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45 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/commandline/pargs.h"
48 #include "gromacs/fileio/tpxio.h"
49 #include "gromacs/fileio/trxio.h"
50 #include "gromacs/utility/cstringutil.h"
54 #include "gromacs/random/random.h"
58 #include "gromacs/fileio/futil.h"
59 #include "gromacs/fileio/matio.h"
61 #include "gromacs/fileio/trnio.h"
65 #include "gromacs/linearalgebra/eigensolver.h"
66 #include "gromacs/math/do_fit.h"
67 #include "gromacs/legacyheaders/gmx_fatal.h"
69 /* print to two file pointers at once (i.e. stderr and log) */
71 void lo_ffprintf(FILE *fp1
, FILE *fp2
, const char *buf
)
73 fprintf(fp1
, "%s", buf
);
74 fprintf(fp2
, "%s", buf
);
77 /* just print a prepared buffer to fp1 and fp2 */
79 void ffprintf(FILE *fp1
, FILE *fp2
, const char *buf
)
81 lo_ffprintf(fp1
, fp2
, buf
);
84 /* prepare buffer with one argument, then print to fp1 and fp2 */
86 void ffprintf_d(FILE *fp1
, FILE *fp2
, char *buf
, const char *fmt
, int arg
)
88 sprintf(buf
, fmt
, arg
);
89 lo_ffprintf(fp1
, fp2
, buf
);
92 /* prepare buffer with one argument, then print to fp1 and fp2 */
94 void ffprintf_g(FILE *fp1
, FILE *fp2
, char *buf
, const char *fmt
, real arg
)
96 sprintf(buf
, fmt
, arg
);
97 lo_ffprintf(fp1
, fp2
, buf
);
100 /* prepare buffer with one argument, then print to fp1 and fp2 */
102 void ffprintf_s(FILE *fp1
, FILE *fp2
, char *buf
, const char *fmt
, const char *arg
)
104 sprintf(buf
, fmt
, arg
);
105 lo_ffprintf(fp1
, fp2
, buf
);
108 /* prepare buffer with two arguments, then print to fp1 and fp2 */
110 void ffprintf_dd(FILE *fp1
, FILE *fp2
, char *buf
, const char *fmt
, int arg1
, int arg2
)
112 sprintf(buf
, fmt
, arg1
, arg2
);
113 lo_ffprintf(fp1
, fp2
, buf
);
116 /* prepare buffer with two arguments, then print to fp1 and fp2 */
118 void ffprintf_gg(FILE *fp1
, FILE *fp2
, char *buf
, const char *fmt
, real arg1
, real arg2
)
120 sprintf(buf
, fmt
, arg1
, arg2
);
121 lo_ffprintf(fp1
, fp2
, buf
);
124 /* prepare buffer with two arguments, then print to fp1 and fp2 */
126 void ffprintf_ss(FILE *fp1
, FILE *fp2
, char *buf
, const char *fmt
, const char *arg1
, const char *arg2
)
128 sprintf(buf
, fmt
, arg1
, arg2
);
129 lo_ffprintf(fp1
, fp2
, buf
);
142 void pr_energy(FILE *fp
, real e
)
144 fprintf(fp
, "Energy: %8.4f\n", e
);
147 void cp_index(int nn
, int from
[], int to
[])
151 for (i
= 0; (i
< nn
); i
++)
157 void mc_optimize(FILE *log
, t_mat
*m
, real
*time
,
158 int maxiter
, int nrandom
,
160 const char *conv
, output_env_t oenv
)
163 real ecur
, enext
, emin
, prob
, enorm
;
164 int i
, j
, iswap
, jswap
, nn
, nuphill
= 0;
170 fprintf(stderr
, "Can not do Monte Carlo optimization with a non-square matrix.\n");
173 printf("\nDoing Monte Carlo optimization to find the smoothest trajectory\n");
174 printf("by reordering the frames to minimize the path between the two structures\n");
175 printf("that have the largest pairwise RMSD.\n");
178 enorm
= m
->mat
[0][0];
179 for (i
= 0; (i
< m
->n1
); i
++)
181 for (j
= 0; (j
< m
->nn
); j
++)
183 if (m
->mat
[i
][j
] > enorm
)
185 enorm
= m
->mat
[i
][j
];
191 if ((iswap
== -1) || (jswap
== -1))
193 fprintf(stderr
, "Matrix contains identical values in all fields\n");
196 swap_rows(m
, 0, iswap
);
197 swap_rows(m
, m
->n1
-1, jswap
);
198 emin
= ecur
= mat_energy(m
);
199 printf("Largest distance %g between %d and %d. Energy: %g.\n",
200 enorm
, iswap
, jswap
, emin
);
202 rng
= gmx_rng_init(seed
);
205 /* Initiate and store global minimum */
206 minimum
= init_mat(nn
, m
->b1D
);
208 copy_t_mat(minimum
, m
);
212 fp
= xvgropen(conv
, "Convergence of the MC optimization",
213 "Energy", "Step", oenv
);
215 for (i
= 0; (i
< maxiter
); i
++)
217 /* Generate new swapping candidates */
220 iswap
= 1+(nn
-2)*gmx_rng_uniform_real(rng
);
221 jswap
= 1+(nn
-2)*gmx_rng_uniform_real(rng
);
223 while ((iswap
== jswap
) || (iswap
>= nn
-1) || (jswap
>= nn
-1));
225 /* Apply swap and compute energy */
226 swap_rows(m
, iswap
, jswap
);
227 enext
= mat_energy(m
);
229 /* Compute probability */
231 if ((enext
< ecur
) || (i
< nrandom
))
236 /* Store global minimum */
237 copy_t_mat(minimum
, m
);
243 /* Try Monte Carlo step */
244 prob
= exp(-(enext
-ecur
)/(enorm
*kT
));
247 if ((prob
== 1) || (gmx_rng_uniform_real(rng
) < prob
))
254 fprintf(log
, "Iter: %d Swapped %4d and %4d (energy: %g prob: %g)\n",
255 i
, iswap
, jswap
, enext
, prob
);
258 fprintf(fp
, "%6d %10g\n", i
, enext
);
264 swap_rows(m
, jswap
, iswap
);
267 fprintf(log
, "%d uphill steps were taken during optimization\n",
270 /* Now swap the matrix to get it into global minimum mode */
271 copy_t_mat(m
, minimum
);
273 fprintf(log
, "Global minimum energy %g\n", mat_energy(minimum
));
274 fprintf(log
, "Global minimum energy %g\n", mat_energy(m
));
275 fprintf(log
, "Swapped time and frame indices and RMSD to next neighbor:\n");
276 for (i
= 0; (i
< m
->nn
); i
++)
278 fprintf(log
, "%10g %5d %10g\n",
281 (i
< m
->nn
-1) ? m
->mat
[m
->m_ind
[i
]][m
->m_ind
[i
+1]] : 0);
290 static void calc_dist(int nind
, rvec x
[], real
**d
)
296 for (i
= 0; (i
< nind
-1); i
++)
299 for (j
= i
+1; (j
< nind
); j
++)
301 /* Should use pbc_dx when analysing multiple molecueles,
302 * but the box is not stored for every frame.
304 rvec_sub(xi
, x
[j
], dx
);
310 static real
rms_dist(int isize
, real
**d
, real
**d_r
)
316 for (i
= 0; (i
< isize
-1); i
++)
318 for (j
= i
+1; (j
< isize
); j
++)
320 r
= d
[i
][j
]-d_r
[i
][j
];
324 r2
/= (isize
*(isize
-1))/2;
329 static int rms_dist_comp(const void *a
, const void *b
)
336 if (da
->dist
- db
->dist
< 0)
340 else if (da
->dist
- db
->dist
> 0)
347 static int clust_id_comp(const void *a
, const void *b
)
354 return da
->clust
- db
->clust
;
357 static int nrnb_comp(const void *a
, const void *b
)
364 /* return the b-a, we want highest first */
365 return db
->nr
- da
->nr
;
368 void gather(t_mat
*m
, real cutoff
, t_clusters
*clust
)
372 int i
, j
, k
, nn
, cid
, n1
, diff
;
375 /* First we sort the entries in the RMSD matrix */
379 for (i
= k
= 0; (i
< n1
); i
++)
381 for (j
= i
+1; (j
< n1
); j
++, k
++)
385 d
[k
].dist
= m
->mat
[i
][j
];
390 gmx_incons("gather algortihm");
392 qsort(d
, nn
, sizeof(d
[0]), rms_dist_comp
);
394 /* Now we make a cluster index for all of the conformations */
397 /* Now we check the closest structures, and equalize their cluster numbers */
398 fprintf(stderr
, "Linking structures ");
401 fprintf(stderr
, "*");
403 for (k
= 0; (k
< nn
) && (d
[k
].dist
< cutoff
); k
++)
405 diff
= c
[d
[k
].j
].clust
- c
[d
[k
].i
].clust
;
411 c
[d
[k
].j
].clust
= c
[d
[k
].i
].clust
;
415 c
[d
[k
].i
].clust
= c
[d
[k
].j
].clust
;
421 fprintf(stderr
, "\nSorting and renumbering clusters\n");
422 /* Sort on cluster number */
423 qsort(c
, n1
, sizeof(c
[0]), clust_id_comp
);
425 /* Renumber clusters */
427 for (k
= 1; k
< n1
; k
++)
429 if (c
[k
].clust
!= c
[k
-1].clust
)
442 for (k
= 0; (k
< n1
); k
++)
444 fprintf(debug
, "Cluster index for conformation %d: %d\n",
445 c
[k
].conf
, c
[k
].clust
);
449 for (k
= 0; k
< n1
; k
++)
451 clust
->cl
[c
[k
].conf
] = c
[k
].clust
;
458 gmx_bool
jp_same(int **nnb
, int i
, int j
, int P
)
464 for (k
= 0; nnb
[i
][k
] >= 0; k
++)
466 bIn
= bIn
|| (nnb
[i
][k
] == j
);
474 for (k
= 0; nnb
[j
][k
] >= 0; k
++)
476 bIn
= bIn
|| (nnb
[j
][k
] == i
);
484 for (ii
= 0; nnb
[i
][ii
] >= 0; ii
++)
486 for (jj
= 0; nnb
[j
][jj
] >= 0; jj
++)
488 if ((nnb
[i
][ii
] == nnb
[j
][jj
]) && (nnb
[i
][ii
] != -1))
498 static void jarvis_patrick(int n1
, real
**mat
, int M
, int P
,
499 real rmsdcut
, t_clusters
*clust
)
504 int i
, j
, k
, cid
, diff
, max
;
513 /* First we sort the entries in the RMSD matrix row by row.
514 * This gives us the nearest neighbor list.
518 for (i
= 0; (i
< n1
); i
++)
520 for (j
= 0; (j
< n1
); j
++)
523 row
[j
].dist
= mat
[i
][j
];
525 qsort(row
, n1
, sizeof(row
[0]), rms_dist_comp
);
528 /* Put the M nearest neighbors in the list */
530 for (j
= k
= 0; (k
< M
) && (j
< n1
) && (mat
[i
][row
[j
].j
] < rmsdcut
); j
++)
534 nnb
[i
][k
] = row
[j
].j
;
542 /* Put all neighbors nearer than rmsdcut in the list */
545 for (j
= 0; (j
< n1
) && (mat
[i
][row
[j
].j
] < rmsdcut
); j
++)
554 nnb
[i
][k
] = row
[j
].j
;
560 srenew(nnb
[i
], max
+1);
568 fprintf(debug
, "Nearest neighborlist. M = %d, P = %d\n", M
, P
);
569 for (i
= 0; (i
< n1
); i
++)
571 fprintf(debug
, "i:%5d nbs:", i
);
572 for (j
= 0; nnb
[i
][j
] >= 0; j
++)
574 fprintf(debug
, "%5d[%5.3f]", nnb
[i
][j
], mat
[i
][nnb
[i
][j
]]);
576 fprintf(debug
, "\n");
581 fprintf(stderr
, "Linking structures ");
582 /* Use mcpy for temporary storage of booleans */
583 mcpy
= mk_matrix(n1
, n1
, FALSE
);
584 for (i
= 0; i
< n1
; i
++)
586 for (j
= i
+1; j
< n1
; j
++)
588 mcpy
[i
][j
] = jp_same(nnb
, i
, j
, P
);
593 fprintf(stderr
, "*");
595 for (i
= 0; i
< n1
; i
++)
597 for (j
= i
+1; j
< n1
; j
++)
601 diff
= c
[j
].clust
- c
[i
].clust
;
607 c
[j
].clust
= c
[i
].clust
;
611 c
[i
].clust
= c
[j
].clust
;
620 fprintf(stderr
, "\nSorting and renumbering clusters\n");
621 /* Sort on cluster number */
622 qsort(c
, n1
, sizeof(c
[0]), clust_id_comp
);
624 /* Renumber clusters */
626 for (k
= 1; k
< n1
; k
++)
628 if (c
[k
].clust
!= c
[k
-1].clust
)
640 for (k
= 0; k
< n1
; k
++)
642 clust
->cl
[c
[k
].conf
] = c
[k
].clust
;
646 for (k
= 0; (k
< n1
); k
++)
648 fprintf(debug
, "Cluster index for conformation %d: %d\n",
649 c
[k
].conf
, c
[k
].clust
);
653 /* Again, I don't see the point in this... (AF) */
654 /* for(i=0; (i<n1); i++) { */
655 /* for(j=0; (j<n1); j++) */
656 /* mcpy[c[i].conf][c[j].conf] = mat[i][j]; */
658 /* for(i=0; (i<n1); i++) { */
659 /* for(j=0; (j<n1); j++) */
660 /* mat[i][j] = mcpy[i][j]; */
662 done_matrix(n1
, &mcpy
);
665 for (i
= 0; (i
< n1
); i
++)
672 static void dump_nnb (FILE *fp
, const char *title
, int n1
, t_nnb
*nnb
)
676 /* dump neighbor list */
677 fprintf(fp
, "%s", title
);
678 for (i
= 0; (i
< n1
); i
++)
680 fprintf(fp
, "i:%5d #:%5d nbs:", i
, nnb
[i
].nr
);
681 for (j
= 0; j
< nnb
[i
].nr
; j
++)
683 fprintf(fp
, "%5d", nnb
[i
].nb
[j
]);
689 static void gromos(int n1
, real
**mat
, real rmsdcut
, t_clusters
*clust
)
693 int i
, j
, k
, j1
, max
;
695 /* Put all neighbors nearer than rmsdcut in the list */
696 fprintf(stderr
, "Making list of neighbors within cutoff ");
699 for (i
= 0; (i
< n1
); i
++)
703 /* put all neighbors within cut-off in list */
704 for (j
= 0; j
< n1
; j
++)
706 if (mat
[i
][j
] < rmsdcut
)
711 srenew(nnb
[i
].nb
, max
);
717 /* store nr of neighbors, we'll need that */
719 if (i
%(1+n1
/100) == 0)
721 fprintf(stderr
, "%3d%%\b\b\b\b", (i
*100+1)/n1
);
724 fprintf(stderr
, "%3d%%\n", 100);
727 /* sort neighbor list on number of neighbors, largest first */
728 qsort(nnb
, n1
, sizeof(nnb
[0]), nrnb_comp
);
732 dump_nnb(debug
, "Nearest neighborlist after sort.\n", n1
, nnb
);
735 /* turn first structure with all its neighbors (largest) into cluster
736 remove them from pool of structures and repeat for all remaining */
737 fprintf(stderr
, "Finding clusters %4d", 0);
738 /* cluster id's start at 1: */
742 /* set cluster id (k) for first item in neighborlist */
743 for (j
= 0; j
< nnb
[0].nr
; j
++)
745 clust
->cl
[nnb
[0].nb
[j
]] = k
;
751 /* adjust number of neighbors for others, taking removals into account: */
752 for (i
= 1; i
< n1
&& nnb
[i
].nr
; i
++)
755 for (j
= 0; j
< nnb
[i
].nr
; j
++)
757 /* if this neighbor wasn't removed */
758 if (clust
->cl
[nnb
[i
].nb
[j
]] == 0)
760 /* shift the rest (j1<=j) */
761 nnb
[i
].nb
[j1
] = nnb
[i
].nb
[j
];
766 /* now j1 is the new number of neighbors */
769 /* sort again on nnb[].nr, because we have new # neighbors: */
770 /* but we only need to sort upto i, i.e. when nnb[].nr>0 */
771 qsort(nnb
, i
, sizeof(nnb
[0]), nrnb_comp
);
773 fprintf(stderr
, "\b\b\b\b%4d", k
);
777 fprintf(stderr
, "\n");
781 fprintf(debug
, "Clusters (%d):\n", k
);
782 for (i
= 0; i
< n1
; i
++)
784 fprintf(debug
, " %3d", clust
->cl
[i
]);
786 fprintf(debug
, "\n");
792 rvec
**read_whole_trj(const char *fn
, int isize
, atom_id index
[], int skip
,
793 int *nframe
, real
**time
, const output_env_t oenv
, gmx_bool bPBC
, gmx_rmpbc_t gpbc
)
798 int i
, i0
, j
, max_nf
;
806 natom
= read_first_x(oenv
, &status
, fn
, &t
, &x
, box
);
813 gmx_rmpbc(gpbc
, natom
, box
, x
);
819 srenew(*time
, max_nf
);
824 /* Store only the interesting atoms */
825 for (j
= 0; (j
< isize
); j
++)
827 copy_rvec(x
[index
[j
]], xx
[i0
][j
]);
834 while (read_next_x(oenv
, status
, &t
, x
, box
));
835 fprintf(stderr
, "Allocated %lu bytes for frames\n",
836 (unsigned long) (max_nf
*isize
*sizeof(**xx
)));
837 fprintf(stderr
, "Read %d frames from trajectory %s\n", i0
, fn
);
844 static int plot_clusters(int nf
, real
**mat
, t_clusters
*clust
,
847 int i
, j
, ncluster
, ci
;
848 int *cl_id
, *nstruct
, *strind
;
853 for (i
= 0; i
< nf
; i
++)
856 cl_id
[i
] = clust
->cl
[i
];
860 for (i
= 0; i
< nf
; i
++)
862 if (nstruct
[i
] >= minstruct
)
865 for (j
= 0; (j
< nf
); j
++)
869 strind
[j
] = ncluster
;
875 fprintf(stderr
, "There are %d clusters with at least %d conformations\n",
876 ncluster
, minstruct
);
878 for (i
= 0; (i
< nf
); i
++)
881 for (j
= 0; j
< i
; j
++)
883 if ((ci
== cl_id
[j
]) && (nstruct
[ci
] >= minstruct
))
885 /* color different clusters with different colors, as long as
886 we don't run out of colors */
887 mat
[i
][j
] = strind
[i
];
902 static void mark_clusters(int nf
, real
**mat
, real val
, t_clusters
*clust
)
906 for (i
= 0; i
< nf
; i
++)
908 for (j
= 0; j
< i
; j
++)
910 if (clust
->cl
[i
] == clust
->cl
[j
])
922 static char *parse_filename(const char *fn
, int maxnr
)
931 gmx_fatal(FARGS
, "will not number filename %s containing '%c'", fn
, '%');
933 /* number of digits needed in numbering */
934 i
= (int)(log(maxnr
)/log(10)) + 1;
935 /* split fn and ext */
936 ext
= strrchr(fn
, '.');
939 gmx_fatal(FARGS
, "cannot separate extension in filename %s", fn
);
942 /* insert e.g. '%03d' between fn and ext */
943 sprintf(buf
, "%s%%0%dd.%s", fn
, i
, ext
);
944 snew(fnout
, strlen(buf
)+1);
950 static void ana_trans(t_clusters
*clust
, int nf
,
951 const char *transfn
, const char *ntransfn
, FILE *log
,
952 t_rgb rlo
, t_rgb rhi
, const output_env_t oenv
)
957 int i
, ntranst
, maxtrans
;
960 snew(ntrans
, clust
->ncl
);
961 snew(trans
, clust
->ncl
);
962 snew(axis
, clust
->ncl
);
963 for (i
= 0; i
< clust
->ncl
; i
++)
966 snew(trans
[i
], clust
->ncl
);
970 for (i
= 1; i
< nf
; i
++)
972 if (clust
->cl
[i
] != clust
->cl
[i
-1])
975 ntrans
[clust
->cl
[i
-1]-1]++;
976 ntrans
[clust
->cl
[i
]-1]++;
977 trans
[clust
->cl
[i
-1]-1][clust
->cl
[i
]-1]++;
978 maxtrans
= max(maxtrans
, trans
[clust
->cl
[i
]-1][clust
->cl
[i
-1]-1]);
981 ffprintf_dd(stderr
, log
, buf
, "Counted %d transitions in total, "
982 "max %d between two specific clusters\n", ntranst
, maxtrans
);
985 fp
= gmx_ffopen(transfn
, "w");
986 i
= min(maxtrans
+1, 80);
987 write_xpm(fp
, 0, "Cluster Transitions", "# transitions",
988 "from cluster", "to cluster",
989 clust
->ncl
, clust
->ncl
, axis
, axis
, trans
,
990 0, maxtrans
, rlo
, rhi
, &i
);
995 fp
= xvgropen(ntransfn
, "Cluster Transitions", "Cluster #", "# transitions",
997 for (i
= 0; i
< clust
->ncl
; i
++)
999 fprintf(fp
, "%5d %5d\n", i
+1, ntrans
[i
]);
1004 for (i
= 0; i
< clust
->ncl
; i
++)
1012 static void analyze_clusters(int nf
, t_clusters
*clust
, real
**rmsd
,
1013 int natom
, t_atoms
*atoms
, rvec
*xtps
,
1014 real
*mass
, rvec
**xx
, real
*time
,
1015 int ifsize
, atom_id
*fitidx
,
1016 int iosize
, atom_id
*outidx
,
1017 const char *trxfn
, const char *sizefn
,
1018 const char *transfn
, const char *ntransfn
,
1019 const char *clustidfn
, gmx_bool bAverage
,
1020 int write_ncl
, int write_nst
, real rmsmin
,
1021 gmx_bool bFit
, FILE *log
, t_rgb rlo
, t_rgb rhi
,
1022 const output_env_t oenv
)
1025 char buf
[STRLEN
], buf1
[40], buf2
[40], buf3
[40], *trxsfn
;
1026 t_trxstatus
*trxout
= NULL
;
1027 t_trxstatus
*trxsout
= NULL
;
1028 int i
, i1
, cl
, nstr
, *structure
, first
= 0, midstr
;
1029 gmx_bool
*bWrite
= NULL
;
1030 real r
, clrmsd
, midrmsd
;
1036 ffprintf_d(stderr
, log
, buf
, "\nFound %d clusters\n\n", clust
->ncl
);
1040 /* do we write all structures? */
1043 trxsfn
= parse_filename(trxfn
, max(write_ncl
, clust
->ncl
));
1046 ffprintf_ss(stderr
, log
, buf
, "Writing %s structure for each cluster to %s\n",
1047 bAverage
? "average" : "middle", trxfn
);
1050 /* find out what we want to tell the user:
1051 Writing [all structures|structures with rmsd > %g] for
1052 {all|first %d} clusters {with more than %d structures} to %s */
1055 sprintf(buf1
, "structures with rmsd > %g", rmsmin
);
1059 sprintf(buf1
, "all structures");
1061 buf2
[0] = buf3
[0] = '\0';
1062 if (write_ncl
>= clust
->ncl
)
1066 sprintf(buf2
, "all ");
1071 sprintf(buf2
, "the first %d ", write_ncl
);
1075 sprintf(buf3
, " with more than %d structures", write_nst
);
1077 sprintf(buf
, "Writing %s for %sclusters%s to %s\n", buf1
, buf2
, buf3
, trxsfn
);
1078 ffprintf(stderr
, log
, buf
);
1081 /* Prepare a reference structure for the orientation of the clusters */
1084 reset_x(ifsize
, fitidx
, natom
, NULL
, xtps
, mass
);
1086 trxout
= open_trx(trxfn
, "w");
1087 /* Calculate the average structure in each cluster, *
1088 * all structures are fitted to the first struture of the cluster */
1092 if (transfn
|| ntransfn
)
1094 ana_trans(clust
, nf
, transfn
, ntransfn
, log
, rlo
, rhi
, oenv
);
1099 fp
= xvgropen(clustidfn
, "Clusters", output_env_get_xvgr_tlabel(oenv
), "Cluster #", oenv
);
1100 if (output_env_get_print_xvgr_codes(oenv
))
1102 fprintf(fp
, "@ s0 symbol 2\n");
1103 fprintf(fp
, "@ s0 symbol size 0.2\n");
1104 fprintf(fp
, "@ s0 linestyle 0\n");
1106 for (i
= 0; i
< nf
; i
++)
1108 fprintf(fp
, "%8g %8d\n", time
[i
], clust
->cl
[i
]);
1114 fp
= xvgropen(sizefn
, "Cluster Sizes", "Cluster #", "# Structures", oenv
);
1115 if (output_env_get_print_xvgr_codes(oenv
))
1117 fprintf(fp
, "@g%d type %s\n", 0, "bar");
1120 snew(structure
, nf
);
1121 fprintf(log
, "\n%3s | %3s %4s | %6s %4s | cluster members\n",
1122 "cl.", "#st", "rmsd", "middle", "rmsd");
1123 for (cl
= 1; cl
<= clust
->ncl
; cl
++)
1125 /* prepare structures (fit, middle, average) */
1128 for (i
= 0; i
< natom
; i
++)
1134 for (i1
= 0; i1
< nf
; i1
++)
1136 if (clust
->cl
[i1
] == cl
)
1138 structure
[nstr
] = i1
;
1140 if (trxfn
&& (bAverage
|| write_ncl
) )
1144 reset_x(ifsize
, fitidx
, natom
, NULL
, xx
[i1
], mass
);
1152 do_fit(natom
, mass
, xx
[first
], xx
[i1
]);
1156 for (i
= 0; i
< natom
; i
++)
1158 rvec_inc(xav
[i
], xx
[i1
][i
]);
1166 fprintf(fp
, "%8d %8d\n", cl
, nstr
);
1171 for (i1
= 0; i1
< nstr
; i1
++)
1176 for (i
= 0; i
< nstr
; i
++)
1180 r
+= rmsd
[structure
[i
]][structure
[i1
]];
1184 r
+= rmsd
[structure
[i1
]][structure
[i
]];
1191 midstr
= structure
[i1
];
1198 /* dump cluster info to logfile */
1201 sprintf(buf1
, "%6.3f", clrmsd
);
1206 sprintf(buf2
, "%5.3f", midrmsd
);
1214 sprintf(buf1
, "%5s", "");
1215 sprintf(buf2
, "%5s", "");
1217 fprintf(log
, "%3d | %3d %s | %6g%s |", cl
, nstr
, buf1
, time
[midstr
], buf2
);
1218 for (i
= 0; i
< nstr
; i
++)
1220 if ((i
% 7 == 0) && i
)
1222 sprintf(buf
, "\n%3s | %3s %4s | %6s %4s |", "", "", "", "", "");
1229 fprintf(log
, "%s %6g", buf
, time
[i1
]);
1233 /* write structures to trajectory file(s) */
1238 for (i
= 0; i
< nstr
; i
++)
1243 if (cl
< write_ncl
+1 && nstr
> write_nst
)
1245 /* Dump all structures for this cluster */
1246 /* generate numbered filename (there is a %d in trxfn!) */
1247 sprintf(buf
, trxsfn
, cl
);
1248 trxsout
= open_trx(buf
, "w");
1249 for (i
= 0; i
< nstr
; i
++)
1254 for (i1
= 0; i1
< i
&& bWrite
[i
]; i1
++)
1258 bWrite
[i
] = rmsd
[structure
[i1
]][structure
[i
]] > rmsmin
;
1264 write_trx(trxsout
, iosize
, outidx
, atoms
, i
, time
[structure
[i
]], zerobox
,
1265 xx
[structure
[i
]], NULL
, NULL
);
1270 /* Dump the average structure for this cluster */
1273 for (i
= 0; i
< natom
; i
++)
1275 svmul(1.0/nstr
, xav
[i
], xav
[i
]);
1280 for (i
= 0; i
< natom
; i
++)
1282 copy_rvec(xx
[midstr
][i
], xav
[i
]);
1286 reset_x(ifsize
, fitidx
, natom
, NULL
, xav
, mass
);
1291 do_fit(natom
, mass
, xtps
, xav
);
1294 write_trx(trxout
, iosize
, outidx
, atoms
, cl
, time
[midstr
], zerobox
, xav
, NULL
, NULL
);
1314 static void convert_mat(t_matrix
*mat
, t_mat
*rms
)
1319 matrix2real(mat
, rms
->mat
);
1320 /* free input xpm matrix data */
1321 for (i
= 0; i
< mat
->nx
; i
++)
1323 sfree(mat
->matrix
[i
]);
1327 for (i
= 0; i
< mat
->nx
; i
++)
1329 for (j
= i
; j
< mat
->nx
; j
++)
1331 rms
->sumrms
+= rms
->mat
[i
][j
];
1332 rms
->maxrms
= max(rms
->maxrms
, rms
->mat
[i
][j
]);
1335 rms
->minrms
= min(rms
->minrms
, rms
->mat
[i
][j
]);
1342 int gmx_cluster(int argc
, char *argv
[])
1344 const char *desc
[] = {
1345 "[THISMODULE] can cluster structures using several different methods.",
1346 "Distances between structures can be determined from a trajectory",
1347 "or read from an [TT].xpm[tt] matrix file with the [TT]-dm[tt] option.",
1348 "RMS deviation after fitting or RMS deviation of atom-pair distances",
1349 "can be used to define the distance between structures.[PAR]",
1351 "single linkage: add a structure to a cluster when its distance to any",
1352 "element of the cluster is less than [TT]cutoff[tt].[PAR]",
1354 "Jarvis Patrick: add a structure to a cluster when this structure",
1355 "and a structure in the cluster have each other as neighbors and",
1356 "they have a least [TT]P[tt] neighbors in common. The neighbors",
1357 "of a structure are the M closest structures or all structures within",
1358 "[TT]cutoff[tt].[PAR]",
1360 "Monte Carlo: reorder the RMSD matrix using Monte Carlo such that",
1361 "the order of the frames is using the smallest possible increments.",
1362 "With this it is possible to make a smooth animation going from one",
1363 "structure to another with the largest possible (e.g.) RMSD between",
1364 "them, however the intermediate steps should be as small as possible.",
1365 "Applications could be to visualize a potential of mean force",
1366 "ensemble of simulations or a pulling simulation. Obviously the user",
1367 "has to prepare the trajectory well (e.g. by not superimposing frames).",
1368 "The final result can be inspect visually by looking at the matrix",
1369 "[TT].xpm[tt] file, which should vary smoothly from bottom to top.[PAR]",
1371 "diagonalization: diagonalize the RMSD matrix.[PAR]",
1373 "gromos: use algorithm as described in Daura [IT]et al.[it]",
1374 "([IT]Angew. Chem. Int. Ed.[it] [BB]1999[bb], [IT]38[it], pp 236-240).",
1375 "Count number of neighbors using cut-off, take structure with",
1376 "largest number of neighbors with all its neighbors as cluster",
1377 "and eliminate it from the pool of clusters. Repeat for remaining",
1378 "structures in pool.[PAR]",
1380 "When the clustering algorithm assigns each structure to exactly one",
1381 "cluster (single linkage, Jarvis Patrick and gromos) and a trajectory",
1382 "file is supplied, the structure with",
1383 "the smallest average distance to the others or the average structure",
1384 "or all structures for each cluster will be written to a trajectory",
1385 "file. When writing all structures, separate numbered files are made",
1386 "for each cluster.[PAR]",
1388 "Two output files are always written:[BR]",
1389 "[TT]-o[tt] writes the RMSD values in the upper left half of the matrix",
1390 "and a graphical depiction of the clusters in the lower right half",
1391 "When [TT]-minstruct[tt] = 1 the graphical depiction is black",
1392 "when two structures are in the same cluster.",
1393 "When [TT]-minstruct[tt] > 1 different colors will be used for each",
1395 "[TT]-g[tt] writes information on the options used and a detailed list",
1396 "of all clusters and their members.[PAR]",
1398 "Additionally, a number of optional output files can be written:[BR]",
1399 "[TT]-dist[tt] writes the RMSD distribution.[BR]",
1400 "[TT]-ev[tt] writes the eigenvectors of the RMSD matrix",
1401 "diagonalization.[BR]",
1402 "[TT]-sz[tt] writes the cluster sizes.[BR]",
1403 "[TT]-tr[tt] writes a matrix of the number transitions between",
1404 "cluster pairs.[BR]",
1405 "[TT]-ntr[tt] writes the total number of transitions to or from",
1406 "each cluster.[BR]",
1407 "[TT]-clid[tt] writes the cluster number as a function of time.[BR]",
1408 "[TT]-cl[tt] writes average (with option [TT]-av[tt]) or central",
1409 "structure of each cluster or writes numbered files with cluster members",
1410 "for a selected set of clusters (with option [TT]-wcl[tt], depends on",
1411 "[TT]-nst[tt] and [TT]-rmsmin[tt]). The center of a cluster is the",
1412 "structure with the smallest average RMSD from all other structures",
1413 "of the cluster.[BR]",
1417 int nf
, i
, i1
, i2
, j
;
1418 gmx_int64_t nrms
= 0;
1421 rvec
*xtps
, *usextps
, *x1
, **xx
= NULL
;
1422 const char *fn
, *trx_out_fn
;
1424 t_mat
*rms
, *orig
= NULL
;
1429 t_matrix
*readmat
= NULL
;
1432 int isize
= 0, ifsize
= 0, iosize
= 0;
1433 atom_id
*index
= NULL
, *fitidx
, *outidx
;
1435 real rmsd
, **d1
, **d2
, *time
= NULL
, time_invfac
, *mass
= NULL
;
1436 char buf
[STRLEN
], buf1
[80], title
[STRLEN
];
1437 gmx_bool bAnalyze
, bUseRmsdCut
, bJP_RMSD
= FALSE
, bReadMat
, bReadTraj
, bPBC
= TRUE
;
1439 int method
, ncluster
= 0;
1440 static const char *methodname
[] = {
1441 NULL
, "linkage", "jarvis-patrick", "monte-carlo",
1442 "diagonalization", "gromos", NULL
1445 m_null
, m_linkage
, m_jarvis_patrick
,
1446 m_monte_carlo
, m_diagonalize
, m_gromos
, m_nr
1448 /* Set colors for plotting: white = zero RMS, black = maximum */
1449 static t_rgb rlo_top
= { 1.0, 1.0, 1.0 };
1450 static t_rgb rhi_top
= { 0.0, 0.0, 0.0 };
1451 static t_rgb rlo_bot
= { 1.0, 1.0, 1.0 };
1452 static t_rgb rhi_bot
= { 0.0, 0.0, 1.0 };
1453 static int nlevels
= 40, skip
= 1;
1454 static real scalemax
= -1.0, rmsdcut
= 0.1, rmsmin
= 0.0;
1455 gmx_bool bRMSdist
= FALSE
, bBinary
= FALSE
, bAverage
= FALSE
, bFit
= TRUE
;
1456 static int niter
= 10000, nrandom
= 0, seed
= 1993, write_ncl
= 0, write_nst
= 1, minstruct
= 1;
1457 static real kT
= 1e-3;
1458 static int M
= 10, P
= 3;
1460 gmx_rmpbc_t gpbc
= NULL
;
1463 { "-dista", FALSE
, etBOOL
, {&bRMSdist
},
1464 "Use RMSD of distances instead of RMS deviation" },
1465 { "-nlevels", FALSE
, etINT
, {&nlevels
},
1466 "Discretize RMSD matrix in this number of levels" },
1467 { "-cutoff", FALSE
, etREAL
, {&rmsdcut
},
1468 "RMSD cut-off (nm) for two structures to be neighbor" },
1469 { "-fit", FALSE
, etBOOL
, {&bFit
},
1470 "Use least squares fitting before RMSD calculation" },
1471 { "-max", FALSE
, etREAL
, {&scalemax
},
1472 "Maximum level in RMSD matrix" },
1473 { "-skip", FALSE
, etINT
, {&skip
},
1474 "Only analyze every nr-th frame" },
1475 { "-av", FALSE
, etBOOL
, {&bAverage
},
1476 "Write average iso middle structure for each cluster" },
1477 { "-wcl", FALSE
, etINT
, {&write_ncl
},
1478 "Write the structures for this number of clusters to numbered files" },
1479 { "-nst", FALSE
, etINT
, {&write_nst
},
1480 "Only write all structures if more than this number of structures per cluster" },
1481 { "-rmsmin", FALSE
, etREAL
, {&rmsmin
},
1482 "minimum rms difference with rest of cluster for writing structures" },
1483 { "-method", FALSE
, etENUM
, {methodname
},
1484 "Method for cluster determination" },
1485 { "-minstruct", FALSE
, etINT
, {&minstruct
},
1486 "Minimum number of structures in cluster for coloring in the [TT].xpm[tt] file" },
1487 { "-binary", FALSE
, etBOOL
, {&bBinary
},
1488 "Treat the RMSD matrix as consisting of 0 and 1, where the cut-off "
1489 "is given by [TT]-cutoff[tt]" },
1490 { "-M", FALSE
, etINT
, {&M
},
1491 "Number of nearest neighbors considered for Jarvis-Patrick algorithm, "
1492 "0 is use cutoff" },
1493 { "-P", FALSE
, etINT
, {&P
},
1494 "Number of identical nearest neighbors required to form a cluster" },
1495 { "-seed", FALSE
, etINT
, {&seed
},
1496 "Random number seed for Monte Carlo clustering algorithm: <= 0 means generate" },
1497 { "-niter", FALSE
, etINT
, {&niter
},
1498 "Number of iterations for MC" },
1499 { "-nrandom", FALSE
, etINT
, {&nrandom
},
1500 "The first iterations for MC may be done complete random, to shuffle the frames" },
1501 { "-kT", FALSE
, etREAL
, {&kT
},
1502 "Boltzmann weighting factor for Monte Carlo optimization "
1503 "(zero turns off uphill steps)" },
1504 { "-pbc", FALSE
, etBOOL
,
1505 { &bPBC
}, "PBC check" }
1508 { efTRX
, "-f", NULL
, ffOPTRD
},
1509 { efTPS
, "-s", NULL
, ffOPTRD
},
1510 { efNDX
, NULL
, NULL
, ffOPTRD
},
1511 { efXPM
, "-dm", "rmsd", ffOPTRD
},
1512 { efXPM
, "-om", "rmsd-raw", ffWRITE
},
1513 { efXPM
, "-o", "rmsd-clust", ffWRITE
},
1514 { efLOG
, "-g", "cluster", ffWRITE
},
1515 { efXVG
, "-dist", "rmsd-dist", ffOPTWR
},
1516 { efXVG
, "-ev", "rmsd-eig", ffOPTWR
},
1517 { efXVG
, "-conv", "mc-conv", ffOPTWR
},
1518 { efXVG
, "-sz", "clust-size", ffOPTWR
},
1519 { efXPM
, "-tr", "clust-trans", ffOPTWR
},
1520 { efXVG
, "-ntr", "clust-trans", ffOPTWR
},
1521 { efXVG
, "-clid", "clust-id.xvg", ffOPTWR
},
1522 { efTRX
, "-cl", "clusters.pdb", ffOPTWR
}
1524 #define NFILE asize(fnm)
1526 if (!parse_common_args(&argc
, argv
,
1527 PCA_CAN_VIEW
| PCA_CAN_TIME
| PCA_TIME_UNIT
| PCA_BE_NICE
,
1528 NFILE
, fnm
, asize(pa
), pa
, asize(desc
), desc
, 0, NULL
,
1535 bReadMat
= opt2bSet("-dm", NFILE
, fnm
);
1536 bReadTraj
= opt2bSet("-f", NFILE
, fnm
) || !bReadMat
;
1537 if (opt2parg_bSet("-av", asize(pa
), pa
) ||
1538 opt2parg_bSet("-wcl", asize(pa
), pa
) ||
1539 opt2parg_bSet("-nst", asize(pa
), pa
) ||
1540 opt2parg_bSet("-rmsmin", asize(pa
), pa
) ||
1541 opt2bSet("-cl", NFILE
, fnm
) )
1543 trx_out_fn
= opt2fn("-cl", NFILE
, fnm
);
1549 if (bReadMat
&& output_env_get_time_factor(oenv
) != 1)
1552 "\nWarning: assuming the time unit in %s is %s\n",
1553 opt2fn("-dm", NFILE
, fnm
), output_env_get_time_unit(oenv
));
1555 if (trx_out_fn
&& !bReadTraj
)
1557 fprintf(stderr
, "\nWarning: "
1558 "cannot write cluster structures without reading trajectory\n"
1559 " ignoring option -cl %s\n", trx_out_fn
);
1563 while (method
< m_nr
&& gmx_strcasecmp(methodname
[0], methodname
[method
]) != 0)
1569 gmx_fatal(FARGS
, "Invalid method");
1572 bAnalyze
= (method
== m_linkage
|| method
== m_jarvis_patrick
||
1573 method
== m_gromos
);
1576 log
= ftp2FILE(efLOG
, NFILE
, fnm
, "w");
1578 fprintf(stderr
, "Using %s method for clustering\n", methodname
[0]);
1579 fprintf(log
, "Using %s method for clustering\n", methodname
[0]);
1581 /* check input and write parameters to log file */
1582 bUseRmsdCut
= FALSE
;
1583 if (method
== m_jarvis_patrick
)
1585 bJP_RMSD
= (M
== 0) || opt2parg_bSet("-cutoff", asize(pa
), pa
);
1586 if ((M
< 0) || (M
== 1))
1588 gmx_fatal(FARGS
, "M (%d) must be 0 or larger than 1", M
);
1592 sprintf(buf1
, "Will use P=%d and RMSD cutoff (%g)", P
, rmsdcut
);
1599 gmx_fatal(FARGS
, "Number of neighbors required (P) must be less than M");
1603 sprintf(buf1
, "Will use P=%d, M=%d and RMSD cutoff (%g)", P
, M
, rmsdcut
);
1608 sprintf(buf1
, "Will use P=%d, M=%d", P
, M
);
1611 ffprintf_s(stderr
, log
, buf
, "%s for determining the neighbors\n\n", buf1
);
1613 else /* method != m_jarvis */
1615 bUseRmsdCut
= ( bBinary
|| method
== m_linkage
|| method
== m_gromos
);
1617 if (bUseRmsdCut
&& method
!= m_jarvis_patrick
)
1619 fprintf(log
, "Using RMSD cutoff %g nm\n", rmsdcut
);
1621 if (method
== m_monte_carlo
)
1623 fprintf(log
, "Using %d iterations\n", niter
);
1628 gmx_fatal(FARGS
, "skip (%d) should be >= 1", skip
);
1634 /* don't read mass-database as masses (and top) are not used */
1635 read_tps_conf(ftp2fn(efTPS
, NFILE
, fnm
), buf
, &top
, &ePBC
, &xtps
, NULL
, box
,
1639 gpbc
= gmx_rmpbc_init(&top
.idef
, ePBC
, top
.atoms
.nr
);
1642 fprintf(stderr
, "\nSelect group for least squares fit%s:\n",
1643 bReadMat
? "" : " and RMSD calculation");
1644 get_index(&(top
.atoms
), ftp2fn_null(efNDX
, NFILE
, fnm
),
1645 1, &ifsize
, &fitidx
, &grpname
);
1648 fprintf(stderr
, "\nSelect group for output:\n");
1649 get_index(&(top
.atoms
), ftp2fn_null(efNDX
, NFILE
, fnm
),
1650 1, &iosize
, &outidx
, &grpname
);
1651 /* merge and convert both index groups: */
1652 /* first copy outidx to index. let outidx refer to elements in index */
1653 snew(index
, iosize
);
1655 for (i
= 0; i
< iosize
; i
++)
1657 index
[i
] = outidx
[i
];
1660 /* now lookup elements from fitidx in index, add them if necessary
1661 and also let fitidx refer to elements in index */
1662 for (i
= 0; i
< ifsize
; i
++)
1665 while (j
< isize
&& index
[j
] != fitidx
[i
])
1671 /* slow this way, but doesn't matter much */
1673 srenew(index
, isize
);
1675 index
[j
] = fitidx
[i
];
1679 else /* !trx_out_fn */
1683 for (i
= 0; i
< ifsize
; i
++)
1685 index
[i
] = fitidx
[i
];
1693 /* Loop over first coordinate file */
1694 fn
= opt2fn("-f", NFILE
, fnm
);
1696 xx
= read_whole_trj(fn
, isize
, index
, skip
, &nf
, &time
, oenv
, bPBC
, gpbc
);
1697 output_env_conv_times(oenv
, nf
, time
);
1698 if (!bRMSdist
|| bAnalyze
)
1700 /* Center all frames on zero */
1702 for (i
= 0; i
< ifsize
; i
++)
1704 mass
[fitidx
[i
]] = top
.atoms
.atom
[index
[fitidx
[i
]]].m
;
1708 for (i
= 0; i
< nf
; i
++)
1710 reset_x(ifsize
, fitidx
, isize
, NULL
, xx
[i
], mass
);
1716 gmx_rmpbc_done(gpbc
);
1722 fprintf(stderr
, "Reading rms distance matrix ");
1723 read_xpm_matrix(opt2fn("-dm", NFILE
, fnm
), &readmat
);
1724 fprintf(stderr
, "\n");
1725 if (readmat
[0].nx
!= readmat
[0].ny
)
1727 gmx_fatal(FARGS
, "Matrix (%dx%d) is not square",
1728 readmat
[0].nx
, readmat
[0].ny
);
1730 if (bReadTraj
&& bAnalyze
&& (readmat
[0].nx
!= nf
))
1732 gmx_fatal(FARGS
, "Matrix size (%dx%d) does not match the number of "
1733 "frames (%d)", readmat
[0].nx
, readmat
[0].ny
, nf
);
1738 time
= readmat
[0].axis_x
;
1739 time_invfac
= output_env_get_time_invfactor(oenv
);
1740 for (i
= 0; i
< nf
; i
++)
1742 time
[i
] *= time_invfac
;
1745 rms
= init_mat(readmat
[0].nx
, method
== m_diagonalize
);
1746 convert_mat(&(readmat
[0]), rms
);
1748 nlevels
= readmat
[0].nmap
;
1750 else /* !bReadMat */
1752 rms
= init_mat(nf
, method
== m_diagonalize
);
1753 nrms
= ((gmx_int64_t
)nf
*((gmx_int64_t
)nf
-1))/2;
1756 fprintf(stderr
, "Computing %dx%d RMS deviation matrix\n", nf
, nf
);
1757 /* Initialize work array */
1759 for (i1
= 0; i1
< nf
; i1
++)
1761 for (i2
= i1
+1; i2
< nf
; i2
++)
1763 for (i
= 0; i
< isize
; i
++)
1765 copy_rvec(xx
[i1
][i
], x1
[i
]);
1769 do_fit(isize
, mass
, xx
[i2
], x1
);
1771 rmsd
= rmsdev(isize
, mass
, xx
[i2
], x1
);
1772 set_mat_entry(rms
, i1
, i2
, rmsd
);
1774 nrms
-= (gmx_int64_t
) (nf
-i1
-1);
1775 fprintf(stderr
, "\r# RMSD calculations left: " "%"GMX_PRId64
" ", nrms
);
1781 fprintf(stderr
, "Computing %dx%d RMS distance deviation matrix\n", nf
, nf
);
1783 /* Initiate work arrays */
1786 for (i
= 0; (i
< isize
); i
++)
1791 for (i1
= 0; i1
< nf
; i1
++)
1793 calc_dist(isize
, xx
[i1
], d1
);
1794 for (i2
= i1
+1; (i2
< nf
); i2
++)
1796 calc_dist(isize
, xx
[i2
], d2
);
1797 set_mat_entry(rms
, i1
, i2
, rms_dist(isize
, d1
, d2
));
1800 fprintf(stderr
, "\r# RMSD calculations left: " "%"GMX_PRId64
" ", nrms
);
1802 /* Clean up work arrays */
1803 for (i
= 0; (i
< isize
); i
++)
1811 fprintf(stderr
, "\n\n");
1813 ffprintf_gg(stderr
, log
, buf
, "The RMSD ranges from %g to %g nm\n",
1814 rms
->minrms
, rms
->maxrms
);
1815 ffprintf_g(stderr
, log
, buf
, "Average RMSD is %g\n", 2*rms
->sumrms
/(nf
*(nf
-1)));
1816 ffprintf_d(stderr
, log
, buf
, "Number of structures for matrix %d\n", nf
);
1817 ffprintf_g(stderr
, log
, buf
, "Energy of the matrix is %g.\n", mat_energy(rms
));
1818 if (bUseRmsdCut
&& (rmsdcut
< rms
->minrms
|| rmsdcut
> rms
->maxrms
) )
1820 fprintf(stderr
, "WARNING: rmsd cutoff %g is outside range of rmsd values "
1821 "%g to %g\n", rmsdcut
, rms
->minrms
, rms
->maxrms
);
1823 if (bAnalyze
&& (rmsmin
< rms
->minrms
) )
1825 fprintf(stderr
, "WARNING: rmsd minimum %g is below lowest rmsd value %g\n",
1826 rmsmin
, rms
->minrms
);
1828 if (bAnalyze
&& (rmsmin
> rmsdcut
) )
1830 fprintf(stderr
, "WARNING: rmsd minimum %g is above rmsd cutoff %g\n",
1834 /* Plot the rmsd distribution */
1835 rmsd_distribution(opt2fn("-dist", NFILE
, fnm
), rms
, oenv
);
1839 for (i1
= 0; (i1
< nf
); i1
++)
1841 for (i2
= 0; (i2
< nf
); i2
++)
1843 if (rms
->mat
[i1
][i2
] < rmsdcut
)
1845 rms
->mat
[i1
][i2
] = 0;
1849 rms
->mat
[i1
][i2
] = 1;
1859 /* Now sort the matrix and write it out again */
1860 gather(rms
, rmsdcut
, &clust
);
1863 /* Do a diagonalization */
1864 snew(eigenvalues
, nf
);
1865 snew(eigenvectors
, nf
*nf
);
1866 memcpy(eigenvectors
, rms
->mat
[0], nf
*nf
*sizeof(real
));
1867 eigensolver(eigenvectors
, nf
, 0, nf
, eigenvalues
, rms
->mat
[0]);
1868 sfree(eigenvectors
);
1870 fp
= xvgropen(opt2fn("-ev", NFILE
, fnm
), "RMSD matrix Eigenvalues",
1871 "Eigenvector index", "Eigenvalues (nm\\S2\\N)", oenv
);
1872 for (i
= 0; (i
< nf
); i
++)
1874 fprintf(fp
, "%10d %10g\n", i
, eigenvalues
[i
]);
1879 orig
= init_mat(rms
->nn
, FALSE
);
1881 copy_t_mat(orig
, rms
);
1882 mc_optimize(log
, rms
, time
, niter
, nrandom
, seed
, kT
,
1883 opt2fn_null("-conv", NFILE
, fnm
), oenv
);
1885 case m_jarvis_patrick
:
1886 jarvis_patrick(rms
->nn
, rms
->mat
, M
, P
, bJP_RMSD
? rmsdcut
: -1, &clust
);
1889 gromos(rms
->nn
, rms
->mat
, rmsdcut
, &clust
);
1892 gmx_fatal(FARGS
, "DEATH HORROR unknown method \"%s\"", methodname
[0]);
1895 if (method
== m_monte_carlo
|| method
== m_diagonalize
)
1897 fprintf(stderr
, "Energy of the matrix after clustering is %g.\n",
1905 ncluster
= plot_clusters(nf
, rms
->mat
, &clust
, minstruct
);
1909 mark_clusters(nf
, rms
->mat
, rms
->maxrms
, &clust
);
1911 init_t_atoms(&useatoms
, isize
, FALSE
);
1912 snew(usextps
, isize
);
1913 useatoms
.resinfo
= top
.atoms
.resinfo
;
1914 for (i
= 0; i
< isize
; i
++)
1916 useatoms
.atomname
[i
] = top
.atoms
.atomname
[index
[i
]];
1917 useatoms
.atom
[i
].resind
= top
.atoms
.atom
[index
[i
]].resind
;
1918 useatoms
.nres
= max(useatoms
.nres
, useatoms
.atom
[i
].resind
+1);
1919 copy_rvec(xtps
[index
[i
]], usextps
[i
]);
1921 useatoms
.nr
= isize
;
1922 analyze_clusters(nf
, &clust
, rms
->mat
, isize
, &useatoms
, usextps
, mass
, xx
, time
,
1923 ifsize
, fitidx
, iosize
, outidx
,
1924 bReadTraj
? trx_out_fn
: NULL
,
1925 opt2fn_null("-sz", NFILE
, fnm
),
1926 opt2fn_null("-tr", NFILE
, fnm
),
1927 opt2fn_null("-ntr", NFILE
, fnm
),
1928 opt2fn_null("-clid", NFILE
, fnm
),
1929 bAverage
, write_ncl
, write_nst
, rmsmin
, bFit
, log
,
1930 rlo_bot
, rhi_bot
, oenv
);
1934 if (bBinary
&& !bAnalyze
)
1936 /* Make the clustering visible */
1937 for (i2
= 0; (i2
< nf
); i2
++)
1939 for (i1
= i2
+1; (i1
< nf
); i1
++)
1941 if (rms
->mat
[i1
][i2
])
1943 rms
->mat
[i1
][i2
] = rms
->maxrms
;
1949 fp
= opt2FILE("-o", NFILE
, fnm
, "w");
1950 fprintf(stderr
, "Writing rms distance/clustering matrix ");
1953 write_xpm(fp
, 0, readmat
[0].title
, readmat
[0].legend
, readmat
[0].label_x
,
1954 readmat
[0].label_y
, nf
, nf
, readmat
[0].axis_x
, readmat
[0].axis_y
,
1955 rms
->mat
, 0.0, rms
->maxrms
, rlo_top
, rhi_top
, &nlevels
);
1959 sprintf(buf
, "Time (%s)", output_env_get_time_unit(oenv
));
1960 sprintf(title
, "RMS%sDeviation / Cluster Index",
1961 bRMSdist
? " Distance " : " ");
1964 write_xpm_split(fp
, 0, title
, "RMSD (nm)", buf
, buf
,
1965 nf
, nf
, time
, time
, rms
->mat
, 0.0, rms
->maxrms
, &nlevels
,
1966 rlo_top
, rhi_top
, 0.0, (real
) ncluster
,
1967 &ncluster
, TRUE
, rlo_bot
, rhi_bot
);
1971 write_xpm(fp
, 0, title
, "RMSD (nm)", buf
, buf
,
1972 nf
, nf
, time
, time
, rms
->mat
, 0.0, rms
->maxrms
,
1973 rlo_top
, rhi_top
, &nlevels
);
1976 fprintf(stderr
, "\n");
1980 fp
= opt2FILE("-om", NFILE
, fnm
, "w");
1981 sprintf(buf
, "Time (%s)", output_env_get_time_unit(oenv
));
1982 sprintf(title
, "RMS%sDeviation", bRMSdist
? " Distance " : " ");
1983 write_xpm(fp
, 0, title
, "RMSD (nm)", buf
, buf
,
1984 nf
, nf
, time
, time
, orig
->mat
, 0.0, orig
->maxrms
,
1985 rlo_top
, rhi_top
, &nlevels
);
1990 /* now show what we've done */
1991 do_view(oenv
, opt2fn("-o", NFILE
, fnm
), "-nxy");
1992 do_view(oenv
, opt2fn_null("-sz", NFILE
, fnm
), "-nxy");
1993 if (method
== m_diagonalize
)
1995 do_view(oenv
, opt2fn_null("-ev", NFILE
, fnm
), "-nxy");
1997 do_view(oenv
, opt2fn("-dist", NFILE
, fnm
), "-nxy");
2000 do_view(oenv
, opt2fn_null("-tr", NFILE
, fnm
), "-nxy");
2001 do_view(oenv
, opt2fn_null("-ntr", NFILE
, fnm
), "-nxy");
2002 do_view(oenv
, opt2fn_null("-clid", NFILE
, fnm
), "-nxy");
2004 do_view(oenv
, opt2fn_null("-conv", NFILE
, fnm
), NULL
);