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/* NOTICE: this source code file has been modified for use with FreeMOL */ |
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|
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#define notKEG_DEBUG |
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|
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#define EXTERN |
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#include "pcwin.h" |
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#include "pcmod.h" |
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#include "energies.h" |
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#include "pot.h" |
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#include "angles.h" |
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|
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#include "rings.h" |
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#include "torsions.h" |
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#include "nonbond.h" |
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#include "bonds_ff.h" |
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#include "derivs.h" |
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#include "hess.h" |
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#include "field.h" |
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#include "atom_k.h" |
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#include "cutoffs.h" |
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#include "solv.h" |
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#include "gmmx.h" |
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#include "fix.h" |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <unistd.h> |
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#include <string.h> |
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//#include <malloc.h> |
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|
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struct t_rotbond { |
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int nbonds, bond[200][2], bond_res[200]; |
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int incl_amide, incl_alkene; |
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} rotbond; |
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struct t_minim_values { |
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int iprint, ndc, nconst; |
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float dielc; |
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} minim_values; |
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|
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struct t_minim_control { |
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int type, method, field, added_const; |
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char added_path[256],added_name[256]; |
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} minim_control; |
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EXTERN struct t_files { |
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int nfiles, append, batch, icurrent, ibatno; |
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} files; |
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char Savename[80]; |
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|
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/* |
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void initialize_pcmodel(char*); |
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void mmp22mod(int,int); |
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void pcmfin(int, int); |
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void initialize(void); |
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void mmxsub(int); |
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void check_numfile(int, char *); |
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void mac2mod(int, int); |
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void bbchk(void); |
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void type(void); |
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void initialize_gmmx(void); |
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void read_gmmxinp(char*, char*, char*, FILE*, int); |
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void run_gmmx(void); |
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void search_rings(int); |
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*/ |
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|
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|
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void usage(void) { |
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printf("\nUsage: mengine [-hvdxi] reads sdf on stdin, writes on stdout\n\n" |
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"-h\tThis help page\n" |
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"-v\tVerbose output\n" |
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"-a\tAdd hydrogen atoms; delete existing ones\n" |
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"-d\tEvaluate dipole moment\n" |
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"-x\tEvaluate XlogP\n" |
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"-i\tEvaluate vibrational data\n\n"); |
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} |
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|
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/* ==================================================== */ |
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int main(int argc, char *argv[]) |
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{ |
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int i; |
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FILE *infile; |
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char *line = NULL; |
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|
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char *infilename = NULL; |
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char *outfilename = NULL; |
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char *mmff94filename = NULL; |
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char *mmxfilename = NULL; |
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char *logfilename = NULL; |
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|
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int c; |
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int flags = 0; |
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|
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while ((c = getopt(argc, argv, "e:o:p:c:havdxi")) != -1) { |
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switch(c) { |
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case 'a': |
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flags = flags | DO_ADDH; |
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break; |
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case 'd': |
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flags = flags | DO_DIPOLE; |
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break; |
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case 'x': |
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flags = flags | DO_XLOGP; |
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break; |
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case 'i': |
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flags = flags | DO_VIBRATION; |
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break; |
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case 'v': |
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VERBOSE = 1; |
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break; |
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case 'h': |
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usage(); |
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exit(-1); |
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case 'o': |
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outfilename = strdup(optarg); |
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break; |
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#if 0 |
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// EXTERNAL PARAM FILES STILL NOT WORKING |
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// SOON THEY WILL |
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case 'p': |
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mmff94filename = strdup(optarg); |
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break; |
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case 'c': |
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mmxfilename = strdup(optarg); |
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break; |
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#endif |
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case 'e': |
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logfilename = strdup(optarg); |
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break; |
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case '?': |
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if (isprint (optopt)) |
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fprintf (stderr, "Unknown option `-%c'.\n", optopt); |
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else |
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fprintf (stderr, |
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"Unknown option character `\\x%x'.\n", |
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optopt); |
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return 1; |
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default: |
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abort (); |
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} |
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} |
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|
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argc -= optind; |
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argv += optind; |
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|
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if (argc == 1) |
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infilename = strdup(argv[0]); |
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|
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#ifdef KEG_DEBUG |
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if(!infilename) |
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infilename = strdup("caffeine.sdf"); |
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if(!outfilename) |
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outfilename = strdup("output.sdf"); |
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#endif |
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|
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/* default behavior is to use the hardcoded parameter files */ |
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|
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if(!mmff94filename) mmff94filename = strdup("|mmff94"); /* hard-coded builtins */ |
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if(!mmxfilename) mmxfilename = strdup("|mmxconst"); /* hard-coded builtins */ |
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|
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/* if no input file provide, then use standard input */ |
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|
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if(infilename) { |
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infile = fopen(infilename,"rb"); |
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} else { |
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infile = stdin; |
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} |
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|
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/* if no output file provided, then use standard output */ |
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|
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if(outfilename) { |
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pcmoutfile = fopen(outfilename,"wb"); |
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} else { |
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pcmoutfile = stdout; |
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} |
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|
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/* if no log file provided, then use standard error */ |
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|
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if(logfilename) { |
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pcmlogfile = fopen(logfilename,"wb"); |
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} else { |
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pcmlogfile = stderr; |
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} |
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|
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/* initialize the system using parameter file */ |
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|
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initialize_pcmodel(mmxfilename); |
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initialize(); |
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minim_values.iprint = 0; //FALSE; |
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initialize_gmmx(); |
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|
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/* run the job */ |
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|
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if (infile) { |
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read_gmmxinp(mmff94filename, infile, flags); |
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} |
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|
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/* release temporary strings */ |
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|
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if(infilename) free(infilename); |
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if(outfilename) free(outfilename); |
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if(mmff94filename) free(mmff94filename); |
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if(mmxfilename) free(mmxfilename); |
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if(logfilename) free(logfilename); |
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|
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/* close file handles */ |
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|
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if(infile && (infile!=stdin)) fclose(infile); |
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if(pcmoutfile && (pcmoutfile!=stdout)) fclose(pcmoutfile); |
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if(pcmlogfile && (pcmlogfile!=stderr)) fclose(pcmlogfile); |
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|
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exit(0); |
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} |
