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43 #include "gromacs/commandline/pargs.h"
44 #include "gromacs/fileio/confio.h"
45 #include "gromacs/fileio/xvgr.h"
46 #include "gromacs/gmxana/gmx_ana.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/statistics/statistics.h"
49 #include "gromacs/topology/topology.h"
50 #include "gromacs/utility/arraysize.h"
51 #include "gromacs/utility/cstringutil.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/futil.h"
54 #include "gromacs/utility/pleasecite.h"
55 #include "gromacs/utility/smalloc.h"
57 static const char *etitles[] = { "E-docked", "Free Energy" };
61 int index, cluster_id;
68 static t_pdbfile *read_pdbf(const char *fn)
76 read_tps_conf(fn, &top, &pdbf->ePBC, &pdbf->x, NULL, pdbf->box, FALSE);
77 pdbf->atoms = top.atoms;
78 fp = gmx_ffopen(fn, "r");
80 while ((ptr = fgets2(buf, 255, fp)) != NULL)
82 if (std::strstr(buf, "Intermolecular") != NULL)
84 ptr = std::strchr(buf, '=');
85 sscanf(ptr+1, "%lf", &e);
88 else if (std::strstr(buf, "Estimated Free") != NULL)
90 ptr = std::strchr(buf, '=');
91 sscanf(ptr+1, "%lf", &e);
100 static t_pdbfile **read_em_all(const char *fn, int *npdbf)
102 t_pdbfile **pdbf = 0;
104 char buf[256], name[256];
107 std::strcpy(buf, fn);
108 buf[std::strlen(buf)-4] = '\0';
114 sprintf(name, "%s_%d.pdb", buf, i+1);
115 if ((bExist = gmx_fexist(name)) == TRUE)
117 pdbf[i] = read_pdbf(name);
118 pdbf[i]->index = i+1;
123 srenew(pdbf, maxpdbf);
131 printf("Found %d pdb files\n", i);
136 static gmx_bool bFreeSort = FALSE;
138 static int pdbf_comp(const void *a, const void *b)
144 pa = *(t_pdbfile **)a;
145 pb = *(t_pdbfile **)b;
147 dc = pa->cluster_id - pb->cluster_id;
153 x = pa->efree - pb->efree;
157 x = pa->edocked - pb->edocked;
179 static void analyse_em_all(int npdb, t_pdbfile *pdbf[], const char *edocked,
180 const char *efree, const gmx_output_env_t *oenv)
185 for (bFreeSort = FALSE; (bFreeSort <= TRUE); bFreeSort++)
187 qsort(pdbf, npdb, sizeof(pdbf[0]), pdbf_comp);
188 fp = xvgropen(bFreeSort ? efree : edocked,
189 etitles[bFreeSort], "()", "E (kJ/mol)", oenv);
190 for (i = 0; (i < npdb); i++)
192 fprintf(fp, "%12lf\n", bFreeSort ? pdbf[i]->efree : pdbf[i]->edocked);
198 static void clust_stat(FILE *fp, int start, int end, t_pdbfile *pdbf[])
204 ed = gmx_stats_init();
205 ef = gmx_stats_init();
206 for (i = start; (i < end); i++)
208 gmx_stats_add_point(ed, i-start, pdbf[i]->edocked, 0, 0);
209 gmx_stats_add_point(ef, i-start, pdbf[i]->efree, 0, 0);
211 gmx_stats_get_ase(ed, &aver, &sigma, NULL);
212 fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[FALSE], aver, sigma);
213 gmx_stats_get_ase(ef, &aver, &sigma, NULL);
214 fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[TRUE], aver, sigma);
219 static real rmsd_dist(t_pdbfile *pa, t_pdbfile *pb, gmx_bool bRMSD)
228 for (i = 0; (i < pa->atoms.nr); i++)
230 rvec_sub(pa->x[i], pb->x[i], dx);
231 rmsd += iprod(dx, dx);
233 rmsd = std::sqrt(rmsd/pa->atoms.nr);
239 for (i = 0; (i < pa->atoms.nr); i++)
241 rvec_inc(acm, pa->x[i]);
242 rvec_inc(bcm, pb->x[i]);
244 rvec_sub(acm, bcm, dx);
245 for (i = 0; (i < DIM); i++)
247 dx[i] /= pa->atoms.nr;
254 static void line(FILE *fp)
256 fprintf(fp, " - - - - - - - - - -\n");
259 static void cluster_em_all(FILE *fp, int npdb, t_pdbfile *pdbf[],
260 gmx_bool bFree, gmx_bool bRMSD, real cutoff)
267 qsort(pdbf, npdb, sizeof(pdbf[0]), pdbf_comp);
269 fprintf(fp, "Statistics over all structures:\n");
270 clust_stat(fp, 0, npdb, pdbf);
273 /* Index to first structure in a cluster */
277 for (i = 1; (i < npdb); i++)
279 for (j = 0; (j < ncluster); j++)
281 rmsd = rmsd_dist(pdbf[cndx[j]], pdbf[i], bRMSD);
284 /* Structure i is in cluster j */
285 pdbf[i]->cluster_id = pdbf[cndx[j]]->cluster_id;
291 /* New cluster! Cool! */
293 pdbf[i]->cluster_id = ncluster;
297 cndx[ncluster] = npdb;
298 qsort(pdbf, npdb, sizeof(pdbf[0]), pdbf_comp);
302 for (i = 1; (i < npdb); i++)
304 if (pdbf[i]->cluster_id != pdbf[i-1]->cluster_id)
312 gmx_fatal(FARGS, "Consistency error: j = %d, ncluster = %d", j, ncluster);
315 fprintf(fp, "I found %d clusters based on %s and %s with a %.3f nm cut-off\n",
316 ncluster, etitles[bFree], bRMSD ? "RMSD" : "distance", cutoff);
318 for (j = 0; (j < ncluster); j++)
320 fprintf(fp, "Cluster: %3d %s: %10.5f kJ/mol %3d elements\n",
322 bFree ? pdbf[cndx[j]]->efree : pdbf[cndx[j]]->edocked,
324 clust_stat(fp, cndx[j], cndx[j+1], pdbf);
325 for (k = cndx[j]; (k < cndx[j+1]); k++)
327 fprintf(fp, " %3d", pdbf[k]->index);
335 int gmx_anadock(int argc, char *argv[])
337 const char *desc[] = {
338 "[THISMODULE] analyses the results of an Autodock run and clusters the",
339 "structures together, based on distance or RMSD. The docked energy",
340 "and free energy estimates are analysed, and for each cluster the",
341 "energy statistics are printed.[PAR]",
342 "An alternative approach to this is to cluster the structures first",
343 "using [gmx-cluster] and then sort the clusters on either lowest",
344 "energy or average energy."
347 { efPDB, "-f", NULL, ffREAD },
348 { efXVG, "-od", "edocked", ffWRITE },
349 { efXVG, "-of", "efree", ffWRITE },
350 { efLOG, "-g", "anadock", ffWRITE }
352 gmx_output_env_t *oenv;
353 #define NFILE asize(fnm)
354 static gmx_bool bFree = FALSE, bRMS = TRUE;
355 static real cutoff = 0.2;
357 { "-free", FALSE, etBOOL, {&bFree},
358 "Use Free energy estimate from autodock for sorting the classes" },
359 { "-rms", FALSE, etBOOL, {&bRMS},
360 "Cluster on RMS or distance" },
361 { "-cutoff", FALSE, etREAL, {&cutoff},
362 "Maximum RMSD/distance for belonging to the same cluster" }
364 #define NPA asize(pa)
367 t_pdbfile **pdbf = NULL;
370 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
376 fp = gmx_ffopen(opt2fn("-g", NFILE, fnm), "w");
377 please_cite(stdout, "Hetenyi2002b");
378 please_cite(fp, "Hetenyi2002b");
380 pdbf = read_em_all(opt2fn("-f", NFILE, fnm), &npdbf);
382 analyse_em_all(npdbf, pdbf, opt2fn("-od", NFILE, fnm), opt2fn("-of", NFILE, fnm),
385 cluster_em_all(fp, npdbf, pdbf, bFree, bRMS, cutoff);