rino 0.1.0
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- data/README +44 -0
- data/Rakefile +123 -0
- data/ext/extconf.rb +26 -0
- data/ext/ruby_inchi_main.so +0 -0
- data/ext/src/aux2atom.h +2786 -0
- data/ext/src/comdef.h +148 -0
- data/ext/src/e_0dstereo.c +3014 -0
- data/ext/src/e_0dstereo.h +31 -0
- data/ext/src/e_comdef.h +57 -0
- data/ext/src/e_ctl_data.h +147 -0
- data/ext/src/e_ichi_io.c +498 -0
- data/ext/src/e_ichi_io.h +40 -0
- data/ext/src/e_ichi_parms.c +37 -0
- data/ext/src/e_ichi_parms.h +41 -0
- data/ext/src/e_ichicomp.h +50 -0
- data/ext/src/e_ichierr.h +40 -0
- data/ext/src/e_ichimain.c +593 -0
- data/ext/src/e_ichisize.h +43 -0
- data/ext/src/e_inchi_atom.c +75 -0
- data/ext/src/e_inchi_atom.h +33 -0
- data/ext/src/e_inpdef.h +41 -0
- data/ext/src/e_mode.h +706 -0
- data/ext/src/e_mol2atom.c +649 -0
- data/ext/src/e_readinch.c +58 -0
- data/ext/src/e_readmol.c +54 -0
- data/ext/src/e_readmol.h +180 -0
- data/ext/src/e_readstru.c +251 -0
- data/ext/src/e_readstru.h +33 -0
- data/ext/src/e_util.c +284 -0
- data/ext/src/e_util.h +61 -0
- data/ext/src/extr_ct.h +251 -0
- data/ext/src/ichi.h +206 -0
- data/ext/src/ichi_bns.c +7999 -0
- data/ext/src/ichi_bns.h +231 -0
- data/ext/src/ichican2.c +5000 -0
- data/ext/src/ichicano.c +2195 -0
- data/ext/src/ichicano.h +49 -0
- data/ext/src/ichicans.c +1625 -0
- data/ext/src/ichicant.h +379 -0
- data/ext/src/ichicomn.h +260 -0
- data/ext/src/ichicomp.h +50 -0
- data/ext/src/ichidrp.h +119 -0
- data/ext/src/ichierr.h +124 -0
- data/ext/src/ichiisot.c +101 -0
- data/ext/src/ichilnct.c +286 -0
- data/ext/src/ichimain.h +132 -0
- data/ext/src/ichimak2.c +1189 -0
- data/ext/src/ichimake.c +3812 -0
- data/ext/src/ichimake.h +205 -0
- data/ext/src/ichimap1.c +851 -0
- data/ext/src/ichimap2.c +2856 -0
- data/ext/src/ichimap4.c +1609 -0
- data/ext/src/ichinorm.c +741 -0
- data/ext/src/ichinorm.h +67 -0
- data/ext/src/ichiparm.c +45 -0
- data/ext/src/ichiparm.h +1441 -0
- data/ext/src/ichiprt1.c +3612 -0
- data/ext/src/ichiprt2.c +1511 -0
- data/ext/src/ichiprt3.c +3011 -0
- data/ext/src/ichiqueu.c +1003 -0
- data/ext/src/ichiring.c +326 -0
- data/ext/src/ichiring.h +49 -0
- data/ext/src/ichisize.h +35 -0
- data/ext/src/ichisort.c +539 -0
- data/ext/src/ichister.c +3538 -0
- data/ext/src/ichister.h +35 -0
- data/ext/src/ichitaut.c +3843 -0
- data/ext/src/ichitaut.h +387 -0
- data/ext/src/ichitime.h +74 -0
- data/ext/src/inchi_api.h +670 -0
- data/ext/src/inchi_dll.c +1480 -0
- data/ext/src/inchi_dll.h +34 -0
- data/ext/src/inchi_dll_main.c +23 -0
- data/ext/src/inchi_dll_main.h +31 -0
- data/ext/src/inpdef.h +328 -0
- data/ext/src/lreadmol.h +1246 -0
- data/ext/src/mode.h +706 -0
- data/ext/src/ruby_inchi_main.c +558 -0
- data/ext/src/runichi.c +4179 -0
- data/ext/src/strutil.c +3861 -0
- data/ext/src/strutil.h +182 -0
- data/ext/src/util.c +1130 -0
- data/ext/src/util.h +85 -0
- data/lib/clean_tempfile.rb +220 -0
- data/lib/rino.rb +111 -0
- data/test/test.rb +386 -0
- metadata +130 -0
data/ext/src/e_ichi_io.c
ADDED
@@ -0,0 +1,498 @@
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/*
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* International Union of Pure and Applied Chemistry (IUPAC)
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* International Chemical Identifier (InChI)
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* Version 1
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* Software version 1.00
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* April 13, 2005
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* Developed at NIST
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <ctype.h>
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#include <limits.h>
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#include <errno.h>
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#include <stdarg.h>
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#include "e_mode.h"
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19
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#include "ichitime.h"
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20
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#include "inchi_api.h"
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#include "e_ctl_data.h"
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#include "e_comdef.h"
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#include "e_ichicomp.h"
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#include "e_util.h"
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#include "e_ichi_io.h"
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#include "e_ichi_parms.h"
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#define LtrimRtrim e_LtrimRtrim
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/**********************************************
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* output " L=V" or " L missing" or ""
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* The fprintf format string must contain %s%s%s%s
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*/
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char e_gsMissing[] = "is missing";
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char e_gsEmpty[] = "";
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char e_gsSpace[] = " ";
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char e_gsEqual[] = "=";
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/********* from inchimain.c *****************************************/
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int e_inchi_print( FILE* f, const char* lpszFormat, ... )
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{
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int ret=0, ret2=0;
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/* char *p=NULL; */
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va_list argList;
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if ( f ) {
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my_va_start( argList, lpszFormat );
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ret = vfprintf( f, lpszFormat, argList );
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va_end( argList );
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} else {
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/* printf( "\r" ); */
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my_va_start( argList, lpszFormat );
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//ret2 = vfprintf( stdout, lpszFormat, argList );
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/* ret2 = vprintf( lpszFormat, argList ); */
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va_end( argList );
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}
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#ifdef INCHI_LIB
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if( FWPRINT )
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{
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my_va_start( argList, lpszFormat );
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FWPRINT( lpszFormat, argList );
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va_end( argList );
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}
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#endif
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return ret? ret : ret2;
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}
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/*****************************************************************/
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int e_my_fprintf( FILE* f, const char* lpszFormat, ... )
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75
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{
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76
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int ret=0, ret2=0;
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va_list argList;
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#ifndef INCHI_LIB
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if ( f ) {
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if ( f == stderr && lpszFormat && lpszFormat[0] && '\r' == lpszFormat[strlen(lpszFormat)-1] ) {
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#define CONSOLE_LINE_LEN 80
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#ifndef INCHI_ANSI_ONLY
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char szLine[CONSOLE_LINE_LEN];
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my_va_start( argList, lpszFormat );
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ret = _vsnprintf( szLine, CONSOLE_LINE_LEN-1, lpszFormat, argList );
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87
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va_end( argList );
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88
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if ( ret < 0 ) {
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89
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/* output is longer than the console line */
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90
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strcpy(szLine+CONSOLE_LINE_LEN-4, "...\r");
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91
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}
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fputs( szLine, f );
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#else
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94
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my_va_start( argList, lpszFormat );
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ret = vfprintf( f, lpszFormat, argList );
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va_end( argList );
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#endif
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#undef CONSOLE_LINE_LEN
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} else {
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my_va_start( argList, lpszFormat );
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ret = vfprintf( f, lpszFormat, argList );
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va_end( argList );
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}
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}
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if ( f != stderr ) {
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my_va_start( argList, lpszFormat );
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//ret2 = vfprintf( stderr, lpszFormat, argList );
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va_end( argList );
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}
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#else
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111
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if ( f ) {
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my_va_start( argList, lpszFormat );
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ret = vfprintf( f, lpszFormat, argList );
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va_end( argList );
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}
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#endif
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return ret? ret : ret2;
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}
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/*******************************************************************/
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void e_PrintFileName( const char *fmt, FILE *output_file, const char *szFname )
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{
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fprintf( output_file, fmt, szFname );
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}
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/************** copied from util.c *********************************/
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char *e_fgetsTab( char *szLine, int len, FILE *f );
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/*******************************************************************/
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/* read up to len or tab or LF; if empty read next until finds non-empty line */
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/* remove leading and trailing white spaces; keep zero termination */
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/*******************************************************************/
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char *e_fgetsTab( char *szLine, int len, FILE *f )
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{
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int length=0, c;
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len --;
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while ( length < len && EOF != (c = fgetc( f )) ) {
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if ( c == '\t' )
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c = '\n';
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szLine[length++] = (char)c;
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if ( c == '\n' )
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break;
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}
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if ( !length && EOF == c ) {
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return NULL;
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}
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szLine[length] = '\0';
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return szLine;
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}
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/*******************************************************************/
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/* read up to len or tab or LF; if empty read next until finds non-empty line */
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/* remove leading and trailing white spaces; keep zero termination */
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/*******************************************************************/
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int e_my_fgetsTab( char *szLine, int len, FILE *f, int *bTooLongLine )
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{
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int length;
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char *p;
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do {
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p = e_fgetsTab( szLine, len-1, f );
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if ( !p ) {
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*bTooLongLine = 0;
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return -1; /* end of file or cannot read */
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}
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szLine[len-1] = '\0';
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/*
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*bTooLongLine = !strchr( szLine, '\n' );
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*/
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p = strchr( szLine, '\n' );
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*bTooLongLine = ( !p && ((int)strlen(szLine)) == len-2 );
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LtrimRtrim( szLine, &length );
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} while ( !length );
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return length;
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}
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/*******************************************************************/
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int e_my_fgetsTab1( char *szLine, int len, FILE *f, int *bTooLongLine )
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{
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int length;
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char *p;
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/*do {*/
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p = e_fgetsTab( szLine, len-1, f );
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if ( !p ) {
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*bTooLongLine = 0;
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return -1; /* end of file or cannot read */
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182
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}
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183
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szLine[len-1] = '\0';
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/*
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185
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*bTooLongLine = !strchr( szLine, '\n' );
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*/
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p = strchr( szLine, '\n' );
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*bTooLongLine = ( !p && ((int)strlen(szLine)) == len-2 );
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LtrimRtrim( szLine, &length );
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/*} while ( !length );*/
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return length;
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}
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/******************************************************************/
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194
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/* read not more than line_len bytes from an lf-terminated line */
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195
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/* if input line is too long quietly ignore the rest of the line */
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196
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char* fgets_up_to_lf( char* line, int line_len, FILE* inp )
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197
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{
|
198
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char *p, *q;
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memset( line, 0, line_len );
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200
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if ( NULL != (p = fgets( line, line_len, inp ) ) && NULL == strchr(p, '\n' ) ){
|
201
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char temp[64]; /* bypass up to '\n' or up to end of file whichever comes first*/
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202
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while ( NULL != fgets( temp, sizeof(temp), inp ) && NULL == strchr(temp,'\n') )
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203
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;
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204
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}
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205
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if ( p && (q = strchr(line, '\r')) ) { /* fix CR CR LF line terminator. */
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q[0] = '\n';
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207
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q[1] = '\0';
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208
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}
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209
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return p;
|
210
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}
|
211
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/********************************************************************/
|
212
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int my_fgetsUpToLfOrTab( char *szLine, int len, FILE *f )
|
213
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+
{
|
214
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int length;
|
215
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+
char *p;
|
216
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char szSkip[256];
|
217
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+
int bTooLongLine = 0;
|
218
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do {
|
219
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p = e_fgetsTab( szLine, len-1, f );
|
220
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+
if ( !p ) {
|
221
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return -1; /* end of file or cannot read */
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222
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+
}
|
223
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szLine[len-1] = '\0';
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224
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/*
|
225
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bTooLongLine = !strchr( szLine, '\n' );
|
226
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*/
|
227
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bTooLongLine = ( !p && ((int)strlen(szLine)) == len-2 );
|
228
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LtrimRtrim( szLine, &length );
|
229
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+
} while ( !length );
|
230
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+
if ( bTooLongLine ) {
|
231
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+
while ( p = e_fgetsTab( szSkip, sizeof(szSkip)-1, f ) ) {
|
232
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+
szSkip[sizeof(szSkip)-1] = '\0';
|
233
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if ( strchr( szSkip, '\n' ) )
|
234
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break;
|
235
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+
}
|
236
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+
}
|
237
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return length;
|
238
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+
}
|
239
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+
|
240
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+
|
241
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+
#ifdef INCHI_ANSI_ONLY
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242
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+
|
243
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static clock_t InchiClock(void);
|
244
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+
|
245
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#ifdef INCHI_USETIMES
|
246
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static clock_t InchiClock(void)
|
247
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{
|
248
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struct tms buf;
|
249
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clock_t c = times( &buf );
|
250
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+
if ( c != (clock_t)-1 ) {
|
251
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+
return buf.tms_utime;
|
252
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+
}
|
253
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return 0;
|
254
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+
}
|
255
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+
#else
|
256
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static clock_t InchiClock(void)
|
257
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{
|
258
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clock_t c = clock();
|
259
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if ( c != (clock_t)-1 ) {
|
260
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return c;
|
261
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+
}
|
262
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return 0;
|
263
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+
}
|
264
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+
#endif
|
265
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+
|
266
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#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X))
|
267
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#define INCHI_CLOCK_T(X) (clock_t)( (double)(X) / 1000.0 * (double)CLOCKS_PER_SEC )
|
268
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const clock_t FullMaxClock = (clock_t)(-1);
|
269
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+
const clock_t HalfMaxClock = (clock_t)(-1) / 2;
|
270
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+
clock_t MaxPositiveClock = 0;
|
271
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clock_t MinNegativeClock = 0;
|
272
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clock_t HalfMaxPositiveClock = 0;
|
273
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clock_t HalfMinNegativeClock = 0;
|
274
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+
|
275
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static void FillMaxMinClock(void); /* keep compiler happy */
|
276
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+
|
277
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static void FillMaxMinClock(void)
|
278
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+
{
|
279
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+
if ( !MaxPositiveClock ) {
|
280
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+
clock_t valPos, val1 = 1;
|
281
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+
while ( 0 < ((val1 <<= 1), (val1 |= 1)) ) {
|
282
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+
valPos = val1;
|
283
|
+
}
|
284
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+
MaxPositiveClock = valPos;
|
285
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+
MinNegativeClock = -valPos;
|
286
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+
HalfMaxPositiveClock = MaxPositiveClock / 2;
|
287
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+
HalfMinNegativeClock = MinNegativeClock / 2;
|
288
|
+
}
|
289
|
+
}
|
290
|
+
|
291
|
+
|
292
|
+
/******** get current process time ****************************************/
|
293
|
+
void InchiTimeGet( inchiTime *TickEnd )
|
294
|
+
{
|
295
|
+
TickEnd->clockTime = InchiClock();
|
296
|
+
}
|
297
|
+
/******** returns difference TickEnd - TickStart in milliseconds **********/
|
298
|
+
long InchiTimeMsecDiff( inchiTime *TickEnd, inchiTime *TickStart )
|
299
|
+
{
|
300
|
+
if ( FullMaxClock > 0 ) {
|
301
|
+
clock_t delta;
|
302
|
+
if ( !TickEnd || !TickStart )
|
303
|
+
return 0;
|
304
|
+
/* clock_t is unsigned */
|
305
|
+
if ( TickEnd->clockTime > TickStart->clockTime ) {
|
306
|
+
if ( TickEnd->clockTime > HalfMaxClock &&
|
307
|
+
TickEnd->clockTime - TickStart->clockTime > HalfMaxClock ) {
|
308
|
+
/* overflow in TickStart->clockTime, actually TickStart->clockTime was later */
|
309
|
+
delta = (FullMaxClock - TickEnd->clockTime) + TickStart->clockTime;
|
310
|
+
return -INCHI_MSEC(delta);
|
311
|
+
}
|
312
|
+
delta = TickEnd->clockTime - TickStart->clockTime;
|
313
|
+
return INCHI_MSEC(delta);
|
314
|
+
} else
|
315
|
+
if ( TickEnd->clockTime < TickStart->clockTime ) {
|
316
|
+
if ( TickStart->clockTime > HalfMaxClock &&
|
317
|
+
TickStart->clockTime - TickEnd->clockTime > HalfMaxClock ) {
|
318
|
+
/* overflow in TickEnd->clockTime, actually TickEnd->clockTime was later */
|
319
|
+
delta = (FullMaxClock - TickStart->clockTime) + TickEnd->clockTime;
|
320
|
+
return INCHI_MSEC(delta);
|
321
|
+
}
|
322
|
+
delta = TickStart->clockTime - TickEnd->clockTime;
|
323
|
+
return -INCHI_MSEC(delta);
|
324
|
+
}
|
325
|
+
return 0; /* TickEnd->clockTime == TickStart->clockTime */
|
326
|
+
} else {
|
327
|
+
/* may happen under Win32 only where clock_t is SIGNED long */
|
328
|
+
clock_t delta;
|
329
|
+
FillMaxMinClock( );
|
330
|
+
if ( !TickEnd || !TickStart )
|
331
|
+
return 0;
|
332
|
+
if ( TickEnd->clockTime >= 0 && TickStart->clockTime >= 0 ||
|
333
|
+
TickEnd->clockTime <= 0 && TickStart->clockTime <= 0) {
|
334
|
+
delta = TickEnd->clockTime - TickStart->clockTime;
|
335
|
+
} else
|
336
|
+
if ( TickEnd->clockTime >= HalfMaxPositiveClock &&
|
337
|
+
TickStart->clockTime <= HalfMinNegativeClock ) {
|
338
|
+
/* end is earlier than start */
|
339
|
+
delta = (MaxPositiveClock - TickEnd->clockTime) + (TickStart->clockTime - MinNegativeClock);
|
340
|
+
delta = -delta;
|
341
|
+
} else
|
342
|
+
if ( TickEnd->clockTime <= HalfMinNegativeClock &&
|
343
|
+
TickStart->clockTime >= HalfMaxPositiveClock ) {
|
344
|
+
/* start was earlier than end */
|
345
|
+
delta = (MaxPositiveClock - TickStart->clockTime) + (TickEnd->clockTime - MinNegativeClock);
|
346
|
+
} else {
|
347
|
+
/* there was no overflow, clock passed zero */
|
348
|
+
delta = TickEnd->clockTime - TickStart->clockTime;
|
349
|
+
}
|
350
|
+
return INCHI_MSEC(delta);
|
351
|
+
}
|
352
|
+
}
|
353
|
+
/******************* get elapsed time from TickStart ************************/
|
354
|
+
long InchiTimeElapsed( inchiTime *TickStart )
|
355
|
+
{
|
356
|
+
inchiTime TickEnd;
|
357
|
+
if ( !TickStart )
|
358
|
+
return 0;
|
359
|
+
InchiTimeGet( &TickEnd );
|
360
|
+
return InchiTimeMsecDiff( &TickEnd, TickStart );
|
361
|
+
}
|
362
|
+
/******************* add number of milliseconds to time *********************/
|
363
|
+
void InchiTimeAddMsec( inchiTime *TickEnd, unsigned long nNumMsec )
|
364
|
+
{
|
365
|
+
clock_t delta;
|
366
|
+
if ( !TickEnd )
|
367
|
+
return;
|
368
|
+
if ( FullMaxClock > 0 ) {
|
369
|
+
/* clock_t is unsigned */
|
370
|
+
delta = INCHI_CLOCK_T(nNumMsec);
|
371
|
+
TickEnd->clockTime += delta;
|
372
|
+
} else {
|
373
|
+
/* may happen under Win32 only where clock_t is SIGNED long */
|
374
|
+
/* clock_t is unsigned */
|
375
|
+
FillMaxMinClock( );
|
376
|
+
delta = INCHI_CLOCK_T(nNumMsec);
|
377
|
+
TickEnd->clockTime += delta;
|
378
|
+
}
|
379
|
+
}
|
380
|
+
/******************* check whether time has expired *********************/
|
381
|
+
int bInchiTimeIsOver( inchiTime *TickStart )
|
382
|
+
{
|
383
|
+
if ( FullMaxClock > 0 ) {
|
384
|
+
clock_t clockCurrTime;
|
385
|
+
if ( !TickStart )
|
386
|
+
return 0;
|
387
|
+
clockCurrTime = InchiClock();
|
388
|
+
/* clock_t is unsigned */
|
389
|
+
if ( TickStart->clockTime > clockCurrTime ) {
|
390
|
+
if ( TickStart->clockTime > HalfMaxClock &&
|
391
|
+
TickStart->clockTime - clockCurrTime > HalfMaxClock ) {
|
392
|
+
/* overflow in clockCurrTime, actually clockCurrTime was later */
|
393
|
+
return 1;
|
394
|
+
}
|
395
|
+
return 0;
|
396
|
+
} else
|
397
|
+
if ( TickStart->clockTime < clockCurrTime ) {
|
398
|
+
if ( clockCurrTime > HalfMaxClock &&
|
399
|
+
clockCurrTime - TickStart->clockTime > HalfMaxClock ) {
|
400
|
+
/* overflow in TickStart->clockTime, actually TickStart->clockTime was later */
|
401
|
+
return 0;
|
402
|
+
}
|
403
|
+
return 1;
|
404
|
+
}
|
405
|
+
return 0; /* TickStart->clockTime == clockCurrTime */
|
406
|
+
} else {
|
407
|
+
/* may happen under Win32 only where clock_t is SIGNED long */
|
408
|
+
clock_t clockCurrTime;
|
409
|
+
FillMaxMinClock( );
|
410
|
+
if ( !TickStart )
|
411
|
+
return 0;
|
412
|
+
clockCurrTime = InchiClock();
|
413
|
+
if ( clockCurrTime >= 0 && TickStart->clockTime >= 0 ||
|
414
|
+
clockCurrTime <= 0 && TickStart->clockTime <= 0) {
|
415
|
+
return (clockCurrTime > TickStart->clockTime);
|
416
|
+
} else
|
417
|
+
if ( clockCurrTime >= HalfMaxPositiveClock &&
|
418
|
+
TickStart->clockTime <= HalfMinNegativeClock ) {
|
419
|
+
/* curr is earlier than start */
|
420
|
+
return 0;
|
421
|
+
} else
|
422
|
+
if ( clockCurrTime <= HalfMinNegativeClock &&
|
423
|
+
TickStart->clockTime >= HalfMaxPositiveClock ) {
|
424
|
+
/* start was earlier than curr */
|
425
|
+
return 1;
|
426
|
+
} else {
|
427
|
+
/* there was no overflow, clock passed zero */
|
428
|
+
return (clockCurrTime > TickStart->clockTime);
|
429
|
+
}
|
430
|
+
}
|
431
|
+
}
|
432
|
+
|
433
|
+
#else
|
434
|
+
|
435
|
+
/******** get current process time ****************************************/
|
436
|
+
void InchiTimeGet( inchiTime *TickEnd )
|
437
|
+
{
|
438
|
+
if ( TickEnd ) {
|
439
|
+
struct _timeb timeb;
|
440
|
+
_ftime( &timeb );
|
441
|
+
TickEnd->clockTime = (unsigned long)timeb.time;
|
442
|
+
TickEnd->millitime = (long)timeb.millitm;
|
443
|
+
}
|
444
|
+
}
|
445
|
+
/******** returns difference TickEnd - TickStart in milliseconds **********/
|
446
|
+
long InchiTimeMsecDiff( inchiTime *TickEnd, inchiTime *TickStart )
|
447
|
+
{
|
448
|
+
long delta;
|
449
|
+
if ( !TickEnd || !TickStart ) {
|
450
|
+
return 0;
|
451
|
+
}
|
452
|
+
if ( TickEnd->clockTime >= TickStart->clockTime ) {
|
453
|
+
delta = (long)(TickEnd->clockTime - TickStart->clockTime);
|
454
|
+
delta *= 1000;
|
455
|
+
delta += TickEnd->millitime - TickStart->millitime;
|
456
|
+
} else {
|
457
|
+
delta = -(long)(TickStart->clockTime - TickEnd->clockTime);
|
458
|
+
delta *= 1000;
|
459
|
+
delta += TickEnd->millitime - TickStart->millitime;
|
460
|
+
}
|
461
|
+
return delta;
|
462
|
+
}
|
463
|
+
/******************* get elapsed time from TickStart ************************/
|
464
|
+
long InchiTimeElapsed( inchiTime *TickStart )
|
465
|
+
{
|
466
|
+
inchiTime TickEnd;
|
467
|
+
if ( !TickStart )
|
468
|
+
return 0;
|
469
|
+
InchiTimeGet( &TickEnd );
|
470
|
+
return InchiTimeMsecDiff( &TickEnd, TickStart );
|
471
|
+
}
|
472
|
+
/******************* add number of milliseconds to time *********************/
|
473
|
+
void InchiTimeAddMsec( inchiTime *TickEnd, unsigned long nNumMsec )
|
474
|
+
{
|
475
|
+
long delta;
|
476
|
+
if ( !TickEnd )
|
477
|
+
return;
|
478
|
+
TickEnd->clockTime += nNumMsec / 1000;
|
479
|
+
delta = nNumMsec % 1000 + TickEnd->millitime;
|
480
|
+
TickEnd->clockTime += delta / 1000;
|
481
|
+
TickEnd->millitime = delta % 1000;
|
482
|
+
}
|
483
|
+
/******************* check whether time has expired *********************/
|
484
|
+
int bInchiTimeIsOver( inchiTime *TickEnd )
|
485
|
+
{
|
486
|
+
struct _timeb timeb;
|
487
|
+
if ( !TickEnd )
|
488
|
+
return 0;
|
489
|
+
_ftime( &timeb );
|
490
|
+
if ( TickEnd->clockTime > (unsigned long)timeb.time )
|
491
|
+
return 0;
|
492
|
+
if ( TickEnd->clockTime < (unsigned long)timeb.time ||
|
493
|
+
TickEnd->millitime < (long)timeb.millitm ) {
|
494
|
+
return 1;
|
495
|
+
}
|
496
|
+
return 0;
|
497
|
+
}
|
498
|
+
#endif
|
data/ext/src/e_ichi_io.h
ADDED
@@ -0,0 +1,40 @@
|
|
1
|
+
/*
|
2
|
+
* International Union of Pure and Applied Chemistry (IUPAC)
|
3
|
+
* International Chemical Identifier (InChI)
|
4
|
+
* Version 1
|
5
|
+
* Software version 1.00
|
6
|
+
* April 13, 2005
|
7
|
+
* Developed at NIST
|
8
|
+
*/
|
9
|
+
|
10
|
+
#ifndef __ICHI_IO_H__
|
11
|
+
#define __ICHI_IO_H__
|
12
|
+
|
13
|
+
|
14
|
+
#ifndef INCHI_ALL_CPP
|
15
|
+
#ifdef __cplusplus
|
16
|
+
extern "C" {
|
17
|
+
#endif
|
18
|
+
#endif
|
19
|
+
|
20
|
+
|
21
|
+
char* fgets_up_to_lf( char* line, int line_len, FILE* inp );
|
22
|
+
int my_fgetsUpToLfOrTab( char *szLine, int len, FILE *f );
|
23
|
+
|
24
|
+
int e_my_fgetsTab( char *szLine, int len, FILE *f, int *bTooLongLine );
|
25
|
+
int e_my_fgetsTab1( char *szLine, int len, FILE *f, int *bTooLongLine );
|
26
|
+
|
27
|
+
int e_inchi_print( FILE* f, const char* lpszFormat, ... );
|
28
|
+
int e_my_fprintf( FILE* f, const char* lpszFormat, ... );
|
29
|
+
void e_PrintFileName( const char *fmt, FILE *output_file, const char *szFname );
|
30
|
+
unsigned long e_ulMyGetTickCount( int bStart );
|
31
|
+
unsigned long e_ulMyTickCountDiff( unsigned long ulTickEnd, unsigned long ulTickStart );
|
32
|
+
|
33
|
+
#ifndef INCHI_ALL_CPP
|
34
|
+
#ifdef __cplusplus
|
35
|
+
}
|
36
|
+
#endif
|
37
|
+
#endif
|
38
|
+
|
39
|
+
|
40
|
+
#endif /* __ICHI_IO_H__ */
|
@@ -0,0 +1,37 @@
|
|
1
|
+
/*
|
2
|
+
* International Union of Pure and Applied Chemistry (IUPAC)
|
3
|
+
* International Chemical Identifier (InChI)
|
4
|
+
* Version 1
|
5
|
+
* Software version 1.00
|
6
|
+
* April 13, 2005
|
7
|
+
* Developed at NIST
|
8
|
+
*/
|
9
|
+
|
10
|
+
#include <stdio.h>
|
11
|
+
#include <stdlib.h>
|
12
|
+
#include <string.h>
|
13
|
+
#include <ctype.h>
|
14
|
+
#include <errno.h>
|
15
|
+
#include <limits.h>
|
16
|
+
|
17
|
+
#include "e_mode.h"
|
18
|
+
#include "inchi_api.h"
|
19
|
+
#include "e_ctl_data.h"
|
20
|
+
#include "e_ichi_io.h"
|
21
|
+
#include "e_ichi_parms.h"
|
22
|
+
#include "e_util.h"
|
23
|
+
#include "e_ichicomp.h"
|
24
|
+
|
25
|
+
#define DetectInputINChIFileType e_DetectInputINChIFileType
|
26
|
+
#define ReadCommandLineParms e_ReadCommandLineParms
|
27
|
+
#define mystrncpy e_mystrncpy
|
28
|
+
#define my_fprintf e_my_fprintf
|
29
|
+
#define LtrimRtrim e_LtrimRtrim
|
30
|
+
#define PrintInputParms e_PrintInputParms
|
31
|
+
#define OpenFiles e_OpenFiles
|
32
|
+
#define PrintFileName e_PrintFileName
|
33
|
+
#define HelpCommandLineParms e_HelpCommandLineParms
|
34
|
+
#define inchi_print_nodisplay fprintf
|
35
|
+
|
36
|
+
#include "ichiparm.h"
|
37
|
+
|
@@ -0,0 +1,41 @@
|
|
1
|
+
/*
|
2
|
+
* International Union of Pure and Applied Chemistry (IUPAC)
|
3
|
+
* International Chemical Identifier (InChI)
|
4
|
+
* Version 1
|
5
|
+
* Software version 1.00
|
6
|
+
* April 13, 2005
|
7
|
+
* Developed at NIST
|
8
|
+
*/
|
9
|
+
|
10
|
+
#ifndef __ICHI_PARMS_H__
|
11
|
+
#define __ICHI_PARMS_H__
|
12
|
+
|
13
|
+
|
14
|
+
|
15
|
+
#ifndef INCHI_ALL_CPP
|
16
|
+
#ifdef __cplusplus
|
17
|
+
extern "C" {
|
18
|
+
#endif
|
19
|
+
#endif
|
20
|
+
|
21
|
+
|
22
|
+
int e_ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *szSdfDataValue,
|
23
|
+
unsigned long *ulDisplTime, int bReleaseVersion, INCHI_FILE *log_file );
|
24
|
+
|
25
|
+
int e_PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip );
|
26
|
+
int e_OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_file, INPUT_PARMS *ip );
|
27
|
+
void e_HelpCommandLineParms( INCHI_FILE *f );
|
28
|
+
|
29
|
+
|
30
|
+
|
31
|
+
|
32
|
+
|
33
|
+
|
34
|
+
|
35
|
+
#ifndef INCHI_ALL_CPP
|
36
|
+
#ifdef __cplusplus
|
37
|
+
}
|
38
|
+
#endif
|
39
|
+
#endif
|
40
|
+
|
41
|
+
#endif /* __ICHI_PARMS_H__ */
|
@@ -0,0 +1,50 @@
|
|
1
|
+
/*
|
2
|
+
* International Union of Pure and Applied Chemistry (IUPAC)
|
3
|
+
* International Chemical Identifier (InChI)
|
4
|
+
* Version 1
|
5
|
+
* Software version 1.00
|
6
|
+
* April 13, 2005
|
7
|
+
* Developed at NIST
|
8
|
+
*/
|
9
|
+
|
10
|
+
#ifndef __INCHI_COMPAT_H__
|
11
|
+
#define __INCHI_COMPAT_H__
|
12
|
+
|
13
|
+
/* compatibility */
|
14
|
+
|
15
|
+
#if( defined(__GNUC__) && defined(__MINGW32__) && __GNUC__ == 3 && __GNUC_MINOR__ == 2 && __GNUC_PATCHLEVEL__ == 0 && defined(_WIN32) )
|
16
|
+
/* replace with the proper definition for GNU gcc & MinGW-2.0.0-3 (mingw special 20020817-1), gcc 3.2 core */
|
17
|
+
#define my_va_start(A,B) ((A)=(va_list)__builtin_next_arg(lpszFormat))
|
18
|
+
#else
|
19
|
+
#define my_va_start va_start
|
20
|
+
#endif
|
21
|
+
|
22
|
+
|
23
|
+
|
24
|
+
/* ANSI redefinitions */
|
25
|
+
#ifdef INCHI_ANSI_ONLY /* { */
|
26
|
+
#ifndef __isascii
|
27
|
+
#define __isascii(val) ((unsigned)(val) <= 0x7F)
|
28
|
+
#endif
|
29
|
+
|
30
|
+
/* #ifndef __GNUC__ */
|
31
|
+
/* these non-ANSI functions are implemented in gcc */
|
32
|
+
#include <stdio.h>
|
33
|
+
/* this #include provides size_t definition */
|
34
|
+
/* implementation is located in util.c */
|
35
|
+
#if ( !defined(_MSC_VER) || defined(__STDC__) && __STDC__ == 1 )
|
36
|
+
/* support (VC++ Language extensions) = OFF && defined(INCHI_ANSI_ONLY) */
|
37
|
+
int memicmp (const void*, const void*, size_t);
|
38
|
+
int stricmp( const char *s1, const char *s2 );
|
39
|
+
char *_strnset( char *string, int c, size_t count );
|
40
|
+
char *_strdup( const char *string );
|
41
|
+
#endif
|
42
|
+
/* #endif */
|
43
|
+
|
44
|
+
#endif /* } */
|
45
|
+
|
46
|
+
#define inchi_max(a,b) (((a)>(b))?(a):(b))
|
47
|
+
#define inchi_min(a,b) (((a)<(b))?(a):(b))
|
48
|
+
|
49
|
+
|
50
|
+
#endif /* __INCHI_COMPAT_H__ */
|
data/ext/src/e_ichierr.h
ADDED
@@ -0,0 +1,40 @@
|
|
1
|
+
/*
|
2
|
+
* International Union of Pure and Applied Chemistry (IUPAC)
|
3
|
+
* International Chemical Identifier (InChI)
|
4
|
+
* Version 1
|
5
|
+
* Software version 1.00
|
6
|
+
* April 13, 2005
|
7
|
+
* Developed at NIST
|
8
|
+
*/
|
9
|
+
|
10
|
+
#ifndef __INCHIERR_H__
|
11
|
+
#define __INCHIERR_H__
|
12
|
+
|
13
|
+
#define _IS_OKAY 0
|
14
|
+
#define _IS_WARNING 1
|
15
|
+
#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */
|
16
|
+
#define _IS_FATAL 3
|
17
|
+
#define _IS_UNKNOWN 4 /* unknown error: used in INChI DLL only */
|
18
|
+
#define _IS_EOF -1 /* end of file */
|
19
|
+
#define _IS_SKIP -2
|
20
|
+
|
21
|
+
|
22
|
+
|
23
|
+
#define INCHI_INP_ERROR_ERR 40
|
24
|
+
#define INCHI_INP_ERROR_RET (-1)
|
25
|
+
|
26
|
+
#define INCHI_INP_FATAL_ERR 1
|
27
|
+
#define INCHI_INP_FATAL_RET 0
|
28
|
+
|
29
|
+
#define INCHI_INP_EOF_ERR 11
|
30
|
+
#define INCHI_INP_EOF_RET 0
|
31
|
+
|
32
|
+
#define LOG_MASK_WARN 1
|
33
|
+
#define LOG_MASK_ERR 2
|
34
|
+
#define LOG_MASK_FATAL 4
|
35
|
+
|
36
|
+
#define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL)
|
37
|
+
#define LOG_MASK_NO_WARN (LOG_MASK_ERR | LOG_MASK_FATAL)
|
38
|
+
|
39
|
+
|
40
|
+
#endif /* __INCHIERR_H__ */
|