ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/freemol/trunk/src/mengine/src/mengine.c
Revision: 58
Committed: Mon Dec 1 06:44:59 2008 UTC (10 years, 11 months ago) by wdelano
File size: 5108 byte(s)
Log Message:
code merge 20081130
Line File contents
1 /* NOTICE: this source code file has been modified for use with FreeMOL */
2
3 /*
4 Kevin: please remove the "not" below or simply define KEG_DEBUG at
5 compile time in order to activate your preferred debug / testing
6 behaviors. This is more robust approach then using comments...
7 */
8
9 #define not KEG_DEBUG
10
11 #define EXTERN
12 #include "pcwin.h"
13 #include "pcmod.h"
14 #include "energies.h"
15 #include "pot.h"
16 #include "angles.h"
17
18 #include "rings.h"
19 #include "torsions.h"
20 #include "nonbond.h"
21 #include "bonds_ff.h"
22 #include "derivs.h"
23 #include "hess.h"
24 #include "field.h"
25 #include "atom_k.h"
26 #include "cutoffs.h"
27 #include "solv.h"
28 #include "gmmx.h"
29 #include "fix.h"
30
31 #include <stdio.h>
32 #include <stdlib.h>
33 #include <unistd.h>
34 #include <string.h>
35 //#include <malloc.h>
36
37 struct t_rotbond {
38 int nbonds, bond[200][2], bond_res[200];
39 int incl_amide, incl_alkene;
40 } rotbond;
41 struct t_minim_values {
42 int iprint, ndc, nconst;
43 float dielc;
44 } minim_values;
45
46 struct t_minim_control {
47 int type, method, field, added_const;
48 char added_path[256],added_name[256];
49 } minim_control;
50 EXTERN struct t_files {
51 int nfiles, append, batch, icurrent, ibatno;
52 } files;
53 char Savename[80];
54
55 /*
56 void initialize_pcmodel(char*);
57 void mmp22mod(int,int);
58 void pcmfin(int, int);
59 void initialize(void);
60 void mmxsub(int);
61 void check_numfile(int, char *);
62 void mac2mod(int, int);
63 void bbchk(void);
64 void type(void);
65 void initialize_gmmx(void);
66 void read_gmmxinp(char*, char*, char*, FILE*, int);
67 void run_gmmx(void);
68 void search_rings(int);
69 */
70
71
72 void usage(void) {
73 printf("\nUsage: mengine [-hvdxi] reads sdf on stdin, writes on stdout\n\n"
74 "-h\tThis help page\n"
75 "-v\tVerbose output\n"
76 "-a\tAdd hydrogen atoms; delete existing ones\n"
77 "-d\tEvaluate dipole moment\n"
78 "-x\tEvaluate XlogP\n"
79 "-i\tEvaluate vibrational data\n\n");
80 }
81
82 /* ==================================================== */
83 int main(int argc, char *argv[])
84 {
85 int i;
86 FILE *infile;
87 char *line = NULL;
88
89 char *infilename = NULL;
90 char *outfilename = NULL;
91 char *mmff94filename = NULL;
92 char *mmxfilename = NULL;
93 char *logfilename = NULL;
94
95 int c;
96 int flags = 0;
97
98 while ((c = getopt(argc, argv, "e:o:p:c:havdxi")) != -1) {
99 switch(c) {
100 case 'a':
101 flags = flags | DO_ADDH;
102 break;
103 case 'd':
104 flags = flags | DO_DIPOLE;
105 break;
106 case 'x':
107 flags = flags | DO_XLOGP;
108 break;
109 case 'i':
110 flags = flags | DO_VIBRATION;
111 break;
112 case 'v':
113 VERBOSE = 1;
114 break;
115 case 'h':
116 usage();
117 exit(-1);
118 case 'o':
119 outfilename = strdup(optarg);
120 break;
121 #if 0
122 // EXTERNAL PARAM FILES STILL NOT WORKING
123 case 'p':
124 mmff94filename = strdup(optarg);
125 break;
126 case 'c':
127 mmxfilename = strdup(optarg);
128 break;
129 #endif
130 case 'e':
131 logfilename = strdup(optarg);
132 break;
133 case '?':
134 if (isprint (optopt))
135 fprintf (stderr, "Unknown option `-%c'.\n", optopt);
136 else
137 fprintf (stderr,
138 "Unknown option character `\\x%x'.\n",
139 optopt);
140 return 1;
141 default:
142 abort ();
143 }
144 }
145
146 argc -= optind;
147 argv += optind;
148
149 if (argc == 1)
150 infilename = strdup(argv[0]);
151
152 #ifdef KEG_DEBUG
153 if(!infilename)
154 infilename = strdup("caffeine.sdf");
155 if(!outfilename)
156 outfilename = strdup("output.sdf");
157 #endif
158
159 /* default behavior is to use the hardcoded parameter files */
160
161 if(!mmff94filename) mmff94filename = strdup("|mmff94"); /* hard-coded builtins */
162 if(!mmxfilename) mmxfilename = strdup("|mmxconst"); /* hard-coded builtins */
163
164 /* if no input file provide, then use standard input */
165
166 if(infilename) {
167 infile = fopen(infilename,"rb");
168 } else {
169 infile = stdin;
170 }
171
172 /* if no output file provided, then use standard output */
173
174 if(outfilename) {
175 pcmoutfile = fopen(outfilename,"wb");
176 } else {
177 pcmoutfile = stdout;
178 }
179
180 /* if no log file provided, then use standard error */
181
182 if(logfilename) {
183 pcmlogfile = fopen(logfilename,"wb");
184 } else {
185 pcmlogfile = stderr;
186 }
187
188 /* initialize the system using parameter file */
189
190 initialize_pcmodel(mmxfilename);
191 initialize();
192 minim_values.iprint = 0; //FALSE;
193 initialize_gmmx();
194
195 /* run the job */
196
197 if (infile) {
198 read_gmmxinp(mmff94filename, infile, flags);
199 }
200
201 /* release temporary strings */
202
203 if(infilename) free(infilename);
204 if(outfilename) free(outfilename);
205 if(mmff94filename) free(mmff94filename);
206 if(mmxfilename) free(mmxfilename);
207 if(logfilename) free(logfilename);
208
209 /* close file handles */
210
211 if(infile && (infile!=stdin)) fclose(infile);
212 if(pcmoutfile && (pcmoutfile!=stdout)) fclose(pcmoutfile);
213 if(pcmlogfile && (pcmlogfile!=stderr)) fclose(pcmlogfile);
214
215 exit(0);
216 }