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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:
# ms.3
# pdb.3
# Makefile
# ms.h
# pdb.h
# pdb_int.h
# pdbrun5_read.i
# pdbrun5_write.i
# pdbrun6_read.i
# pdbrun6_write.i
# read_format.i
# write_format.i
# ms.c
# pdb_read.c
# pdb_sprntf.c
# pdb_sscanf.c
# pdb_write.c
# pdbrun.c
# This archive created: Wed Nov 1 20:29:01 1995
export PATH; PATH=/bin:/usr/bin:$PATH
echo shar: "extracting 'ms.3'" '(2081 characters)'
if test -f 'ms.3'
then
echo shar: "will not over-write existing file 'ms.3'"
else
sed 's/^ X//' << \SHAR_EOF > 'ms.3'
X.\" Copyright (c) 1984,1989 by the Regents of the University of California.
X.\" All Rights Reserved.
X.\" $Id: ms.3,v 1.1 94/11/02 13:10:21 gregc Exp $
X.TH MS 3 "14 Sept 1989"
X.SH NAME
Xms_read_record, ms_parse, ms_write_record \- read and write Molecular Surface (ms) records
X.SH SYNOPSIS
X.nf
X.B #include
X.PP
X.B ms_record ms_read_record(f)
X.B FILE *f;
X.PP
X.B ms_record ms_parse(line_buffer)
X.B char *line_buffer;
X.PP
X.B void ms_write_record(f, m)
X.B FILE *f;
X.B ms_record *m;
X.fi
X.SH DESCRIPTION
XThe routines listed above
Xare subroutines for Molecular Surface record I/O
Xand are available in the pdb library, typically
X.IR "-L/usr/local/lib/midas -lpdb" .
X.PP
XAlthough the header file is too long to reproduce here, it should be
Xperused before using any of the above routines.
XIt is typically found in
X.IR /usr/local/midas/include .
X.PP
X\fBms_read_record\fP reads the next line of input from the file \fBf\fP,
Xand returns the contents parsed into a C structure.
X\fBms_parse\fP parses the contents of the line buffer
Xand returns a C structure.
X\fBms_write_record\fP writes the contents of the MS record (\fB*m\fP) to
Xthe file \fBf\fP.
X.SH "SEE ALSO"
Xdms(1)
X.SH DIAGNOSTICS
XUpon reaching the end of the file, \fBms_read_record\fP will return
Xa record with MS_END as its type.
X.SH COPYRIGHT
XCopyright \(co 1992 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 2081 -ne "`wc -c < 'ms.3'`"
then
echo shar: "error transmitting 'ms.3'" '(should have been 2081 characters)'
fi
fi
echo shar: "extracting 'pdb.3'" '(3650 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 (c) 1984,1989 by the Regents of the University of California.
X.\" All Rights Reserved.
X.\" $Id: pdb.3,v 1.16 94/11/06 19:55:29 gregc Exp $
X.TH PDB 3 "14 Sept 1989"
X.SH NAME
Xpdb_read_record, pdb_parse, pdb_write_record \- read and write Brookhaven Protein DataBank records
X.SH SYNOPSIS
X.nf
X.B #include
X.PP
X.B pdb_record pdb_read_record(f)
X.B FILE *f;
X.PP
X.B pdb_record pdb_parse(line_buffer)
X.B char *line_buffer;
X.PP
X.B "void pdb_write_record(f, r, name, line_num)"
X.B FILE *f;
X.B pdb_record *r;
X.B char *name;
X.B int line_num;
X.fi
X.SH DESCRIPTION
XThe routines listed above
Xare subroutines for Brookhaven Protein Data Bank record I/O
Xand are available in the pdb library, typically
X.IR "-L/usr/local/lib/midas -lpdb" .
X.PP
XAlthough the header file is too long to reproduce here, it should be
Xperused before using any of the above routines.
XIt is typically found in
X.IR /usr/local/midas/include .
X\fBpdb_read_record\fP reads the next line of input from the file \fBf\fP,
Xand returns the contents parsed into a C structure.
X\fBpdb_parse\fP parses the contents of the line buffer
Xand returns a C structure.
X\fBpdb_write_record\fP writes the contents of the PDB record (\fB*r\fP) to
Xthe file \fBf\fP. If the \fBname\fP is non-null, then it and the line
Xnumber given (\fBline_num\fP) are placed in columns 72 through 80 on the
Xline in standard PDB format.
X.PP
X\fBpdb_read_record\fP and \fBpdb_write_record\fP automatically
Xhandle versions 5 and 6 of the UCSFCGL's PDB scene annotation records.
XThe version number is automatically changed when a USER PDBRUN record is read
Xor written.
XAny other version number turns off the parsing of scene annotation records.
X.SH "SEE ALSO"
X``Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description,'' Febuary 1992,
XBrookhaven National Laboratory
X(URL: ftp://ftp.pdb.bnl.gov/pub/format_desc.ps),
Xthe January 1993 Protein Data Bank Quarterly Newsletter,
Xand Couch, \fIet. al\fP, ``Annotating PDB Files with Scene Information'',
X(in press)
X(URL: http://cgl.ucsf.edu/????).
X.SH DIAGNOSTICS
XUpon reaching the end of the file, \fBpdb_read_record\fP will return
Xa record with PDB_END as its type.
X.SH NOTES
XThe subtype field of USERxx structure tells what the \fIxx\fP part 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 usually have leading blanks and sometimes have embedded blanks.
XResidue names occasionally have leading blanks too.
XTo be entirely consistent with the PDB format, the programmer should put those
Xblanks in before using \fBpdb_write_record\fP.
X.SH BUGS
XDoesn't allow exact duplication of the PDB card image sorting field
X(columns 73 through 80).
X.PP
XRoutines are needed to convert to and from PDB typesetting conventions
Xin COMPND, SOURCE, AUTHOR, and JRNL records.
X.SH COPYRIGHT
XCopyright \(co 1989 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 3650 -ne "`wc -c < 'pdb.3'`"
then
echo shar: "error transmitting 'pdb.3'" '(should have been 3650 characters)'
fi
fi
echo shar: "extracting 'Makefile'" '(1069 characters)'
if test -f 'Makefile'
then
echo shar: "will not over-write existing file 'Makefile'"
else
sed 's/^ X//' << \SHAR_EOF > 'Makefile'
X#
X# For machines that don't have lint, remove $(LINTLIB) from the
X# "all" target.
X#
X# On BSD machines, LINTOPT should be '-C', RANLIB should be 'ranlib'
X#
X# On System V machines, LINTOPT should be '-o $(NOTHING)',
X# RANLIB should be ':'
X#
XSHELL = /bin/sh
XRANLIB = :
XNOTHING =
XLINTOPT = -o $(NOTHING)
X
XOPT = -O -g
XDEBUG =
XCFLAGS = $(OPT) $(DEBUG)
XLIBRARY = pdb
X
XLIBARCH = lib$(LIBRARY).a
XLINTLIB = llib-l$(LIBRARY).ln
XOBJS = pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o pdbrun.o ms.o
XSRCS = pdb_read.c pdb_sprntf.c pdb_sscanf.c pdb_write.c pdbrun.c ms.c
X
Xall: $(LIBARCH) $(LINTLIB)
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) $(LIBARCH)
X @echo "done"
X
X$(LINTLIB): $(SRCS) $(HDRS)
X @echo "Creating $(LINTLIB) ... "
X @lint $(LINTOPT)$(LIBRARY) $(SRCS)
X @echo "done"
X
Xclean:; @rm -f $(OBJS)
X
Xspotless:; @rm -f $(OBJS) $(LIBARCH) $(LINTLIB)
X
Xlint: $(SRCS)
X lint -u $(SRCS)
X
Xtags: $(HDRS) $(SRCS); @ctags -w $(HDRS) $(SRCS)
SHAR_EOF
if test 1069 -ne "`wc -c < 'Makefile'`"
then
echo shar: "error transmitting 'Makefile'" '(should have been 1069 characters)'
fi
fi
echo shar: "extracting 'ms.h'" '(2307 characters)'
if test -f 'ms.h'
then
echo shar: "will not over-write existing file 'ms.h'"
else
sed 's/^ X//' << \SHAR_EOF > 'ms.h'
X/*
X * Copyright (c) 1989 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: ms.h,v 2.2 94/01/27 12:41:26 gregc Exp $
X */
X
X#ifndef MS_H
X#define MS_H
X
X#include
X
X#ifdef __cplusplus
Xextern "C" {
X#endif
X
X#define MS_RECLEN 128
X#define MS_BUFSIZ (MS_RECLEN + 2)
X
X#define MS_MAX_RESTYPE 8
X#define MS_MAX_RESSEQ 8
X#define MS_MAX_ATNAME 8
X
X#define MS_UNKNOWN 0
X#define MS_END 1
X#define MS_ATOM 2
X#define MS_SURFACE 3
X#define MS_USER 4
X
X#define MS_NUM_R 5
X
Xtypedef struct ms_atom {
X char residue_type[MS_MAX_RESTYPE];
X char residue_sequence[MS_MAX_RESSEQ];
X char atom_name[MS_MAX_ATNAME];
X float coord[3];
X} ms_atom;
X
Xtypedef struct ms_surf {
X char residue_type[MS_MAX_RESTYPE];
X char residue_sequence[MS_MAX_RESSEQ];
X char atom_name[MS_MAX_ATNAME];
X float coord[3];
X float normal[3];
X float area;
X float extra;
X char has_normal;
X char type;
X char level;
X} ms_surface;
X
Xtypedef struct ms_user {
X char string[MS_BUFSIZ];
X} ms_user;
X
X#define ms_unknown ms_user
X
Xtypedef struct ms_record {
X int record_type;
X union {
X ms_unknown unknown;
X ms_atom atom;
X ms_surface surface;
X ms_user user;
X } ms;
X} ms_record;
X
X#if defined(__STDC__) || defined(__cplusplus)
Xextern ms_record ms_read_record(FILE *);
Xextern ms_record ms_read_string(const char *);
Xextern void ms_write_record(FILE *, const ms_record *);
Xextern void ms_write_string(char *, const ms_record *);
X#else
Xextern ms_record ms_read_record();
Xextern ms_record ms_read_string();
Xextern void ms_write_record();
Xextern void ms_write_string();
X#endif
X
X#ifdef __cplusplus
X}
X#endif
X#endif
SHAR_EOF
if test 2307 -ne "`wc -c < 'ms.h'`"
then
echo shar: "error transmitting 'ms.h'" '(should have been 2307 characters)'
fi
fi
echo shar: "extracting 'pdb.h'" '(12494 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) 1989 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 2.11 1995/01/20 01:20:36 gregc Exp $
X *
X * Based on Brookhaven National Laboratory Protein Data Bank, March 1989
X *
X * C structure declarations
X */
X
X#ifndef PDB_H
X# define PDB_H
X
X# include
X
X# ifdef __cplusplus
Xextern "C" {
X# endif
X
X# define PDB_RECLEN 80 /* PDB record length */
X# define PDB_BUFSIZ PDB_RECLEN + 2 /* + '\n' + '\0' */
X
X# define PDB_PDBRUN_VERSION 6
X
X# define PDB_UNKNOWN 0
X
X/* records originally in alphabetical order */
X
X# define PDB_ANISOU 1
X# define PDB_ATOM 2
X# define PDB_AUTHOR 3
X# define PDB_COMPND 4
X# define PDB_CONECT 5
X# define PDB_CRYST1 6
X# define PDB_END 7
X# define PDB_FORMUL 8
X# define PDB_FTNOTE 9
X# define PDB_HEADER 10
X# define PDB_HELIX 11
X# define PDB_HET 12
X# define PDB_HETATM 13
X# define PDB_JRNL 14
X# define PDB_MASTER 15
X# define PDB_MTRIX 16
X# define PDB_OBSLTE 17
X# define PDB_ORIGX 18
X# define PDB_REMARK 19
X# define PDB_REVDAT 20
X# define PDB_SCALE 21
X# define PDB_SEQRES 22
X# define PDB_SHEET 23
X# define PDB_SIGATM 24
X# define PDB_SIGUIJ 25
X# define PDB_SITE 26
X# define PDB_SOURCE 27
X# define PDB_SPRSDE 28
X# define PDB_SSBOND 29
X# define PDB_TER 30
X# define PDB_TURN 31
X# define PDB_TVECT 32
X# define PDB_USER 33
X# define PDB_MODEL 34
X# define PDB_ENDMDL 35
X# define PDB_EXPDTA 36
X# define PDB_SYMDES 37
X# define PDB_SYMOP 38
X# define PDB_MTXDES 39
X# define PDB_CMPDES 40
X# define PDB_CMPONT 41
X# define PDB_TRNSFM 42
X# define PDB_AGRDES 43
X# define PDB_AGGRGT 44
X
X# define PDB_NUM_R 45
X
X# define PDB_USER_PDBRUN 0x100
X# define PDB_USER_EYEPOS 0x101
X# define PDB_USER_ATPOS 0x102
X# define PDB_USER_WINDOW 0x103
X# define PDB_USER_FOCUS 0x104
X# define PDB_USER_VIEWPORT 0x105
X# define PDB_USER_BGCOLOR 0x106
X# define PDB_USER_ANGLE 0x107
X# define PDB_USER_DISTANCE 0x108
X# define PDB_USER_FILE 0x109
X# define PDB_USER_MARKNAME 0x10a
X# define PDB_USER_MARK 0x10b
X# define PDB_USER_CNAME 0x10c
X# define PDB_USER_COLOR 0x10d
X# define PDB_USER_RADIUS 0x10e
X# define PDB_USER_OBJECT 0x10f
X# define PDB_USER_ENDOBJ 0x110
X# define PDB_USER_CHAIN 0x111
X# define PDB_USER_GFX_BEGIN 0x112
X# define PDB_USER_GFX_END 0x113
X# define PDB_USER_GFX_COLOR 0x114
X# define PDB_USER_GFX_NORMAL 0x115
X# define PDB_USER_GFX_VERTEX 0x116
X# define PDB_USER_GFX_FONT 0x117
X# define PDB_USER_GFX_TEXTPOS 0x118
X# define PDB_USER_GFX_LABEL 0x119
X# define PDB_USER_GFX_MOVE 0x11a /* obsolete */
X# define PDB_USER_GFX_DRAW 0x11b /* obsolete */
X# define PDB_USER_GFX_MARKER 0x11c /* obsolete */
X# define PDB_USER_GFX_POINT 0x11d /* obsolete */
X
X# define PDB_NUM_USER_R (PDB_USER_GFX_POINT-PDB_USER_PDBRUN+1)
X
X# define PDB_GFX_UNKNOWN 0x0
X# define PDB_GFX_POINTS 0x1
X# define PDB_GFX_MARKERS 0x2
X# define PDB_GFX_LINES 0x3
X# define PDB_GFX_LINE_STRIP 0x4
X# define PDB_GFX_LINE_LOOP 0x5
X# define PDB_GFX_TRIANGLES 0x6
X# define PDB_GFX_TRIANGLE_STRIP 0x7
X# define PDB_GFX_TRIANGLE_FAN 0x8
X# define PDB_GFX_QUADS 0x9
X# define PDB_GFX_QUAD_STRIP 0xa
X# define PDB_GFX_POLYGON 0xb
X
Xtypedef char pdb_date[10];
Xtypedef char pdb_aname[5]; /* atom name - NO2* */
Xtypedef char pdb_rname[5]; /* residue name - ALA */
Xtypedef char pdb_pname[5]; /* pdb name - 9lyz */
Xtypedef char pdb_id[4]; /* generic short id field */
Xtypedef double pdb_float; /* size of floating point */
X
Xtypedef struct { /* residue info */
X pdb_rname name;
X char chain_id;
X int seq_num;
X char insert_code;
X} pdb_residue;
X
X/*
X * structures declarations for each record type
X */
X
Xstruct pdb_unknown {
X char junk[81];
X};
Xstruct pdb_aggrgt {
X int serial_num;
X int num_components;
X int cmpont_serial_nums[14];
X};
X# define pdb_agrdes pdb_ftnote
Xstruct pdb_anisou {
X int serial_num;
X pdb_aname name;
X char alt_loc;
X pdb_residue residue;
X int u[6];
X};
Xstruct pdb_atom {
X int serial_num;
X pdb_aname name;
X char alt_loc;
X pdb_residue residue;
X pdb_float x, y, z;
X pdb_float occupancy, temp_factor;
X int ftnote_num;
X};
Xstruct pdb_author {
X char data[61];
X char continuation;
X};
X# define pdb_cmpdes pdb_ftnote
Xstruct pdb_cmpont {
X int seq_num;
X pdb_residue residues[2];
X};
X# define pdb_compnd pdb_author
Xstruct pdb_conect {
X int serial_num;
X int covalent[4];
X struct {
X int hydrogen[2];
X int salt;
X } bonds[2];
X};
Xstruct pdb_cryst1 {
X pdb_float a, b, c;
X pdb_float alpha, beta, gamma;
X char space_grp[12];
X int z;
X};
X/* no structure for PDB_END */
X/* no structure for PDB_ENDMDL */
X# define pdb_expdta pdb_author
Xstruct pdb_formul {
X int component;
X pdb_rname het_id;
X int continuation;
X char exclude; /* * to exclude */
X char formula[52];
X};
Xstruct pdb_ftnote {
X int num;
X char text[60];
X};
Xstruct pdb_header {
X char class[41];
X pdb_date date;
X pdb_pname id;
X char type;
X};
Xstruct pdb_helix {
X int serial_num;
X pdb_id id;
X pdb_residue residues[2];
X int class;
X char comment[31];
X};
Xstruct pdb_het {
X pdb_residue het_grp;
X int num_atoms;
X char text[41];
X};
X# define pdb_hetatm pdb_atom
X# define pdb_jrnl pdb_author
Xstruct pdb_master {
X int num_remark;
X int num_ftnote;
X int num_het;
X int num_helix;
X int num_sheet;
X int num_turn;
X int num_site;
X int num_transform;
X int num_coordinate;
X int num_ter;
X int num_conect;
X int num_seqres;
X};
Xstruct pdb_model {
X int num;
X};
Xstruct pdb_mtrix {
X int row_num;
X int serial_num;
X pdb_float m1, m2, m3, v;
X int given;
X};
X# define pdb_mtxdes pdb_ftnote
Xstruct pdb_obslte {
X int continuation;
X pdb_date date;
X pdb_pname old_id;
X pdb_pname id_map[8];
X};
Xstruct pdb_origx {
X int row_num;
X pdb_float o1, o2, o3, t;
X};
X# define pdb_remark pdb_ftnote
Xstruct pdb_revdat {
X int modification;
X int continuation;
X pdb_date date;
X char id[8];
X char mod_type;
X char corrections[31];
X};
Xstruct pdb_scale {
X int row_num;
X pdb_float s1, s2, s3, u;
X};
Xstruct pdb_seqres {
X int serial_num;
X char chain_id;
X int count;
X pdb_rname names[13];
X};
Xstruct pdb_sheet {
X int strand_num;
X pdb_id id;
X int count;
X pdb_residue residues[2];
X int sense;
X struct {
X pdb_aname name;
X pdb_residue residue;
X } atoms[2];
X};
X# define pdb_sigatm pdb_atom
X# define pdb_siguij pdb_anisou
Xstruct pdb_site {
X int seq_num;
X pdb_id id;
X int count;
X pdb_residue residues[4];
X};
X# define pdb_source pdb_author
Xstruct pdb_sprsde {
X int continuation;
X pdb_date date;
X pdb_pname id;
X pdb_pname supersede[8];
X};
Xstruct pdb_ssbond {
X int seq_num;
X pdb_residue residues[2];
X char comment[31];
X};
X# define pdb_symdes pdb_ftnote
Xstruct pdb_symop {
X int row_num;
X int serial_num;
X pdb_float s1, s2, s3, t;
X};
Xstruct pdb_ter {
X int serial_num;
X pdb_residue residue;
X};
Xstruct pdb_trnsfm {
X int result_serial_num;
X int apply_serial_num;
X int source_serial_num;
X};
Xstruct pdb_turn {
X int seq_num;
X pdb_id id;
X pdb_residue residues[2];
X char comment[31];
X};
Xstruct pdb_tvect {
X int serial_num;
X pdb_float t1, t2, t3;
X char comment[31];
X};
Xstruct pdb_user {
X char subtype[3];
X char text[67];
X};
Xstruct pdb_user_pdbrun {
X int version;
X};
Xstruct pdb_user_eyepos {
X pdb_float xyz[3];
X};
X# define pdb_user_atpos pdb_user_eyepos
Xstruct pdb_user_window {
X pdb_float left, right, bottom, top, hither, yon;
X};
Xstruct pdb_user_focus {
X pdb_float focus;
X};
Xstruct pdb_user_viewport {
X pdb_float xmin, xmax, ymin, ymax;
X};
Xstruct pdb_user_bgcolor {
X pdb_float rgb[3];
X};
Xstruct pdb_user_angle {
X int atom0, atom1, atom2, atom3;
X pdb_float angle;
X int which; /* version 5 -- obsolete */
X};
Xstruct pdb_user_distance {
X int atom0, atom1;
X pdb_float distance;
X int which; /* version 5 -- obsolete */
X};
Xstruct pdb_user_file {
X char filename[62]; /* 57 in version 6 */
X int model; /* not in version 5 */
X};
Xstruct pdb_user_markname {
X char markname[58];
X};
X# define pdb_user_mark pdb_user_markname
Xstruct pdb_user_cname {
X pdb_float rgb[3];
X char name[39];
X};
Xstruct pdb_user_color {
X pdb_float rgb[3];
X char spec[39];
X};
Xstruct pdb_user_radius {
X pdb_float radius;
X};
Xstruct pdb_user_object {
X int model; /* version 5 -- obsolete */
X};
Xstruct pdb_user_endobj {
X int model; /* version 5 -- obsolete */
X};
Xstruct pdb_user_chain {
X int atom0, atom1;
X};
Xstruct pdb_user_gfx_begin { /* not in version 5 */
X int primitive;
X char unknown[33];
X};
X/* no structure for USER GFX END */
X# define pdb_user_gfx_color pdb_user_color
Xstruct pdb_user_gfx_normal {
X pdb_float xyz[3];
X};
X# define pdb_user_gfx_vertex pdb_user_gfx_normal
Xstruct pdb_user_gfx_font {
X int size;
X char name[54];
X};
Xstruct pdb_user_gfx_textpos { /* not in version 5 */
X pdb_float xyz[3];
X};
Xstruct pdb_user_gfx_label {
X pdb_float xyz[3]; /* version 5 -- obsolete */
X char text[57]; /* 27 in version 5 */
X};
Xstruct pdb_user_gfx_move { /* version 5 -- obsolete */
X pdb_float xyz[3];
X};
X# define pdb_user_gfx_draw pdb_user_gfx_move /* version 5 -- obsolete */
X# define pdb_user_gfx_marker pdb_user_gfx_move /* "" */
X# define pdb_user_gfx_point pdb_user_gfx_move /* "" */
X
Xtypedef struct pdb_record {
X int record_type;
X union {
X struct pdb_unknown unknown;
X struct pdb_agrdes agrdes;
X struct pdb_aggrgt aggrgt;
X struct pdb_anisou anisou;
X struct pdb_atom atom;
X struct pdb_author author;
X struct pdb_cmpdes cmpdes;
X struct pdb_cmpont cmpont;
X struct pdb_compnd compnd;
X struct pdb_conect conect;
X struct pdb_cryst1 cryst1;
X /* no pdb_end structure */
X /* no pdb_endmdl structure */
X struct pdb_expdta expdta;
X struct pdb_formul formul;
X struct pdb_ftnote ftnote;
X struct pdb_header header;
X struct pdb_helix helix;
X struct pdb_het het;
X struct pdb_hetatm hetatm;
X struct pdb_jrnl jrnl;
X struct pdb_master master;
X struct pdb_model model;
X struct pdb_mtrix mtrix;
X struct pdb_mtxdes mtxdes;
X struct pdb_obslte obslte;
X struct pdb_origx origx;
X struct pdb_remark remark;
X struct pdb_revdat revdat;
X struct pdb_scale scale;
X struct pdb_seqres seqres;
X struct pdb_sheet sheet;
X struct pdb_sigatm sigatm;
X struct pdb_siguij siguij;
X struct pdb_site site;
X struct pdb_source source;
X struct pdb_sprsde sprsde;
X struct pdb_ssbond ssbond;
X struct pdb_symdes symdes;
X struct pdb_symop symop;
X struct pdb_ter ter;
X struct pdb_trnsfm trnsfm;
X struct pdb_turn turn;
X struct pdb_tvect tvect;
X struct pdb_user user;
X struct pdb_user_pdbrun user_pdbrun;
X struct pdb_user_eyepos user_eyepos;
X struct pdb_user_atpos user_atpos;
X struct pdb_user_window user_window;
X struct pdb_user_focus user_focus;
X struct pdb_user_viewport user_viewport;
X struct pdb_user_bgcolor user_bgcolor;
X struct pdb_user_angle user_angle;
X struct pdb_user_distance user_distance;
X struct pdb_user_file user_file;
X struct pdb_user_markname user_markname;
X struct pdb_user_mark user_mark;
X struct pdb_user_cname user_cname;
X struct pdb_user_color user_color;
X struct pdb_user_radius user_radius;
X struct pdb_user_object user_object;
X struct pdb_user_endobj user_endobj;
X struct pdb_user_chain user_chain;
X struct pdb_user_gfx_begin user_gfx_begin;
X struct pdb_user_gfx_color user_gfx_color;
X struct pdb_user_gfx_normal user_gfx_normal;
X struct pdb_user_gfx_vertex user_gfx_vertex;
X struct pdb_user_gfx_font user_gfx_font;
X struct pdb_user_gfx_textpos user_gfx_textpos;
X struct pdb_user_gfx_label user_gfx_label;
X struct pdb_user_gfx_move user_gfx_move;
X struct pdb_user_gfx_draw user_gfx_draw;
X struct pdb_user_gfx_marker user_gfx_marker;
X struct pdb_user_gfx_point user_gfx_point;
X } pdb;
X} pdb_record;
X
X# if defined(__STDC__) || defined(__cplusplus)
Xextern pdb_record pdb_read_record(FILE *);
Xextern pdb_record pdb_read_string(const char *);
Xextern void pdb_write_record(FILE *, const pdb_record *, const char *, int);
Xextern void pdb_write_string(char *, const pdb_record *);
X# else
Xextern pdb_record pdb_read_record();
Xextern pdb_record pdb_read_string();
Xextern void pdb_write_record();
Xextern void pdb_write_string();
X# endif
X
X# ifdef __cplusplus
X}
X# endif
X#endif /* PDB_H */
SHAR_EOF
if test 12494 -ne "`wc -c < 'pdb.h'`"
then
echo shar: "error transmitting 'pdb.h'" '(should have been 12494 characters)'
fi
fi
echo shar: "extracting 'pdb_int.h'" '(1312 characters)'
if test -f 'pdb_int.h'
then
echo shar: "will not over-write existing file 'pdb_int.h'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_int.h'
X/*
X * Copyright (c) 1989 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_int.h,v 2.4 1994/11/17 00:58:58 gregc Exp $
X */
X
X#include "pdb.h"
X
X#ifndef __STDC__
X# define const
X#endif
X
Xextern int pdb_pdbrun_version;
X
X#ifdef __STDC__
Xextern int pdb_sscanf(const char *, const char *, ...);
Xextern void pdb_sprintf(char *, const char *, ...);
Xextern const char *pdb_gfx_string(int i);
Xextern int pdb_gfx_type(const char *type);
X#else
Xextern int pdb_sscanf();
Xextern void pdb_sprintf();
Xextern char *pdb_gfx_string();
Xextern int pdb_gfx_type();
X#endif
SHAR_EOF
if test 1312 -ne "`wc -c < 'pdb_int.h'`"
then
echo shar: "error transmitting 'pdb_int.h'" '(should have been 1312 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 'ms.c'" '(6563 characters)'
if test -f 'ms.c'
then
echo shar: "will not over-write existing file 'ms.c'"
else
sed 's/^ X//' << \SHAR_EOF > 'ms.c'
X/*
X * Copyright (c) 1989 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: ms.c,v 2.4 94/05/19 16:01:16 conrad Exp $
X */
X
X#include
X#include
X#include
X#include
X#include "pdb_int.h"
X#include "ms.h"
X
X#ifndef TRUE
X#define TRUE 1
X#define FALSE 0
X#endif
X
X/*
X * ms_read_record:
X * Read an ms record from a file and return the corresponding
X * data structure
X */
Xms_record
X#ifdef __STDC__
Xms_read_record(FILE *fp)
X#else
Xms_read_record(fp)
X FILE *fp;
X#endif
X{
X char buf[MS_BUFSIZ];
X char *cp;
X int c;
X ms_record record;
X
X /*
X * If at end of file, just set the record type and return
X */
X if (fgets(buf, sizeof buf, fp) == NULL) {
X record.record_type = MS_END;
X return record;
X }
X
X cp = strchr(buf, '\n');
X if (cp != NULL)
X *cp = '\0';
X else
X /* discard extra characters since line too long */
X while ((c = getc(fp)) != '\n' && c != EOF)
X continue;
X
X return ms_read_string(buf);
X}
X
X#ifdef __STDC__
X static void crunch(char *);
X#else
X static void crunch();
X#endif
X
X/*
X * ms_read_string
X * Construct the data structure corresponding to the given line
X */
Xms_record
X#ifdef __STDC__
Xms_read_string(const char *buf)
X#else
Xms_read_string(buf)
X char *buf;
X#endif
X{
X int i;
X const char *cp;
X char *sp;
X int nfield;
X double area, extra;
X double coord[3], normal[3];
X ms_record record;
X ms_atom *map;
X ms_surface *msp;
X char type;
X const char *atom_fmt, *surf_fmt;
X
X /*
X * If the head of the string is "user" (case-independently),
X * we copy the buffer into the string and return
X */
X if (strncasecmp(buf, "user", 4) == 0) {
X record.record_type = MS_USER;
X for (cp = buf + 4; isspace(*cp); cp++)
X continue;
X sp = record.ms.user.string;
X while (*cp != '\0' && *cp != '\n')
X *sp++ = *cp++;
X *sp = '\0';
X return record;
X }
X
X /*
X * This is either an atom line, surface line, or an error
X */
X if (strlen(buf) < 41) {
X record.record_type = MS_UNKNOWN;
X (void) strcpy(record.ms.unknown.string, buf);
X return record;
X }
X type = buf[40];
X atom_fmt = "%3s %4s %4s%8f %8f %8f A";
X surf_fmt = "%3s %4s %4s%8f %8f %8f S%c%c %6f %6f %6f %6f %6f";
X if (isspace(type)) {
X type = buf[41];
X atom_fmt = "%3s %5s %4s%8f %8f %8f A";
X surf_fmt = "%3s %5s %4s%8f %8f %8f S%c%c %6f %6f %6f %6f %6f";
X }
X switch (type) {
X case 'A':
X record.record_type = MS_ATOM;
X map = &record.ms.atom;
X nfield = pdb_sscanf(buf, atom_fmt,
X map->residue_type, map->residue_sequence,
X map->atom_name, &coord[0], &coord[1], &coord[2]);
X if (nfield == 6) {
X for (i = 0; i < 3; i++)
X map->coord[i] = coord[i];
X crunch(map->residue_type);
X crunch(map->residue_sequence);
X crunch(map->atom_name);
X return record;
X }
X break;
X case 'S':
X record.record_type = MS_SURFACE;
X msp = &record.ms.surface;
X nfield = pdb_sscanf(buf, surf_fmt,
X msp->residue_type, msp->residue_sequence,
X msp->atom_name, &coord[0], &coord[1], &coord[2],
X &msp->type, &msp->level, &area,
X &normal[0], &normal[1], &normal[2], &extra);
X switch (nfield) {
X case 9:
X normal[0] = 0;
X /* FALLTHROUGH */
X case 10:
X msp->has_normal = FALSE;
X for (i = 0; i < 3; i++)
X msp->coord[i] = coord[i];
X msp->area = area;
X msp->extra = normal[0];
X crunch(msp->residue_type);
X crunch(msp->residue_sequence);
X crunch(msp->atom_name);
X return record;
X case 12:
X extra = 0;
X /* FALLTHROUGH */
X case 13:
X msp->has_normal = TRUE;
X for (i = 0; i < 3; i++) {
X msp->coord[i] = coord[i];
X msp->normal[i] = normal[i];
X }
X msp->area = area;
X msp->extra = extra;
X crunch(msp->residue_type);
X crunch(msp->residue_sequence);
X crunch(msp->atom_name);
X return record;
X }
X break;
X }
X
X /*
X * Okay. We must not have recognized the record. Set the
X * record type, copy the string into the string and return
X */
X record.record_type = MS_UNKNOWN;
X (void) strcpy(record.ms.unknown.string, buf);
X return record;
X}
X
X/*
X * crunch:
X * Remove blanks from a string
X */
Xstatic
Xvoid
X#ifdef __STDC__
Xcrunch(char *s)
X#else
Xcrunch(s)
X char *s;
X#endif
X{
X char *last;
X
X for (last = s; *s != '\0'; s++)
X if (!isspace(*s))
X *last++ = *s;
X *last = '\0';
X}
X
X/*
X * ms_write_record:
X * Write an ms record to a file from the corresponding
X * data structure
X */
Xvoid
X#ifdef __STDC__
Xms_write_record(FILE *fp, const ms_record *mp)
X#else
Xms_write_record(fp, mp)
X FILE *fp;
X ms_record *mp;
X#endif
X{
X char buffer[MS_RECLEN];
X
X ms_write_string(buffer, mp);
X fprintf(fp, "%s\n", buffer);
X}
X
X/*
X * ms_write_string:
X * Write an ms record to a string from the corresponding
X * data structure
X */
Xvoid
X#ifdef __STDC__
Xms_write_string(char *buffer, const ms_record *mp)
X#else
Xms_write_string(buffer, mp)
X char *buffer;
X ms_record *mp;
X#endif
X{
X const ms_atom *map;
X const ms_surface *msp;
X char *cp;
X
X switch (mp->record_type) {
X case MS_ATOM:
X map = &mp->ms.atom;
X (void) sprintf(buffer, "%-3s %4s %4s %7.3f %7.3f %7.3f A",
X map->residue_type, map->residue_sequence,
X map->atom_name, map->coord[0], map->coord[1],
X map->coord[2]);
X break;
X case MS_SURFACE:
X msp = &mp->ms.surface;
X (void) sprintf(buffer,
X "%-3s %4s %4s %7.3f %7.3f %7.3f S%c%c %6.3f",
X msp->residue_type, msp->residue_sequence,
X msp->atom_name, msp->coord[0], msp->coord[1],
X msp->coord[2], msp->type, msp->level, msp->area);
X cp = strchr(buffer, '\0');
X if (msp->has_normal) {
X (void) sprintf(cp, " %6.3f %6.3f %6.3f",
X msp->normal[0], msp->normal[1], msp->normal[2]);
X cp = strchr(cp, '\0');
X }
X if (msp->extra != 0) {
X if (msp->extra >= 1000 || msp->extra <= -100)
X (void) sprintf(cp, " %6.1f", msp->extra);
X else if (msp->extra >= 100 || msp->extra <= -10)
X (void) sprintf(cp, " %6.2f", msp->extra);
X else
X (void) sprintf(cp, " %6.3f", msp->extra);
X }
X break;
X case MS_USER:
X (void) sprintf(buffer, "USER %s\n", mp->ms.user.string);
X break;
X }
X}
SHAR_EOF
if test 6563 -ne "`wc -c < 'ms.c'`"
then
echo shar: "error transmitting 'ms.c'" '(should have been 6563 characters)'
fi
fi
echo shar: "extracting 'pdb_read.c'" '(30391 characters)'
if test -f 'pdb_read.c'
then
echo shar: "will not over-write existing file 'pdb_read.c'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_read.c'
X/*
X * Copyright (c) 1989 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.c,v 2.20 1995/07/22 02:03:18 gregc Exp $
X *
X * subroutine for reading PDB format files
X *
X */
X
X/* LINTLIBRARY */
X
X# include
X# include
X# include
X# include "pdb_int.h"
X
X# ifndef _tolower
X# define _tolower tolower
X# endif
X
X# define STREQN(a,b,n) (strncmp(a, b, n) == 0)
X
Xstatic const char * const pdb_record_format[PDB_NUM_R] = {
X#include "read_format.i"
X};
X
Xstatic char const * const pdbrun5[] = {
X#include "pdbrun5_read.i"
X};
X
Xstatic char const * const pdbrun6[] = {
X#include "pdbrun6_read.i"
X};
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
Xpdb_record
X# ifdef __STDC__
Xpdb_read_record(FILE *f)
X# else
Xpdb_read_record(f)
X FILE *f;
X# endif
X{
X
X char buffer[PDB_BUFSIZ];
X char *cp;
X int c;
X static pdb_record r_end = { PDB_END };
X
X if (fgets(buffer, PDB_BUFSIZ, f) == NULL) {
X /* at eof or error - default to eof */
X return r_end;
X }
X
X cp = strchr(buffer, '\n');
X if (cp != NULL)
X *cp = '\0';
X else
X /* discard extra characters since line too long */
X while ((c = getc(f)) != '\n' && c != EOF)
X continue;
X
X return pdb_read_string(buffer);
X}
X
Xstatic int
X#ifdef __STDC__
Xpdbrun5_type(const char *buf)
X#else
Xpdbrun5_type(buf)
X char *buf;
X#endif
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 int
X#ifdef __STDC__
Xpdbrun6_type(const char *buf)
X#else
Xpdbrun6_type(buf)
X char *buf;
X#endif
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_record
X# ifdef __STDC__
Xpdb_read_string(const char *buffer)
X# else
Xpdb_read_string(buffer)
X char *buffer;
X# endif
X{
X
X pdb_record r;
X const char *fmt;
X struct pdb_sheet *sh;
X pdb_residue *sha0, *sha1;
X char record_type[4];
X int i;
X char new_buffer[PDB_BUFSIZ];
X
X# if defined(__STDC__) || defined(vms)
X (void) memset(&r, 0, sizeof r);
X# else
X bzero((char *) &r, sizeof r);
X# endif
X
X# ifdef DEBUG
X printf("%s", buffer);
X# endif /* DEBUG */
X
X /* convert pdb record to C structure */
X
X for (i = 0; buffer[i] != '\0' && buffer[i] != '\n' && i < 4; i += 1) {
X if (isupper(buffer[i]))
X record_type[i] = _tolower(buffer[i]);
X else
X record_type[i] = buffer[i];
X }
X if (i < 4)
X for (; i < 4; i += 1)
X record_type[i] = ' ';
X
X r.record_type = PDB_UNKNOWN;
X switch (record_type[0]) {
X
X case 'a':
X if (STREQN(record_type + 1, "tom", 3))
X r.record_type = PDB_ATOM;
X else if (STREQN(record_type + 1, "uth", 3))
X r.record_type = PDB_AUTHOR;
X else if (STREQN(record_type + 1, "nis", 3))
X r.record_type = PDB_ANISOU;
X else if (STREQN(record_type + 1, "grd", 3))
X r.record_type = PDB_AGRDES;
X else if (STREQN(record_type + 1, "ggr", 3))
X r.record_type = PDB_AGGRGT;
X break;
X
X case 'c':
X if (STREQN(record_type + 1, "omp", 3))
X r.record_type = PDB_COMPND;
X else if (STREQN(record_type + 1, "rys", 3))
X r.record_type = PDB_CRYST1;
X else if (STREQN(record_type + 1, "one", 3))
X r.record_type = PDB_CONECT;
X else if (STREQN(record_type + 1, "mpd", 3))
X r.record_type = PDB_CMPDES;
X else if (STREQN(record_type + 1, "mpo", 3))
X r.record_type = PDB_CMPONT;
X break;
X
X case 'e':
X if (STREQN(record_type + 1, "nd ", 3))
X r.record_type = PDB_END;
X else if (STREQN(record_type + 1, "ndm", 3))
X r.record_type = PDB_ENDMDL;
X else if (STREQN(record_type + 1, "xpd", 3))
X r.record_type = PDB_EXPDTA;
X break;
X
X case 'f':
X if (STREQN(record_type + 1, "tno", 3))
X r.record_type = PDB_FTNOTE;
X else if (STREQN(record_type + 1, "orm", 3))
X r.record_type = PDB_FORMUL;
X break;
X
X case 'h':
X if (STREQN(record_type + 1, "eta", 3))
X r.record_type = PDB_HETATM;
X else if (STREQN(record_type + 1, "ead", 3))
X r.record_type = PDB_HEADER;
X else if (STREQN(record_type + 1, "et ", 3))
X r.record_type = PDB_HET;
X else if (STREQN(record_type + 1, "eli", 3))
X r.record_type = PDB_HELIX;
X break;
X
X case 'j':
X if (STREQN(record_type + 1, "rnl", 3))
X r.record_type = PDB_JRNL;
X break;
X
X case 'm':
X if (STREQN(record_type + 1, "tri", 3))
X r.record_type = PDB_MTRIX;
X else if (STREQN(record_type + 1, "ast", 3))
X r.record_type = PDB_MASTER;
X else if (STREQN(record_type + 1, "ode", 3))
X r.record_type = PDB_MODEL;
X else if (STREQN(record_type + 1, "txd", 3))
X r.record_type = PDB_MTXDES;
X break;
X
X case 'o':
X if (STREQN(record_type + 1, "bsl", 3))
X r.record_type = PDB_OBSLTE;
X else if (STREQN(record_type + 1, "rig", 3))
X r.record_type = PDB_ORIGX;
X break;
X
X case 'r':
X if (STREQN(record_type + 1, "ema", 3))
X r.record_type = PDB_REMARK;
X else if (STREQN(record_type + 1, "evd", 3))
X r.record_type = PDB_REVDAT;
X break;
X
X case 's':
X switch (record_type[1]) {
X
X case 'c':
X if (STREQN(record_type + 2, "al", 2))
X r.record_type = PDB_SCALE;
X break;
X
X case 'e':
X if (STREQN(record_type + 2, "qr", 2))
X r.record_type = PDB_SEQRES;
X break;
X
X case 'h':
X if (STREQN(record_type + 2, "ee", 2))
X r.record_type = PDB_SHEET;
X break;
X
X case 'i':
X if (STREQN(record_type + 2, "te", 2))
X r.record_type = PDB_SITE;
X else if (STREQN(record_type + 2, "ga", 2))
X r.record_type = PDB_SIGATM;
X else if (STREQN(record_type + 2, "gu", 2))
X r.record_type = PDB_SIGUIJ;
X break;
X
X case 'o':
X if (STREQN(record_type + 2, "ur", 2))
X r.record_type = PDB_SOURCE;
X break;
X
X case 'p':
X if (STREQN(record_type + 2, "rs", 2))
X r.record_type = PDB_SPRSDE;
X break;
X
X case 's':
X if (STREQN(record_type + 2, "bo", 2))
X r.record_type = PDB_SSBOND;
X break;
X
X case 'y':
X if (STREQN(record_type + 2, "md", 2))
X r.record_type = PDB_SYMDES;
X else if (STREQN(record_type + 2, "mo", 2))
X r.record_type = PDB_SYMOP;
X break;
X }
X break;
X
X case 't':
X if (STREQN(record_type + 1, "urn", 3))
X r.record_type = PDB_TURN;
X else if (STREQN(record_type + 1, "vec", 3))
X r.record_type = PDB_TVECT;
X else if (STREQN(record_type + 1, "er ", 3))
X r.record_type = PDB_TER;
X else if (STREQN(record_type + 1, "rns", 3))
X r.record_type = PDB_TRNSFM;
X break;
X
X case 'u':
X if (STREQN(record_type + 1, "ser", 3)) {
X r.record_type = PDB_USER;
X switch (pdb_pdbrun_version) {
X case 1: case 2: case 3: case 4: case 5:
X r.record_type = pdbrun5_type(buffer + 6);
X break;
X case 6:
X r.record_type = pdbrun6_type(buffer + 6);
X break;
X default:
X if (strncasecmp(buffer + 6, "PDBRUN ", 7) == 0)
X r.record_type = PDB_USER_PDBRUN;
X break;
X }
X }
X break;
X }
X
X if (r.record_type < PDB_USER_PDBRUN)
X fmt = pdb_record_format[r.record_type];
X else if (pdb_pdbrun_version < 6)
X fmt = pdbrun5[r.record_type - PDB_USER_PDBRUN];
X else
X fmt = pdbrun6[r.record_type - PDB_USER_PDBRUN];
X switch (r.record_type) {
X
X default:
X case PDB_UNKNOWN:
Xunknown:
X r.record_type = PDB_UNKNOWN; /* in case of goto */
X (void) pdb_sscanf(buffer, "%72s", r.pdb.unknown.junk);
X break;
X
X case PDB_AGGRGT:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.aggrgt.serial_num,
X &r.pdb.aggrgt.num_components,
X &r.pdb.aggrgt.cmpont_serial_nums[0],
X &r.pdb.aggrgt.cmpont_serial_nums[1],
X &r.pdb.aggrgt.cmpont_serial_nums[2],
X &r.pdb.aggrgt.cmpont_serial_nums[3],
X &r.pdb.aggrgt.cmpont_serial_nums[4],
X &r.pdb.aggrgt.cmpont_serial_nums[5],
X &r.pdb.aggrgt.cmpont_serial_nums[6],
X &r.pdb.aggrgt.cmpont_serial_nums[7],
X &r.pdb.aggrgt.cmpont_serial_nums[8],
X &r.pdb.aggrgt.cmpont_serial_nums[9],
X &r.pdb.aggrgt.cmpont_serial_nums[10],
X &r.pdb.aggrgt.cmpont_serial_nums[11],
X &r.pdb.aggrgt.cmpont_serial_nums[12],
X &r.pdb.aggrgt.cmpont_serial_nums[13]))
X goto unknown;
X break;
X case PDB_ANISOU:
X case PDB_SIGUIJ:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.anisou.serial_num,
X r.pdb.anisou.name, &r.pdb.anisou.alt_loc,
X r.pdb.anisou.residue.name,
X &r.pdb.anisou.residue.chain_id,
X &r.pdb.anisou.residue.seq_num,
X &r.pdb.anisou.residue.insert_code,
X &r.pdb.anisou.u[0], &r.pdb.anisou.u[1],
X &r.pdb.anisou.u[2], &r.pdb.anisou.u[3],
X &r.pdb.anisou.u[4], &r.pdb.anisou.u[5]))
X goto unknown;
X break;
X
X case PDB_ATOM:
X case PDB_HETATM:
X case PDB_SIGATM:
X if (0 <= pdb_sscanf(buffer, fmt, &r.pdb.atom.serial_num,
X r.pdb.atom.name, &r.pdb.atom.alt_loc,
X r.pdb.atom.residue.name,
X &r.pdb.atom.residue.chain_id,
X &r.pdb.atom.residue.seq_num,
X &r.pdb.atom.residue.insert_code,
X &r.pdb.atom.x, &r.pdb.atom.y, &r.pdb.atom.z,
X &r.pdb.atom.occupancy, &r.pdb.atom.temp_factor,
X &r.pdb.atom.ftnote_num))
X break;
X /* handle atom serial number overflows */
X if (strncmp(&buffer[6], "*****", 5) != 0)
X goto unknown;
X strncpy(new_buffer, buffer, PDB_BUFSIZ);
X strncpy(&new_buffer[6], "00000", 5);
X if (0 <= pdb_sscanf(new_buffer, fmt, &r.pdb.atom.serial_num,
X r.pdb.atom.name, &r.pdb.atom.alt_loc,
X r.pdb.atom.residue.name,
X &r.pdb.atom.residue.chain_id,
X &r.pdb.atom.residue.seq_num,
X &r.pdb.atom.residue.insert_code,
X &r.pdb.atom.x, &r.pdb.atom.y, &r.pdb.atom.z,
X &r.pdb.atom.occupancy, &r.pdb.atom.temp_factor,
X &r.pdb.atom.ftnote_num)) {
X static int atom_serial_number = 10000;
X r.pdb.atom.serial_num = atom_serial_number++;
X break;
X }
X goto unknown;
X
X case PDB_AUTHOR:
X case PDB_COMPND:
X case PDB_JRNL:
X case PDB_SOURCE:
X case PDB_EXPDTA:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.author.continuation,
X r.pdb.author.data))
X goto unknown;
X break;
X
X case PDB_CMPONT:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.cmpont.seq_num,
X r.pdb.cmpont.residues[0].name,
X &r.pdb.cmpont.residues[0].chain_id,
X &r.pdb.cmpont.residues[0].seq_num,
X &r.pdb.cmpont.residues[0].insert_code,
X r.pdb.cmpont.residues[1].name,
X &r.pdb.cmpont.residues[1].chain_id,
X &r.pdb.cmpont.residues[1].seq_num,
X &r.pdb.cmpont.residues[1].insert_code))
X goto unknown;
X break;
X
X case PDB_CONECT:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.conect.serial_num,
X &r.pdb.conect.covalent[0],
X &r.pdb.conect.covalent[1],
X &r.pdb.conect.covalent[2],
X &r.pdb.conect.covalent[3],
X &r.pdb.conect.bonds[0].hydrogen[0],
X &r.pdb.conect.bonds[0].hydrogen[1],
X &r.pdb.conect.bonds[0].salt,
X &r.pdb.conect.bonds[1].hydrogen[0],
X &r.pdb.conect.bonds[1].hydrogen[1],
X &r.pdb.conect.bonds[1].salt))
X goto unknown;
X break;
X
X case PDB_CRYST1:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.cryst1.a,
X &r.pdb.cryst1.b, &r.pdb.cryst1.c,
X &r.pdb.cryst1.alpha, &r.pdb.cryst1.beta,
X &r.pdb.cryst1.gamma, r.pdb.cryst1.space_grp,
X &r.pdb.cryst1.z))
X goto unknown;
X break;
X
X case PDB_END:
X case PDB_ENDMDL:
X break;
X
X case PDB_FORMUL:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.formul.component,
X r.pdb.formul.het_id, &r.pdb.formul.continuation,
X &r.pdb.formul.exclude, r.pdb.formul.formula))
X goto unknown;
X break;
X
X case PDB_FTNOTE:
X case PDB_REMARK:
X case PDB_SYMDES:
X case PDB_MTXDES:
X case PDB_CMPDES:
X case PDB_AGRDES:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.ftnote.num,
X r.pdb.ftnote.text))
X goto unknown;
X break;
X
X case PDB_HEADER:
X if (0 > pdb_sscanf(buffer, fmt, r.pdb.header.class,
X r.pdb.header.date, &r.pdb.header.type,
X r.pdb.header.id))
X goto unknown;
X break;
X
X case PDB_HELIX:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.helix.serial_num,
X r.pdb.helix.id,
X r.pdb.helix.residues[0].name,
X &r.pdb.helix.residues[0].chain_id,
X &r.pdb.helix.residues[0].seq_num,
X &r.pdb.helix.residues[0].insert_code,
X r.pdb.helix.residues[1].name,
X &r.pdb.helix.residues[1].chain_id,
X &r.pdb.helix.residues[1].seq_num,
X &r.pdb.helix.residues[1].insert_code,
X &r.pdb.helix.class, r.pdb.helix.comment))
X goto unknown;
X break;
X
X case PDB_HET:
X if (0 > pdb_sscanf(buffer, fmt, r.pdb.het.het_grp.name,
X &r.pdb.het.het_grp.chain_id,
X &r.pdb.het.het_grp.seq_num,
X &r.pdb.het.het_grp.insert_code,
X &r.pdb.het.num_atoms, r.pdb.het.text))
X goto unknown;
X break;
X
X case PDB_MASTER:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.master.num_remark,
X &r.pdb.master.num_ftnote,
X &r.pdb.master.num_het, &r.pdb.master.num_helix,
X &r.pdb.master.num_sheet, &r.pdb.master.num_turn,
X &r.pdb.master.num_site,
X &r.pdb.master.num_transform,
X &r.pdb.master.num_coordinate,
X &r.pdb.master.num_ter, &r.pdb.master.num_conect,
X &r.pdb.master.num_seqres))
X goto unknown;
X break;
X
X case PDB_MODEL:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.model.num))
X goto unknown;
X break;
X
X case PDB_MTRIX:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.mtrix.row_num,
X &r.pdb.mtrix.serial_num, &r.pdb.mtrix.m1,
X &r.pdb.mtrix.m2, &r.pdb.mtrix.m3,
X &r.pdb.mtrix.v, &r.pdb.mtrix.given))
X goto unknown;
X break;
X
X case PDB_OBSLTE:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.obslte.continuation,
X r.pdb.obslte.date, r.pdb.obslte.old_id,
X r.pdb.obslte.id_map[0], r.pdb.obslte.id_map[1],
X r.pdb.obslte.id_map[2], r.pdb.obslte.id_map[3],
X r.pdb.obslte.id_map[4], r.pdb.obslte.id_map[2],
X r.pdb.obslte.id_map[6], r.pdb.obslte.id_map[7]))
X goto unknown;
X break;
X
X case PDB_ORIGX:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.origx.row_num,
X &r.pdb.origx.o1, &r.pdb.origx.o2,
X &r.pdb.origx.o3, &r.pdb.origx.t))
X goto unknown;
X break;
X
X case PDB_REVDAT:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.revdat.modification,
X &r.pdb.revdat.continuation, r.pdb.revdat.date,
X r.pdb.revdat.id, &r.pdb.revdat.mod_type,
X r.pdb.revdat.corrections))
X goto unknown;
X break;
X
X case PDB_SCALE:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.scale.row_num,
X &r.pdb.scale.s1, &r.pdb.scale.s2,
X &r.pdb.scale.s3, &r.pdb.scale.u))
X goto unknown;
X break;
X
X case PDB_SEQRES:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.seqres.serial_num,
X &r.pdb.seqres.chain_id, &r.pdb.seqres.count,
X r.pdb.seqres.names[0], r.pdb.seqres.names[1],
X r.pdb.seqres.names[2], r.pdb.seqres.names[3],
X r.pdb.seqres.names[4], r.pdb.seqres.names[5],
X r.pdb.seqres.names[6], r.pdb.seqres.names[7],
X r.pdb.seqres.names[8], r.pdb.seqres.names[9],
X r.pdb.seqres.names[10], r.pdb.seqres.names[11],
X r.pdb.seqres.names[12]))
X goto unknown;
X break;
X
X case PDB_SHEET:
X sh = &r.pdb.sheet;
X sha0 = &sh->atoms[0].residue;
X sha1 = &sh->atoms[1].residue;
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.sheet.strand_num,
X sh->id, &r.pdb.sheet.count,
X sh->residues[0].name, &sh->residues[0].chain_id,
X &sh->residues[0].seq_num,
X &sh->residues[0].insert_code,
X sh->residues[1].name, &sh->residues[1].chain_id,
X &sh->residues[1].seq_num,
X &sh->residues[1].insert_code, &sh->sense,
X sh->atoms[0].name, sha0->name, &sha0->chain_id,
X &sha0->seq_num, &sha0->insert_code,
X sh->atoms[1].name, sha1->name,
X &sha1->chain_id, &sha1->seq_num,
X &sha1->insert_code))
X goto unknown;
X break;
X
X case PDB_SITE:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.site.seq_num,
X r.pdb.site.id, &r.pdb.site.count,
X r.pdb.site.residues[0].name,
X &r.pdb.site.residues[0].chain_id,
X &r.pdb.site.residues[0].seq_num,
X &r.pdb.site.residues[0].insert_code,
X r.pdb.site.residues[1].name,
X &r.pdb.site.residues[1].chain_id,
X &r.pdb.site.residues[1].seq_num,
X &r.pdb.site.residues[1].insert_code,
X r.pdb.site.residues[2].name,
X &r.pdb.site.residues[2].chain_id,
X &r.pdb.site.residues[2].seq_num,
X &r.pdb.site.residues[2].insert_code,
X r.pdb.site.residues[3].name,
X &r.pdb.site.residues[3].chain_id,
X &r.pdb.site.residues[3].seq_num,
X &r.pdb.site.residues[3].insert_code))
X goto unknown;
X break;
X
X case PDB_SPRSDE:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.sprsde.continuation,
X r.pdb.sprsde.date, r.pdb.sprsde.id,
X r.pdb.sprsde.supersede[0],
X r.pdb.sprsde.supersede[1],
X r.pdb.sprsde.supersede[2],
X r.pdb.sprsde.supersede[3],
X r.pdb.sprsde.supersede[4],
X r.pdb.sprsde.supersede[5],
X r.pdb.sprsde.supersede[6],
X r.pdb.sprsde.supersede[7]))
X goto unknown;
X break;
X
X case PDB_SSBOND:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.ssbond.seq_num,
X r.pdb.ssbond.residues[0].name,
X &r.pdb.ssbond.residues[0].chain_id,
X &r.pdb.ssbond.residues[0].seq_num,
X &r.pdb.ssbond.residues[0].insert_code,
X r.pdb.ssbond.residues[1].name,
X &r.pdb.ssbond.residues[1].chain_id,
X &r.pdb.ssbond.residues[1].seq_num,
X &r.pdb.ssbond.residues[1].insert_code,
X r.pdb.ssbond.comment))
X goto unknown;
X break;
X
X case PDB_SYMOP:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.symop.row_num,
X &r.pdb.symop.serial_num, &r.pdb.symop.s1,
X &r.pdb.symop.s2, &r.pdb.symop.s3,
X &r.pdb.symop.t))
X goto unknown;
X break;
X
X case PDB_TER:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.ter.serial_num,
X r.pdb.ter.residue.name,
X &r.pdb.ter.residue.chain_id,
X &r.pdb.ter.residue.seq_num,
X &r.pdb.ter.residue.insert_code))
X goto unknown;
X break;
X
X case PDB_TRNSFM:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.trnsfm.result_serial_num,
X &r.pdb.trnsfm.apply_serial_num,
X &r.pdb.trnsfm.source_serial_num))
X goto unknown;
X break;
X
X case PDB_TURN:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.turn.seq_num,
X r.pdb.turn.id, r.pdb.turn.residues[0].name,
X &r.pdb.turn.residues[0].chain_id,
X &r.pdb.turn.residues[0].seq_num,
X &r.pdb.turn.residues[0].insert_code,
X r.pdb.turn.residues[1].name,
X &r.pdb.turn.residues[1].chain_id,
X &r.pdb.turn.residues[1].seq_num,
X &r.pdb.turn.residues[1].insert_code,
X r.pdb.turn.comment))
X goto unknown;
X break;
X
X case PDB_TVECT:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.tvect.serial_num,
X &r.pdb.tvect.t1, &r.pdb.tvect.t2,
X &r.pdb.tvect.t3, r.pdb.tvect.comment))
X goto unknown;
X break;
X
Xuser:
X r.record_type = PDB_USER;
X fmt = pdb_record_format[r.record_type];
X case PDB_USER:
X if (0 > pdb_sscanf(buffer, fmt, r.pdb.user.subtype,
X r.pdb.user.text))
X goto unknown;
X break;
X
X case PDB_USER_PDBRUN:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_pdbrun.version))
X goto user;
X pdb_pdbrun_version = r.pdb.user_pdbrun.version;
X break;
X
X case PDB_USER_EYEPOS:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_eyepos.xyz[0],
X &r.pdb.user_eyepos.xyz[1],
X &r.pdb.user_eyepos.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_ATPOS:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_atpos.xyz[0],
X &r.pdb.user_atpos.xyz[1],
X &r.pdb.user_atpos.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_WINDOW:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_window.left,
X &r.pdb.user_window.right,
X &r.pdb.user_window.bottom,
X &r.pdb.user_window.top,
X &r.pdb.user_window.hither,
X &r.pdb.user_window.yon))
X goto user;
X break;
X
X case PDB_USER_FOCUS:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_focus.focus))
X goto user;
X break;
X
X case PDB_USER_VIEWPORT:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_viewport.xmin,
X &r.pdb.user_viewport.xmax,
X &r.pdb.user_viewport.ymin,
X &r.pdb.user_viewport.ymax))
X goto user;
X break;
X
X case PDB_USER_BGCOLOR:
X if (pdb_pdbrun_version < 6) {
X if (0 > sscanf(buffer, fmt, &r.pdb.user_bgcolor.rgb[0],
X &r.pdb.user_bgcolor.rgb[1],
X &r.pdb.user_bgcolor.rgb[2]))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt,
X &r.pdb.user_bgcolor.rgb[0],
X &r.pdb.user_bgcolor.rgb[1],
X &r.pdb.user_bgcolor.rgb[2]))
X goto user;
X break;
X
X case PDB_USER_ANGLE:
X if (pdb_pdbrun_version < 6) {
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_angle.which,
X &r.pdb.user_angle.atom0,
X &r.pdb.user_angle.atom1,
X &r.pdb.user_angle.atom2,
X &r.pdb.user_angle.atom3,
X &r.pdb.user_angle.angle))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_angle.atom0,
X &r.pdb.user_angle.atom1,
X &r.pdb.user_angle.atom2,
X &r.pdb.user_angle.atom3,
X &r.pdb.user_angle.angle))
X goto user;
X break;
X
X case PDB_USER_DISTANCE:
X if (pdb_pdbrun_version < 6) {
X if (0 > pdb_sscanf(buffer, fmt,
X &r.pdb.user_distance.which,
X &r.pdb.user_distance.atom0,
X &r.pdb.user_distance.atom1,
X &r.pdb.user_distance.distance))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt,
X &r.pdb.user_distance.atom0,
X &r.pdb.user_distance.atom1,
X &r.pdb.user_distance.distance))
X goto user;
X break;
X
X case PDB_USER_FILE:
X if (pdb_pdbrun_version < 6) {
X if (0 > pdb_sscanf(buffer, fmt,
X r.pdb.user_file.filename))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_file.model,
X r.pdb.user_file.filename))
X goto user;
X break;
X
X case PDB_USER_MARKNAME:
X if (0 > pdb_sscanf(buffer, fmt, r.pdb.user_markname.markname))
X goto user;
X break;
X
X case PDB_USER_MARK:
X if (0 > pdb_sscanf(buffer, fmt, r.pdb.user_mark.markname))
X goto user;
X break;
X
X case PDB_USER_CNAME:
X if (pdb_pdbrun_version < 6) {
X if (0 > sscanf(buffer, fmt, r.pdb.user_cname.name,
X &r.pdb.user_cname.rgb[0],
X &r.pdb.user_cname.rgb[1],
X &r.pdb.user_cname.rgb[2]))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_cname.rgb[0],
X &r.pdb.user_cname.rgb[1],
X &r.pdb.user_cname.rgb[2],
X r.pdb.user_cname.name))
X goto user;
X break;
X
X case PDB_USER_COLOR:
X if (pdb_pdbrun_version < 6) {
X if (0 > sscanf(buffer, fmt, r.pdb.user_color.spec,
X &r.pdb.user_color.rgb[0],
X &r.pdb.user_color.rgb[1],
X &r.pdb.user_color.rgb[2]))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_color.rgb[0],
X &r.pdb.user_color.rgb[1],
X &r.pdb.user_color.rgb[2],
X r.pdb.user_color.spec))
X goto user;
X break;
X
X case PDB_USER_RADIUS:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_radius.radius))
X goto user;
X break;
X
X case PDB_USER_OBJECT:
X if (pdb_pdbrun_version < 6) {
X if (0 > pdb_sscanf(buffer, fmt,
X &r.pdb.user_object.model))
X goto user;
X }
X break;
X
X case PDB_USER_ENDOBJ:
X if (pdb_pdbrun_version < 6) {
X if (0 > pdb_sscanf(buffer, fmt,
X &r.pdb.user_endobj.model))
X goto user;
X }
X break;
X
X case PDB_USER_CHAIN:
X if (pdb_pdbrun_version < 6) {
X if (0 > sscanf(buffer, fmt, &r.pdb.user_chain.atom0,
X &r.pdb.user_chain.atom1))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_chain.atom0,
X &r.pdb.user_chain.atom1))
X goto user;
X break;
X
X case PDB_USER_GFX_BEGIN:
X if (0 > pdb_sscanf(buffer, fmt, r.pdb.user_gfx_begin.unknown))
X goto user;
X r.pdb.user_gfx_begin.primitive
X = pdb_gfx_type(r.pdb.user_gfx_begin.unknown);
X break;
X
X case PDB_USER_GFX_END:
X break;
X
X case PDB_USER_GFX_COLOR:
X if (pdb_pdbrun_version < 6) {
X if (0 > sscanf(buffer, fmt, r.pdb.user_gfx_color.spec,
X &r.pdb.user_gfx_color.rgb[0],
X &r.pdb.user_gfx_color.rgb[1],
X &r.pdb.user_gfx_color.rgb[2]))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt,
X &r.pdb.user_gfx_color.rgb[0],
X &r.pdb.user_gfx_color.rgb[1],
X &r.pdb.user_gfx_color.rgb[2],
X r.pdb.user_gfx_color.spec))
X goto user;
X break;
X
X case PDB_USER_GFX_NORMAL:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_gfx_normal.xyz[0],
X &r.pdb.user_gfx_normal.xyz[1],
X &r.pdb.user_gfx_normal.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_GFX_VERTEX:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_gfx_vertex.xyz[0],
X &r.pdb.user_gfx_vertex.xyz[1],
X &r.pdb.user_gfx_vertex.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_GFX_FONT:
X if (pdb_pdbrun_version < 6) {
X if (0 > sscanf(buffer, fmt, r.pdb.user_gfx_font.name,
X &r.pdb.user_gfx_font.size))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt,
X &r.pdb.user_gfx_font.size,
X r.pdb.user_gfx_font.name))
X goto user;
X break;
X
X case PDB_USER_GFX_TEXTPOS:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_gfx_textpos.xyz[0],
X &r.pdb.user_gfx_textpos.xyz[1],
X &r.pdb.user_gfx_textpos.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_GFX_LABEL:
X if (pdb_pdbrun_version < 6) {
X if (0 > sscanf(buffer, fmt,
X &r.pdb.user_gfx_label.xyz[0],
X &r.pdb.user_gfx_label.xyz[1],
X &r.pdb.user_gfx_label.xyz[2],
X r.pdb.user_gfx_label.text))
X goto user;
X } else if (0 > pdb_sscanf(buffer, fmt,
X r.pdb.user_gfx_label.text))
X goto user;
X /* TODO: process text? */
X break;
X
X case PDB_USER_GFX_MOVE:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_gfx_move.xyz[0],
X &r.pdb.user_gfx_move.xyz[1],
X &r.pdb.user_gfx_move.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_GFX_DRAW:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_gfx_draw.xyz[0],
X &r.pdb.user_gfx_draw.xyz[1],
X &r.pdb.user_gfx_draw.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_GFX_MARKER:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_gfx_marker.xyz[0],
X &r.pdb.user_gfx_marker.xyz[1],
X &r.pdb.user_gfx_marker.xyz[2]))
X goto user;
X break;
X
X case PDB_USER_GFX_POINT:
X if (0 > pdb_sscanf(buffer, fmt, &r.pdb.user_gfx_point.xyz[0],
X &r.pdb.user_gfx_point.xyz[1],
X &r.pdb.user_gfx_point.xyz[2]))
X goto user;
X break;
X }
X
X return r;
X}
X
X# ifdef vms
Xpdb_read_dummy()
X{
X pdb_fmt_dummy();
X}
X# endif
SHAR_EOF
if test 30391 -ne "`wc -c < 'pdb_read.c'`"
then
echo shar: "error transmitting 'pdb_read.c'" '(should have been 30391 characters)'
fi
fi
echo shar: "extracting 'pdb_sprntf.c'" '(10000 characters)'
if test -f 'pdb_sprntf.c'
then
echo shar: "will not over-write existing file 'pdb_sprntf.c'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_sprntf.c'
X/*
X * Copyright (c) 1989 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.c,v 2.4 1994/04/15 22:34:24 gregc Exp $
X */
X
X/* LINTLIBRARY */
X
X# include
X# include
X# include
X# ifdef __STDC__
X# include
X# else
X# include
X# endif
X
Xstatic char scratch[BUFSIZ];
X
X# define OVERFLOW_CHAR '*'
X
X# ifdef __STDC__
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# else
Xstatic char *outint(), *outunsigned(), *outstr(), *outfloat(), *outexp();
Xstatic char *e_out();
X# endif
X
X# ifdef __STDC__
Xvoid
Xpdb_sprintf(char *outbuf, const char *fmt, ...)
X# else
X/*VARARGS2*/
Xvoid
Xpdb_sprintf(outbuf, fmt, va_alist)
Xchar *outbuf;
Xchar *fmt;
Xva_dcl
X# endif
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# ifdef __STDC__
X va_start(argv, fmt);
X# else
X va_start(argv);
X# endif
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}
X
Xstatic char *
X# ifdef __STDC__
Xe_out(int width, char *where)
X# else
Xe_out(width, where)
X int width;
X char *where;
X# endif
X{
X while (width-- > 0)
X *where++ = OVERFLOW_CHAR;
X return where;
X}
X
Xstatic char *
X# ifdef __STDC__
Xoutint(int value, int width, int radix, char fill_char, char hex,
X int left_justify, char *p, char zero)
X# else
Xoutint(value, width, radix, fill_char, hex, left_justify, p, zero)
X int value, width;
X int radix;
X char fill_char;
X char hex;
X int left_justify;
X char *p;
X char zero;
X# endif
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 *
X# ifdef __STDC__
Xoutunsigned(unsigned int value, int width, char fill_char, int left_justify,
X char *p)
X# else
Xoutunsigned(value, width, fill_char, left_justify, p)
X unsigned int value;
X int width;
X char fill_char;
X int left_justify;
X char *p;
X# endif
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 *
X# ifdef __STDC__
Xoutstr(char *s, int width, int maxstr, char fill_char, int left_justify, char *p)
X# else
Xoutstr(s, width, maxstr, fill_char, left_justify, p)
X char *s;
X int width;
X int maxstr;
X char fill_char;
X int left_justify;
X char *p;
X# endif
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 *
X# ifdef __STDC__
Xoutfloat(double value, int width, int nplace, char fill_char, int left_justify,
X char *p)
X# else
Xoutfloat(value, width, nplace, fill_char, left_justify, p)
X double value;
X int width, nplace;
X char fill_char;
X int left_justify;
X char *p;
X# endif
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 = 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 *
X# ifdef __STDC__
Xoutexp(double value, int width, int nplace, char fill_char, int left_justify,
X char *p)
X# else
Xoutexp(value, width, nplace, fill_char, left_justify, p)
X double value;
X int width, nplace;
X char *p;
X char fill_char;
X int left_justify;
X# endif
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 10000 -ne "`wc -c < 'pdb_sprntf.c'`"
then
echo shar: "error transmitting 'pdb_sprntf.c'" '(should have been 10000 characters)'
fi
fi
echo shar: "extracting 'pdb_sscanf.c'" '(5183 characters)'
if test -f 'pdb_sscanf.c'
then
echo shar: "will not over-write existing file 'pdb_sscanf.c'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_sscanf.c'
X/*
X * Copyright (c) 1989 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.c,v 2.8 1994/04/15 22:34:24 gregc Exp $
X */
X
X/* LINTLIBRARY */
X
X# include
X# include
X# ifdef __STDC__
X# include
X# include
X# else
X# include
X
Xextern int atoi();
Xextern double atof();
X# endif
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
X# ifdef __STDC__
Xpdb_sscanf(const char *buffer, const char *fmt, ...)
X# else
X/*VARARGS2*/
Xpdb_sscanf(buffer, fmt, va_alist)
X char *buffer;
X char *fmt;
X va_dcl
X# endif
X{
X va_list ap;
X int i, field_width;
X int nmatch;
X char *s, *t;
X char tmp[MAXFIELDSIZE];
X
X# ifdef __STDC__
X va_start(ap, fmt);
X# else
X va_start(ap);
X# endif
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#ifndef __STDC__
X *(va_arg(ap, int *)) = atoi(tmp);
X#else
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#endif
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#ifndef __STDC__
X *(va_arg(ap, double *)) = atof(tmp);
X#else
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#endif
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 fprintf(stderr, "bad format '%c' in pdb_sscanf\n",
X *fmt);
X va_end(ap);
X return -1;
X }
X }
X va_end(ap);
X return nmatch;
X}
SHAR_EOF
if test 5183 -ne "`wc -c < 'pdb_sscanf.c'`"
then
echo shar: "error transmitting 'pdb_sscanf.c'" '(should have been 5183 characters)'
fi
fi
echo shar: "extracting 'pdb_write.c'" '(18051 characters)'
if test -f 'pdb_write.c'
then
echo shar: "will not over-write existing file 'pdb_write.c'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdb_write.c'
X/*
X * Copyright (c) 1989 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_write.c,v 2.11 1995/01/20 01:20:36 gregc Exp $
X *
X * subroutine for writing PDB format files
X *
X */
X
X/* LINTLIBRARY */
X
X# include
X# include
X# include "pdb_int.h"
X
Xstatic const char * const pdb_record_format[PDB_NUM_R] = {
X#include "write_format.i"
X};
X
Xstatic char const * const pdbrun5[] = {
X#include "pdbrun5_write.i"
X};
X
Xstatic char const * const pdbrun6[] = {
X#include "pdbrun6_write.i"
X};
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
Xvoid
X# ifdef __STDC__
Xpdb_write_record(FILE *f, const pdb_record *r, const char *name, int line_num)
X# else
Xpdb_write_record(f, r, name, line_num)
X FILE *f;
X pdb_record *r;
X char *name; /* if NULL, don't print */
X int line_num; /* if name == NULL, don't print */
X# endif
X{
X char buffer[PDB_BUFSIZ];
X
X pdb_write_string(buffer, r);
X if (name == NULL)
X (void) fprintf(f, "%s\n", buffer);
X else if (line_num >= 10000)
X (void) fprintf(f, "%-72.72s%-4.4s%04d\n", buffer, name,
X line_num % 10000);
X else
X (void) fprintf(f, "%-72.72s%-4.4s%4d\n", buffer, name,
X line_num);
X}
X
Xvoid
X# ifdef __STDC__
Xpdb_write_string(char *buffer, const pdb_record *r)
X# else
Xpdb_write_string(buffer, r)
X char *buffer;
X pdb_record *r;
X# endif
X{
X const char *fmt;
X const struct pdb_sheet *sh;
X const pdb_residue *shr0, *shr1, *sha0, *sha1;
X char *s, *t;
X
X /* convert C structure to pdb record */
X
X
X if (r->record_type < PDB_USER_PDBRUN)
X fmt = pdb_record_format[r->record_type];
X else if (pdb_pdbrun_version < 6)
X fmt = pdbrun5[r->record_type - PDB_USER_PDBRUN];
X else
X fmt = pdbrun6[r->record_type - PDB_USER_PDBRUN];
X switch (r->record_type) {
X
X case PDB_UNKNOWN:
X pdb_sprintf(buffer, fmt, r->pdb.unknown.junk);
X break;
X
X case PDB_AGGRGT:
X pdb_sprintf(buffer, fmt, r->pdb.aggrgt.serial_num,
X r->pdb.aggrgt.num_components,
X r->pdb.aggrgt.cmpont_serial_nums[0],
X r->pdb.aggrgt.cmpont_serial_nums[1],
X r->pdb.aggrgt.cmpont_serial_nums[2],
X r->pdb.aggrgt.cmpont_serial_nums[3],
X r->pdb.aggrgt.cmpont_serial_nums[4],
X r->pdb.aggrgt.cmpont_serial_nums[5],
X r->pdb.aggrgt.cmpont_serial_nums[6],
X r->pdb.aggrgt.cmpont_serial_nums[7],
X r->pdb.aggrgt.cmpont_serial_nums[8],
X r->pdb.aggrgt.cmpont_serial_nums[9],
X r->pdb.aggrgt.cmpont_serial_nums[10],
X r->pdb.aggrgt.cmpont_serial_nums[11],
X r->pdb.aggrgt.cmpont_serial_nums[12],
X r->pdb.aggrgt.cmpont_serial_nums[13]);
X break;
X
X case PDB_ANISOU:
X case PDB_SIGUIJ:
X pdb_sprintf(buffer, fmt, r->pdb.anisou.serial_num,
X r->pdb.anisou.name, r->pdb.anisou.alt_loc,
X r->pdb.anisou.residue.name,
X r->pdb.anisou.residue.chain_id,
X r->pdb.anisou.residue.seq_num,
X r->pdb.anisou.residue.insert_code,
X r->pdb.anisou.u[0], r->pdb.anisou.u[1],
X r->pdb.anisou.u[2], r->pdb.anisou.u[3],
X r->pdb.anisou.u[4], r->pdb.anisou.u[5]);
X break;
X
X case PDB_ATOM:
X case PDB_HETATM:
X case PDB_SIGATM:
X pdb_sprintf(buffer, fmt, r->pdb.atom.serial_num,
X r->pdb.atom.name, r->pdb.atom.alt_loc,
X r->pdb.atom.residue.name,
X r->pdb.atom.residue.chain_id,
X r->pdb.atom.residue.seq_num,
X r->pdb.atom.residue.insert_code,
X r->pdb.atom.x, r->pdb.atom.y, r->pdb.atom.z,
X r->pdb.atom.occupancy, r->pdb.atom.temp_factor,
X r->pdb.atom.ftnote_num);
X break;
X
X case PDB_AUTHOR:
X case PDB_COMPND:
X case PDB_JRNL:
X case PDB_SOURCE:
X case PDB_EXPDTA:
X pdb_sprintf(buffer, fmt, r->pdb.author.continuation,
X r->pdb.author.data);
X break;
X
X case PDB_CONECT:
X pdb_sprintf(buffer, fmt, r->pdb.conect.serial_num,
X r->pdb.conect.covalent[0], r->pdb.conect.covalent[1],
X r->pdb.conect.covalent[2], r->pdb.conect.covalent[3],
X r->pdb.conect.bonds[0].hydrogen[0],
X r->pdb.conect.bonds[0].hydrogen[1],
X r->pdb.conect.bonds[0].salt,
X r->pdb.conect.bonds[1].hydrogen[0],
X r->pdb.conect.bonds[1].hydrogen[1],
X r->pdb.conect.bonds[1].salt);
X break;
X
X case PDB_CMPONT:
X pdb_sprintf(buffer, fmt, r->pdb.cmpont.seq_num,
X r->pdb.cmpont.residues[0].name,
X r->pdb.cmpont.residues[0].chain_id,
X r->pdb.cmpont.residues[0].seq_num,
X r->pdb.cmpont.residues[0].insert_code,
X r->pdb.cmpont.residues[1].name,
X r->pdb.cmpont.residues[1].chain_id,
X r->pdb.cmpont.residues[1].seq_num,
X r->pdb.cmpont.residues[1].insert_code);
X break;
X
X case PDB_CRYST1:
X pdb_sprintf(buffer, fmt, r->pdb.cryst1.a, r->pdb.cryst1.b,
X r->pdb.cryst1.c, r->pdb.cryst1.alpha,
X r->pdb.cryst1.beta, r->pdb.cryst1.gamma,
X r->pdb.cryst1.space_grp, r->pdb.cryst1.z);
X break;
X
X case PDB_END:
X case PDB_ENDMDL:
X pdb_sprintf(buffer, fmt);
X break;
X
X case PDB_FORMUL:
X pdb_sprintf(buffer, fmt, r->pdb.formul.component,
X r->pdb.formul.het_id, r->pdb.formul.continuation,
X r->pdb.formul.exclude, r->pdb.formul.formula);
X break;
X
X case PDB_FTNOTE:
X case PDB_REMARK:
X case PDB_SYMDES:
X case PDB_MTXDES:
X case PDB_CMPDES:
X case PDB_AGRDES:
X pdb_sprintf(buffer, fmt, r->pdb.ftnote.num, r->pdb.ftnote.text);
X break;
X
X case PDB_HEADER:
X pdb_sprintf(buffer, fmt, r->pdb.header.class,
X r->pdb.header.date, r->pdb.header.type,
X r->pdb.header.id);
X break;
X
X case PDB_HELIX:
X pdb_sprintf(buffer, fmt, r->pdb.helix.serial_num,
X r->pdb.helix.id,
X r->pdb.helix.residues[0].name,
X r->pdb.helix.residues[0].chain_id,
X r->pdb.helix.residues[0].seq_num,
X r->pdb.helix.residues[0].insert_code,
X r->pdb.helix.residues[1].name,
X r->pdb.helix.residues[1].chain_id,
X r->pdb.helix.residues[1].seq_num,
X r->pdb.helix.residues[1].insert_code,
X r->pdb.helix.class, r->pdb.helix.comment);
X break;
X
X case PDB_HET:
X pdb_sprintf(buffer, fmt, r->pdb.het.het_grp.name,
X r->pdb.het.het_grp.chain_id, r->pdb.het.het_grp.seq_num,
X r->pdb.het.het_grp.insert_code, r->pdb.het.num_atoms,
X r->pdb.het.text);
X break;
X
X case PDB_MASTER:
X pdb_sprintf(buffer, fmt, r->pdb.master.num_remark,
X r->pdb.master.num_ftnote, r->pdb.master.num_het,
X r->pdb.master.num_helix, r->pdb.master.num_sheet,
X r->pdb.master.num_turn, r->pdb.master.num_site,
X r->pdb.master.num_transform,
X r->pdb.master.num_coordinate, r->pdb.master.num_ter,
X r->pdb.master.num_conect, r->pdb.master.num_seqres);
X break;
X
X case PDB_MODEL:
X pdb_sprintf(buffer, fmt, r->pdb.model.num);
X break;
X
X case PDB_MTRIX:
X pdb_sprintf(buffer, fmt, r->pdb.mtrix.row_num,
X r->pdb.mtrix.serial_num, r->pdb.mtrix.m1,
X r->pdb.mtrix.m2, r->pdb.mtrix.m3, r->pdb.mtrix.v,
X r->pdb.mtrix.given);
X break;
X
X case PDB_OBSLTE:
X pdb_sprintf(buffer, fmt, r->pdb.obslte.continuation,
X r->pdb.obslte.date, r->pdb.obslte.old_id,
X r->pdb.obslte.id_map[0], r->pdb.obslte.id_map[1],
X r->pdb.obslte.id_map[2], r->pdb.obslte.id_map[3],
X r->pdb.obslte.id_map[4], r->pdb.obslte.id_map[2],
X r->pdb.obslte.id_map[6], r->pdb.obslte.id_map[7]);
X break;
X
X case PDB_ORIGX:
X pdb_sprintf(buffer, fmt, r->pdb.origx.row_num, r->pdb.origx.o1,
X r->pdb.origx.o2, r->pdb.origx.o3, r->pdb.origx.t);
X break;
X
X case PDB_REVDAT:
X pdb_sprintf(buffer, fmt, r->pdb.revdat.modification,
X r->pdb.revdat.continuation, r->pdb.revdat.date,
X r->pdb.revdat.id, r->pdb.revdat.mod_type,
X r->pdb.revdat.corrections);
X break;
X
X case PDB_SCALE:
X pdb_sprintf(buffer, fmt, r->pdb.scale.row_num, r->pdb.scale.s1,
X r->pdb.scale.s2, r->pdb.scale.s3, r->pdb.scale.u);
X break;
X
X case PDB_SEQRES:
X pdb_sprintf(buffer, fmt, r->pdb.seqres.serial_num,
X r->pdb.seqres.chain_id, r->pdb.seqres.count,
X r->pdb.seqres.names[0], r->pdb.seqres.names[1],
X r->pdb.seqres.names[2], r->pdb.seqres.names[3],
X r->pdb.seqres.names[4], r->pdb.seqres.names[5],
X r->pdb.seqres.names[6], r->pdb.seqres.names[7],
X r->pdb.seqres.names[8], r->pdb.seqres.names[9],
X r->pdb.seqres.names[10], r->pdb.seqres.names[11],
X r->pdb.seqres.names[12]);
X break;
X
X case PDB_SHEET:
X sh = &r->pdb.sheet;
X shr0 = &sh->residues[0];
X shr1 = &sh->residues[1];
X sha0 = &sh->atoms[0].residue;
X sha1 = &sh->atoms[1].residue;
X pdb_sprintf(buffer, fmt, sh->strand_num,
X sh->id, sh->count,
X shr0->name, shr0->chain_id, shr0->seq_num,
X shr0->insert_code,
X shr1->name, shr1->chain_id, shr1->seq_num,
X shr1->insert_code,
X sh->sense,
X sh->atoms[0].name,
X sha0->name, sha0->chain_id, sha0->seq_num,
X sha0->insert_code,
X sh->atoms[1].name,
X sha1->name, sha1->chain_id, sha1->seq_num,
X sha1->insert_code);
X break;
X
X case PDB_SITE:
X shr0 = &r->pdb.site.residues[0];
X shr1 = &r->pdb.site.residues[1];
X sha0 = &r->pdb.site.residues[2];
X sha1 = &r->pdb.site.residues[3];
X pdb_sprintf(buffer, fmt, r->pdb.site.seq_num,
X r->pdb.site.id, r->pdb.site.count,
X shr0->name, shr0->chain_id, shr0->seq_num,
X shr0->insert_code,
X shr1->name, shr1->chain_id, shr1->seq_num,
X shr1->insert_code,
X sha0->name, sha0->chain_id, sha0->seq_num,
X sha0->insert_code,
X sha1->name, sha1->chain_id, sha1->seq_num,
X sha1->insert_code);
X break;
X
X case PDB_SPRSDE:
X pdb_sprintf(buffer, fmt, r->pdb.sprsde.continuation,
X r->pdb.sprsde.date, r->pdb.sprsde.id,
X r->pdb.sprsde.supersede[0], r->pdb.sprsde.supersede[1],
X r->pdb.sprsde.supersede[2], r->pdb.sprsde.supersede[3],
X r->pdb.sprsde.supersede[4], r->pdb.sprsde.supersede[5],
X r->pdb.sprsde.supersede[6], r->pdb.sprsde.supersede[7]);
X break;
X
X case PDB_SSBOND:
X pdb_sprintf(buffer, fmt, r->pdb.ssbond.seq_num,
X r->pdb.ssbond.residues[0].name,
X r->pdb.ssbond.residues[0].chain_id,
X r->pdb.ssbond.residues[0].seq_num,
X r->pdb.ssbond.residues[0].insert_code,
X r->pdb.ssbond.residues[1].name,
X r->pdb.ssbond.residues[1].chain_id,
X r->pdb.ssbond.residues[1].seq_num,
X r->pdb.ssbond.residues[1].insert_code,
X r->pdb.ssbond.comment);
X break;
X
X case PDB_SYMOP:
X pdb_sprintf(buffer, fmt, r->pdb.symop.row_num,
X r->pdb.symop.serial_num, r->pdb.symop.s1,
X r->pdb.symop.s2, r->pdb.symop.s3, r->pdb.symop.t);
X break;
X
X case PDB_TER:
X pdb_sprintf(buffer, fmt, r->pdb.ter.serial_num,
X r->pdb.ter.residue.name, r->pdb.ter.residue.chain_id,
X r->pdb.ter.residue.seq_num,
X r->pdb.ter.residue.insert_code);
X break;
X
X case PDB_TRNSFM:
X pdb_sprintf(buffer, fmt, r->pdb.trnsfm.result_serial_num,
X r->pdb.trnsfm.apply_serial_num,
X r->pdb.trnsfm.source_serial_num);
X break;
X
X case PDB_TURN:
X pdb_sprintf(buffer, fmt, r->pdb.turn.seq_num,
X r->pdb.turn.id,
X r->pdb.turn.residues[0].name,
X r->pdb.turn.residues[0].chain_id,
X r->pdb.turn.residues[0].seq_num,
X r->pdb.turn.residues[0].insert_code,
X r->pdb.turn.residues[1].name,
X r->pdb.turn.residues[1].chain_id,
X r->pdb.turn.residues[1].seq_num,
X r->pdb.turn.residues[1].insert_code,
X r->pdb.turn.comment);
X break;
X
X case PDB_TVECT:
X pdb_sprintf(buffer, fmt, r->pdb.tvect.serial_num,
X r->pdb.tvect.t1, r->pdb.tvect.t2, r->pdb.tvect.t3,
X r->pdb.tvect.comment);
X break;
X
X case PDB_USER:
X pdb_sprintf(buffer, fmt, r->pdb.user.subtype, r->pdb.user.text);
X break;
X
X case PDB_USER_PDBRUN:
X pdb_sprintf(buffer, fmt, r->pdb.user_pdbrun.version);
X pdb_pdbrun_version = r->pdb.user_pdbrun.version;
X break;
X
X case PDB_USER_EYEPOS:
X pdb_sprintf(buffer, fmt, r->pdb.user_eyepos.xyz[0],
X r->pdb.user_eyepos.xyz[1], r->pdb.user_eyepos.xyz[2]);
X break;
X
X case PDB_USER_ATPOS:
X pdb_sprintf(buffer, fmt, r->pdb.user_atpos.xyz[0],
X r->pdb.user_atpos.xyz[1], r->pdb.user_atpos.xyz[2]);
X break;
X
X case PDB_USER_WINDOW:
X pdb_sprintf(buffer, fmt, r->pdb.user_window.left,
X r->pdb.user_window.right, r->pdb.user_window.bottom,
X r->pdb.user_window.top, r->pdb.user_window.hither,
X r->pdb.user_window.yon);
X break;
X
X case PDB_USER_FOCUS:
X pdb_sprintf(buffer, fmt, r->pdb.user_focus.focus);
X break;
X
X case PDB_USER_VIEWPORT:
X pdb_sprintf(buffer, fmt, r->pdb.user_viewport.xmin,
X r->pdb.user_viewport.xmax, r->pdb.user_viewport.ymin,
X r->pdb.user_viewport.ymax);
X break;
X
X case PDB_USER_BGCOLOR:
X if (pdb_pdbrun_version < 6)
X sprintf(buffer, fmt, r->pdb.user_bgcolor.rgb[0],
X r->pdb.user_bgcolor.rgb[1],
X r->pdb.user_bgcolor.rgb[2]);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_bgcolor.rgb[0],
X r->pdb.user_bgcolor.rgb[1],
X r->pdb.user_bgcolor.rgb[2]);
X break;
X
X case PDB_USER_ANGLE:
X if (pdb_pdbrun_version < 6)
X pdb_sprintf(buffer, fmt, r->pdb.user_angle.which,
X r->pdb.user_angle.atom0,
X r->pdb.user_angle.atom1,
X r->pdb.user_angle.atom2,
X r->pdb.user_angle.atom3,
X r->pdb.user_angle.angle);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_angle.atom0,
X r->pdb.user_angle.atom1,
X r->pdb.user_angle.atom2,
X r->pdb.user_angle.atom3,
X r->pdb.user_angle.angle);
X break;
X
X case PDB_USER_DISTANCE:
X if (pdb_pdbrun_version < 6)
X pdb_sprintf(buffer, fmt, r->pdb.user_distance.which,
X r->pdb.user_distance.atom0,
X r->pdb.user_distance.atom1,
X r->pdb.user_distance.distance);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_distance.atom0,
X r->pdb.user_distance.atom1,
X r->pdb.user_distance.distance);
X break;
X
X case PDB_USER_FILE:
X if (pdb_pdbrun_version < 6)
X pdb_sprintf(buffer, fmt, r->pdb.user_file.filename);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_file.model,
X r->pdb.user_file.filename);
X break;
X
X case PDB_USER_MARKNAME:
X pdb_sprintf(buffer, fmt, r->pdb.user_markname.markname);
X break;
X
X case PDB_USER_MARK:
X pdb_sprintf(buffer, fmt, r->pdb.user_mark.markname);
X break;
X
X case PDB_USER_CNAME:
X if (pdb_pdbrun_version < 6)
X sprintf(buffer, fmt, r->pdb.user_cname.name,
X r->pdb.user_cname.rgb[0],
X r->pdb.user_cname.rgb[1],
X r->pdb.user_cname.rgb[2]);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_cname.rgb[0],
X r->pdb.user_cname.rgb[1],
X r->pdb.user_cname.rgb[2],
X r->pdb.user_cname.name);
X break;
X
X case PDB_USER_COLOR:
X if (pdb_pdbrun_version < 6)
X sprintf(buffer, fmt, r->pdb.user_color.spec,
X r->pdb.user_color.rgb[0],
X r->pdb.user_color.rgb[1],
X r->pdb.user_color.rgb[2]);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_color.rgb[0],
X r->pdb.user_color.rgb[1],
X r->pdb.user_color.rgb[2],
X r->pdb.user_color.spec);
X break;
X
X case PDB_USER_RADIUS:
X pdb_sprintf(buffer, fmt, r->pdb.user_radius.radius);
X break;
X
X case PDB_USER_OBJECT:
X pdb_sprintf(buffer, fmt, r->pdb.user_object.model);
X break;
X
X case PDB_USER_ENDOBJ:
X pdb_sprintf(buffer, fmt, r->pdb.user_endobj.model);
X break;
X
X case PDB_USER_CHAIN:
X if (pdb_pdbrun_version < 6)
X sprintf(buffer, fmt, r->pdb.user_chain.atom0,
X r->pdb.user_chain.atom1);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_chain.atom0,
X r->pdb.user_chain.atom1);
X break;
X
X case PDB_USER_GFX_BEGIN:
X if (r->pdb.user_gfx_begin.primitive == PDB_GFX_UNKNOWN)
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_begin.unknown);
X else
X pdb_sprintf(buffer, fmt, pdb_gfx_string(
X r->pdb.user_gfx_begin.primitive));
X break;
X
X case PDB_USER_GFX_END:
X pdb_sprintf(buffer, fmt);
X break;
X
X case PDB_USER_GFX_COLOR:
X if (pdb_pdbrun_version < 6)
X sprintf(buffer, fmt, r->pdb.user_gfx_color.spec,
X r->pdb.user_gfx_color.rgb[0],
X r->pdb.user_gfx_color.rgb[1],
X r->pdb.user_gfx_color.rgb[2]);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_color.rgb[0],
X r->pdb.user_gfx_color.rgb[1],
X r->pdb.user_gfx_color.rgb[2],
X r->pdb.user_gfx_color.spec);
X break;
X
X case PDB_USER_GFX_NORMAL:
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_normal.xyz[0],
X r->pdb.user_gfx_normal.xyz[1],
X r->pdb.user_gfx_normal.xyz[2]);
X break;
X
X case PDB_USER_GFX_VERTEX:
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_vertex.xyz[0],
X r->pdb.user_gfx_vertex.xyz[1],
X r->pdb.user_gfx_vertex.xyz[2]);
X break;
X
X case PDB_USER_GFX_FONT:
X if (pdb_pdbrun_version < 6)
X sprintf(buffer, fmt, r->pdb.user_gfx_font.name,
X r->pdb.user_gfx_font.size);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_font.size,
X r->pdb.user_gfx_font.name);
X break;
X
X case PDB_USER_GFX_TEXTPOS:
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_textpos.xyz[0],
X r->pdb.user_gfx_textpos.xyz[1],
X r->pdb.user_gfx_textpos.xyz[2]);
X break;
X
X case PDB_USER_GFX_LABEL:
X if (pdb_pdbrun_version < 6)
X sprintf(buffer, fmt, r->pdb.user_gfx_label.xyz[0],
X r->pdb.user_gfx_label.xyz[1],
X r->pdb.user_gfx_label.xyz[2],
X r->pdb.user_gfx_label.text);
X else
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_label.text);
X break;
X
X case PDB_USER_GFX_MOVE:
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_move.xyz[0],
X r->pdb.user_gfx_move.xyz[1],
X r->pdb.user_gfx_move.xyz[2]);
X break;
X
X case PDB_USER_GFX_DRAW:
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_draw.xyz[0],
X r->pdb.user_gfx_draw.xyz[1],
X r->pdb.user_gfx_draw.xyz[2]);
X break;
X
X case PDB_USER_GFX_MARKER:
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_marker.xyz[0],
X r->pdb.user_gfx_marker.xyz[1],
X r->pdb.user_gfx_marker.xyz[2]);
X break;
X
X case PDB_USER_GFX_POINT:
X pdb_sprintf(buffer, fmt, r->pdb.user_gfx_point.xyz[0],
X r->pdb.user_gfx_point.xyz[1],
X r->pdb.user_gfx_point.xyz[2]);
X break;
X
X default:
X (void) sprintf(buffer, "unknown pdb record #%d",
X r->record_type);
X break;
X }
X
X /* find last non-blank in buffer, and shorten it */
X t = NULL;
X for (s = buffer; *s != '\0'; s++)
X if (!isspace(*s))
X t = s + 1;
X if (t == NULL) /* this should never happen, but ... */
X t = buffer;
X *t = '\0';
X}
X
X# ifdef vms
Xpdb_write_dummy()
X{
X pdb_fmt_dummy();
X}
X# endif
SHAR_EOF
if test 18051 -ne "`wc -c < 'pdb_write.c'`"
then
echo shar: "error transmitting 'pdb_write.c'" '(should have been 18051 characters)'
fi
fi
echo shar: "extracting 'pdbrun.c'" '(2700 characters)'
if test -f 'pdbrun.c'
then
echo shar: "will not over-write existing file 'pdbrun.c'"
else
sed 's/^ X//' << \SHAR_EOF > 'pdbrun.c'
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: pdbrun.c,v 1.4 1994/11/18 01:00:57 gregc Exp $
X *
X * subroutine for reading PDB format files
X *
X */
X
X/* LINTLIBRARY */
X
X# include "pdb_int.h"
X# include
X
Xint pdb_pdbrun_version = PDB_PDBRUN_VERSION;
X
X#ifdef __STDC__
Xconst char *
Xpdb_gfx_string(int i)
X#else
Xchar *
Xpdb_gfx_string(i)
X int i;
X#endif
X{
X switch (i) {
X default: return "UNKNOWN";
X case PDB_GFX_POINTS: return "POINTS";
X case PDB_GFX_MARKERS: return "MARKERS";
X case PDB_GFX_LINES: return "LINES";
X case PDB_GFX_LINE_STRIP: return "LINE-STRIP";
X case PDB_GFX_LINE_LOOP: return "LINE-LOOP";
X case PDB_GFX_TRIANGLES: return "TRIANGLES";
X case PDB_GFX_TRIANGLE_STRIP: return "TRIANGLE-STRIP";
X case PDB_GFX_TRIANGLE_FAN: return "TRIANGLE-FAN";
X case PDB_GFX_QUADS: return "QUADS";
X case PDB_GFX_QUAD_STRIP: return "QUAD-STRIP";
X case PDB_GFX_POLYGON: return "POLYGON";
X }
X}
X
X#ifdef __STDC__
Xint
Xpdb_gfx_type(const char *type)
X#else
Xint
Xpdb_gfx_type(type)
X char *type;
X#endif
X{
X switch (type[0]) {
X case 'L':
X if (strcmp(type + 1, "INE-LOOP") == 0)
X return PDB_GFX_LINE_LOOP;
X if (strcmp(type + 1, "INE-STRIP") == 0)
X return PDB_GFX_LINE_STRIP;
X if (strcmp(type + 1, "INES") == 0)
X return PDB_GFX_LINES;
X break;
X case 'M':
X if (strcmp(type + 1, "ARKERS") == 0)
X return PDB_GFX_MARKERS;
X break;
X case 'P':
X if (strcmp(type + 1, "OINTS") == 0)
X return PDB_GFX_POINTS;
X if (strcmp(type + 1, "OLYGON") == 0)
X return PDB_GFX_POLYGON;
X break;
X case 'Q':
X if (strcmp(type + 1, "UAD-STRIP") == 0)
X return PDB_GFX_QUAD_STRIP;
X if (strcmp(type + 1, "UADS") == 0)
X return PDB_GFX_QUADS;
X break;
X case 'T':
X if (strcmp(type + 1, "RIANGLE-FAN") == 0)
X return PDB_GFX_TRIANGLE_FAN;
X if (strcmp(type + 1, "RIANGLE-STRIP") == 0)
X return PDB_GFX_TRIANGLE_STRIP;
X if (strcmp(type + 1, "RIANGLES") == 0)
X return PDB_GFX_TRIANGLES;
X break;
X }
X return PDB_GFX_UNKNOWN;
X}
SHAR_EOF
if test 2700 -ne "`wc -c < 'pdbrun.c'`"
then
echo shar: "error transmitting 'pdbrun.c'" '(should have been 2700 characters)'
fi
fi
exit 0
# End of shell archive
|
