s%c%4d%c %7D%7D%7D%7D%7D%7D", /* ANISOU */
X"SITE %3d %3s %2d %-4s%c%4D%c %-4s%c%4D%c %-4s%c%4D%c %-4s%c%4D%c",
X"SOURCE %c%-60s", /* AUTHOR */
X"SPRSDE %2D %-9s %-10s%-5s%-5s%-5s%-5s%-5s%-5s%-5s%-4s",
X"SSBOND %3D %-4s%c %4d%c %-4s%c %4D%c %-30s",
X"TER %5d %-4s%c%4d%c",
X"TURN %3D %3s %-4s%c%4d%c %-4s%c%4d%c %-30s",
X"TVECT %3D%10.5f%10.5f%10.5f%-30s",
X"USER%-2s%-66s",
X"MODEL %5d",
X"ENDMDL",
X"EXPDTA %c%-60s", /* AUTHOR */
X"SYMDES %3d %59s", /* FTNOTE */
X"SYMOP%1d %3d%10.6f%10.6f%10.6f %10.5f",
X"MTXDES %3d %59s", /* FTNOTE */
X"CMPDES %3d %59s", /* FTNOTE */
X"CMPONT %3d %4s%c %4d%c %4s%c %4d%c",
X"TRNSFM %3d %3d %3d",
X"AGRDES %3d %59s", /* FTNOTE */
X"AGGRGT %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d",
SHAR_EOF
if test 2897 -ne "`wc -c < 'write_format.i'`"
then
echo shar: "error transmitting 'write_format.i'" '(should have been 2897 characters)'
fi
fi
echo shar: "extracting 'pdb++.cc'" '(1306 characters)'
if test -f 'pdb++.cc'
then
echo shar: "will not over-write existing file 'pdb++.cc'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb++.cc'
X//
X// Copyright (c) 1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdb++.cc,v 1.6 1994/12/13 22:41:17 gregc Exp $
X//
X
X#include "pdb++.h"
X
Xextern "C" {
X#include
X}
X
Xvoid
XPDB::type(RecordType t)
X{
X if (t == UNKNOWN) {
X // optimize default case (skip memset())
X rType = t;
X unknown.junk[0] = '\0';
X return;
X }
X memset(this, 0, sizeof *this);
X rType = t;
X switch (t) {
X default:
X break;
X case ATOM:
X atom.occupancy = 1.0;
X break;
X }
X}
X
Xint
XPDB::byteCmp(const PDB &l, const PDB &r)
X{
X return memcmp(&l, &r, sizeof (PDB));
X}
SHAR_EOF
if test 1306 -ne "`wc -c < 'pdb++.cc'`"
then
echo shar: "error transmitting 'pdb++.cc'" '(should have been 1306 characters)'
fi
fi
echo shar: "extracting 'pdb_chars.cc'" '(14454 characters)'
if test -f 'pdb_chars.cc'
then
echo shar: "will not over-write existing file 'pdb_chars.cc'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_chars.cc'
X//
X// Copyright (c) 1989,1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdb_chars.cc,v 1.8 95/02/28 14:09:52 gregc Exp $
X//
X// subroutine for writing PDB format files
X//
X
X# include "pdb++.h"
Xextern "C" {
X# include
X}
Xextern "C" int sprintf(char *, const char *, ...);
X
Xstatic char const * const pdbRecordFormat[PDB::NUM_TYPES] = {
X#include "write_format.i"
X};
X
Xstatic char const * const pdbrun5[PDB::NUM_USER] = {
X#include "pdbrun5_write.i"
X};
X
Xstatic char const * const pdbrun6[PDB::NUM_USER] = {
X#include "pdbrun6_write.i"
X};
X
Xconst char *
XPDB::chars(void) const
X{
X static char buf[BufLen];
X const char *fmt;
X const Sheet *sh;
X const Residue *shr0, *shr1, *sha0, *sha1;
X int count;
X
X // convert C structure to pdb record
X
X if (rType < USER_PDBRUN)
X fmt = pdbRecordFormat[rType];
X else if (pdbrunOutputVersion < 6)
X fmt = pdbrun5[rType - USER_PDBRUN];
X else
X fmt = pdbrun6[rType - USER_PDBRUN];
X switch (rType) {
X
X case UNKNOWN:
X count = sprintf(buf, fmt, unknown.junk);
X break;
X
X case AGGRGT:
X count = sprintf(buf, fmt, aggrgt.serialNum,
X aggrgt.numComponents, aggrgt.cmpontSerialNums[0],
X aggrgt.cmpontSerialNums[1],
X aggrgt.cmpontSerialNums[2],
X aggrgt.cmpontSerialNums[3],
X aggrgt.cmpontSerialNums[4],
X aggrgt.cmpontSerialNums[5],
X aggrgt.cmpontSerialNums[6],
X aggrgt.cmpontSerialNums[7],
X aggrgt.cmpontSerialNums[8],
X aggrgt.cmpontSerialNums[9],
X aggrgt.cmpontSerialNums[10],
X aggrgt.cmpontSerialNums[11],
X aggrgt.cmpontSerialNums[12],
X aggrgt.cmpontSerialNums[13]);
X break;
X
X case AGRDES:
X case CMPDES:
X case FTNOTE:
X case MTXDES:
X case REMARK:
X case SYMDES:
X count = sprintf(buf, fmt, agrdes.num, agrdes.text);
X break;
X
X case ANISOU:
X case SIGUIJ:
X count = sprintf(buf, fmt, anisou.serialNum, anisou.name,
X anisou.altLoc, anisou.residue.name,
X anisou.residue.chainId, anisou.residue.seqNum,
X anisou.residue.insertCode, anisou.u[0], anisou.u[1],
X anisou.u[2], anisou.u[3], anisou.u[4], anisou.u[5]);
X break;
X
X case ATOM:
X case HETATM:
X case SIGATM:
X count = sprintf(buf, fmt, atom.serialNum, atom.name,
X atom.altLoc, atom.residue.name, atom.residue.chainId,
X atom.residue.seqNum, atom.residue.insertCode,
X atom.xyz[0], atom.xyz[1], atom.xyz[2], atom.occupancy,
X atom.tempFactor, atom.ftnoteNum);
X break;
X
X case AUTHOR:
X case COMPND:
X case JRNL:
X case SOURCE:
X case EXPDTA:
X count = sprintf(buf, fmt, author.continuation, author.data);
X break;
X
X case CONECT:
X count = sprintf(buf, fmt, conect.serialNum,
X conect.covalent[0], conect.covalent[1],
X conect.covalent[2], conect.covalent[3],
X conect.bonds[0].hydrogen[0],
X conect.bonds[0].hydrogen[1], conect.bonds[0].salt,
X conect.bonds[1].hydrogen[0],
X conect.bonds[1].hydrogen[1], conect.bonds[1].salt);
X break;
X
X case CMPONT:
X count = sprintf(buf, fmt, cmpont.seqNum,
X cmpont.residues[0].name, cmpont.residues[0].chainId,
X cmpont.residues[0].seqNum,
X cmpont.residues[0].insertCode,
X cmpont.residues[1].name, cmpont.residues[1].chainId,
X cmpont.residues[1].seqNum,
X cmpont.residues[1].insertCode);
X break;
X
X case CRYST1:
X count = sprintf(buf, fmt, cryst1.a, cryst1.b, cryst1.c,
X cryst1.alpha, cryst1.beta, cryst1.gamma,
X cryst1.spaceGrp, cryst1.z);
X break;
X
X case END:
X case ENDMDL:
X count = sprintf(buf, fmt);
X break;
X
X case FORMUL:
X count = sprintf(buf, fmt, formul.component, formul.hetId,
X formul.continuation, formul.exclude, formul.formula);
X break;
X
X case HEADER:
X count = sprintf(buf, fmt, header.classification,
X header.timestamp, header.type, header.id);
X break;
X
X case HELIX:
X count = sprintf(buf, fmt, helix.serialNum, helix.id,
X helix.residues[0].name, helix.residues[0].chainId,
X helix.residues[0].seqNum,
X helix.residues[0].insertCode, helix.residues[1].name,
X helix.residues[1].chainId, helix.residues[1].seqNum,
X helix.residues[1].insertCode, helix.type,
X helix.comment);
X break;
X
X case HET:
X count = sprintf(buf, fmt, het.hetGrp.name,
X het.hetGrp.chainId, het.hetGrp.seqNum,
X het.hetGrp.insertCode, het.numAtoms, het.text);
X break;
X
X case MASTER:
X count = sprintf(buf, fmt, master.numRemark, master.numFtnote,
X master.numHet, master.numHelix, master.numSheet,
X master.numTurn, master.numSite, master.numTransform,
X master.numCoordinate, master.numTer,
X master.numConect, master.numSeqres);
X break;
X
X case MODEL:
X count = sprintf(buf, fmt, model.num);
X break;
X
X case MTRIX:
X count = sprintf(buf, fmt, mtrix.rowNum, mtrix.serialNum,
X mtrix.m1, mtrix.m2, mtrix.m3, mtrix.v, mtrix.given);
X break;
X
X case OBSLTE:
X count = sprintf(buf, fmt, obslte.continuation, obslte.timestamp,
X obslte.oldId, obslte.idMap[0], obslte.idMap[1],
X obslte.idMap[2], obslte.idMap[3], obslte.idMap[4],
X obslte.idMap[2], obslte.idMap[6], obslte.idMap[7]);
X break;
X
X case ORIGX:
X count = sprintf(buf, fmt, origx.rowNum, origx.o1, origx.o2,
X origx.o3, origx.t);
X break;
X
X case REVDAT:
X count = sprintf(buf, fmt, revdat.modification,
X revdat.continuation, revdat.timestamp, revdat.id,
X revdat.modType, revdat.corrections);
X break;
X
X case SCALE:
X count = sprintf(buf, fmt, scale.rowNum, scale.s1, scale.s2,
X scale.s3, scale.u);
X break;
X
X case SEQRES:
X count = sprintf(buf, fmt, seqres.serialNum, seqres.chainId,
X seqres.count, seqres.names[0], seqres.names[1],
X seqres.names[2], seqres.names[3], seqres.names[4],
X seqres.names[5], seqres.names[6], seqres.names[7],
X seqres.names[8], seqres.names[9], seqres.names[10],
X seqres.names[11], seqres.names[12]);
X break;
X
X case SHEET:
X sh = &sheet;
X shr0 = &sh->residues[0];
X shr1 = &sh->residues[1];
X sha0 = &sh->atoms[0].residue;
X sha1 = &sh->atoms[1].residue;
X count = sprintf(buf, fmt, sh->strandNum, sh->id, sh->count,
X shr0->name, shr0->chainId, shr0->seqNum,
X shr0->insertCode, shr1->name, shr1->chainId,
X shr1->seqNum, shr1->insertCode, sh->sense,
X sh->atoms[0].name, sha0->name, sha0->chainId,
X sha0->seqNum, sha0->insertCode, sh->atoms[1].name,
X sha1->name, sha1->chainId, sha1->seqNum,
X sha1->insertCode);
X break;
X
X case SITE:
X shr0 = &site.residues[0];
X shr1 = &site.residues[1];
X sha0 = &site.residues[2];
X sha1 = &site.residues[3];
X count = sprintf(buf, fmt, site.seqNum, site.id, site.count,
X shr0->name, shr0->chainId, shr0->seqNum,
X shr0->insertCode,
X shr1->name, shr1->chainId, shr1->seqNum,
X shr1->insertCode,
X sha0->name, sha0->chainId, sha0->seqNum,
X sha0->insertCode,
X sha1->name, sha1->chainId, sha1->seqNum,
X sha1->insertCode);
X break;
X
X case SPRSDE:
X count = sprintf(buf, fmt, sprsde.continuation, sprsde.timestamp,
X sprsde.id, sprsde.supersede[0], sprsde.supersede[1],
X sprsde.supersede[2], sprsde.supersede[3],
X sprsde.supersede[4], sprsde.supersede[5],
X sprsde.supersede[6], sprsde.supersede[7]);
X break;
X
X case SSBOND:
X count = sprintf(buf, fmt, ssbond.seqNum,
X ssbond.residues[0].name, ssbond.residues[0].chainId,
X ssbond.residues[0].seqNum,
X ssbond.residues[0].insertCode,
X ssbond.residues[1].name, ssbond.residues[1].chainId,
X ssbond.residues[1].seqNum,
X ssbond.residues[1].insertCode, ssbond.comment);
X break;
X
X case SYMOP:
X count = sprintf(buf, fmt, symop.rowNum, symop.serialNum,
X symop.s1, symop.s2, symop.s3, symop.t);
X break;
X
X case TER:
X count = sprintf(buf, fmt, ter.serialNum, ter.residue.name,
X ter.residue.chainId, ter.residue.seqNum,
X ter.residue.insertCode);
X break;
X
X case TRNSFM:
X count = sprintf(buf, fmt, trnsfm.resultSerialNum,
X trnsfm.applySerialNum, trnsfm.sourceSerialNum);
X break;
X
X case TURN:
X count = sprintf(buf, fmt, turn.seqNum, turn.id,
X turn.residues[0].name, turn.residues[0].chainId,
X turn.residues[0].seqNum, turn.residues[0].insertCode,
X turn.residues[1].name, turn.residues[1].chainId,
X turn.residues[1].seqNum, turn.residues[1].insertCode,
X turn.comment);
X break;
X
X case TVECT:
X count = sprintf(buf, fmt, tvect.serialNum, tvect.t1, tvect.t2,
X tvect.t3, tvect.comment);
X break;
X
X case USER:
X count = sprintf(buf, fmt, user.subtype, user.text);
X break;
X
X case USER_PDBRUN:
X count = sprintf(buf, fmt, userPdbrun.version);
X pdbrunOutputVersion = userPdbrun.version;
X break;
X
X case USER_EYEPOS:
X count = sprintf(buf, fmt, userEyePos.xyz[0], userEyePos.xyz[1],
X userEyePos.xyz[2]);
X break;
X
X case USER_ATPOS:
X count = sprintf(buf, fmt, userAtPos.xyz[0], userAtPos.xyz[1],
X userAtPos.xyz[2]);
X break;
X
X case USER_WINDOW:
X count = sprintf(buf, fmt, userWindow.left, userWindow.right,
X userWindow.bottom, userWindow.top, userWindow.hither,
X userWindow.yon);
X break;
X
X case USER_FOCUS:
X count = sprintf(buf, fmt, userFocus.focus);
X break;
X
X case USER_VIEWPORT:
X count = sprintf(buf, fmt, userViewport.xmin, userViewport.xmax,
X userViewport.ymin, userViewport.ymax);
X break;
X
X case USER_BGCOLOR:
X if (pdbrunOutputVersion < 6)
X count = ::sprintf(buf, fmt, userBgColor.rgb[0],
X userBgColor.rgb[1], userBgColor.rgb[2]);
X else
X count = sprintf(buf, fmt, userBgColor.rgb[0],
X userBgColor.rgb[1], userBgColor.rgb[2]);
X break;
X
X case USER_ANGLE:
X if (pdbrunOutputVersion < 6)
X count = sprintf(buf, fmt, userAngle.which,
X userAngle.atom0, userAngle.atom1,
X userAngle.atom2, userAngle.atom3,
X userAngle.angle);
X else
X count = sprintf(buf, fmt, userAngle.atom0,
X userAngle.atom1, userAngle.atom2,
X userAngle.atom3, userAngle.angle);
X break;
X
X case USER_DISTANCE:
X if (pdbrunOutputVersion < 6)
X count = sprintf(buf, fmt, userDistance.which,
X userDistance.atom0, userDistance.atom1,
X userDistance.distance);
X else
X count = sprintf(buf, fmt, userDistance.atom0,
X userDistance.atom1, userDistance.distance);
X break;
X
X case USER_FILE:
X if (pdbrunOutputVersion < 6)
X count = sprintf(buf, fmt, userFile.filename);
X else
X count = sprintf(buf, fmt, userFile.model,
X userFile.filename);
X break;
X
X case USER_MARKNAME:
X if (pdbrunOutputVersion < 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userMarkname.markname);
X break;
X
X case USER_MARK:
X if (pdbrunOutputVersion < 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userMark.markname);
X break;
X
X case USER_CNAME:
X if (pdbrunOutputVersion < 6)
X count = ::sprintf(buf, fmt, userCName.name,
X userCName.rgb[0], userCName.rgb[1],
X userCName.rgb[2]);
X else
X count = sprintf(buf, fmt, userCName.rgb[0],
X userCName.rgb[1], userCName.rgb[2],
X userCName.name);
X break;
X
X case USER_COLOR:
X if (pdbrunOutputVersion < 6)
X count = ::sprintf(buf, fmt, userColor.spec,
X userColor.rgb[0], userColor.rgb[1],
X userColor.rgb[2]);
X else
X count = sprintf(buf, fmt, userColor.rgb[0],
X userColor.rgb[1], userColor.rgb[2],
X userColor.spec);
X break;
X
X case USER_RADIUS:
X count = sprintf(buf, fmt, userRadius.radius);
X break;
X
X case USER_OBJECT:
X count = sprintf(buf, fmt, userObject.model);
X break;
X
X case USER_ENDOBJ:
X count = sprintf(buf, fmt, userEndObj.model);
X break;
X
X case USER_CHAIN:
X if (pdbrunOutputVersion < 6)
X count = ::sprintf(buf, fmt, userChain.atom0,
X userChain.atom1);
X else
X count = sprintf(buf, fmt, userChain.atom0,
X userChain.atom1);
X break;
X
X case USER_GFX_BEGIN:
X if (pdbrunOutputVersion < 6)
X count = 0;
X else if (userGfxBegin.primitive == GFX_UNKNOWN)
X count = sprintf(buf, fmt, userGfxBegin.unknown);
X else
X count = sprintf(buf, fmt,
X gfxChars(userGfxBegin.primitive));
X break;
X
X case USER_GFX_END:
X if (pdbrunOutputVersion < 6)
X count = 0;
X else
X count = sprintf(buf, fmt);
X break;
X
X case USER_GFX_COLOR:
X if (pdbrunOutputVersion < 6)
X count = ::sprintf(buf, fmt, userGfxColor.spec,
X userGfxColor.rgb[0], userGfxColor.rgb[1],
X userGfxColor.rgb[2]);
X else
X count = sprintf(buf, fmt, userGfxColor.rgb[0],
X userGfxColor.rgb[1], userGfxColor.rgb[2],
X userGfxColor.spec);
X break;
X
X case USER_GFX_NORMAL:
X if (pdbrunOutputVersion < 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userGfxNormal.xyz[0],
X userGfxNormal.xyz[1], userGfxNormal.xyz[2]);
X break;
X
X case USER_GFX_VERTEX:
X if (pdbrunOutputVersion < 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userGfxVertex.xyz[0],
X userGfxVertex.xyz[1], userGfxVertex.xyz[2]);
X break;
X
X case USER_GFX_FONT:
X if (pdbrunOutputVersion < 6)
X count = ::sprintf(buf, fmt, userGfxFont.name,
X userGfxFont.size);
X else
X count = sprintf(buf, fmt, userGfxFont.size,
X userGfxFont.name);
X break;
X
X case USER_GFX_TEXTPOS:
X if (pdbrunOutputVersion < 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userGfxTextPos.xyz[0],
X userGfxTextPos.xyz[1], userGfxTextPos.xyz[2]);
X break;
X
X case USER_GFX_LABEL:
X if (pdbrunOutputVersion < 6)
X count = ::sprintf(buf, fmt, userGfxLabel.xyz[0],
X userGfxLabel.xyz[1], userGfxLabel.xyz[2],
X userGfxLabel.text);
X else
X count = sprintf(buf, fmt, userGfxLabel.text);
X break;
X
X case USER_GFX_MOVE:
X if (pdbrunOutputVersion >= 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userGfxMove.xyz[0],
X userGfxMove.xyz[1], userGfxMove.xyz[2]);
X break;
X
X case USER_GFX_DRAW:
X if (pdbrunOutputVersion >= 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userGfxDraw.xyz[0],
X userGfxDraw.xyz[1], userGfxDraw.xyz[2]);
X break;
X
X case USER_GFX_MARKER:
X if (pdbrunOutputVersion >= 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userGfxMarker.xyz[0],
X userGfxMarker.xyz[1], userGfxMarker.xyz[2]);
X break;
X
X case USER_GFX_POINT:
X if (pdbrunOutputVersion >= 6)
X count = 0;
X else
X count = sprintf(buf, fmt, userGfxPoint.xyz[0],
X userGfxPoint.xyz[1], userGfxPoint.xyz[2]);
X break;
X
X default:
X count = sprintf(buf, "unknown pdb record #%d", rType);
X break;
X }
X
X // find last non-blank in buf, and shorten it
X while (count > 1 && isspace(buf[count - 1]))
X count -= 1;
X buf[count] = '\0';
X return buf;
X}
SHAR_EOF
if test 14454 -ne "`wc -c < 'pdb_chars.cc'`"
then
echo shar: "error transmitting 'pdb_chars.cc'" '(should have been 14454 characters)'
fi
fi
echo shar: "extracting 'pdb_read.cc'" '(16032 characters)'
if test -f 'pdb_read.cc'
then
echo shar: "will not over-write existing file 'pdb_read.cc'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_read.cc'
X//
X// Copyright (c) 1989, 1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdb_read.cc,v 1.8 95/02/28 14:09:28 gregc Exp $
X//
X// subroutine for reading PDB format files
X//
X
X# include "pdb++.h"
X# include
X
X# ifndef NULL
X# define NULL 0
X# endif
X
Xextern "C" int sscanf(const char *, const char *, ...);
X
X//
X// for each pdb record type there is a format reading in the
X// record values and for printing them out.
X//
X// The actual format of a line written, is the print format
X// followed by blank padding to 72 characters, followed by
X// 8 characters of file and line information.
X//
X
Xstatic char const * const pdbRecordFormat[PDB::NUM_TYPES] = {
X#include "read_format.i"
X};
X
Xstatic char const * const pdbrun5[PDB::NUM_USER] = {
X#include "pdbrun5_read.i"
X};
X
Xstatic char const * const pdbrun6[PDB::NUM_USER] = {
X#include "pdbrun6_read.i"
X};
X
XPDB::PDB(const char *buf)
X{
X const char *fmt;
X Sheet *sh;
X Residue *sha0, *sha1;
X
X // convert pdb record to C structure
X
X memset(this, 0, sizeof *this);
X rType = getType(buf);
X if (rType < USER_PDBRUN)
X fmt = pdbRecordFormat[rType];
X else if (pdbrunInputVersion < 6)
X fmt = pdbrun5[rType - USER_PDBRUN];
X else
X fmt = pdbrun6[rType - USER_PDBRUN];
X switch (rType) {
X
X default:
X case UNKNOWN:
Xunknown:
X rType = UNKNOWN; // in case of goto
X (void) sprintf(unknown.junk, "%72s", buf);
X break;
X
X case AGGRGT:
X if (0 > sscanf(buf, fmt, &aggrgt.serialNum,
X &aggrgt.numComponents,
X &aggrgt.cmpontSerialNums[0],
X &aggrgt.cmpontSerialNums[1],
X &aggrgt.cmpontSerialNums[2],
X &aggrgt.cmpontSerialNums[3],
X &aggrgt.cmpontSerialNums[4],
X &aggrgt.cmpontSerialNums[5],
X &aggrgt.cmpontSerialNums[6],
X &aggrgt.cmpontSerialNums[7],
X &aggrgt.cmpontSerialNums[8],
X &aggrgt.cmpontSerialNums[9],
X &aggrgt.cmpontSerialNums[10],
X &aggrgt.cmpontSerialNums[11],
X &aggrgt.cmpontSerialNums[12],
X &aggrgt.cmpontSerialNums[13]))
X goto unknown;
X break;
X
X case AGRDES:
X case CMPDES:
X case FTNOTE:
X case MTXDES:
X case REMARK:
X case SYMDES:
X if (0 > sscanf(buf, fmt, &agrdes.num, agrdes.text))
X goto unknown;
X break;
X
X case ANISOU:
X case SIGUIJ:
X if (0 > sscanf(buf, fmt, &anisou.serialNum, anisou.name,
X &anisou.altLoc, anisou.residue.name,
X &anisou.residue.chainId,
X &anisou.residue.seqNum,
X &anisou.residue.insertCode,
X &anisou.u[0], &anisou.u[1], &anisou.u[2],
X &anisou.u[3], &anisou.u[4], &anisou.u[5]))
X goto unknown;
X break;
X
X case ATOM:
X case HETATM:
X case SIGATM:
X if (0 > sscanf(buf, fmt, &atom.serialNum, atom.name,
X &atom.altLoc, atom.residue.name,
X &atom.residue.chainId, &atom.residue.seqNum,
X &atom.residue.insertCode, &atom.xyz[0],
X &atom.xyz[1], &atom.xyz[2], &atom.occupancy,
X &atom.tempFactor, &atom.ftnoteNum))
X goto unknown;
X break;
X
X case AUTHOR:
X case COMPND:
X case EXPDTA:
X case JRNL:
X case SOURCE:
X if (0 > sscanf(buf, fmt, &author.continuation, author.data))
X goto unknown;
X break;
X
X case CONECT:
X if (0 > sscanf(buf, fmt, &conect.serialNum,
X &conect.covalent[0], &conect.covalent[1],
X &conect.covalent[2], &conect.covalent[3],
X &conect.bonds[0].hydrogen[0],
X &conect.bonds[0].hydrogen[1],
X &conect.bonds[0].salt,
X &conect.bonds[1].hydrogen[0],
X &conect.bonds[1].hydrogen[1],
X &conect.bonds[1].salt))
X goto unknown;
X break;
X
X case CMPONT:
X if (0 > sscanf(buf, fmt, &cmpont.seqNum,
X cmpont.residues[0].name,
X &cmpont.residues[0].chainId,
X &cmpont.residues[0].seqNum,
X &cmpont.residues[0].insertCode,
X cmpont.residues[1].name,
X &cmpont.residues[1].chainId,
X &cmpont.residues[1].seqNum,
X &cmpont.residues[1].insertCode))
X goto unknown;
X break;
X
X case CRYST1:
X if (0 > sscanf(buf, fmt, &cryst1.a, &cryst1.b, &cryst1.c,
X &cryst1.alpha, &cryst1.beta, &cryst1.gamma,
X cryst1.spaceGrp, &cryst1.z))
X goto unknown;
X break;
X
X case END:
X case ENDMDL:
X break;
X
X case FORMUL:
X if (0 > sscanf(buf, fmt, &formul.component, formul.hetId,
X &formul.continuation, &formul.exclude,
X formul.formula))
X goto unknown;
X break;
X
X case HEADER:
X if (0 > sscanf(buf, fmt, header.classification,
X header.timestamp, &header.type, header.id))
X goto unknown;
X break;
X
X case HELIX:
X if (0 > sscanf(buf, fmt, &helix.serialNum, helix.id,
X helix.residues[0].name,
X &helix.residues[0].chainId,
X &helix.residues[0].seqNum,
X &helix.residues[0].insertCode,
X helix.residues[1].name,
X &helix.residues[1].chainId,
X &helix.residues[1].seqNum,
X &helix.residues[1].insertCode,
X &helix.type, helix.comment))
X goto unknown;
X break;
X
X case HET:
X if (0 > sscanf(buf, fmt, het.hetGrp.name,
X &het.hetGrp.chainId, &het.hetGrp.seqNum,
X &het.hetGrp.insertCode, &het.numAtoms,
X het.text))
X goto unknown;
X break;
X
X case MASTER:
X if (0 > sscanf(buf, fmt, &master.numRemark, &master.numFtnote,
X &master.numHet, &master.numHelix,
X &master.numSheet, &master.numTurn,
X &master.numSite, &master.numTransform,
X &master.numCoordinate, &master.numTer,
X &master.numConect, &master.numSeqres))
X goto unknown;
X break;
X
X case MODEL:
X if (0 > sscanf(buf, fmt, &model.num))
X goto unknown;
X break;
X
X case MTRIX:
X if (0 > sscanf(buf, fmt, &mtrix.rowNum, &mtrix.serialNum,
X &mtrix.m1, &mtrix.m2, &mtrix.m3, &mtrix.v,
X &mtrix.given))
X goto unknown;
X break;
X
X case OBSLTE:
X if (0 > sscanf(buf, fmt, &obslte.continuation, obslte.timestamp,
X obslte.oldId, obslte.idMap[0],
X obslte.idMap[1], obslte.idMap[2],
X obslte.idMap[3], obslte.idMap[4],
X obslte.idMap[2], obslte.idMap[6],
X obslte.idMap[7]))
X goto unknown;
X break;
X
X case ORIGX:
X if (0 > sscanf(buf, fmt, &origx.rowNum, &origx.o1, &origx.o2,
X &origx.o3, &origx.t))
X goto unknown;
X break;
X
X case REVDAT:
X if (0 > sscanf(buf, fmt, &revdat.modification,
X &revdat.continuation, revdat.timestamp,
X revdat.id, &revdat.modType,
X revdat.corrections))
X goto unknown;
X break;
X
X case SCALE:
X if (0 > sscanf(buf, fmt, &scale.rowNum, &scale.s1, &scale.s2,
X &scale.s3, &scale.u))
X goto unknown;
X break;
X
X case SEQRES:
X if (0 > sscanf(buf, fmt, &seqres.serialNum, &seqres.chainId,
X &seqres.count, seqres.names[0], seqres.names[1],
X seqres.names[2], seqres.names[3],
X seqres.names[4], seqres.names[5],
X seqres.names[6], seqres.names[7],
X seqres.names[8], seqres.names[9],
X seqres.names[10], seqres.names[11],
X seqres.names[12]))
X goto unknown;
X break;
X
X case SHEET:
X sh = &sheet;
X sha0 = &sh->atoms[0].residue;
X sha1 = &sh->atoms[1].residue;
X if (0 > sscanf(buf, fmt, &sh->strandNum, sh->id, &sh->count,
X sh->residues[0].name, &sh->residues[0].chainId,
X &sh->residues[0].seqNum,
X &sh->residues[0].insertCode,
X sh->residues[1].name, &sh->residues[1].chainId,
X &sh->residues[1].seqNum,
X &sh->residues[1].insertCode, &sh->sense,
X sh->atoms[0].name, sha0->name, &sha0->chainId,
X &sha0->seqNum, &sha0->insertCode,
X sh->atoms[1].name, sha1->name, &sha1->chainId,
X &sha1->seqNum, &sha1->insertCode))
X goto unknown;
X break;
X
X case SITE:
X if (0 > sscanf(buf, fmt, &site.seqNum, site.id, &site.count,
X site.residues[0].name,
X &site.residues[0].chainId,
X &site.residues[0].seqNum,
X &site.residues[0].insertCode,
X site.residues[1].name,
X &site.residues[1].chainId,
X &site.residues[1].seqNum,
X &site.residues[1].insertCode,
X site.residues[2].name,
X &site.residues[2].chainId,
X &site.residues[2].seqNum,
X &site.residues[2].insertCode,
X site.residues[3].name,
X &site.residues[3].chainId,
X &site.residues[3].seqNum,
X &site.residues[3].insertCode))
X goto unknown;
X break;
X
X case SPRSDE:
X if (0 > sscanf(buf, fmt, &sprsde.continuation,
X sprsde.timestamp, sprsde.id,
X sprsde.supersede[0], sprsde.supersede[1],
X sprsde.supersede[2], sprsde.supersede[3],
X sprsde.supersede[4], sprsde.supersede[5],
X sprsde.supersede[6], sprsde.supersede[7]))
X goto unknown;
X break;
X
X case SSBOND:
X if (0 > sscanf(buf, fmt, &ssbond.seqNum,
X ssbond.residues[0].name,
X &ssbond.residues[0].chainId,
X &ssbond.residues[0].seqNum,
X &ssbond.residues[0].insertCode,
X ssbond.residues[1].name,
X &ssbond.residues[1].chainId,
X &ssbond.residues[1].seqNum,
X &ssbond.residues[1].insertCode,
X ssbond.comment))
X goto unknown;
X break;
X
X case SYMOP:
X if (0 > sscanf(buf, fmt, &symop.rowNum, &symop.serialNum,
X &symop.s1, &symop.s2, &symop.s3, &symop.t))
X goto unknown;
X break;
X
X case TER:
X if (0 > sscanf(buf, fmt, &ter.serialNum, ter.residue.name,
X &ter.residue.chainId, &ter.residue.seqNum,
X &ter.residue.insertCode))
X goto unknown;
X break;
X
X case TRNSFM:
X if (0 > sscanf(buf, fmt, &trnsfm.resultSerialNum,
X &trnsfm.applySerialNum,
X &trnsfm.sourceSerialNum))
X goto unknown;
X break;
X
X case TURN:
X if (0 > sscanf(buf, fmt, &turn.seqNum, turn.id,
X turn.residues[0].name,
X &turn.residues[0].chainId,
X &turn.residues[0].seqNum,
X &turn.residues[0].insertCode,
X turn.residues[1].name,
X &turn.residues[1].chainId,
X &turn.residues[1].seqNum,
X &turn.residues[1].insertCode, turn.comment))
X goto unknown;
X break;
X
X case TVECT:
X if (0 > sscanf(buf, fmt, &tvect.serialNum, &tvect.t1,
X &tvect.t2, &tvect.t3, tvect.comment))
X goto unknown;
X break;
X
Xuser:
X rType = USER;
X fmt = pdbRecordFormat[rType];
X case USER:
X if (0 > sscanf(buf, fmt, user.subtype, user.text))
X goto unknown;
X break;
X
X case USER_PDBRUN:
X if (0 > sscanf(buf, fmt, &userPdbrun.version))
X goto user;
X pdbrunInputVersion = userPdbrun.version;
X break;
X
X case USER_EYEPOS:
X if (0 > sscanf(buf, fmt, &userEyePos.xyz[0],
X &userEyePos.xyz[1], &userEyePos.xyz[2]))
X goto user;
X break;
X
X case USER_ATPOS:
X if (0 > sscanf(buf, fmt, &userAtPos.xyz[0],
X &userAtPos.xyz[1], &userAtPos.xyz[2]))
X goto user;
X break;
X
X case USER_WINDOW:
X if (0 > sscanf(buf, fmt, &userWindow.left, &userWindow.right,
X &userWindow.bottom, &userWindow.top,
X &userWindow.hither, &userWindow.yon))
X goto user;
X break;
X
X case USER_FOCUS:
X if (0 > sscanf(buf, fmt, &userFocus.focus))
X goto user;
X break;
X
X case USER_VIEWPORT:
X if (0 > sscanf(buf, fmt, &userViewport.xmin, &userViewport.xmax,
X &userViewport.ymin, &userViewport.ymax))
X goto user;
X break;
X
X case USER_BGCOLOR:
X if (pdbrunInputVersion < 6) {
X if (0 > ::sscanf(buf, fmt, &userBgColor.rgb[0],
X &userBgColor.rgb[1],
X &userBgColor.rgb[2]))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userBgColor.rgb[0],
X &userBgColor.rgb[1], &userBgColor.rgb[2]))
X goto user;
X break;
X
X case USER_ANGLE:
X if (pdbrunInputVersion < 6) {
X if (0 > sscanf(buf, fmt, &userAngle.which,
X &userAngle.atom0, &userAngle.atom1,
X &userAngle.atom2, &userAngle.atom3,
X &userAngle.angle))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userAngle.atom0,
X &userAngle.atom1, &userAngle.atom2,
X &userAngle.atom3, &userAngle.angle))
X goto user;
X break;
X
X case USER_DISTANCE:
X if (pdbrunInputVersion < 6) {
X if (0 > sscanf(buf, fmt, &userDistance.which,
X &userDistance.atom0,
X &userDistance.atom1,
X &userDistance.distance))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userDistance.atom0,
X &userDistance.atom1, &userDistance.distance))
X goto user;
X break;
X
X case USER_FILE:
X if (pdbrunInputVersion < 6) {
X if (0 > sscanf(buf, fmt, userFile.filename))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userFile.model,
X userFile.filename))
X goto user;
X break;
X
X case USER_MARKNAME:
X if (pdbrunInputVersion < 6
X || 0 > sscanf(buf, fmt, userMarkname.markname))
X goto user;
X break;
X
X case USER_MARK:
X if (pdbrunInputVersion < 6
X || 0 > sscanf(buf, fmt, userMark.markname))
X goto user;
X break;
X
X case USER_CNAME:
X if (pdbrunInputVersion < 6) {
X if (0 > ::sscanf(buf, fmt, userCName.name,
X &userCName.rgb[0], &userCName.rgb[1],
X &userCName.rgb[2]))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userCName.rgb[0],
X &userCName.rgb[1], &userCName.rgb[2],
X userCName.name))
X goto user;
X break;
X
X case USER_COLOR:
X if (pdbrunInputVersion < 6) {
X if (0 > ::sscanf(buf, fmt, userColor.spec,
X &userColor.rgb[0], &userColor.rgb[1],
X &userColor.rgb[2]))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userColor.rgb[0],
X &userColor.rgb[1], &userColor.rgb[2],
X userColor.spec))
X goto user;
X break;
X
X case USER_RADIUS:
X if (0 > sscanf(buf, fmt, &userRadius.radius))
X goto user;
X break;
X
X case USER_OBJECT:
X if (pdbrunInputVersion < 6) {
X if (0 > sscanf(buf, fmt, &userObject.model))
X goto user;
X }
X break;
X
X case USER_ENDOBJ:
X if (pdbrunInputVersion < 6) {
X if (0 > sscanf(buf, fmt, &userEndObj.model))
X goto user;
X }
X break;
X
X case USER_CHAIN:
X if (pdbrunInputVersion < 6) {
X if (0 > ::sscanf(buf, fmt, &userChain.atom0,
X &userChain.atom1))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userChain.atom0,
X &userChain.atom1))
X goto user;
X break;
X
X case USER_GFX_BEGIN:
X if (pdbrunInputVersion < 6
X || 0 > sscanf(buf, fmt, userGfxBegin.unknown))
X goto user;
X userGfxBegin.primitive = getGfxType(userGfxBegin.unknown);
X break;
X
X case USER_GFX_END:
X if (pdbrunInputVersion < 6)
X goto user;
X break;
X
X case USER_GFX_COLOR:
X if (pdbrunInputVersion < 6) {
X if (0 > ::sscanf(buf, fmt, userGfxColor.spec,
X &userGfxColor.rgb[0],
X &userGfxColor.rgb[1],
X &userGfxColor.rgb[2]))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userGfxColor.rgb[0],
X &userGfxColor.rgb[1], &userGfxColor.rgb[2],
X userGfxColor.spec))
X goto user;
X break;
X
X case USER_GFX_NORMAL:
X if (pdbrunInputVersion < 6
X || 0 > sscanf(buf, fmt, &userGfxNormal.xyz[0],
X &userGfxNormal.xyz[1],
X &userGfxNormal.xyz[2]))
X goto user;
X break;
X
X case USER_GFX_VERTEX:
X if (pdbrunInputVersion < 6
X || 0 > sscanf(buf, fmt, &userGfxVertex.xyz[0],
X &userGfxVertex.xyz[1],
X &userGfxVertex.xyz[2]))
X goto user;
X break;
X
X case USER_GFX_FONT:
X if (pdbrunInputVersion < 6) {
X if (0 > ::sscanf(buf, fmt, userGfxFont.name,
X &userGfxFont.size))
X goto user;
X } else if (0 > sscanf(buf, fmt, &userGfxFont.size,
X userGfxFont.name))
X goto user;
X break;
X
X case USER_GFX_TEXTPOS:
X if (pdbrunInputVersion < 6
X || 0 > sscanf(buf, fmt, &userGfxTextPos.xyz[0],
X &userGfxTextPos.xyz[1], &userGfxTextPos.xyz[2]))
X goto user;
X break;
X
X case USER_GFX_LABEL:
X if (pdbrunInputVersion < 6) {
X if (0 > ::sscanf(buf, fmt, &userGfxLabel.xyz[0],
X &userGfxLabel.xyz[1],
X &userGfxLabel.xyz[2],
X userGfxLabel.text))
X goto user;
X } else if (0 > sscanf(buf, fmt, userGfxLabel.text))
X goto user;
X // TODO: process text?
X break;
X
X case USER_GFX_MOVE:
X if (pdbrunInputVersion >= 6
X || 0 > sscanf(buf, fmt, &userGfxMove.xyz[0],
X &userGfxMove.xyz[1], &userGfxMove.xyz[2]))
X goto user;
X break;
X
X case USER_GFX_DRAW:
X if (pdbrunInputVersion >= 6
X || 0 > sscanf(buf, fmt, &userGfxDraw.xyz[0],
X &userGfxDraw.xyz[1], &userGfxDraw.xyz[2]))
X goto user;
X break;
X
X case USER_GFX_MARKER:
X if (pdbrunInputVersion >= 6
X || 0 > sscanf(buf, fmt, &userGfxMarker.xyz[0],
X &userGfxMarker.xyz[1],
X &userGfxMarker.xyz[2]))
X goto user;
X break;
X
X case USER_GFX_POINT:
X if (pdbrunInputVersion >= 6
X || 0 > sscanf(buf, fmt, &userGfxPoint.xyz[0],
X &userGfxPoint.xyz[1], &userGfxPoint.xyz[2]))
X goto user;
X break;
X }
X}
SHAR_EOF
if test 16032 -ne "`wc -c < 'pdb_read.cc'`"
then
echo shar: "error transmitting 'pdb_read.cc'" '(should have been 16032 characters)'
fi
fi
echo shar: "extracting 'pdb_sprntf.cc'" '(8760 characters)'
if test -f 'pdb_sprntf.cc'
then
echo shar: "will not over-write existing file 'pdb_sprntf.cc'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_sprntf.cc'
X//
X// Copyright (c) 1989,1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdb_sprntf.cc,v 1.4 94/09/06 15:03:07 gregc Exp $
X//
X
X#include "pdb++.h"
X#include
X#include
X#include
X
X // scratch must be big enough to hold the largest number
Xstatic char scratch[256];
X
X#define OVERFLOW_CHAR '*'
X
Xstatic char *outint(int, int, int, char, char, int, char *, char);
Xstatic char *outunsigned(unsigned int, int, char, int, char *);
Xstatic char *outstr(char *, int, int, char, int, char *);
Xstatic char *outfloat(double, int, int, char, int, char *);
Xstatic char *outexp(double, int, int, char, int, char *);
Xstatic char *e_out(int, char *);
X
Xint
XPDB::sprintf(char *outbuf, const char *fmt, ...)
X{
X va_list argv;
X char *p;
X const char *f;
X int field1, field2;
X char c, fill_char;
X int inum;
X unsigned unum;
X double fnum;
X int left_justify;
X
X va_start(argv, fmt);
X f = fmt;
X p = outbuf;
X while (*f) {
X if (*f == '%') {
X f++;
X if (*f == '-')
X left_justify = 1, f++;
X else
X left_justify = 0;
X
X if (*f == '0')
X fill_char = '0', f++;
X else
X fill_char = ' ';
X
X if (isdigit(*f)) {
X field1 = *f++ - '0';
X while (isdigit(*f))
X field1 = field1 * 10 + *f++ - '0';
X }
X else
X field1 = -1;
X
X if (*f == '.') {
X f++;
X field2 = 0;
X while (isdigit(*f))
X field2 = field2 * 10 + *f++ - '0';
X }
X else
X field2 = -1;
X
X if (*f == 'l' || *f == 'h')
X f++;
X
X while (isspace(*f))
X f++;
X switch (*f) {
X case 'c':
X c = (char) va_arg(argv, int);
X if (c == '\0')
X c = ' ';
X if (left_justify)
X *p++ = c;
X while (--field1 > 0)
X *p++ = fill_char;
X if (!left_justify)
X *p++ = c;
X break;
X case 'd':
X case 'D':
X inum = va_arg(argv, int);
X p = outint(inum, field1, 10, fill_char, 'a',
X left_justify, p, (*f == 'D') ? ' ':'0');
X break;
X case 'e':
X fnum = va_arg(argv, double);
X if (field2 < 0)
X field2 = 6;
X p = outexp(fnum, field1, field2, fill_char,
X left_justify, p);
X break;
X case 'f':
X fnum = va_arg(argv, double);
X if (field2 < 0)
X field2 = 6;
X p = outfloat(fnum, field1, field2, fill_char,
X left_justify, p);
X break;
X case 'o':
X inum = va_arg(argv, int);
X p = outint(inum, field1, 8, fill_char, 'a',
X left_justify, p, '0');
X break;
X case 's':
X p = outstr(va_arg(argv, char *), field1, field2,
X fill_char, left_justify, p);
X break;
X case 'u':
X unum = va_arg(argv, unsigned);
X p = outunsigned(unum, field1, fill_char,
X left_justify, p);
X break;
X case 'x':
X inum = va_arg(argv, int);
X p = outint(inum, field1, 16, fill_char, 'a',
X left_justify, p, '0');
X break;
X case 'X':
X inum = va_arg(argv, int);
X p = outint(inum, field1, 16, fill_char, 'A',
X left_justify, p, '0');
X break;
X default:
X if (left_justify)
X *p++ = *f;
X while (--field1 > 0)
X *p++ = fill_char;
X if (!left_justify)
X *p++ = *f;
X break;
X }
X f++;
X }
X else if (*f == '\\') { /* Special character */
X switch (*++f) {
X case 'n':
X *p++ = '\n';
X break;
X case 'r':
X *p++ = '\r';
X break;
X case 'b':
X *p++ = '\b';
X break;
X case 't':
X *p++ = '\t';
X break;
X case 'f':
X *p++ = '\f';
X break;
X case '0': case '1': case '2': case '3':
X case '4': case '5': case '6': case '7':
X inum = *f++ - '0';
X if (*f >= '0' && *f <= '7') {
X inum = inum * 8 + *f++ - '0';
X if (*f >= '0' && *f <= '7')
X inum = inum * 8 + *f++ - '0';
X }
X f--;
X *p++ = (char) inum;
X break;
X default:
X *p++ = *f;
X }
X f++;
X }
X else /* Normal character */
X *p++ = *f++;
X }
X *p = '\0';
X va_end(argv);
X return p - outbuf;
X}
X
Xstatic char *
Xe_out(int width, char *where)
X{
X while (width-- > 0)
X *where++ = OVERFLOW_CHAR;
X return where;
X}
X
Xstatic char *
Xoutint(int value, int width, int radix, char fill_char, char hex,
X int left_justify, char *p, char zero)
X{
X char *s;
X int n;
X int negative;
X
X if (value < 0)
X negative = 1, value = -value, width--;
X else
X negative = 0;
X s = scratch;
X if (value)
X do {
X n = value % radix;
X *s++ = n < 10 ? '0' + n : hex + n - 10;
X value /= radix;
X } while (value);
X else
X *s++ = zero;
X n = s - scratch;
X if (width != -1 && n > width)
X return e_out(width + negative, p);
X
X if (negative && fill_char == '0')
X *p++ = '-';
X if (!left_justify)
X while (width-- > n)
X *p++ = fill_char;
X if (negative && fill_char == ' ')
X *p++ = '-';
X while (--s >= scratch)
X *p++ = *s;
X if (left_justify)
X while (width-- > n)
X *p++ = fill_char;
X return p;
X}
X
Xstatic char *
Xoutunsigned(unsigned int value, int width, char fill_char, int left_justify,
X char *p)
X{
X char *s;
X int n;
X
X s = scratch;
X while (value) {
X *s++ = value % 10 + '0';
X value /= 10;
X }
X n = s - scratch;
X if (n == 0)
X *s++ = '0', n = 1;
X if (width != -1 && n > width)
X return e_out(width, p);
X
X if (!left_justify)
X while (width-- > n)
X *p++ = fill_char;
X while (--s >= scratch)
X *p++ = *s;
X if (left_justify)
X while (width-- > n)
X *p++ = fill_char;
X return p;
X}
X
Xstatic char *
Xoutstr(char *s, int width, int maxstr, char fill_char, int left_justify, char *p)
X{
X int len;
X
X len = strlen(s);
X if (maxstr >= 0 && len > maxstr)
X len = maxstr;
X if (width != -1 && len > width)
X return e_out(width, p);
X
X if (!left_justify)
X while (width-- > len)
X *p++ = fill_char;
X else
X width -= len;
X while (len--)
X *p++ = *s++;
X if (left_justify)
X while (width-- > 0)
X *p++ = fill_char;
X return p;
X}
X
Xstatic char *
Xoutfloat(double value, int width, int nplace, char fill_char, int left_justify,
X char *p)
X{
X int i, intval;
X char *place, *to, *from;
X int negative;
X
X negative = value < 0.0 ? 1 : 0;
X
X if (negative)
X value = -value;
X
X for (i = 0; i < nplace; i++)
X value *= 10.0;
X
X intval = (int) (value + 0.5);
X
X if (width == -1)
X width = nplace + 4; /* TODO: fix */
X else if (nplace + (nplace == 0 ? 1 : 2) > width)
X return e_out(width, p);
X
X for (place = p + width - 1; place >= p + width - nplace; place--) {
X *place = '0' + intval % 10;
X intval /= 10;
X }
X
X if (nplace > 0)
X *place-- = '.';
X
X if (intval == 0)
X *place-- = '0';
X
X for (; place >= p; place--) {
X if (intval == 0)
X break;
X else {
X *place = '0' + intval % 10;
X intval /= 10;
X }
X }
X
X if (intval != 0)
X return e_out(width, p);
X
X if (place < p && negative)
X return e_out(width, p);
X
X if (left_justify) {
X for (from = place + 1, to = (negative ? p + 1 : p);
X from < p + width; from++, to++)
X *to = *from;
X for (; to < p + width; to++)
X *to = fill_char;
X if (negative)
X *p = '-';
X } else {
X for (to = place; to >= p; to--)
X *to = fill_char;
X if (negative)
X if (fill_char == ' ')
X *place = '-';
X else
X *p = '-';
X }
X
X return p + width;
X}
X
Xstatic char *
Xoutexp(double value, int width, int nplace, char fill_char, int left_justify,
X char *p)
X{
X int n;
X char *s;
X int negative;
X double fraction;
X
X if (value < 0)
X negative = 1, value = -value, width--;
X else
X negative = 0;
X
X n = 0;
X while (value > 10)
X n++, value /= 10;
X if (value)
X while (value < 1)
X n--, value *= 10;
X
X s = scratch;
X if (n < 0) {
X n = -n;
X *s++ = n % 10 + '0';
X *s++ = n / 10 + '0';
X *s++ = '-';
X }
X else {
X *s++ = n % 10 + '0';
X *s++ = n / 10 + '0';
X *s++ = '+';
X }
X *s = 'e';
X
X s = scratch + nplace + 4; /* 4 == strlen("e+00") */
X fraction = value - (int) value;
X for (n = 0; n < nplace; n++) {
X fraction *= 10.0;
X *--s = '0' + (int) fraction;
X fraction -= (int) fraction;
X }
X
X s = scratch + nplace + 4;
X if (nplace)
X *s++ = '.';
X n = (int) value;
X if (n)
X *s++ = n % 10 + '0';
X else
X *s++ = '0';
X n = s - scratch;
X if (width != -1 && n > width)
X return e_out(width + negative, p);
X
X if (negative && fill_char == '0')
X *p++ = '-';
X if (!left_justify)
X while (width-- > n)
X *p++ = fill_char;
X if (negative && fill_char == ' ')
X *p++ = '-';
X while (--s >= scratch)
X *p++ = *s;
X if (left_justify)
X while (width-- > n)
X *p++ = fill_char;
X return p;
X}
SHAR_EOF
if test 8760 -ne "`wc -c < 'pdb_sprntf.cc'`"
then
echo shar: "error transmitting 'pdb_sprntf.cc'" '(should have been 8760 characters)'
fi
fi
echo shar: "extracting 'pdb_sscanf.cc'" '(4650 characters)'
if test -f 'pdb_sscanf.cc'
then
echo shar: "will not over-write existing file 'pdb_sscanf.cc'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_sscanf.cc'
X//
X// Copyright (c) 1989,1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdb_sscanf.cc,v 1.8 94/09/06 15:03:23 gregc Exp $
X//
X
X#include "pdb++.h"
X#include
X#include
X#include
X
X//
X// pdb_sscanf performs similarly to sscanf, execept that fields are of
X// fixed length and a complete line is always consumed. The field
X// width defaults to one. If the line is shorter than expected then
X// the default is returned.
X//
X// d get an integer. Default: 0.
X// f get a floating point number (C double). Default: 0.0.
X// (space) ignore characters within field
X// s get a C string, leading and trailing spaces are
X// stripped; the field width is used as a limit on
X// the string length, the null character is appended
X// to the end of the string. Default: empty string.
X// c get a character(s); no stripping of spaces, nor is
X// a null character appended. Default: space(s).
X//
X
X#define MAXFIELDSIZE 64
X
Xint
XPDB::sscanf(const char *buffer, const char *fmt, ...)
X{
X va_list ap;
X int i, field_width;
X int nmatch;
X char *s, *t;
X char tmp[MAXFIELDSIZE];
X
X va_start(ap, fmt);
X nmatch = 0;
X for (; *fmt != '\0'; fmt++) {
X if (*fmt != '%') {
X if (*buffer == *fmt)
X buffer++;
X else if (*buffer != '\0' && *buffer != '\n')
X return -1;
X continue;
X }
X
X // calculate field_width
X field_width = 0;
X for (++fmt; isdigit(*fmt); fmt++)
X field_width = field_width * 10 + *fmt - '0';
X if (field_width == 0)
X field_width = 1; // default
X if (*buffer != '\0' && *buffer != '\n')
X nmatch++;
X
X switch (*fmt) {
X
X case 'd': // integer
X // if we've already seen the end of the buffer, don't
X // try to get anymore characters
X if (*buffer == '\0' || *buffer == '\n') {
X *(va_arg(ap, int *)) = 0;
X break;
X }
X
X s = tmp;
X for (i = 0; i < field_width; i++) {
X if (*buffer == '\0' || *buffer == '\n')
X break;
X *s++ = *buffer++;
X }
X *s = '\0';
X // remove trailing spaces
X while (s > tmp && isspace(*(s - 1)))
X *--s = '\0';
X *(va_arg(ap, int *)) = (int) strtol(tmp, &t, 10);
X if (t != s)
X return -1;
X break;
X
X case 'f': // floating point
X // if we've already seen the end of the buffer, don't
X // try to get anymore characters
X if (*buffer == '\0' || *buffer == '\n') {
X *(va_arg(ap, double *)) = 0.0;
X break;
X }
X
X s = tmp;
X for (i = 0; i < field_width; i++) {
X if (*buffer == '\0' || *buffer == '\n')
X break;
X *s++ = *buffer++;
X }
X *s = '\0';
X // remove trailing spaces
X while (s > tmp && isspace(*(s - 1)))
X *--s = '\0';
X *(va_arg(ap, double *)) = strtod(tmp, &t);
X if (t != s)
X return -1;
X break;
X
X case 's': // string
X // if we've already seen the end of the buffer, don't
X // try to get anymore characters
X if (*buffer == '\0' || *buffer == '\n') {
X *(va_arg(ap, char *)) = '\0';
X break;
X }
X
X s = t = va_arg(ap, char *);
X for (i = 0; i < field_width; i++) {
X if (*buffer == '\0' || *buffer == '\n')
X break;
X *s++ = *buffer++;
X }
X *s = '\0';
X // remove trailing spaces
X while (s > t && isspace(*--s))
X *s = '\0';
X break;
X
X case 'c': // character(s)
X s = va_arg(ap, char *);
X for (i = 0; i < field_width; i++)
X s[i] = ' '; // default
X
X // if we've already seen the end of the buffer, don't
X // try to get anymore characters
X if (*buffer == '\0' || *buffer == '\n')
X break;
X
X for (i = 0; i < field_width; i++) {
X if (*buffer == '\0' || *buffer == '\n')
X break;
X *s++ = *buffer++;
X }
X break;
X
X case ' ': // space (ignore)
X // if we've already seen the end of the buffer, don't
X // try to get anymore characters
X if (*buffer == '\0' || *buffer == '\n')
X break;
X
X for (i = 0; i < field_width; i++, buffer++)
X if (*buffer == '\0' || *buffer == '\n')
X break;
X break;
X
X default:
X va_end(ap);
X return -1;
X }
X }
X va_end(ap);
X return nmatch;
X}
SHAR_EOF
if test 4650 -ne "`wc -c < 'pdb_sscanf.cc'`"
then
echo shar: "error transmitting 'pdb_sscanf.cc'" '(should have been 4650 characters)'
fi
fi
echo shar: "extracting 'pdb_type.cc'" '(12195 characters)'
if test -f 'pdb_type.cc'
then
echo shar: "will not over-write existing file 'pdb_type.cc'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_type.cc'
X//
X// Copyright (c) 1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdb_type.cc,v 1.14 1995/05/22 19:53:09 gregc Exp $
X//
X// subroutine for reading PDB format files
X//
X
X# include "pdb++.h"
Xextern "C" {
X# include
X# include
X}
X#if 0
Xextern "C" int strcasecmp (const char *s1, const char *s2);
Xextern "C" int strncasecmp (const char *s1, const char *s2, size_t n);
X#endif
X
X# ifndef _toupper
X# define _toupper toupper
X# endif
X
Xint PDB::pdbrunInputVersion = PDB::PDBRUNVersion; // just in case
Xint PDB::pdbrunOutputVersion = PDB::PDBRUNVersion; // just in case
X
XPDB::GfxType
XPDB::getGfxType(const char *buf)
X{
X switch (buf[0]) {
X case 'L': case 'l':
X if (strcasecmp(buf + 1, "INE-LOOP") == 0)
X return GFX_LINE_LOOP;
X if (strcasecmp(buf + 1, "INE-STRIP") == 0)
X return GFX_LINE_STRIP;
X if (strcasecmp(buf + 1, "INES") == 0)
X return GFX_LINES;
X break;
X case 'M': case 'm':
X if (strcasecmp(buf + 1, "ARKERS") == 0)
X return GFX_MARKERS;
X break;
X case 'P': case 'p':
X if (strcasecmp(buf + 1, "OINTS") == 0)
X return GFX_POINTS;
X if (strcasecmp(buf + 1, "OLYGON") == 0)
X return GFX_POLYGON;
X break;
X case 'Q': case 'q':
X if (strcasecmp(buf + 1, "UAD-STRIP") == 0)
X return GFX_QUAD_STRIP;
X if (strcasecmp(buf + 1, "UADS") == 0)
X return GFX_QUADS;
X break;
X case 'T': case 't':
X if (strcasecmp(buf + 1, "RIANGLE-FAN") == 0)
X return GFX_TRIANGLE_FAN;
X if (strcasecmp(buf + 1, "RIANGLE-STRIP") == 0)
X return GFX_TRIANGLE_STRIP;
X if (strcasecmp(buf + 1, "RIANGLES") == 0)
X return GFX_TRIANGLES;
X break;
X }
X return GFX_UNKNOWN;
X}
X
Xconst char *
XPDB::gfxChars(GfxType gt)
X{
X switch (gt) {
X default: return "UNKNOWN";
X case GFX_POINTS: return "POINTS";
X case GFX_MARKERS: return "MARKERS";
X case GFX_LINES: return "LINES";
X case GFX_LINE_STRIP: return "LINE-STRIP";
X case GFX_LINE_LOOP: return "LINE-LOOP";
X case GFX_TRIANGLES: return "TRIANGLES";
X case GFX_TRIANGLE_STRIP: return "TRIANGLE-STRIP";
X case GFX_TRIANGLE_FAN: return "TRIANGLE-FAN";
X case GFX_QUADS: return "QUADS";
X case GFX_QUAD_STRIP: return "QUAD-STRIP";
X case GFX_POLYGON: return "POLYGON";
X }
X}
X
Xstatic PDB::RecordType
Xpdbrun5Type(const char *buf)
X{
X switch (buf[0]) {
X case 'A': case 'a':
X if (strncasecmp(buf + 1, "NGLE ", 5) == 0)
X return PDB::USER_ANGLE;
X if (strncasecmp(buf + 1, "TPOS ", 5) == 0)
X return PDB::USER_ATPOS;
X break;
X case 'B': case 'b':
X if (strncasecmp(buf + 1, "GCOLOR ", 7) == 0)
X return PDB::USER_BGCOLOR;
X break;
X case 'C': case 'c':
X if (strncasecmp(buf + 1, "HAIN ", 5) == 0)
X return PDB::USER_CHAIN;
X if (strncasecmp(buf + 1, "NAME ", 5) == 0)
X return PDB::USER_CNAME;
X if (strncasecmp(buf + 1, "OLOR ", 5) == 0)
X return PDB::USER_COLOR;
X break;
X case 'D': case 'd':
X if (strncasecmp(buf + 1, "ISTANCE ", 8) == 0)
X return PDB::USER_DISTANCE;
X break;
X case 'E': case 'e':
X if (strncasecmp(buf + 1, "NDOBJ ", 6) == 0)
X return PDB::USER_ENDOBJ;
X if (strncasecmp(buf + 1, "YEPOS ", 6) == 0)
X return PDB::USER_EYEPOS;
X break;
X case 'F': case 'f':
X if (strncasecmp(buf + 1, "ILE ", 4) == 0)
X return PDB::USER_FILE;
X if (strncasecmp(buf + 1, "OCUS ", 5) == 0)
X return PDB::USER_FOCUS;
X break;
X case 'G': case 'g':
X if (strncasecmp(buf + 1, "FX ", 3) != 0)
X break;
X if (strncasecmp(buf + 4, "COLOR ", 6) == 0)
X return PDB::USER_GFX_COLOR;
X if (strncasecmp(buf + 4, "DRAW ", 5) == 0)
X return PDB::USER_GFX_DRAW;
X if (strncasecmp(buf + 4, "FONT ", 5) == 0)
X return PDB::USER_GFX_FONT;
X if (strncasecmp(buf + 4, "LABEL ", 6) == 0)
X return PDB::USER_GFX_LABEL;
X if (strncasecmp(buf + 4, "MARKER ", 7) == 0)
X return PDB::USER_GFX_MARKER;
X if (strncasecmp(buf + 4, "MOVE ", 5) == 0)
X return PDB::USER_GFX_MOVE;
X if (strncasecmp(buf + 4, "POINT ", 6) == 0)
X return PDB::USER_GFX_POINT;
X break;
X case 'O': case 'o':
X if (strncasecmp(buf + 1, "BJECT ", 6) == 0)
X return PDB::USER_OBJECT;
X break;
X case 'P': case 'p':
X if (strncasecmp(buf + 1, "DBRUN ", 6) == 0)
X return PDB::USER_PDBRUN;
X break;
X case 'R': case 'r':
X if (strncasecmp(buf + 1, "ADIUS ", 6) == 0)
X return PDB::USER_RADIUS;
X break;
X case 'V': case 'v':
X if (strncasecmp(buf + 1, "IEWPORT ", 8) == 0)
X return PDB::USER_VIEWPORT;
X break;
X case 'W': case 'w':
X if (strncasecmp(buf + 1, "INDOW ", 6) == 0)
X return PDB::USER_WINDOW;
X break;
X }
X return PDB::USER;
X}
X
Xstatic PDB::RecordType
Xpdbrun6Type(const char *buf)
X{
X switch (buf[0]) {
X case 'A': case 'a':
X if (strncasecmp(buf + 1, "NGLE ", 5) == 0)
X return PDB::USER_ANGLE;
X if (strncasecmp(buf + 1, "TPOS ", 5) == 0)
X return PDB::USER_ATPOS;
X break;
X case 'B': case 'b':
X if (strncasecmp(buf + 1, "GCOLOR ", 7) == 0)
X return PDB::USER_BGCOLOR;
X break;
X case 'C': case 'c':
X if (strncasecmp(buf + 1, "HAIN ", 5) == 0)
X return PDB::USER_CHAIN;
X if (strncasecmp(buf + 1, "NAME ", 5) == 0)
X return PDB::USER_CNAME;
X if (strncasecmp(buf + 1, "OLOR ", 5) == 0)
X return PDB::USER_COLOR;
X break;
X case 'D': case 'd':
X if (strncasecmp(buf + 1, "ISTANCE ", 8) == 0)
X return PDB::USER_DISTANCE;
X break;
X case 'E': case 'e':
X if (strncasecmp(buf + 1, "NDOBJ", 5) == 0
X && (buf[6] == '\0' || buf[6] == '\n' || buf[6] == ' '))
X return PDB::USER_ENDOBJ;
X if (strncasecmp(buf + 1, "YEPOS ", 6) == 0)
X return PDB::USER_EYEPOS;
X break;
X case 'F': case 'f':
X if (strncasecmp(buf + 1, "ILE ", 4) == 0)
X return PDB::USER_FILE;
X if (strncasecmp(buf + 1, "OCUS ", 5) == 0)
X return PDB::USER_FOCUS;
X break;
X case 'G': case 'g':
X if (buf[1] != 'F' || buf[2] != 'X' || buf[3] != ' ')
X break;
X switch (buf[4]) {
X case 'B': case 'b':
X if (strncasecmp(buf + 5, "EGIN ", 5) == 0)
X return PDB::USER_GFX_BEGIN;
X break;
X case 'C': case 'c':
X if (strncasecmp(buf + 5, "OLOR ", 5) == 0)
X return PDB::USER_GFX_COLOR;
X break;
X case 'E': case 'e':
X if (buf[5] == 'N' && buf[6] == 'D'
X && (buf[7] == '\0' || buf[7] == '\n' || buf[7] == ' '))
X return PDB::USER_GFX_END;
X break;
X case 'F': case 'f':
X if (strncasecmp(buf + 5, "ONT ", 4) == 0)
X return PDB::USER_GFX_FONT;
X break;
X case 'L': case 'l':
X if (strncasecmp(buf + 5, "ABEL ", 5) == 0)
X return PDB::USER_GFX_LABEL;
X break;
X case 'N': case 'n':
X if (strncasecmp(buf + 5, "ORMAL ", 6) == 0)
X return PDB::USER_GFX_NORMAL;
X break;
X case 'T': case 't':
X if (strncasecmp(buf + 5, "EXTPOS ", 7) == 0)
X return PDB::USER_GFX_TEXTPOS;
X break;
X case 'V': case 'v':
X if (strncasecmp(buf + 5, "ERTEX ", 6) == 0)
X return PDB::USER_GFX_VERTEX;
X break;
X }
X break;
X case 'M': case 'm':
X if (strncasecmp(buf + 1, "ARK ", 4) == 0)
X return PDB::USER_MARK;
X if (strncasecmp(buf + 1, "ARKNAME ", 6) == 0)
X return PDB::USER_MARKNAME;
X break;
X case 'O': case 'o':
X if (strncasecmp(buf + 1, "BJECT", 5) == 0
X && (buf[6] == '\0' || buf[6] == '\n' || buf[6] == ' '))
X return PDB::USER_OBJECT;
X break;
X case 'P': case 'p':
X if (strncasecmp(buf + 1, "DBRUN ", 6) == 0)
X return PDB::USER_PDBRUN;
X break;
X case 'R': case 'r':
X if (strncasecmp(buf + 1, "ADIUS ", 6) == 0)
X return PDB::USER_RADIUS;
X break;
X case 'V': case 'v':
X if (strncasecmp(buf + 1, "IEWPORT ", 6) == 0)
X return PDB::USER_VIEWPORT;
X break;
X case 'W': case 'w':
X if (strncasecmp(buf + 1, "INDOW ", 6) == 0)
X return PDB::USER_WINDOW;
X break;
X }
X return PDB::USER;
X}
X
XPDB::RecordType
XPDB::getType(const char *buf)
X{
X char rt[4]; // PDB record type
X int i;
X
X for (i = 0; buf[i] != '\0' && buf[i] != '\n' && i < 4; i += 1) {
X if (islower(buf[i]))
X rt[i] = _toupper(buf[i]);
X else
X rt[i] = buf[i];
X }
X if (i < 4)
X for (; i < 4; i += 1)
X rt[i] = ' ';
X
X switch (rt[0]) {
X
X case 'A':
X switch (rt[1]) {
X case 'G':
X if (rt[2] == 'R' && rt[3] == 'D')
X return AGRDES;
X if (rt[2] == 'G' && rt[3] == 'R')
X return AGGRGT;
X break;
X case 'N':
X if (rt[2] == 'I' && rt[3] == 'S')
X return ANISOU;
X break;
X case 'T':
X if (rt[2] == 'O' && rt[3] == 'M')
X return ATOM;
X break;
X case 'U':
X if (rt[2] == 'T' && rt[3] == 'H')
X return AUTHOR;
X break;
X }
X break;
X
X case 'C':
X switch (rt[1]) {
X case 'M':
X if (rt[2] == 'P' && rt[3] == 'D')
X return CMPDES;
X if (rt[2] == 'P' && rt[3] == 'O')
X return CMPONT;
X break;
X case 'O':
X if (rt[2] == 'M' && rt[3] == 'P')
X return COMPND;
X if (rt[2] == 'N' && rt[3] == 'E')
X return CONECT;
X break;
X case 'R':
X if (rt[2] == 'Y' && rt[3] == 'S')
X return CRYST1;
X break;
X }
X break;
X
X case 'E':
X switch (rt[1]) {
X case 'N':
X if (rt[2] == 'D' && rt[3] == ' ')
X return END;
X if (rt[2] == 'D' && rt[3] == 'M')
X return ENDMDL;
X break;
X case 'X':
X if (rt[2] == 'P' && rt[3] == 'D')
X return EXPDTA;
X break;
X }
X break;
X
X case 'F':
X switch (rt[1]) {
X case 'T':
X if (rt[2] == 'N' && rt[3] == 'O')
X return FTNOTE;
X break;
X case 'O':
X if (rt[2] == 'R' && rt[3] == 'M')
X return FORMUL;
X break;
X }
X break;
X
X case 'H':
X if (rt[1] != 'E')
X break;
X if (rt[2] == 'T' && rt[3] == 'A')
X return HETATM;
X if (rt[2] == 'A' && rt[3] == 'D')
X return HEADER;
X if (rt[2] == 'T' && rt[3] == ' ')
X return HET;
X if (rt[2] == 'L' && rt[3] == 'I')
X return HELIX;
X break;
X
X case 'J':
X if (rt[1] == 'R' && rt[2] == 'N' && rt[3] == 'L')
X return JRNL;
X break;
X
X case 'M':
X switch (rt[1]) {
X case 'A':
X if (rt[2] == 'S' && rt[3] == 'T')
X return MASTER;
X break;
X case 'O':
X if (rt[2] == 'D' && rt[3] == 'E')
X return MODEL;
X break;
X case 'T':
X if (rt[2] == 'R' && rt[3] == 'I')
X return MTRIX;
X if (rt[2] == 'X' && rt[3] == 'D')
X return MTXDES;
X break;
X }
X break;
X
X case 'O':
X switch (rt[1]) {
X case 'B':
X if (rt[2] == 'S' && rt[3] == 'L')
X return OBSLTE;
X break;
X case 'R':
X if (rt[2] == 'I' && rt[3] == 'G')
X return ORIGX;
X break;
X }
X break;
X
X case 'R':
X if (rt[1] != 'E')
X break;
X if (rt[2] == 'M' && rt[3] == 'A')
X return REMARK;
X if (rt[2] == 'V' && rt[3] == 'D')
X return REVDAT;
X break;
X
X case 'S':
X switch (rt[1]) {
X
X case 'C':
X if (rt[2] == 'A' && rt[3] == 'L')
X return SCALE;
X break;
X
X case 'E':
X if (rt[2] == 'Q' && rt[3] == 'R')
X return SEQRES;
X break;
X
X case 'H':
X if (rt[2] == 'E' && rt[3] == 'E')
X return SHEET;
X break;
X
X case 'I':
X if (rt[2] == 'T' && rt[3] == 'E')
X return SITE;
X if (rt[2] == 'G' && rt[3] == 'A')
X return SIGATM;
X if (rt[2] == 'G' && rt[3] == 'U')
X return SIGUIJ;
X break;
X
X case 'O':
X if (rt[2] == 'U' && rt[3] == 'R')
X return SOURCE;
X break;
X
X case 'P':
X if (rt[2] == 'R' && rt[3] == 'S')
X return SPRSDE;
X break;
X
X case 'S':
X if (rt[2] == 'B' && rt[3] == 'O')
X return SSBOND;
X break;
X
X case 'Y':
X if (rt[2] == 'M' && rt[3] == 'D')
X return SYMDES;
X if (rt[2] == 'M' && rt[3] == 'O')
X return SYMOP;
X break;
X }
X break;
X
X case 'T':
X switch (rt[1]) {
X case 'E':
X if (rt[2] == 'R' && rt[3] == ' ')
X return TER;
X break;
X case 'R':
X if (rt[2] == 'N' && rt[3] == 'S')
X return TRNSFM;
X break;
X case 'U':
X if (rt[2] == 'R' && rt[3] == 'N')
X return TURN;
X break;
X case 'V':
X if (rt[2] == 'E' && rt[3] == 'C')
X return TVECT;
X break;
X }
X break;
X
X case 'U':
X if (rt[1] == 'S' && rt[2] == 'E' && rt[3] == 'R')
X switch (pdbrunInputVersion) {
X case 1: case 2: case 3: case 4: case 5:
X return pdbrun5Type(buf + 6);
X case 6:
X return pdbrun6Type(buf + 6);
X default:
X if (strncasecmp(buf + 6, "PDBRUN ", 7) == 0)
X return USER_PDBRUN;
X return USER;
X }
X break;
X }
X return UNKNOWN;
X}
SHAR_EOF
if test 12195 -ne "`wc -c < 'pdb_type.cc'`"
then
echo shar: "error transmitting 'pdb_type.cc'" '(should have been 12195 characters)'
fi
fi
echo shar: "extracting 'pdbinput.cc'" '(1052 characters)'
if test -f 'pdbinput.cc'
then
echo shar: "will not over-write existing file 'pdbinput.cc'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdbinput.cc'
X//
X// Copyright (c) 1992 The Regents of the University of California.
X// All rights reserved.
X//
X// Redistribution and use in source and binary forms are permitted
X// provided that the above copyright notice and this paragraph are
X// duplicated in all such forms and that any documentation,
X// advertising materials, and other materials related to such
X// distribution and use acknowledge that the software was developed
X// by the University of California, San Francisco. The name of the
X// University may not be used to endorse or promote products derived
X// from this software without specific prior written permission.
X// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
X// IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
X// WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
X//
X// $Id: pdbinput.cc,v 1.1 94/02/22 17:09:27 gregc Exp $
X//
X
X#include "pdb++.h"
X
Xistream &
Xoperator>>(istream &s, PDB &p)
X{
X char buf[4 * PDB::BufLen];
X
X s.getline(buf, 4 * PDB::BufLen);
X if (s)
X p = PDB(buf);
X return s;
X}
SHAR_EOF
if test 1052 -ne "`wc -c < 'pdbinput.cc'`"
then
echo shar: "error transmitting 'pdbinput.cc'" '(should have been 1052 characters)'
fi
fi
exit 0
# End of shell archive
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