3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
24 * be called official GROMACS. Details are found in the README & COPYING
25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * For more info, check our website at http://www.gromacs.org
33 * GROningen Mixture of Alchemy and Childrens' Stories
61 const char gmx_residuetype_undefined
[]="Other";
63 struct gmx_residuetype
72 static gmx_bool
gmx_ask_yesno(gmx_bool bASK
)
78 c
=toupper(fgetc(stdin
));
79 } while ((c
!= 'Y') && (c
!= 'N'));
87 t_blocka
*new_blocka(void)
97 void write_index(const char *outf
, t_blocka
*b
,char **gnames
)
102 out
=gmx_fio_fopen(outf
,"w");
103 /* fprintf(out,"%5d %5d\n",b->nr,b->nra); */
104 for(i
=0; (i
<b
->nr
); i
++) {
105 fprintf(out
,"[ %s ]\n",gnames
[i
]);
106 for(k
=0,j
=b
->index
[i
]; j
<b
->index
[i
+1]; j
++,k
++) {
107 fprintf(out
,"%4d ",b
->a
[j
]+1);
116 void add_grp(t_blocka
*b
,char ***gnames
,int nra
,atom_id a
[],const char *name
)
120 srenew(b
->index
,b
->nr
+2);
121 srenew(*gnames
,b
->nr
+1);
122 (*gnames
)[b
->nr
]=strdup(name
);
124 srenew(b
->a
,b
->nra
+nra
);
125 for(i
=0; (i
<nra
); i
++)
128 b
->index
[b
->nr
]=b
->nra
;
131 /* compare index in `a' with group in `b' at `index',
132 when `index'<0 it is relative to end of `b' */
133 static gmx_bool
grp_cmp(t_blocka
*b
, int nra
, atom_id a
[], int index
)
138 index
= b
->nr
-1+index
;
140 gmx_fatal(FARGS
,"no such index group %d in t_blocka (nr=%d)",index
,b
->nr
);
142 if ( nra
!= b
->index
[index
+1] - b
->index
[index
] )
145 if ( a
[i
] != b
->a
[b
->index
[index
]+i
] )
151 p_status(const char **restype
, int nres
, const char **typenames
, int ntypes
)
158 snew(counter
,ntypes
);
159 for(i
=0;i
<ntypes
;i
++)
166 for(j
=0;j
<ntypes
;j
++)
168 if(!gmx_strcasecmp(restype
[i
],typenames
[j
]))
175 for(i
=0; (i
<ntypes
); i
++)
179 printf("There are: %5d %10s residues\n",counter
[i
],typenames
[i
]);
188 mk_aid(t_atoms
*atoms
,const char ** restype
,const char * typestring
,int *nra
,gmx_bool bMatch
)
189 /* Make an array of atom_ids for all atoms with residuetypes matching typestring, or the opposite if bMatch is false */
197 for(i
=0; (i
<atoms
->nr
); i
++)
199 res
=!gmx_strcasecmp(restype
[atoms
->atom
[i
].resind
],typestring
);
219 static void analyse_other(const char ** restype
,t_atoms
*atoms
,
220 t_blocka
*gb
,char ***gn
,gmx_bool bASK
,gmx_bool bVerb
)
225 atom_id
*other_ndx
,*aid
,*aaid
;
226 int i
,j
,k
,l
,resind
,naid
,naaid
,natp
,nrestp
=0;
228 for(i
=0; (i
<atoms
->nres
); i
++)
230 if (gmx_strcasecmp(restype
[i
],"Protein") && gmx_strcasecmp(restype
[i
],"DNA") && gmx_strcasecmp(restype
[i
],"RNA") && gmx_strcasecmp(restype
[i
],"Water"))
235 if (i
< atoms
->nres
) {
238 printf("Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n");
239 snew(other_ndx
,atoms
->nr
);
240 for(k
=0; (k
<atoms
->nr
); k
++) {
241 resind
= atoms
->atom
[k
].resind
;
242 rname
= *atoms
->resinfo
[resind
].name
;
243 if (gmx_strcasecmp(restype
[resind
],"Protein") && gmx_strcasecmp(restype
[resind
],"DNA") &&
244 gmx_strcasecmp(restype
[resind
],"RNA") && gmx_strcasecmp(restype
[resind
],"Water"))
247 for(l
=0; (l
<nrestp
); l
++)
248 if (strcmp(restp
[l
].rname
,rname
) == 0)
251 srenew(restp
,nrestp
+1);
252 restp
[nrestp
].rname
= strdup(rname
);
253 restp
[nrestp
].bNeg
= FALSE
;
254 restp
[nrestp
].gname
= strdup(rname
);
260 for(i
=0; (i
<nrestp
); i
++) {
263 for(j
=0; (j
<atoms
->nr
); j
++) {
264 rname
= *atoms
->resinfo
[atoms
->atom
[j
].resind
].name
;
265 if ((strcmp(restp
[i
].rname
,rname
) == 0 && !restp
[i
].bNeg
) ||
266 (strcmp(restp
[i
].rname
,rname
) != 0 && restp
[i
].bNeg
)) {
270 add_grp(gb
,gn
,naid
,aid
,restp
[i
].gname
);
272 printf("split %s into atoms (y/n) ? ",restp
[i
].gname
);
274 if (gmx_ask_yesno(bASK
)) {
276 for(k
=0; (k
<naid
); k
++) {
277 aname
=*atoms
->atomname
[aid
[k
]];
278 for(l
=0; (l
<natp
); l
++)
279 if (strcmp(aname
,attp
[l
]) == 0)
287 for(l
=0; (l
<natp
); l
++) {
290 for(k
=0; (k
<naid
); k
++) {
291 aname
=*atoms
->atomname
[aid
[k
]];
292 if (strcmp(aname
,attp
[l
])==0)
293 aaid
[naaid
++]=aid
[k
];
295 add_grp(gb
,gn
,naaid
,aaid
,attp
[l
]);
309 /*! /brief Instances of this struct contain the data necessary to
310 * construct a single (protein) index group in
312 typedef struct gmx_help_make_index_group
314 /* The set of atom names that will be used to form this index group */
315 const char **defining_atomnames
;
316 /* Size of the defining_atomnames array */
317 const int num_defining_atomnames
;
318 /* Name of this index group */
319 const char *group_name
;
320 /* Whether the above atom names name the atoms in the group, or
321 * those not in the group */
322 gmx_bool bTakeComplement
;
323 /* The index in wholename gives the first item in the arrays of
324 * atomnames that should be tested with 'gmx_strncasecmp' in stead of
325 * gmx_strcasecmp, or -1 if all items should be tested with strcasecmp
326 * This is comparable to using a '*' wildcard at the end of specific
327 * atom names, but that is more involved to implement...
330 /* Only create this index group if it differs from the one specified in compareto,
331 where -1 means to always create this group. */
333 } t_gmx_help_make_index_group
;
335 static void analyse_prot(const char ** restype
,t_atoms
*atoms
,
336 t_blocka
*gb
,char ***gn
,gmx_bool bASK
,gmx_bool bVerb
)
338 /* lists of atomnames to be used in constructing index groups: */
339 static const char *pnoh
[] = { "H", "HN" };
340 static const char *pnodum
[] = { "MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
341 "MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2" };
342 static const char *calpha
[] = { "CA" };
343 static const char *bb
[] = { "N","CA","C" };
344 static const char *mc
[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT" };
345 static const char *mcb
[] = { "N","CA","CB","C","O","O1","O2","OC1","OC2","OT","OXT" };
346 static const char *mch
[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT",
347 "H1","H2","H3","H","HN" };
349 static const t_gmx_help_make_index_group constructing_data
[] =
350 {{ NULL
, 0, "Protein", TRUE
, -1, -1},
351 { pnoh
, asize(pnoh
), "Protein-H", TRUE
, 0, -1},
352 { calpha
, asize(calpha
), "C-alpha", FALSE
, -1, -1},
353 { bb
, asize(bb
), "Backbone", FALSE
, -1, -1},
354 { mc
, asize(mc
), "MainChain", FALSE
, -1, -1},
355 { mcb
, asize(mcb
), "MainChain+Cb", FALSE
, -1, -1},
356 { mch
, asize(mch
), "MainChain+H", FALSE
, -1, -1},
357 { mch
, asize(mch
), "SideChain", TRUE
, -1, -1},
358 { mch
, asize(mch
), "SideChain-H", TRUE
, 11, -1},
359 { pnodum
, asize(pnodum
), "Prot-Masses", TRUE
, -1, 0},
361 const int num_index_groups
= asize(constructing_data
);
365 int nra
,nnpres
,npres
;
367 char ndx_name
[STRLEN
],*atnm
;
372 printf("Analysing Protein...\n");
376 /* calculate the number of protein residues */
378 for(i
=0; (i
<atoms
->nres
); i
++) {
379 if (0 == gmx_strcasecmp(restype
[i
],"Protein")) {
383 /* find matching or complement atoms */
384 for(i
=0; (i
<(int)num_index_groups
); i
++) {
386 for(n
=0; (n
<atoms
->nr
); n
++) {
387 if (0 == gmx_strcasecmp(restype
[atoms
->atom
[n
].resind
],"Protein")) {
389 for(j
=0; (j
<constructing_data
[i
].num_defining_atomnames
); j
++) {
390 /* skip digits at beginning of atomname, e.g. 1H */
391 atnm
=*atoms
->atomname
[n
];
392 while (isdigit(atnm
[0])) {
395 if ( (constructing_data
[i
].wholename
==-1) || (j
<constructing_data
[i
].wholename
) ) {
396 if (0 == gmx_strcasecmp(constructing_data
[i
].defining_atomnames
[j
],atnm
)) {
400 if (0 == gmx_strncasecmp(constructing_data
[i
].defining_atomnames
[j
],atnm
,strlen(constructing_data
[i
].defining_atomnames
[j
]))) {
405 if (constructing_data
[i
].bTakeComplement
!= match
) {
410 /* if we want to add this group always or it differs from previous
412 if ( -1 == constructing_data
[i
].compareto
|| !grp_cmp(gb
,nra
,aid
,constructing_data
[i
].compareto
-i
) ) {
413 add_grp(gb
,gn
,nra
,aid
,constructing_data
[i
].group_name
);
418 for(i
=0; (i
<(int)num_index_groups
); i
++) {
419 printf("Split %12s into %5d residues (y/n) ? ",constructing_data
[i
].group_name
,npres
);
420 if (gmx_ask_yesno(bASK
)) {
423 for(n
=0;((atoms
->atom
[n
].resind
< npres
) && (n
<atoms
->nr
));) {
424 resind
= atoms
->atom
[n
].resind
;
425 for(;((atoms
->atom
[n
].resind
==resind
) && (n
<atoms
->nr
));n
++) {
427 for(j
=0;(j
<constructing_data
[i
].num_defining_atomnames
); j
++) {
428 if (0 == gmx_strcasecmp(constructing_data
[i
].defining_atomnames
[j
],*atoms
->atomname
[n
])) {
432 if (constructing_data
[i
].bTakeComplement
!= match
) {
436 /* copy the residuename to the tail of the groupname */
439 ri
= &atoms
->resinfo
[resind
];
440 sprintf(ndx_name
,"%s_%s%d%c",
441 constructing_data
[i
].group_name
,*ri
->name
,ri
->nr
,ri
->ic
==' ' ? '\0' : ri
->ic
);
442 add_grp(gb
,gn
,nra
,aid
,ndx_name
);
448 printf("Make group with sidechain and C=O swapped (y/n) ? ");
449 if (gmx_ask_yesno(bASK
)) {
450 /* Make swap sidechain C=O index */
453 for(n
=0;((atoms
->atom
[n
].resind
< npres
) && (n
<atoms
->nr
));) {
454 resind
= atoms
->atom
[n
].resind
;
456 for(;((atoms
->atom
[n
].resind
==resind
) && (n
<atoms
->nr
));n
++)
457 if (strcmp("CA",*atoms
->atomname
[n
]) == 0) {
461 } else if (strcmp("C",*atoms
->atomname
[n
]) == 0) {
463 gmx_incons("Atom naming problem");
466 } else if (strcmp("O",*atoms
->atomname
[n
]) == 0) {
468 gmx_incons("Atom naming problem");
471 } else if (strcmp("O1",*atoms
->atomname
[n
]) == 0) {
473 gmx_incons("Atom naming problem");
479 /* copy the residuename to the tail of the groupname */
481 add_grp(gb
,gn
,nra
,aid
,"SwapSC-CO");
492 /* Return 0 if the name was found, otherwise -1.
493 * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
496 gmx_residuetype_get_type(gmx_residuetype_t rt
,const char * resname
, const char ** p_restype
)
501 for(i
=0;i
<rt
->n
&& rc
;i
++)
503 rc
=gmx_strcasecmp(rt
->resname
[i
],resname
);
506 *p_restype
= (rc
==0) ? rt
->restype
[i
-1] : gmx_residuetype_undefined
;
512 gmx_residuetype_add(gmx_residuetype_t rt
,const char *newresname
, const char *newrestype
)
516 const char * p_oldtype
;
518 found
= !gmx_residuetype_get_type(rt
,newresname
,&p_oldtype
);
520 if(found
&& gmx_strcasecmp(p_oldtype
,newrestype
))
522 fprintf(stderr
,"Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
523 newresname
,p_oldtype
,newrestype
);
528 srenew(rt
->resname
,rt
->n
+1);
529 srenew(rt
->restype
,rt
->n
+1);
530 rt
->resname
[rt
->n
]=strdup(newresname
);
531 rt
->restype
[rt
->n
]=strdup(newrestype
);
540 gmx_residuetype_init(gmx_residuetype_t
*prt
)
544 char resname
[STRLEN
],restype
[STRLEN
],dum
[STRLEN
];
547 struct gmx_residuetype
*rt
;
556 db
=libopen("residuetypes.dat");
558 while(get_a_line(db
,line
,STRLEN
))
564 if(sscanf(line
,"%s %s %s",resname
,restype
,dum
)!=2)
566 gmx_fatal(FARGS
,"Incorrect number of columns (2 expected) for line in residuetypes.dat");
568 gmx_residuetype_add(rt
,resname
,restype
);
580 gmx_residuetype_destroy(gmx_residuetype_t rt
)
586 free(rt
->resname
[i
]);
587 free(rt
->restype
[i
]);
595 gmx_residuetype_get_alltypes(gmx_residuetype_t rt
,
596 const char *** p_typenames
,
601 const char ** my_typename
;
611 for(j
=0;j
<n
&& !found
;j
++)
613 found
=!gmx_strcasecmp(p
,my_typename
[j
]);
618 srenew(my_typename
,n
+1);
624 *p_typenames
=my_typename
;
632 gmx_residuetype_is_protein(gmx_residuetype_t rt
, const char *resnm
)
637 if(gmx_residuetype_get_type(rt
,resnm
,&p_type
)==0 &&
638 gmx_strcasecmp(p_type
,"Protein")==0)
650 gmx_residuetype_is_dna(gmx_residuetype_t rt
, const char *resnm
)
655 if(gmx_residuetype_get_type(rt
,resnm
,&p_type
)==0 &&
656 gmx_strcasecmp(p_type
,"DNA")==0)
668 gmx_residuetype_is_rna(gmx_residuetype_t rt
, const char *resnm
)
673 if(gmx_residuetype_get_type(rt
,resnm
,&p_type
)==0 &&
674 gmx_strcasecmp(p_type
,"RNA")==0)
685 /* Return the size of the arrays */
687 gmx_residuetype_get_size(gmx_residuetype_t rt
)
692 /* Search for a residuetype with name resnm within the
693 * gmx_residuetype database. Return the index if found,
697 gmx_residuetype_get_index(gmx_residuetype_t rt
, const char *resnm
)
702 for(i
=0;i
<rt
->n
&& rc
;i
++)
704 rc
=gmx_strcasecmp(rt
->resname
[i
],resnm
);
707 return (0 == rc
) ? i
-1 : -1;
710 /* Return the name of the residuetype with the given index, or
711 * NULL if not found. */
713 gmx_residuetype_get_name(gmx_residuetype_t rt
, int index
)
715 if(index
>= 0 && index
< rt
->n
) {
716 return rt
->resname
[index
];
724 void analyse(t_atoms
*atoms
,t_blocka
*gb
,char ***gn
,gmx_bool bASK
,gmx_bool bVerb
)
726 gmx_residuetype_t rt
;
729 const char ** restype
;
735 const char ** p_typename
;
742 printf("Analysing residue names:\n");
744 /* Create system group, every single atom */
746 for(i
=0;i
<atoms
->nr
;i
++)
750 add_grp(gb
,gn
,atoms
->nr
,aid
,"System");
753 /* For every residue, get a pointer to the residue type name */
754 gmx_residuetype_init(&rt
);
756 snew(restype
,atoms
->nres
);
759 for(i
=0;i
<atoms
->nres
;i
++)
761 resnm
= *atoms
->resinfo
[i
].name
;
762 gmx_residuetype_get_type(rt
,resnm
,&(restype
[i
]));
764 /* Note that this does not lead to a N*N loop, but N*K, where
765 * K is the number of residue _types_, which is small and independent of N.
768 for(k
=0;k
<ntypes
&& !found
;k
++)
770 found
= !strcmp(restype
[i
],p_typename
[k
]);
774 srenew(p_typename
,ntypes
+1);
775 p_typename
[ntypes
++] = strdup(restype
[i
]);
781 p_status(restype
,atoms
->nres
,p_typename
,ntypes
);
784 for(k
=0;k
<ntypes
;k
++)
786 aid
=mk_aid(atoms
,restype
,p_typename
[k
],&nra
,TRUE
);
788 /* Check for special types to do fancy stuff with */
790 if(!gmx_strcasecmp(p_typename
[k
],"Protein") && nra
>0)
794 analyse_prot(restype
,atoms
,gb
,gn
,bASK
,bVerb
);
796 /* Create a Non-Protein group */
797 aid
=mk_aid(atoms
,restype
,"Protein",&nra
,FALSE
);
798 if ((nra
> 0) && (nra
< atoms
->nr
))
800 add_grp(gb
,gn
,nra
,aid
,"non-Protein");
804 else if(!gmx_strcasecmp(p_typename
[k
],"Water") && nra
>0)
806 add_grp(gb
,gn
,nra
,aid
,p_typename
[k
]);
807 /* Add this group as 'SOL' too, for backward compatibility with older gromacs versions */
808 add_grp(gb
,gn
,nra
,aid
,"SOL");
812 /* Solvent, create a negated group too */
813 aid
=mk_aid(atoms
,restype
,"Water",&nra
,FALSE
);
814 if ((nra
> 0) && (nra
< atoms
->nr
))
816 add_grp(gb
,gn
,nra
,aid
,"non-Water");
823 add_grp(gb
,gn
,nra
,aid
,p_typename
[k
]);
825 analyse_other(restype
,atoms
,gb
,gn
,bASK
,bVerb
);
831 gmx_residuetype_destroy(rt
);
833 /* Create a merged water_and_ions group */
839 for(i
=0;i
<gb
->nr
;i
++)
841 if(!gmx_strcasecmp((*gn
)[i
],"Water"))
844 nwater
= gb
->index
[i
+1]-gb
->index
[i
];
846 else if(!gmx_strcasecmp((*gn
)[i
],"Ion"))
849 nion
= gb
->index
[i
+1]-gb
->index
[i
];
853 if(nwater
>0 && nion
>0)
855 srenew(gb
->index
,gb
->nr
+2);
856 srenew(*gn
,gb
->nr
+1);
857 (*gn
)[gb
->nr
] = strdup("Water_and_ions");
858 srenew(gb
->a
,gb
->nra
+nwater
+nion
);
861 for(i
=gb
->index
[iwater
];i
<gb
->index
[iwater
+1];i
++)
863 gb
->a
[gb
->nra
++] = gb
->a
[i
];
868 for(i
=gb
->index
[iion
];i
<gb
->index
[iion
+1];i
++)
870 gb
->a
[gb
->nra
++] = gb
->a
[i
];
874 gb
->index
[gb
->nr
]=gb
->nra
;
879 void check_index(char *gname
,int n
,atom_id index
[],char *traj
,int natoms
)
884 if (index
[i
] >= natoms
)
885 gmx_fatal(FARGS
,"%s atom number (index[%d]=%d) is larger than the number of atoms in %s (%d)",
886 gname
? gname
: "Index",i
+1, index
[i
]+1,
887 traj
? traj
: "the trajectory",natoms
);
888 else if (index
[i
] < 0)
889 gmx_fatal(FARGS
,"%s atom number (index[%d]=%d) is less than zero",
890 gname
? gname
: "Index",i
+1, index
[i
]+1);
893 t_blocka
*init_index(const char *gfile
, char ***grpname
)
899 char line
[STRLEN
],*pt
,str
[STRLEN
];
901 in
=gmx_fio_fopen(gfile
,"r");
903 get_a_line(in
,line
,STRLEN
);
904 if ( line
[0]=='[' ) {
913 if (get_header(line
,str
)) {
915 srenew(b
->index
,b
->nr
+1);
916 srenew(*grpname
,b
->nr
);
919 b
->index
[b
->nr
]=b
->index
[b
->nr
-1];
920 (*grpname
)[b
->nr
-1]=strdup(str
);
923 while ((i
=sscanf(pt
,"%s",str
)) == 1) {
927 srenew(b
->a
,maxentries
);
929 b
->a
[i
]=strtol(str
, NULL
, 10)-1;
932 pt
=strstr(pt
,str
)+strlen(str
);
935 } while (get_a_line(in
,line
,STRLEN
));
939 sscanf(line
,"%d%d",&b
->nr
,&b
->nra
);
940 snew(b
->index
,b
->nr
+1);
941 snew(*grpname
,b
->nr
);
944 for (i
=0; (i
<b
->nr
); i
++) {
945 nread
=fscanf(in
,"%s%d",str
,&ng
);
946 (*grpname
)[i
]=strdup(str
);
947 b
->index
[i
+1]=b
->index
[i
]+ng
;
948 if (b
->index
[i
+1] > b
->nra
)
949 gmx_fatal(FARGS
,"Something wrong in your indexfile at group %s",str
);
950 for(j
=0; (j
<ng
); j
++) {
951 nread
=fscanf(in
,"%d",&a
);
952 b
->a
[b
->index
[i
]+j
]=a
;
958 for(i
=0; (i
<b
->nr
); i
++) {
959 for(j
=b
->index
[i
]; (j
<b
->index
[i
+1]); j
++) {
961 fprintf(stderr
,"\nWARNING: negative index %d in group %s\n\n",
962 b
->a
[j
],(*grpname
)[i
]);
969 static void minstring(char *str
)
973 for (i
=0; (i
< (int)strlen(str
)); i
++)
978 int find_group(char s
[], int ngrps
, char **grpname
)
987 /* first look for whole name match */
989 for(i
=0; i
<ngrps
; i
++)
990 if (gmx_strcasecmp_min(s
,grpname
[i
])==0) {
995 /* second look for first string match */
997 for(i
=0; i
<ngrps
; i
++)
998 if (gmx_strncasecmp_min(s
,grpname
[i
],n
)==0) {
1003 /* last look for arbitrary substring match */
1007 for(i
=0; i
<ngrps
; i
++) {
1008 strcpy(string
, grpname
[i
]);
1011 if (strstr(string
,s
)!=NULL
) {
1019 printf("Error: Multiple groups '%s' selected\n", s
);
1025 static int qgroup(int *a
, int ngrps
, char **grpname
)
1033 fprintf(stderr
,"Select a group: ");
1035 if ( scanf("%s",s
)!=1 )
1036 gmx_fatal(FARGS
,"Cannot read from input");
1037 trim(s
); /* remove spaces */
1038 } while (strlen(s
)==0);
1039 aa
= strtol(s
, &end
, 10);
1040 if (aa
==0 && end
[0] != '\0') /* string entered */
1041 aa
= find_group(s
, ngrps
, grpname
);
1042 bInRange
= (aa
>= 0 && aa
< ngrps
);
1044 printf("Error: No such group '%s'\n", s
);
1045 } while (!bInRange
);
1046 printf("Selected %d: '%s'\n", aa
, grpname
[aa
]);
1051 static void rd_groups(t_blocka
*grps
,char **grpname
,char *gnames
[],
1052 int ngrps
,int isize
[],atom_id
*index
[],int grpnr
[])
1057 gmx_fatal(FARGS
,"Error: no groups in indexfile");
1058 for(i
=0; (i
<grps
->nr
); i
++)
1059 fprintf(stderr
,"Group %5d (%15s) has %5d elements\n",i
,grpname
[i
],
1060 grps
->index
[i
+1]-grps
->index
[i
]);
1061 for(i
=0; (i
<ngrps
); i
++) {
1064 gnr1
=qgroup(&grpnr
[i
], grps
->nr
, grpname
);
1065 if ((gnr1
<0) || (gnr1
>=grps
->nr
))
1066 fprintf(stderr
,"Select between %d and %d.\n",0,grps
->nr
-1);
1067 } while ((gnr1
<0) || (gnr1
>=grps
->nr
));
1069 fprintf(stderr
,"There is one group in the index\n");
1072 gnames
[i
]=strdup(grpname
[gnr1
]);
1073 isize
[i
]=grps
->index
[gnr1
+1]-grps
->index
[gnr1
];
1074 snew(index
[i
],isize
[i
]);
1075 for(j
=0; (j
<isize
[i
]); j
++)
1076 index
[i
][j
]=grps
->a
[grps
->index
[gnr1
]+j
];
1080 void rd_index(const char *statfile
,int ngrps
,int isize
[],
1081 atom_id
*index
[],char *grpnames
[])
1089 gmx_fatal(FARGS
,"No index file specified");
1090 grps
=init_index(statfile
,&gnames
);
1091 rd_groups(grps
,gnames
,grpnames
,ngrps
,isize
,index
,grpnr
);
1094 void rd_index_nrs(char *statfile
,int ngrps
,int isize
[],
1095 atom_id
*index
[],char *grpnames
[],int grpnr
[])
1101 gmx_fatal(FARGS
,"No index file specified");
1102 grps
=init_index(statfile
,&gnames
);
1104 rd_groups(grps
,gnames
,grpnames
,ngrps
,isize
,index
,grpnr
);
1107 void get_index(t_atoms
*atoms
, const char *fnm
, int ngrps
,
1108 int isize
[], atom_id
*index
[],char *grpnames
[])
1111 t_blocka
*grps
= NULL
;
1117 grps
=init_index(fnm
,gnames
);
1121 snew(grps
->index
,1);
1122 analyse(atoms
,grps
,gnames
,FALSE
,FALSE
);
1125 gmx_incons("You need to supply a valid atoms structure or a valid index file name");
1127 rd_groups(grps
,*gnames
,grpnames
,ngrps
,isize
,index
,grpnr
);
1130 t_cluster_ndx
*cluster_index(FILE *fplog
,const char *ndx
)
1136 c
->clust
= init_index(ndx
,&c
->grpname
);
1138 for(i
=0; (i
<c
->clust
->nra
); i
++)
1139 c
->maxframe
= max(c
->maxframe
,c
->clust
->a
[i
]);
1140 fprintf(fplog
? fplog
: stdout
,
1141 "There are %d clusters containing %d structures, highest framenr is %d\n",
1142 c
->clust
->nr
,c
->clust
->nra
,c
->maxframe
);
1144 pr_blocka(debug
,0,"clust",c
->clust
,TRUE
);
1145 for(i
=0; (i
<c
->clust
->nra
); i
++)
1146 if ((c
->clust
->a
[i
] < 0) || (c
->clust
->a
[i
] > c
->maxframe
))
1147 gmx_fatal(FARGS
,"Range check error for c->clust->a[%d] = %d\n"
1148 "should be within 0 and %d",i
,c
->clust
->a
[i
],c
->maxframe
+1);
1150 c
->inv_clust
=make_invblocka(c
->clust
,c
->maxframe
);