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48 #include "gromacs/fileio/gmxfio.h"
49 #include "gromacs/fileio/strdb.h"
50 #include "gromacs/legacyheaders/txtdump.h"
51 #include "gromacs/topology/atoms.h"
52 #include "gromacs/topology/block.h"
53 #include "gromacs/topology/invblock.h"
54 #include "gromacs/topology/residuetypes.h"
55 #include "gromacs/utility/arraysize.h"
56 #include "gromacs/utility/cstringutil.h"
57 #include "gromacs/utility/fatalerror.h"
58 #include "gromacs/utility/smalloc.h"
60 static gmx_bool
gmx_ask_yesno(gmx_bool bASK
)
68 c
= toupper(fgetc(stdin
));
70 while ((c
!= 'Y') && (c
!= 'N'));
80 void write_index(const char *outf
, t_blocka
*b
, char **gnames
, gmx_bool bDuplicate
, int natoms
)
85 out
= gmx_fio_fopen(outf
, "w");
86 /* fprintf(out,"%5d %5d\n",b->nr,b->nra); */
87 for (i
= 0; (i
< b
->nr
); i
++)
89 fprintf(out
, "[ %s ]\n", gnames
[i
]);
90 for (k
= 0, j
= b
->index
[i
]; j
< b
->index
[i
+1]; j
++, k
++)
92 fprintf(out
, "%4d ", b
->a
[j
]+1);
101 /* Duplicate copy, useful for computational electrophysiology double-layer setups */
104 fprintf(stderr
, "Duplicating the whole system with an atom offset of %d atoms.\n", natoms
);
105 for (i
= 0; (i
< b
->nr
); i
++)
107 fprintf(out
, "[ %s_copy ]\n", gnames
[i
]);
108 for (k
= 0, j
= b
->index
[i
]; j
< b
->index
[i
+1]; j
++, k
++)
110 fprintf(out
, "%4d ", b
->a
[j
]+1 + natoms
);
123 void add_grp(t_blocka
*b
, char ***gnames
, int nra
, atom_id a
[], const char *name
)
127 srenew(b
->index
, b
->nr
+2);
128 srenew(*gnames
, b
->nr
+1);
129 (*gnames
)[b
->nr
] = gmx_strdup(name
);
131 srenew(b
->a
, b
->nra
+nra
);
132 for (i
= 0; (i
< nra
); i
++)
134 b
->a
[b
->nra
++] = a
[i
];
137 b
->index
[b
->nr
] = b
->nra
;
140 /* compare index in `a' with group in `b' at `index',
141 when `index'<0 it is relative to end of `b' */
142 static gmx_bool
grp_cmp(t_blocka
*b
, int nra
, atom_id a
[], int index
)
148 index
= b
->nr
-1+index
;
152 gmx_fatal(FARGS
, "no such index group %d in t_blocka (nr=%d)", index
, b
->nr
);
155 if (nra
!= b
->index
[index
+1] - b
->index
[index
])
159 for (i
= 0; i
< nra
; i
++)
161 if (a
[i
] != b
->a
[b
->index
[index
]+i
])
170 p_status(const char *const *restype
, int nres
,
171 const char *const *typenames
, int ntypes
)
176 snew(counter
, ntypes
);
177 for (i
= 0; i
< ntypes
; i
++)
181 for (i
= 0; i
< nres
; i
++)
183 for (j
= 0; j
< ntypes
; j
++)
185 if (!gmx_strcasecmp(restype
[i
], typenames
[j
]))
192 for (i
= 0; (i
< ntypes
); i
++)
196 printf("There are: %5d %10s residues\n", counter
[i
], typenames
[i
]);
205 mk_aid(t_atoms
*atoms
, const char ** restype
, const char * typestring
, int *nra
, gmx_bool bMatch
)
206 /* Make an array of atom_ids for all atoms with residuetypes matching typestring, or the opposite if bMatch is false */
214 for (i
= 0; (i
< atoms
->nr
); i
++)
216 res
= !gmx_strcasecmp(restype
[atoms
->atom
[i
].resind
], typestring
);
236 static void analyse_other(const char ** restype
, t_atoms
*atoms
,
237 t_blocka
*gb
, char ***gn
, gmx_bool bASK
, gmx_bool bVerb
)
239 restp_t
*restp
= NULL
;
243 int i
, j
, k
, l
, resind
, naid
, naaid
, natp
, nrestp
= 0;
245 for (i
= 0; (i
< atoms
->nres
); i
++)
247 if (gmx_strcasecmp(restype
[i
], "Protein") && gmx_strcasecmp(restype
[i
], "DNA") && gmx_strcasecmp(restype
[i
], "RNA") && gmx_strcasecmp(restype
[i
], "Water"))
257 printf("Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n");
259 for (k
= 0; (k
< atoms
->nr
); k
++)
261 resind
= atoms
->atom
[k
].resind
;
262 rname
= *atoms
->resinfo
[resind
].name
;
263 if (gmx_strcasecmp(restype
[resind
], "Protein") && gmx_strcasecmp(restype
[resind
], "DNA") &&
264 gmx_strcasecmp(restype
[resind
], "RNA") && gmx_strcasecmp(restype
[resind
], "Water"))
267 for (l
= 0; (l
< nrestp
); l
++)
269 if (strcmp(restp
[l
].rname
, rname
) == 0)
276 srenew(restp
, nrestp
+1);
277 restp
[nrestp
].rname
= gmx_strdup(rname
);
278 restp
[nrestp
].bNeg
= FALSE
;
279 restp
[nrestp
].gname
= gmx_strdup(rname
);
284 for (i
= 0; (i
< nrestp
); i
++)
286 snew(aid
, atoms
->nr
);
288 for (j
= 0; (j
< atoms
->nr
); j
++)
290 rname
= *atoms
->resinfo
[atoms
->atom
[j
].resind
].name
;
291 if ((strcmp(restp
[i
].rname
, rname
) == 0 && !restp
[i
].bNeg
) ||
292 (strcmp(restp
[i
].rname
, rname
) != 0 && restp
[i
].bNeg
))
297 add_grp(gb
, gn
, naid
, aid
, restp
[i
].gname
);
300 printf("split %s into atoms (y/n) ? ", restp
[i
].gname
);
302 if (gmx_ask_yesno(bASK
))
305 for (k
= 0; (k
< naid
); k
++)
307 aname
= *atoms
->atomname
[aid
[k
]];
308 for (l
= 0; (l
< natp
); l
++)
310 if (strcmp(aname
, attp
[l
]) == 0)
317 srenew(attp
, ++natp
);
318 attp
[natp
-1] = aname
;
323 for (l
= 0; (l
< natp
); l
++)
327 for (k
= 0; (k
< naid
); k
++)
329 aname
= *atoms
->atomname
[aid
[k
]];
330 if (strcmp(aname
, attp
[l
]) == 0)
332 aaid
[naaid
++] = aid
[k
];
335 add_grp(gb
, gn
, naaid
, aaid
, attp
[l
]);
344 sfree(restp
[i
].rname
);
345 sfree(restp
[i
].gname
);
352 * Cata necessary to construct a single (protein) index group in
355 typedef struct gmx_help_make_index_group
357 /** The set of atom names that will be used to form this index group */
358 const char **defining_atomnames
;
359 /** Size of the defining_atomnames array */
360 int num_defining_atomnames
;
361 /** Name of this index group */
362 const char *group_name
;
363 /** Whether the above atom names name the atoms in the group, or
364 those not in the group */
365 gmx_bool bTakeComplement
;
366 /** The index in wholename gives the first item in the arrays of
367 atomnames that should be tested with 'gmx_strncasecmp' in stead of
368 gmx_strcasecmp, or -1 if all items should be tested with strcasecmp
369 This is comparable to using a '*' wildcard at the end of specific
370 atom names, but that is more involved to implement...
373 /** Only create this index group if it differs from the one specified in compareto,
374 where -1 means to always create this group. */
376 } t_gmx_help_make_index_group
;
378 static void analyse_prot(const char ** restype
, t_atoms
*atoms
,
379 t_blocka
*gb
, char ***gn
, gmx_bool bASK
, gmx_bool bVerb
)
381 /* lists of atomnames to be used in constructing index groups: */
382 static const char *pnoh
[] = { "H", "HN" };
383 static const char *pnodum
[] = {
384 "MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
385 "MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2"
387 static const char *calpha
[] = { "CA" };
388 static const char *bb
[] = { "N", "CA", "C" };
389 static const char *mc
[] = { "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
390 static const char *mcb
[] = { "N", "CA", "CB", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
391 static const char *mch
[] = {
392 "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT",
393 "H1", "H2", "H3", "H", "HN"
396 static const t_gmx_help_make_index_group constructing_data
[] =
397 {{ NULL
, 0, "Protein", TRUE
, -1, -1},
398 { pnoh
, asize(pnoh
), "Protein-H", TRUE
, 0, -1},
399 { calpha
, asize(calpha
), "C-alpha", FALSE
, -1, -1},
400 { bb
, asize(bb
), "Backbone", FALSE
, -1, -1},
401 { mc
, asize(mc
), "MainChain", FALSE
, -1, -1},
402 { mcb
, asize(mcb
), "MainChain+Cb", FALSE
, -1, -1},
403 { mch
, asize(mch
), "MainChain+H", FALSE
, -1, -1},
404 { mch
, asize(mch
), "SideChain", TRUE
, -1, -1},
405 { mch
, asize(mch
), "SideChain-H", TRUE
, 11, -1},
406 { pnodum
, asize(pnodum
), "Prot-Masses", TRUE
, -1, 0}, };
407 const int num_index_groups
= asize(constructing_data
);
413 char ndx_name
[STRLEN
], *atnm
;
418 printf("Analysing Protein...\n");
420 snew(aid
, atoms
->nr
);
422 /* calculate the number of protein residues */
424 for (i
= 0; (i
< atoms
->nres
); i
++)
426 if (0 == gmx_strcasecmp(restype
[i
], "Protein"))
431 /* find matching or complement atoms */
432 for (i
= 0; (i
< (int)num_index_groups
); i
++)
435 for (n
= 0; (n
< atoms
->nr
); n
++)
437 if (0 == gmx_strcasecmp(restype
[atoms
->atom
[n
].resind
], "Protein"))
440 for (j
= 0; (j
< constructing_data
[i
].num_defining_atomnames
); j
++)
442 /* skip digits at beginning of atomname, e.g. 1H */
443 atnm
= *atoms
->atomname
[n
];
444 while (isdigit(atnm
[0]))
448 if ( (constructing_data
[i
].wholename
== -1) || (j
< constructing_data
[i
].wholename
) )
450 if (0 == gmx_strcasecmp(constructing_data
[i
].defining_atomnames
[j
], atnm
))
457 if (0 == gmx_strncasecmp(constructing_data
[i
].defining_atomnames
[j
], atnm
, strlen(constructing_data
[i
].defining_atomnames
[j
])))
463 if (constructing_data
[i
].bTakeComplement
!= match
)
469 /* if we want to add this group always or it differs from previous
471 if (-1 == constructing_data
[i
].compareto
|| !grp_cmp(gb
, nra
, aid
, constructing_data
[i
].compareto
-i
) )
473 add_grp(gb
, gn
, nra
, aid
, constructing_data
[i
].group_name
);
479 for (i
= 0; (i
< (int)num_index_groups
); i
++)
481 printf("Split %12s into %5d residues (y/n) ? ", constructing_data
[i
].group_name
, npres
);
482 if (gmx_ask_yesno(bASK
))
486 for (n
= 0; ((atoms
->atom
[n
].resind
< npres
) && (n
< atoms
->nr
)); )
488 resind
= atoms
->atom
[n
].resind
;
489 for (; ((atoms
->atom
[n
].resind
== resind
) && (n
< atoms
->nr
)); n
++)
492 for (j
= 0; (j
< constructing_data
[i
].num_defining_atomnames
); j
++)
494 if (0 == gmx_strcasecmp(constructing_data
[i
].defining_atomnames
[j
], *atoms
->atomname
[n
]))
499 if (constructing_data
[i
].bTakeComplement
!= match
)
504 /* copy the residuename to the tail of the groupname */
508 ri
= &atoms
->resinfo
[resind
];
509 sprintf(ndx_name
, "%s_%s%d%c",
510 constructing_data
[i
].group_name
, *ri
->name
, ri
->nr
, ri
->ic
== ' ' ? '\0' : ri
->ic
);
511 add_grp(gb
, gn
, nra
, aid
, ndx_name
);
517 printf("Make group with sidechain and C=O swapped (y/n) ? ");
518 if (gmx_ask_yesno(bASK
))
520 /* Make swap sidechain C=O index */
523 for (n
= 0; ((atoms
->atom
[n
].resind
< npres
) && (n
< atoms
->nr
)); )
525 resind
= atoms
->atom
[n
].resind
;
527 for (; ((atoms
->atom
[n
].resind
== resind
) && (n
< atoms
->nr
)); n
++)
529 if (strcmp("CA", *atoms
->atomname
[n
]) == 0)
535 else if (strcmp("C", *atoms
->atomname
[n
]) == 0)
539 gmx_incons("Atom naming problem");
543 else if (strcmp("O", *atoms
->atomname
[n
]) == 0)
547 gmx_incons("Atom naming problem");
551 else if (strcmp("O1", *atoms
->atomname
[n
]) == 0)
555 gmx_incons("Atom naming problem");
565 /* copy the residuename to the tail of the groupname */
568 add_grp(gb
, gn
, nra
, aid
, "SwapSC-CO");
576 void analyse(t_atoms
*atoms
, t_blocka
*gb
, char ***gn
, gmx_bool bASK
, gmx_bool bVerb
)
578 gmx_residuetype_t
*rt
= NULL
;
581 const char ** restype
;
592 printf("Analysing residue names:\n");
594 /* Create system group, every single atom */
595 snew(aid
, atoms
->nr
);
596 for (i
= 0; i
< atoms
->nr
; i
++)
600 add_grp(gb
, gn
, atoms
->nr
, aid
, "System");
603 /* For every residue, get a pointer to the residue type name */
604 gmx_residuetype_init(&rt
);
607 snew(restype
, atoms
->nres
);
610 for (i
= 0; i
< atoms
->nres
; i
++)
612 resnm
= *atoms
->resinfo
[i
].name
;
613 gmx_residuetype_get_type(rt
, resnm
, &(restype
[i
]));
615 /* Note that this does not lead to a N*N loop, but N*K, where
616 * K is the number of residue _types_, which is small and independent of N.
619 for (k
= 0; k
< ntypes
&& !found
; k
++)
621 assert(p_typename
!= NULL
);
622 found
= !strcmp(restype
[i
], p_typename
[k
]);
626 srenew(p_typename
, ntypes
+1);
627 p_typename
[ntypes
++] = gmx_strdup(restype
[i
]);
633 p_status(restype
, atoms
->nres
, p_typename
, ntypes
);
636 for (k
= 0; k
< ntypes
; k
++)
638 aid
= mk_aid(atoms
, restype
, p_typename
[k
], &nra
, TRUE
);
640 /* Check for special types to do fancy stuff with */
642 if (!gmx_strcasecmp(p_typename
[k
], "Protein") && nra
> 0)
646 analyse_prot(restype
, atoms
, gb
, gn
, bASK
, bVerb
);
648 /* Create a Non-Protein group */
649 aid
= mk_aid(atoms
, restype
, "Protein", &nra
, FALSE
);
650 if ((nra
> 0) && (nra
< atoms
->nr
))
652 add_grp(gb
, gn
, nra
, aid
, "non-Protein");
656 else if (!gmx_strcasecmp(p_typename
[k
], "Water") && nra
> 0)
658 add_grp(gb
, gn
, nra
, aid
, p_typename
[k
]);
659 /* Add this group as 'SOL' too, for backward compatibility with older gromacs versions */
660 add_grp(gb
, gn
, nra
, aid
, "SOL");
664 /* Solvent, create a negated group too */
665 aid
= mk_aid(atoms
, restype
, "Water", &nra
, FALSE
);
666 if ((nra
> 0) && (nra
< atoms
->nr
))
668 add_grp(gb
, gn
, nra
, aid
, "non-Water");
675 add_grp(gb
, gn
, nra
, aid
, p_typename
[k
]);
677 analyse_other(restype
, atoms
, gb
, gn
, bASK
, bVerb
);
679 sfree(p_typename
[k
]);
684 gmx_residuetype_destroy(rt
);
686 /* Create a merged water_and_ions group */
692 for (i
= 0; i
< gb
->nr
; i
++)
694 if (!gmx_strcasecmp((*gn
)[i
], "Water"))
697 nwater
= gb
->index
[i
+1]-gb
->index
[i
];
699 else if (!gmx_strcasecmp((*gn
)[i
], "Ion"))
702 nion
= gb
->index
[i
+1]-gb
->index
[i
];
706 if (nwater
> 0 && nion
> 0)
708 srenew(gb
->index
, gb
->nr
+2);
709 srenew(*gn
, gb
->nr
+1);
710 (*gn
)[gb
->nr
] = gmx_strdup("Water_and_ions");
711 srenew(gb
->a
, gb
->nra
+nwater
+nion
);
714 for (i
= gb
->index
[iwater
]; i
< gb
->index
[iwater
+1]; i
++)
716 gb
->a
[gb
->nra
++] = gb
->a
[i
];
721 for (i
= gb
->index
[iion
]; i
< gb
->index
[iion
+1]; i
++)
723 gb
->a
[gb
->nra
++] = gb
->a
[i
];
727 gb
->index
[gb
->nr
] = gb
->nra
;
732 void check_index(char *gname
, int n
, atom_id index
[], char *traj
, int natoms
)
736 for (i
= 0; i
< n
; i
++)
738 if (index
[i
] >= natoms
)
740 gmx_fatal(FARGS
, "%s atom number (index[%d]=%d) is larger than the number of atoms in %s (%d)",
741 gname
? gname
: "Index", i
+1, index
[i
]+1,
742 traj
? traj
: "the trajectory", natoms
);
744 else if (index
[i
] < 0)
746 gmx_fatal(FARGS
, "%s atom number (index[%d]=%d) is less than zero",
747 gname
? gname
: "Index", i
+1, index
[i
]+1);
752 t_blocka
*init_index(const char *gfile
, char ***grpname
)
758 char line
[STRLEN
], *pt
, str
[STRLEN
];
760 in
= gmx_fio_fopen(gfile
, "r");
768 while (get_a_line(in
, line
, STRLEN
))
770 if (get_header(line
, str
))
773 srenew(b
->index
, b
->nr
+1);
774 srenew(*grpname
, b
->nr
);
779 b
->index
[b
->nr
] = b
->index
[b
->nr
-1];
780 (*grpname
)[b
->nr
-1] = gmx_strdup(str
);
786 gmx_fatal(FARGS
, "The first header of your indexfile is invalid");
789 while (sscanf(pt
, "%s", str
) == 1)
795 srenew(b
->a
, maxentries
);
797 assert(b
->a
!= NULL
); // for clang analyzer
798 b
->a
[i
] = strtol(str
, NULL
, 10)-1;
801 pt
= strstr(pt
, str
)+strlen(str
);
807 for (i
= 0; (i
< b
->nr
); i
++)
809 assert(b
->a
!= NULL
); // for clang analyzer
810 for (j
= b
->index
[i
]; (j
< b
->index
[i
+1]); j
++)
814 fprintf(stderr
, "\nWARNING: negative index %d in group %s\n\n",
815 b
->a
[j
], (*grpname
)[i
]);
823 static void minstring(char *str
)
827 for (i
= 0; (i
< (int)strlen(str
)); i
++)
836 int find_group(const char *s
, int ngrps
, char **grpname
)
844 /* first look for whole name match */
847 for (i
= 0; i
< ngrps
; i
++)
849 if (gmx_strcasecmp_min(s
, grpname
[i
]) == 0)
859 /* second look for first string match */
862 for (i
= 0; i
< ngrps
; i
++)
864 if (gmx_strncasecmp_min(s
, grpname
[i
], n
) == 0)
874 /* last look for arbitrary substring match */
878 strncpy(key
, s
, sizeof(key
)-1);
879 key
[STRLEN
-1] = '\0';
882 for (i
= 0; i
< ngrps
; i
++)
884 strcpy(string
, grpname
[i
]);
887 if (strstr(string
, key
) != NULL
)
899 printf("Error: Multiple groups '%s' selected\n", s
);
905 static int qgroup(int *a
, int ngrps
, char **grpname
)
914 fprintf(stderr
, "Select a group: ");
917 if (scanf("%s", s
) != 1)
919 gmx_fatal(FARGS
, "Cannot read from input");
921 trim(s
); /* remove spaces */
923 while (strlen(s
) == 0);
924 aa
= strtol(s
, &end
, 10);
925 if (aa
== 0 && end
[0] != '\0') /* string entered */
927 aa
= find_group(s
, ngrps
, grpname
);
929 bInRange
= (aa
>= 0 && aa
< ngrps
);
932 printf("Error: No such group '%s'\n", s
);
936 printf("Selected %d: '%s'\n", aa
, grpname
[aa
]);
941 static void rd_groups(t_blocka
*grps
, char **grpname
, char *gnames
[],
942 int ngrps
, int isize
[], atom_id
*index
[], int grpnr
[])
948 gmx_fatal(FARGS
, "Error: no groups in indexfile");
950 for (i
= 0; (i
< grps
->nr
); i
++)
952 fprintf(stderr
, "Group %5d (%15s) has %5d elements\n", i
, grpname
[i
],
953 grps
->index
[i
+1]-grps
->index
[i
]);
955 for (i
= 0; (i
< ngrps
); i
++)
961 gnr1
= qgroup(&grpnr
[i
], grps
->nr
, grpname
);
962 if ((gnr1
< 0) || (gnr1
>= grps
->nr
))
964 fprintf(stderr
, "Select between %d and %d.\n", 0, grps
->nr
-1);
967 while ((gnr1
< 0) || (gnr1
>= grps
->nr
));
971 fprintf(stderr
, "There is one group in the index\n");
974 gnames
[i
] = gmx_strdup(grpname
[gnr1
]);
975 isize
[i
] = grps
->index
[gnr1
+1]-grps
->index
[gnr1
];
976 snew(index
[i
], isize
[i
]);
977 for (j
= 0; (j
< isize
[i
]); j
++)
979 index
[i
][j
] = grps
->a
[grps
->index
[gnr1
]+j
];
984 void rd_index(const char *statfile
, int ngrps
, int isize
[],
985 atom_id
*index
[], char *grpnames
[])
994 gmx_fatal(FARGS
, "No index file specified");
996 grps
= init_index(statfile
, &gnames
);
997 rd_groups(grps
, gnames
, grpnames
, ngrps
, isize
, index
, grpnr
);
1000 void rd_index_nrs(char *statfile
, int ngrps
, int isize
[],
1001 atom_id
*index
[], char *grpnames
[], int grpnr
[])
1008 gmx_fatal(FARGS
, "No index file specified");
1010 grps
= init_index(statfile
, &gnames
);
1012 rd_groups(grps
, gnames
, grpnames
, ngrps
, isize
, index
, grpnr
);
1015 void get_index(t_atoms
*atoms
, const char *fnm
, int ngrps
,
1016 int isize
[], atom_id
*index
[], char *grpnames
[])
1019 t_blocka
*grps
= NULL
;
1026 grps
= init_index(fnm
, gnames
);
1031 snew(grps
->index
, 1);
1032 analyse(atoms
, grps
, gnames
, FALSE
, FALSE
);
1036 gmx_incons("You need to supply a valid atoms structure or a valid index file name");
1039 rd_groups(grps
, *gnames
, grpnames
, ngrps
, isize
, index
, grpnr
);
1042 t_cluster_ndx
*cluster_index(FILE *fplog
, const char *ndx
)
1048 c
->clust
= init_index(ndx
, &c
->grpname
);
1050 for (i
= 0; (i
< c
->clust
->nra
); i
++)
1052 c
->maxframe
= std::max(c
->maxframe
, c
->clust
->a
[i
]);
1054 fprintf(fplog
? fplog
: stdout
,
1055 "There are %d clusters containing %d structures, highest framenr is %d\n",
1056 c
->clust
->nr
, c
->clust
->nra
, c
->maxframe
);
1059 pr_blocka(debug
, 0, "clust", c
->clust
, TRUE
);
1060 for (i
= 0; (i
< c
->clust
->nra
); i
++)
1062 if ((c
->clust
->a
[i
] < 0) || (c
->clust
->a
[i
] > c
->maxframe
))
1064 gmx_fatal(FARGS
, "Range check error for c->clust->a[%d] = %d\n"
1065 "should be within 0 and %d", i
, c
->clust
->a
[i
], c
->maxframe
+1);
1069 c
->inv_clust
= make_invblocka(c
->clust
, c
->maxframe
);