/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
#define MAXNAMES 30
#define NAME_LEN 30
-gmx_bool bCase=FALSE;
+gmx_bool bCase = FALSE;
-static int or_groups(atom_id nr1,atom_id *at1,atom_id nr2,atom_id *at2,
- atom_id *nr,atom_id *at)
+static int or_groups(atom_id nr1, atom_id *at1, atom_id nr2, atom_id *at2,
+ atom_id *nr, atom_id *at)
{
- atom_id i1,i2,max=0;
- gmx_bool bNotIncr;
-
- *nr=0;
-
- bNotIncr=FALSE;
- for(i1=0; i1<nr1; i1++) {
- if ((i1>0) && (at1[i1] <= max))
- bNotIncr=TRUE;
- max=at1[i1];
- }
- for(i1=0; i1<nr2; i1++) {
- if ((i1>0) && (at2[i1] <= max))
- bNotIncr=TRUE;
- max=at2[i1];
- }
-
- if (bNotIncr)
- printf("One of your groups is not ascending\n");
- else {
- i1=0;
- i2=0;
- *nr=0;
- while ((i1 < nr1) || (i2 < nr2)) {
- if ((i2 == nr2) || ((i1<nr1) && (at1[i1] < at2[i2]))) {
- at[*nr]=at1[i1];
- (*nr)++;
- i1++;
- }
- else {
- if ((i2<nr2) && ((i1==nr1) || (at1[i1] > at2[i2]))) {
- at[*nr]=at2[i2];
- (*nr)++;
- }
- i2++;
- }
- }
-
- printf("Merged two groups with OR: %u %u -> %u\n",nr1,nr2,*nr);
- }
-
- return *nr;
+ atom_id i1, i2, max = 0;
+ gmx_bool bNotIncr;
+
+ *nr = 0;
+
+ bNotIncr = FALSE;
+ for (i1 = 0; i1 < nr1; i1++)
+ {
+ if ((i1 > 0) && (at1[i1] <= max))
+ {
+ bNotIncr = TRUE;
+ }
+ max = at1[i1];
+ }
+ for (i1 = 0; i1 < nr2; i1++)
+ {
+ if ((i1 > 0) && (at2[i1] <= max))
+ {
+ bNotIncr = TRUE;
+ }
+ max = at2[i1];
+ }
+
+ if (bNotIncr)
+ {
+ printf("One of your groups is not ascending\n");
+ }
+ else
+ {
+ i1 = 0;
+ i2 = 0;
+ *nr = 0;
+ while ((i1 < nr1) || (i2 < nr2))
+ {
+ if ((i2 == nr2) || ((i1 < nr1) && (at1[i1] < at2[i2])))
+ {
+ at[*nr] = at1[i1];
+ (*nr)++;
+ i1++;
+ }
+ else
+ {
+ if ((i2 < nr2) && ((i1 == nr1) || (at1[i1] > at2[i2])))
+ {
+ at[*nr] = at2[i2];
+ (*nr)++;
+ }
+ i2++;
+ }
+ }
+
+ printf("Merged two groups with OR: %u %u -> %u\n", nr1, nr2, *nr);
+ }
+
+ return *nr;
}
-static int and_groups(atom_id nr1,atom_id *at1,atom_id nr2,atom_id *at2,
- atom_id *nr,atom_id *at)
+static int and_groups(atom_id nr1, atom_id *at1, atom_id nr2, atom_id *at2,
+ atom_id *nr, atom_id *at)
{
- atom_id i1,i2;
-
- *nr=0;
- for (i1=0; i1<nr1; i1++) {
- for (i2=0; i2<nr2; i2++) {
- if (at1[i1]==at2[i2]) {
- at[*nr]=at1[i1];
- (*nr)++;
- }
+ atom_id i1, i2;
+
+ *nr = 0;
+ for (i1 = 0; i1 < nr1; i1++)
+ {
+ for (i2 = 0; i2 < nr2; i2++)
+ {
+ if (at1[i1] == at2[i2])
+ {
+ at[*nr] = at1[i1];
+ (*nr)++;
+ }
+ }
}
- }
- printf("Merged two groups with AND: %u %u -> %u\n",nr1,nr2,*nr);
+ printf("Merged two groups with AND: %u %u -> %u\n", nr1, nr2, *nr);
- return *nr;
+ return *nr;
}
static gmx_bool is_name_char(char c)
{
- /* This string should contain all characters that can not be
- * the first letter of a name due to the make_ndx syntax.
- */
- const char *spec=" !&|";
+ /* This string should contain all characters that can not be
+ * the first letter of a name due to the make_ndx syntax.
+ */
+ const char *spec = " !&|";
- return (c != '\0' && strchr(spec,c) == NULL);
+ return (c != '\0' && strchr(spec, c) == NULL);
}
-static int parse_names(char **string,int *n_names,char **names)
+static int parse_names(char **string, int *n_names, char **names)
{
- int i;
-
- *n_names=0;
- while (is_name_char((*string)[0]) || (*string)[0] == ' ') {
- if (is_name_char((*string)[0])) {
- if (*n_names >= MAXNAMES)
- gmx_fatal(FARGS,"To many names: %d\n",*n_names+1);
- i=0;
- while (is_name_char((*string)[i])) {
- names[*n_names][i]=(*string)[i];
- i++;
- if (i > NAME_LEN) {
- printf("Name is too long, the maximum is %d characters\n",NAME_LEN);
- return 0;
- }
- }
- names[*n_names][i]='\0';
- if (!bCase)
- upstring(names[*n_names]);
- *string += i;
- (*n_names)++;
+ int i;
+
+ *n_names = 0;
+ while (is_name_char((*string)[0]) || (*string)[0] == ' ')
+ {
+ if (is_name_char((*string)[0]))
+ {
+ if (*n_names >= MAXNAMES)
+ {
+ gmx_fatal(FARGS, "To many names: %d\n", *n_names+1);
+ }
+ i = 0;
+ while (is_name_char((*string)[i]))
+ {
+ names[*n_names][i] = (*string)[i];
+ i++;
+ if (i > NAME_LEN)
+ {
+ printf("Name is too long, the maximum is %d characters\n", NAME_LEN);
+ return 0;
+ }
+ }
+ names[*n_names][i] = '\0';
+ if (!bCase)
+ {
+ upstring(names[*n_names]);
+ }
+ *string += i;
+ (*n_names)++;
+ }
+ else
+ {
+ (*string)++;
+ }
}
- else
- (*string)++;
- }
- return *n_names;
+ return *n_names;
}
-static gmx_bool parse_int_char(char **string,int *nr,char *c)
+static gmx_bool parse_int_char(char **string, int *nr, char *c)
{
- char *orig;
- gmx_bool bRet;
+ char *orig;
+ gmx_bool bRet;
- orig = *string;
+ orig = *string;
- while ((*string)[0]==' ')
- (*string)++;
+ while ((*string)[0] == ' ')
+ {
+ (*string)++;
+ }
- bRet=FALSE;
+ bRet = FALSE;
- *c = ' ';
+ *c = ' ';
- if (isdigit((*string)[0])) {
- *nr=(*string)[0]-'0';
- (*string)++;
- while (isdigit((*string)[0])) {
- *nr = (*nr)*10+(*string)[0]-'0';
- (*string)++;
- }
- if (isalpha((*string)[0])) {
- *c = (*string)[0];
- (*string)++;
+ if (isdigit((*string)[0]))
+ {
+ *nr = (*string)[0]-'0';
+ (*string)++;
+ while (isdigit((*string)[0]))
+ {
+ *nr = (*nr)*10+(*string)[0]-'0';
+ (*string)++;
+ }
+ if (isalpha((*string)[0]))
+ {
+ *c = (*string)[0];
+ (*string)++;
+ }
+ /* Check if there is at most one non-digit character */
+ if (!isalnum((*string)[0]))
+ {
+ bRet = TRUE;
+ }
+ else
+ {
+ *string = orig;
+ }
}
- /* Check if there is at most one non-digit character */
- if (!isalnum((*string)[0])) {
- bRet = TRUE;
- } else {
- *string = orig;
+ else
+ {
+ *nr = NOTSET;
}
- }
- else
- *nr=NOTSET;
- return bRet;
+ return bRet;
}
-static gmx_bool parse_int(char **string,int *nr)
+static gmx_bool parse_int(char **string, int *nr)
{
- char *orig,c;
- gmx_bool bRet;
+ char *orig, c;
+ gmx_bool bRet;
- orig = *string;
- bRet = parse_int_char(string,nr,&c);
- if (bRet && c != ' ') {
- *string = orig;
- bRet = FALSE;
- }
+ orig = *string;
+ bRet = parse_int_char(string, nr, &c);
+ if (bRet && c != ' ')
+ {
+ *string = orig;
+ bRet = FALSE;
+ }
- return bRet;
+ return bRet;
}
static gmx_bool isquote(char c)
{
- return (c == '\"');
+ return (c == '\"');
}
-static gmx_bool parse_string(char **string,int *nr, int ngrps, char **grpname)
+static gmx_bool parse_string(char **string, int *nr, int ngrps, char **grpname)
{
- char *s, *sp;
- char c;
-
- while ((*string)[0]==' ')
- (*string)++;
-
- (*nr) = NOTSET;
- if (isquote((*string)[0])) {
- c=(*string)[0];
- (*string)++;
- s = strdup((*string));
- sp = strchr(s, c);
- if (sp!=NULL) {
- (*string) += sp-s + 1;
- sp[0]='\0';
- (*nr) = find_group(s, ngrps, grpname);
- }
- }
-
- return (*nr) != NOTSET;
+ char *s, *sp;
+ char c;
+
+ while ((*string)[0] == ' ')
+ {
+ (*string)++;
+ }
+
+ (*nr) = NOTSET;
+ if (isquote((*string)[0]))
+ {
+ c = (*string)[0];
+ (*string)++;
+ s = strdup((*string));
+ sp = strchr(s, c);
+ if (sp != NULL)
+ {
+ (*string) += sp-s + 1;
+ sp[0] = '\0';
+ (*nr) = find_group(s, ngrps, grpname);
+ }
+ }
+
+ return (*nr) != NOTSET;
}
-static int select_atomnumbers(char **string,t_atoms *atoms,atom_id n1,
- atom_id *nr,atom_id *index,char *gname)
+static int select_atomnumbers(char **string, t_atoms *atoms, atom_id n1,
+ atom_id *nr, atom_id *index, char *gname)
{
- char buf[STRLEN];
- int i,up;
-
- *nr=0;
- while ((*string)[0]==' ')
- (*string)++;
- if ((*string)[0]=='-') {
- (*string)++;
- parse_int(string,&up);
- if ((n1<1) || (n1>atoms->nr) || (up<1) || (up>atoms->nr))
- printf("Invalid atom range\n");
- else {
- for(i=n1-1; i<=up-1; i++) {
- index[*nr]=i;
- (*nr)++;
- }
- printf("Found %u atom%s in range %u-%d\n",*nr,(*nr==1)?"":"s",n1,up);
- if (n1==up)
- sprintf(buf,"a_%u",n1);
- else
- sprintf(buf,"a_%u-%d",n1,up);
- strcpy(gname,buf);
- }
- }
- else {
- i=n1;
- sprintf(gname,"a");
- do {
- if ((i-1>=0) && (i-1<atoms->nr)) {
- index[*nr] = i-1;
- (*nr)++;
- sprintf(buf,"_%d",i);
- strcat(gname,buf);
- } else {
- printf("Invalid atom number %d\n",i);
- *nr = 0;
- }
- } while ((*nr!=0) && (parse_int(string,&i)));
- }
-
- return *nr;
+ char buf[STRLEN];
+ int i, up;
+
+ *nr = 0;
+ while ((*string)[0] == ' ')
+ {
+ (*string)++;
+ }
+ if ((*string)[0] == '-')
+ {
+ (*string)++;
+ parse_int(string, &up);
+ if ((n1 < 1) || (n1 > atoms->nr) || (up < 1) || (up > atoms->nr))
+ {
+ printf("Invalid atom range\n");
+ }
+ else
+ {
+ for (i = n1-1; i <= up-1; i++)
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ printf("Found %u atom%s in range %u-%d\n", *nr, (*nr == 1) ? "" : "s", n1, up);
+ if (n1 == up)
+ {
+ sprintf(buf, "a_%u", n1);
+ }
+ else
+ {
+ sprintf(buf, "a_%u-%d", n1, up);
+ }
+ strcpy(gname, buf);
+ }
+ }
+ else
+ {
+ i = n1;
+ sprintf(gname, "a");
+ do
+ {
+ if ((i-1 >= 0) && (i-1 < atoms->nr))
+ {
+ index[*nr] = i-1;
+ (*nr)++;
+ sprintf(buf, "_%d", i);
+ strcat(gname, buf);
+ }
+ else
+ {
+ printf("Invalid atom number %d\n", i);
+ *nr = 0;
+ }
+ }
+ while ((*nr != 0) && (parse_int(string, &i)));
+ }
+
+ return *nr;
}
-static int select_residuenumbers(char **string,t_atoms *atoms,
- atom_id n1,char c,
- atom_id *nr,atom_id *index,char *gname)
+static int select_residuenumbers(char **string, t_atoms *atoms,
+ atom_id n1, char c,
+ atom_id *nr, atom_id *index, char *gname)
{
- char buf[STRLEN];
- int i,j,up;
- t_resinfo *ri;
-
- *nr=0;
- while ((*string)[0]==' ')
- (*string)++;
- if ((*string)[0]=='-') {
- /* Residue number range selection */
- if (c != ' ') {
- printf("Error: residue insertion codes can not be used with residue range selection\n");
- return 0;
- }
- (*string)++;
- parse_int(string,&up);
-
- for(i=0; i<atoms->nr; i++) {
- ri = &atoms->resinfo[atoms->atom[i].resind];
- for(j=n1; (j<=up); j++) {
- if (ri->nr == j && (c == ' ' || ri->ic == c)) {
- index[*nr]=i;
- (*nr)++;
- }
- }
- }
- printf("Found %u atom%s with res.nr. in range %u-%d\n",
- *nr,(*nr==1)?"":"s",n1,up);
- if (n1==up)
- sprintf(buf,"r_%u",n1);
+ char buf[STRLEN];
+ int i, j, up;
+ t_resinfo *ri;
+
+ *nr = 0;
+ while ((*string)[0] == ' ')
+ {
+ (*string)++;
+ }
+ if ((*string)[0] == '-')
+ {
+ /* Residue number range selection */
+ if (c != ' ')
+ {
+ printf("Error: residue insertion codes can not be used with residue range selection\n");
+ return 0;
+ }
+ (*string)++;
+ parse_int(string, &up);
+
+ for (i = 0; i < atoms->nr; i++)
+ {
+ ri = &atoms->resinfo[atoms->atom[i].resind];
+ for (j = n1; (j <= up); j++)
+ {
+ if (ri->nr == j && (c == ' ' || ri->ic == c))
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ }
+ }
+ printf("Found %u atom%s with res.nr. in range %u-%d\n",
+ *nr, (*nr == 1) ? "" : "s", n1, up);
+ if (n1 == up)
+ {
+ sprintf(buf, "r_%u", n1);
+ }
+ else
+ {
+ sprintf(buf, "r_%u-%d", n1, up);
+ }
+ strcpy(gname, buf);
+ }
else
- sprintf(buf,"r_%u-%d",n1,up);
- strcpy(gname,buf);
- }
- else {
- /* Individual residue number/insertion code selection */
- j=n1;
- sprintf(gname,"r");
- do {
- for(i=0; i<atoms->nr; i++) {
- ri = &atoms->resinfo[atoms->atom[i].resind];
- if (ri->nr == j && ri->ic == c) {
- index[*nr]=i;
- (*nr)++;
- }
- }
- sprintf(buf,"_%d",j);
- strcat(gname,buf);
- } while (parse_int_char(string,&j,&c));
- }
-
- return *nr;
+ {
+ /* Individual residue number/insertion code selection */
+ j = n1;
+ sprintf(gname, "r");
+ do
+ {
+ for (i = 0; i < atoms->nr; i++)
+ {
+ ri = &atoms->resinfo[atoms->atom[i].resind];
+ if (ri->nr == j && ri->ic == c)
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ }
+ sprintf(buf, "_%d", j);
+ strcat(gname, buf);
+ }
+ while (parse_int_char(string, &j, &c));
+ }
+
+ return *nr;
}
-static int select_residueindices(char **string,t_atoms *atoms,
- atom_id n1,char c,
- atom_id *nr,atom_id *index,char *gname)
+static int select_residueindices(char **string, t_atoms *atoms,
+ atom_id n1, char c,
+ atom_id *nr, atom_id *index, char *gname)
{
- /*this should be similar to select_residuenumbers except select by index (sequential numbering in file)*/
- /*resind+1 for 1-indexing*/
- char buf[STRLEN];
- int i,j,up;
- t_resinfo *ri;
-
- *nr=0;
- while ((*string)[0]==' ')
- (*string)++;
- if ((*string)[0]=='-') {
- /* Residue number range selection */
- if (c != ' ') {
- printf("Error: residue insertion codes can not be used with residue range selection\n");
- return 0;
- }
- (*string)++;
- parse_int(string,&up);
-
- for(i=0; i<atoms->nr; i++) {
- ri = &atoms->resinfo[atoms->atom[i].resind];
- for(j=n1; (j<=up); j++) {
- if (atoms->atom[i].resind+1 == j && (c == ' ' || ri->ic == c)) {
- index[*nr]=i;
- (*nr)++;
- }
- }
- }
- printf("Found %u atom%s with resind.+1 in range %u-%d\n",
- *nr,(*nr==1)?"":"s",n1,up);
- if (n1==up)
- sprintf(buf,"r_%u",n1);
+ /*this should be similar to select_residuenumbers except select by index (sequential numbering in file)*/
+ /*resind+1 for 1-indexing*/
+ char buf[STRLEN];
+ int i, j, up;
+ t_resinfo *ri;
+
+ *nr = 0;
+ while ((*string)[0] == ' ')
+ {
+ (*string)++;
+ }
+ if ((*string)[0] == '-')
+ {
+ /* Residue number range selection */
+ if (c != ' ')
+ {
+ printf("Error: residue insertion codes can not be used with residue range selection\n");
+ return 0;
+ }
+ (*string)++;
+ parse_int(string, &up);
+
+ for (i = 0; i < atoms->nr; i++)
+ {
+ ri = &atoms->resinfo[atoms->atom[i].resind];
+ for (j = n1; (j <= up); j++)
+ {
+ if (atoms->atom[i].resind+1 == j && (c == ' ' || ri->ic == c))
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ }
+ }
+ printf("Found %u atom%s with resind.+1 in range %u-%d\n",
+ *nr, (*nr == 1) ? "" : "s", n1, up);
+ if (n1 == up)
+ {
+ sprintf(buf, "r_%u", n1);
+ }
+ else
+ {
+ sprintf(buf, "r_%u-%d", n1, up);
+ }
+ strcpy(gname, buf);
+ }
else
- sprintf(buf,"r_%u-%d",n1,up);
- strcpy(gname,buf);
- }
- else {
- /* Individual residue number/insertion code selection */
- j=n1;
- sprintf(gname,"r");
- do {
- for(i=0; i<atoms->nr; i++) {
- ri = &atoms->resinfo[atoms->atom[i].resind];
- if (atoms->atom[i].resind+1 == j && ri->ic == c) {
- index[*nr]=i;
- (*nr)++;
- }
- }
- sprintf(buf,"_%d",j);
- strcat(gname,buf);
- } while (parse_int_char(string,&j,&c));
- }
-
- return *nr;
+ {
+ /* Individual residue number/insertion code selection */
+ j = n1;
+ sprintf(gname, "r");
+ do
+ {
+ for (i = 0; i < atoms->nr; i++)
+ {
+ ri = &atoms->resinfo[atoms->atom[i].resind];
+ if (atoms->atom[i].resind+1 == j && ri->ic == c)
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ }
+ sprintf(buf, "_%d", j);
+ strcat(gname, buf);
+ }
+ while (parse_int_char(string, &j, &c));
+ }
+
+ return *nr;
}
-static gmx_bool atoms_from_residuenumbers(t_atoms *atoms,int group,t_blocka *block,
- atom_id *nr,atom_id *index,char *gname)
+static gmx_bool atoms_from_residuenumbers(t_atoms *atoms, int group, t_blocka *block,
+ atom_id *nr, atom_id *index, char *gname)
{
- int i,j,j0,j1,resnr,nres;
-
- j0=block->index[group];
- j1=block->index[group+1];
- nres = atoms->nres;
- for(j=j0; j<j1; j++)
- if (block->a[j]>=nres) {
- printf("Index %s contains number>nres (%d>%d)\n",
- gname,block->a[j]+1,nres);
- return FALSE;
- }
- for(i=0; i<atoms->nr; i++) {
- resnr = atoms->resinfo[atoms->atom[i].resind].nr;
- for (j=j0; j<j1; j++)
- if (block->a[j]+1 == resnr) {
- index[*nr]=i;
- (*nr)++;
- break;
- }
- }
- printf("Found %u atom%s in %d residues from group %s\n",
- *nr,(*nr==1)?"":"s",j1-j0,gname);
- return *nr;
+ int i, j, j0, j1, resnr, nres;
+
+ j0 = block->index[group];
+ j1 = block->index[group+1];
+ nres = atoms->nres;
+ for (j = j0; j < j1; j++)
+ {
+ if (block->a[j] >= nres)
+ {
+ printf("Index %s contains number>nres (%d>%d)\n",
+ gname, block->a[j]+1, nres);
+ return FALSE;
+ }
+ }
+ for (i = 0; i < atoms->nr; i++)
+ {
+ resnr = atoms->resinfo[atoms->atom[i].resind].nr;
+ for (j = j0; j < j1; j++)
+ {
+ if (block->a[j]+1 == resnr)
+ {
+ index[*nr] = i;
+ (*nr)++;
+ break;
+ }
+ }
+ }
+ printf("Found %u atom%s in %d residues from group %s\n",
+ *nr, (*nr == 1) ? "" : "s", j1-j0, gname);
+ return *nr;
}
-static gmx_bool comp_name(char *name,char *search)
+static gmx_bool comp_name(char *name, char *search)
{
- while (name[0] != '\0' && search[0] != '\0') {
- switch (search[0]) {
- case '?':
- /* Always matches */
- break;
- case '*':
- if (search[1] != '\0') {
- printf("WARNING: Currently '*' is only supported at the end of an expression\n");
- return FALSE;
- } else {
- return TRUE;
- }
- break;
- default:
- /* Compare a single character */
- if (( bCase && strncmp(name,search,1)) ||
- (!bCase && gmx_strncasecmp(name,search,1))) {
- return FALSE;
- }
- }
- name++;
- search++;
- }
-
- return (name[0] == '\0' && (search[0] == '\0' || search[0] == '*'));
+ while (name[0] != '\0' && search[0] != '\0')
+ {
+ switch (search[0])
+ {
+ case '?':
+ /* Always matches */
+ break;
+ case '*':
+ if (search[1] != '\0')
+ {
+ printf("WARNING: Currently '*' is only supported at the end of an expression\n");
+ return FALSE;
+ }
+ else
+ {
+ return TRUE;
+ }
+ break;
+ default:
+ /* Compare a single character */
+ if (( bCase && strncmp(name, search, 1)) ||
+ (!bCase && gmx_strncasecmp(name, search, 1)))
+ {
+ return FALSE;
+ }
+ }
+ name++;
+ search++;
+ }
+
+ return (name[0] == '\0' && (search[0] == '\0' || search[0] == '*'));
}
-static int select_chainnames(t_atoms *atoms,int n_names,char **names,
- atom_id *nr,atom_id *index)
+static int select_chainnames(t_atoms *atoms, int n_names, char **names,
+ atom_id *nr, atom_id *index)
{
- char name[2];
- int j;
- atom_id i;
-
- name[1]=0;
- *nr=0;
- for(i=0; i<atoms->nr; i++) {
- name[0] = atoms->resinfo[atoms->atom[i].resind].chainid;
- j=0;
- while (j<n_names && !comp_name(name,names[j]))
- j++;
- if (j<n_names) {
- index[*nr]=i;
- (*nr)++;
- }
- }
- printf("Found %u atom%s with chain identifier%s",
- *nr,(*nr==1)?"":"s",(n_names==1)?"":"s");
- for(j=0; (j<n_names); j++)
- printf(" %s",names[j]);
- printf("\n");
-
- return *nr;
+ char name[2];
+ int j;
+ atom_id i;
+
+ name[1] = 0;
+ *nr = 0;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ name[0] = atoms->resinfo[atoms->atom[i].resind].chainid;
+ j = 0;
+ while (j < n_names && !comp_name(name, names[j]))
+ {
+ j++;
+ }
+ if (j < n_names)
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ }
+ printf("Found %u atom%s with chain identifier%s",
+ *nr, (*nr == 1) ? "" : "s", (n_names == 1) ? "" : "s");
+ for (j = 0; (j < n_names); j++)
+ {
+ printf(" %s", names[j]);
+ }
+ printf("\n");
+
+ return *nr;
}
-static int select_atomnames(t_atoms *atoms,int n_names,char **names,
- atom_id *nr,atom_id *index,gmx_bool bType)
+static int select_atomnames(t_atoms *atoms, int n_names, char **names,
+ atom_id *nr, atom_id *index, gmx_bool bType)
{
- char *name;
- int j;
- atom_id i;
-
- *nr=0;
- for(i=0; i<atoms->nr; i++) {
- if (bType)
- name=*(atoms->atomtype[i]);
- else
- name=*(atoms->atomname[i]);
- j=0;
- while (j<n_names && !comp_name(name,names[j]))
- j++;
- if (j<n_names) {
- index[*nr]=i;
- (*nr)++;
- }
- }
- printf("Found %u atoms with %s%s",
- *nr,bType ? "type" : "name",(n_names==1)?"":"s");
- for(j=0; (j<n_names); j++)
- printf(" %s",names[j]);
- printf("\n");
-
- return *nr;
+ char *name;
+ int j;
+ atom_id i;
+
+ *nr = 0;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ if (bType)
+ {
+ name = *(atoms->atomtype[i]);
+ }
+ else
+ {
+ name = *(atoms->atomname[i]);
+ }
+ j = 0;
+ while (j < n_names && !comp_name(name, names[j]))
+ {
+ j++;
+ }
+ if (j < n_names)
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ }
+ printf("Found %u atoms with %s%s",
+ *nr, bType ? "type" : "name", (n_names == 1) ? "" : "s");
+ for (j = 0; (j < n_names); j++)
+ {
+ printf(" %s", names[j]);
+ }
+ printf("\n");
+
+ return *nr;
}
-static int select_residuenames(t_atoms *atoms,int n_names,char **names,
- atom_id *nr,atom_id *index)
+static int select_residuenames(t_atoms *atoms, int n_names, char **names,
+ atom_id *nr, atom_id *index)
{
- char *name;
- int j;
- atom_id i;
-
- *nr=0;
- for(i=0; i<atoms->nr; i++) {
- name = *(atoms->resinfo[atoms->atom[i].resind].name);
- j=0;
- while (j<n_names && !comp_name(name,names[j]))
- j++;
- if (j<n_names) {
- index[*nr]=i;
- (*nr)++;
- }
- }
- printf("Found %u atoms with residue name%s",*nr,(n_names==1)?"":"s");
- for(j=0; (j<n_names); j++)
- printf(" %s",names[j]);
- printf("\n");
-
- return *nr;
+ char *name;
+ int j;
+ atom_id i;
+
+ *nr = 0;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ name = *(atoms->resinfo[atoms->atom[i].resind].name);
+ j = 0;
+ while (j < n_names && !comp_name(name, names[j]))
+ {
+ j++;
+ }
+ if (j < n_names)
+ {
+ index[*nr] = i;
+ (*nr)++;
+ }
+ }
+ printf("Found %u atoms with residue name%s", *nr, (n_names == 1) ? "" : "s");
+ for (j = 0; (j < n_names); j++)
+ {
+ printf(" %s", names[j]);
+ }
+ printf("\n");
+
+ return *nr;
}
-static void copy2block(int n,atom_id *index,t_blocka *block)
+static void copy2block(int n, atom_id *index, t_blocka *block)
{
- int i,n0;
-
- block->nr++;
- n0=block->nra;
- block->nra=n0+n;
- srenew(block->index,block->nr+1);
- block->index[block->nr]=n0+n;
- srenew(block->a,n0+n);
- for(i=0; (i<n); i++)
- block->a[n0+i]=index[i];
+ int i, n0;
+
+ block->nr++;
+ n0 = block->nra;
+ block->nra = n0+n;
+ srenew(block->index, block->nr+1);
+ block->index[block->nr] = n0+n;
+ srenew(block->a, n0+n);
+ for (i = 0; (i < n); i++)
+ {
+ block->a[n0+i] = index[i];
+ }
}
-static void make_gname(int n,char **names,char *gname)
+static void make_gname(int n, char **names, char *gname)
{
- int i;
-
- strcpy(gname,names[0]);
- for (i=1; i<n; i++) {
- strcat(gname,"_");
- strcat(gname,names[i]);
- }
+ int i;
+
+ strcpy(gname, names[0]);
+ for (i = 1; i < n; i++)
+ {
+ strcat(gname, "_");
+ strcat(gname, names[i]);
+ }
}
-static void copy_group(int g,t_blocka *block,atom_id *nr,atom_id *index)
+static void copy_group(int g, t_blocka *block, atom_id *nr, atom_id *index)
{
- int i,i0;
-
- i0=block->index[g];
- *nr=block->index[g+1]-i0;
- for (i=0; i<*nr; i++)
- index[i]=block->a[i0+i];
+ int i, i0;
+
+ i0 = block->index[g];
+ *nr = block->index[g+1]-i0;
+ for (i = 0; i < *nr; i++)
+ {
+ index[i] = block->a[i0+i];
+ }
}
-static void remove_group(int nr,int nr2,t_blocka *block,char ***gn)
+static void remove_group(int nr, int nr2, t_blocka *block, char ***gn)
{
- int i,j,shift;
- char *name;
-
- if (nr2==NOTSET)
- nr2=nr;
-
- for(j=0; j<=nr2-nr; j++) {
- if ((nr<0) || (nr>=block->nr))
- printf("Group %d does not exist\n",nr+j);
- else {
- shift=block->index[nr+1]-block->index[nr];
- for(i=block->index[nr+1]; i<block->nra; i++)
- block->a[i-shift]=block->a[i];
-
- for(i=nr; i<block->nr; i++)
- block->index[i]=block->index[i+1]-shift;
- name = strdup((*gn)[nr]);
- sfree((*gn)[nr]);
- for(i=nr; i<block->nr-1; i++) {
- (*gn)[i]=(*gn)[i+1];
- }
- block->nr--;
- block->nra=block->index[block->nr];
- printf("Removed group %d '%s'\n",nr+j,name);
- sfree(name);
- }
- }
+ int i, j, shift;
+ char *name;
+
+ if (nr2 == NOTSET)
+ {
+ nr2 = nr;
+ }
+
+ for (j = 0; j <= nr2-nr; j++)
+ {
+ if ((nr < 0) || (nr >= block->nr))
+ {
+ printf("Group %d does not exist\n", nr+j);
+ }
+ else
+ {
+ shift = block->index[nr+1]-block->index[nr];
+ for (i = block->index[nr+1]; i < block->nra; i++)
+ {
+ block->a[i-shift] = block->a[i];
+ }
+
+ for (i = nr; i < block->nr; i++)
+ {
+ block->index[i] = block->index[i+1]-shift;
+ }
+ name = strdup((*gn)[nr]);
+ sfree((*gn)[nr]);
+ for (i = nr; i < block->nr-1; i++)
+ {
+ (*gn)[i] = (*gn)[i+1];
+ }
+ block->nr--;
+ block->nra = block->index[block->nr];
+ printf("Removed group %d '%s'\n", nr+j, name);
+ sfree(name);
+ }
+ }
}
-static void split_group(t_atoms *atoms,int sel_nr,t_blocka *block,char ***gn,
- gmx_bool bAtom)
+static void split_group(t_atoms *atoms, int sel_nr, t_blocka *block, char ***gn,
+ gmx_bool bAtom)
{
- char buf[STRLEN],*name;
- int i,resind;
- atom_id a,n0,n1;
-
- printf("Splitting group %d '%s' into %s\n",sel_nr,(*gn)[sel_nr],
- bAtom ? "atoms" : "residues");
-
- n0=block->index[sel_nr];
- n1=block->index[sel_nr+1];
- srenew(block->a,block->nra+n1-n0);
- for (i=n0; i<n1; i++) {
- a=block->a[i];
- resind = atoms->atom[a].resind;
- name = *(atoms->resinfo[resind].name);
- if (bAtom || (i==n0) || (atoms->atom[block->a[i-1]].resind!=resind)) {
- if (i>n0)
- block->index[block->nr]=block->nra;
- block->nr++;
- srenew(block->index,block->nr+1);
- srenew(*gn,block->nr);
- if (bAtom)
- sprintf(buf,"%s_%s_%u",(*gn)[sel_nr],*atoms->atomname[a],a+1);
- else
- sprintf(buf,"%s_%s_%d",(*gn)[sel_nr],name,atoms->resinfo[resind].nr);
- (*gn)[block->nr-1]=strdup(buf);
- }
- block->a[block->nra]=a;
- block->nra++;
- }
- block->index[block->nr]=block->nra;
+ char buf[STRLEN], *name;
+ int i, resind;
+ atom_id a, n0, n1;
+
+ printf("Splitting group %d '%s' into %s\n", sel_nr, (*gn)[sel_nr],
+ bAtom ? "atoms" : "residues");
+
+ n0 = block->index[sel_nr];
+ n1 = block->index[sel_nr+1];
+ srenew(block->a, block->nra+n1-n0);
+ for (i = n0; i < n1; i++)
+ {
+ a = block->a[i];
+ resind = atoms->atom[a].resind;
+ name = *(atoms->resinfo[resind].name);
+ if (bAtom || (i == n0) || (atoms->atom[block->a[i-1]].resind != resind))
+ {
+ if (i > n0)
+ {
+ block->index[block->nr] = block->nra;
+ }
+ block->nr++;
+ srenew(block->index, block->nr+1);
+ srenew(*gn, block->nr);
+ if (bAtom)
+ {
+ sprintf(buf, "%s_%s_%u", (*gn)[sel_nr], *atoms->atomname[a], a+1);
+ }
+ else
+ {
+ sprintf(buf, "%s_%s_%d", (*gn)[sel_nr], name, atoms->resinfo[resind].nr);
+ }
+ (*gn)[block->nr-1] = strdup(buf);
+ }
+ block->a[block->nra] = a;
+ block->nra++;
+ }
+ block->index[block->nr] = block->nra;
}
-static int split_chain(t_atoms *atoms,rvec *x,
- int sel_nr,t_blocka *block,char ***gn)
+static int split_chain(t_atoms *atoms, rvec *x,
+ int sel_nr, t_blocka *block, char ***gn)
{
- char buf[STRLEN];
- int j,nchain;
- atom_id i,a,natoms,*start=NULL,*end=NULL,ca_start,ca_end;
- rvec vec;
-
- natoms=atoms->nr;
- nchain=0;
- ca_start=0;
-
- while (ca_start<natoms) {
- while((ca_start<natoms) && strcmp(*atoms->atomname[ca_start],"CA"))
- ca_start++;
- if (ca_start<natoms) {
- srenew(start,nchain+1);
- srenew(end,nchain+1);
- start[nchain]=ca_start;
- while ((start[nchain]>0) &&
- (atoms->atom[start[nchain]-1].resind ==
- atoms->atom[ca_start].resind))
- start[nchain]--;
-
- i=ca_start;
- do {
- ca_end=i;
- do {
- i++;
- } while ((i<natoms) && strcmp(*atoms->atomname[i],"CA"));
- if (i<natoms)
- rvec_sub(x[ca_end],x[i],vec);
- } while ((i<natoms) && (norm(vec)<0.45));
-
- end[nchain]=ca_end;
- while ((end[nchain]+1<natoms) &&
- (atoms->atom[end[nchain]+1].resind==atoms->atom[ca_end].resind))
- end[nchain]++;
- ca_start=end[nchain]+1;
- nchain++;
- }
- }
- if (nchain==1)
- printf("Found 1 chain, will not split\n");
- else
- printf("Found %d chains\n",nchain);
- for (j=0; j<nchain; j++)
- printf("%d:%6u atoms (%u to %u)\n",
- j+1,end[j]-start[j]+1,start[j]+1,end[j]+1);
-
- if (nchain > 1) {
- srenew(block->a,block->nra+block->index[sel_nr+1]-block->index[sel_nr]);
- for (j=0; j<nchain; j++) {
- block->nr++;
- srenew(block->index,block->nr+1);
- srenew(*gn,block->nr);
- sprintf(buf,"%s_chain%d",(*gn)[sel_nr],j+1);
- (*gn)[block->nr-1]=strdup(buf);
- for (i=block->index[sel_nr]; i<block->index[sel_nr+1]; i++) {
- a=block->a[i];
- if ((a>=start[j]) && (a<=end[j])) {
- block->a[block->nra]=a;
- block->nra++;
- }
- }
- block->index[block->nr]=block->nra;
- if (block->index[block->nr-1]==block->index[block->nr])
- remove_group(block->nr-1,NOTSET,block,gn);
- }
- }
- sfree(start);
- sfree(end);
-
- return nchain;
+ char buf[STRLEN];
+ int j, nchain;
+ atom_id i, a, natoms, *start = NULL, *end = NULL, ca_start, ca_end;
+ rvec vec;
+
+ natoms = atoms->nr;
+ nchain = 0;
+ ca_start = 0;
+
+ while (ca_start < natoms)
+ {
+ while ((ca_start < natoms) && strcmp(*atoms->atomname[ca_start], "CA"))
+ {
+ ca_start++;
+ }
+ if (ca_start < natoms)
+ {
+ srenew(start, nchain+1);
+ srenew(end, nchain+1);
+ start[nchain] = ca_start;
+ while ((start[nchain] > 0) &&
+ (atoms->atom[start[nchain]-1].resind ==
+ atoms->atom[ca_start].resind))
+ {
+ start[nchain]--;
+ }
+
+ i = ca_start;
+ do
+ {
+ ca_end = i;
+ do
+ {
+ i++;
+ }
+ while ((i < natoms) && strcmp(*atoms->atomname[i], "CA"));
+ if (i < natoms)
+ {
+ rvec_sub(x[ca_end], x[i], vec);
+ }
+ }
+ while ((i < natoms) && (norm(vec) < 0.45));
+
+ end[nchain] = ca_end;
+ while ((end[nchain]+1 < natoms) &&
+ (atoms->atom[end[nchain]+1].resind == atoms->atom[ca_end].resind))
+ {
+ end[nchain]++;
+ }
+ ca_start = end[nchain]+1;
+ nchain++;
+ }
+ }
+ if (nchain == 1)
+ {
+ printf("Found 1 chain, will not split\n");
+ }
+ else
+ {
+ printf("Found %d chains\n", nchain);
+ }
+ for (j = 0; j < nchain; j++)
+ {
+ printf("%d:%6u atoms (%u to %u)\n",
+ j+1, end[j]-start[j]+1, start[j]+1, end[j]+1);
+ }
+
+ if (nchain > 1)
+ {
+ srenew(block->a, block->nra+block->index[sel_nr+1]-block->index[sel_nr]);
+ for (j = 0; j < nchain; j++)
+ {
+ block->nr++;
+ srenew(block->index, block->nr+1);
+ srenew(*gn, block->nr);
+ sprintf(buf, "%s_chain%d", (*gn)[sel_nr], j+1);
+ (*gn)[block->nr-1] = strdup(buf);
+ for (i = block->index[sel_nr]; i < block->index[sel_nr+1]; i++)
+ {
+ a = block->a[i];
+ if ((a >= start[j]) && (a <= end[j]))
+ {
+ block->a[block->nra] = a;
+ block->nra++;
+ }
+ }
+ block->index[block->nr] = block->nra;
+ if (block->index[block->nr-1] == block->index[block->nr])
+ {
+ remove_group(block->nr-1, NOTSET, block, gn);
+ }
+ }
+ }
+ sfree(start);
+ sfree(end);
+
+ return nchain;
}
static gmx_bool check_have_atoms(t_atoms *atoms, char *string)
{
- if ( atoms==NULL ) {
- printf("Can not process '%s' without atom info, use option -f\n", string);
- return FALSE;
- } else
- return TRUE;
+ if (atoms == NULL)
+ {
+ printf("Can not process '%s' without atom info, use option -f\n", string);
+ return FALSE;
+ }
+ else
+ {
+ return TRUE;
+ }
}
-static gmx_bool parse_entry(char **string,int natoms,t_atoms *atoms,
- t_blocka *block,char ***gn,
- atom_id *nr,atom_id *index,char *gname)
+static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
+ t_blocka *block, char ***gn,
+ atom_id *nr, atom_id *index, char *gname)
{
- static char **names, *ostring;
- static gmx_bool bFirst=TRUE;
- int j,n_names,sel_nr1;
- atom_id i,nr1,*index1;
- char c;
- gmx_bool bRet,bCompl;
-
- if (bFirst) {
- bFirst=FALSE;
- snew(names,MAXNAMES);
- for (i=0; i<MAXNAMES; i++)
- snew(names[i],NAME_LEN+1);
- }
-
- bRet=FALSE;
- sel_nr1=NOTSET;
-
- while(*string[0]==' ')
- (*string)++;
-
- if ((*string)[0]=='!') {
- bCompl=TRUE;
- (*string)++;
- while(*string[0]==' ')
- (*string)++;
- } else
- bCompl=FALSE;
-
- ostring = *string;
-
- if (parse_int(string,&sel_nr1) ||
- parse_string(string,&sel_nr1,block->nr,*gn)) {
- if ((sel_nr1>=0) && (sel_nr1<block->nr)) {
- copy_group(sel_nr1,block,nr,index);
- strcpy(gname,(*gn)[sel_nr1]);
- printf("Copied index group %d '%s'\n",sel_nr1,(*gn)[sel_nr1]);
- bRet=TRUE;
- } else
- printf("Group %d does not exist\n",sel_nr1);
- }
- else if ((*string)[0]=='a') {
- (*string)++;
- if (check_have_atoms(atoms, ostring)) {
- if (parse_int(string,&sel_nr1)) {
- bRet=select_atomnumbers(string,atoms,sel_nr1,nr,index,gname);
- }
- else if (parse_names(string,&n_names,names)) {
- bRet=select_atomnames(atoms,n_names,names,nr,index,FALSE);
- make_gname(n_names,names,gname);
- }
- }
- }
- else if ((*string)[0]=='t') {
- (*string)++;
- if (check_have_atoms(atoms, ostring) &&
- parse_names(string,&n_names,names)) {
- if (atoms->atomtype == NULL)
- printf("Need a run input file to select atom types\n");
- else {
- bRet=select_atomnames(atoms,n_names,names,nr,index,TRUE);
- make_gname(n_names,names,gname);
- }
- }
- }
- else if (strncmp(*string,"res",3)==0) {
- (*string)+=3;
- if ( check_have_atoms(atoms, ostring) &&
- parse_int(string,&sel_nr1) &&
- (sel_nr1>=0) && (sel_nr1<block->nr) ) {
- bRet=atoms_from_residuenumbers(atoms,
- sel_nr1,block,nr,index,(*gn)[sel_nr1]);
- sprintf(gname,"atom_%s",(*gn)[sel_nr1]);
- }
- }
- else if (strncmp(*string,"ri",2)==0) {
- (*string)+=2;
- if (check_have_atoms(atoms, ostring) &&
- parse_int_char(string,&sel_nr1,&c)) {
- bRet=select_residueindices(string,atoms,sel_nr1,c,nr,index,gname);
- }
- }
- else if ((*string)[0]=='r') {
- (*string)++;
- if (check_have_atoms(atoms, ostring)) {
- if (parse_int_char(string,&sel_nr1,&c)) {
- bRet=select_residuenumbers(string,atoms,sel_nr1,c,nr,index,gname);
- }
- else if (parse_names(string,&n_names,names)) {
- bRet=select_residuenames(atoms,n_names,names,nr,index);
- make_gname(n_names,names,gname);
- }
- }
- }
- else if (strncmp(*string,"chain",5)==0) {
- (*string)+=5;
- if (check_have_atoms(atoms, ostring) &&
- parse_names(string,&n_names,names)) {
- bRet=select_chainnames(atoms,n_names,names,nr,index);
- sprintf(gname,"ch%s",names[0]);
- for (i=1; i<n_names; i++)
- strcat(gname,names[i]);
- }
- }
- if (bRet && bCompl) {
- snew(index1,natoms-*nr);
- nr1=0;
- for(i=0; i<natoms; i++) {
- j=0;
- while ((j<*nr) && (index[j] != i))
- j++;
- if (j==*nr) {
- if (nr1 >= natoms-*nr) {
- printf("There are double atoms in your index group\n");
- break;
- }
- index1[nr1]=i;
- nr1++;
- }
- }
- *nr=nr1;
- for(i=0; i<nr1; i++)
- index[i]=index1[i];
- sfree(index1);
-
- for (i=strlen(gname)+1; i>0; i--)
- gname[i]=gname[i-1];
- gname[0]='!';
- printf("Complemented group: %u atoms\n",*nr);
- }
-
- return bRet;
+ static char **names, *ostring;
+ static gmx_bool bFirst = TRUE;
+ int j, n_names, sel_nr1;
+ atom_id i, nr1, *index1;
+ char c;
+ gmx_bool bRet, bCompl;
+
+ if (bFirst)
+ {
+ bFirst = FALSE;
+ snew(names, MAXNAMES);
+ for (i = 0; i < MAXNAMES; i++)
+ {
+ snew(names[i], NAME_LEN+1);
+ }
+ }
+
+ bRet = FALSE;
+ sel_nr1 = NOTSET;
+
+ while (*string[0] == ' ')
+ {
+ (*string)++;
+ }
+
+ if ((*string)[0] == '!')
+ {
+ bCompl = TRUE;
+ (*string)++;
+ while (*string[0] == ' ')
+ {
+ (*string)++;
+ }
+ }
+ else
+ {
+ bCompl = FALSE;
+ }
+
+ ostring = *string;
+
+ if (parse_int(string, &sel_nr1) ||
+ parse_string(string, &sel_nr1, block->nr, *gn))
+ {
+ if ((sel_nr1 >= 0) && (sel_nr1 < block->nr))
+ {
+ copy_group(sel_nr1, block, nr, index);
+ strcpy(gname, (*gn)[sel_nr1]);
+ printf("Copied index group %d '%s'\n", sel_nr1, (*gn)[sel_nr1]);
+ bRet = TRUE;
+ }
+ else
+ {
+ printf("Group %d does not exist\n", sel_nr1);
+ }
+ }
+ else if ((*string)[0] == 'a')
+ {
+ (*string)++;
+ if (check_have_atoms(atoms, ostring))
+ {
+ if (parse_int(string, &sel_nr1))
+ {
+ bRet = select_atomnumbers(string, atoms, sel_nr1, nr, index, gname);
+ }
+ else if (parse_names(string, &n_names, names))
+ {
+ bRet = select_atomnames(atoms, n_names, names, nr, index, FALSE);
+ make_gname(n_names, names, gname);
+ }
+ }
+ }
+ else if ((*string)[0] == 't')
+ {
+ (*string)++;
+ if (check_have_atoms(atoms, ostring) &&
+ parse_names(string, &n_names, names))
+ {
+ if (atoms->atomtype == NULL)
+ {
+ printf("Need a run input file to select atom types\n");
+ }
+ else
+ {
+ bRet = select_atomnames(atoms, n_names, names, nr, index, TRUE);
+ make_gname(n_names, names, gname);
+ }
+ }
+ }
+ else if (strncmp(*string, "res", 3) == 0)
+ {
+ (*string) += 3;
+ if (check_have_atoms(atoms, ostring) &&
+ parse_int(string, &sel_nr1) &&
+ (sel_nr1 >= 0) && (sel_nr1 < block->nr) )
+ {
+ bRet = atoms_from_residuenumbers(atoms,
+ sel_nr1, block, nr, index, (*gn)[sel_nr1]);
+ sprintf(gname, "atom_%s", (*gn)[sel_nr1]);
+ }
+ }
+ else if (strncmp(*string, "ri", 2) == 0)
+ {
+ (*string) += 2;
+ if (check_have_atoms(atoms, ostring) &&
+ parse_int_char(string, &sel_nr1, &c))
+ {
+ bRet = select_residueindices(string, atoms, sel_nr1, c, nr, index, gname);
+ }
+ }
+ else if ((*string)[0] == 'r')
+ {
+ (*string)++;
+ if (check_have_atoms(atoms, ostring))
+ {
+ if (parse_int_char(string, &sel_nr1, &c))
+ {
+ bRet = select_residuenumbers(string, atoms, sel_nr1, c, nr, index, gname);
+ }
+ else if (parse_names(string, &n_names, names))
+ {
+ bRet = select_residuenames(atoms, n_names, names, nr, index);
+ make_gname(n_names, names, gname);
+ }
+ }
+ }
+ else if (strncmp(*string, "chain", 5) == 0)
+ {
+ (*string) += 5;
+ if (check_have_atoms(atoms, ostring) &&
+ parse_names(string, &n_names, names))
+ {
+ bRet = select_chainnames(atoms, n_names, names, nr, index);
+ sprintf(gname, "ch%s", names[0]);
+ for (i = 1; i < n_names; i++)
+ {
+ strcat(gname, names[i]);
+ }
+ }
+ }
+ if (bRet && bCompl)
+ {
+ snew(index1, natoms-*nr);
+ nr1 = 0;
+ for (i = 0; i < natoms; i++)
+ {
+ j = 0;
+ while ((j < *nr) && (index[j] != i))
+ {
+ j++;
+ }
+ if (j == *nr)
+ {
+ if (nr1 >= natoms-*nr)
+ {
+ printf("There are double atoms in your index group\n");
+ break;
+ }
+ index1[nr1] = i;
+ nr1++;
+ }
+ }
+ *nr = nr1;
+ for (i = 0; i < nr1; i++)
+ {
+ index[i] = index1[i];
+ }
+ sfree(index1);
+
+ for (i = strlen(gname)+1; i > 0; i--)
+ {
+ gname[i] = gname[i-1];
+ }
+ gname[0] = '!';
+ printf("Complemented group: %u atoms\n", *nr);
+ }
+
+ return bRet;
}
static void list_residues(t_atoms *atoms)
{
- int i,j,start,end,prev_resind,resind;
- gmx_bool bDiff;
-
- /* Print all the residues, assuming continuous resnr count */
- start = atoms->atom[0].resind;
- prev_resind = start;
- for(i=0; i<atoms->nr; i++) {
- resind = atoms->atom[i].resind;
- if ((resind != prev_resind) || (i==atoms->nr-1)) {
- if ((bDiff=strcmp(*atoms->resinfo[resind].name,
- *atoms->resinfo[start].name)) ||
- (i==atoms->nr-1)) {
- if (bDiff)
- end = prev_resind;
- else
- end = resind;
- if (end < start+3)
- for(j=start; j<=end; j++)
- printf("%4d %-5s",
- j+1,*(atoms->resinfo[j].name));
- else
- printf(" %4d - %4d %-5s ",
- start+1,end+1,*(atoms->resinfo[start].name));
- start = resind;
- }
- }
- prev_resind = resind;
- }
- printf("\n");
+ int i, j, start, end, prev_resind, resind;
+ gmx_bool bDiff;
+
+ /* Print all the residues, assuming continuous resnr count */
+ start = atoms->atom[0].resind;
+ prev_resind = start;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ resind = atoms->atom[i].resind;
+ if ((resind != prev_resind) || (i == atoms->nr-1))
+ {
+ if ((bDiff = strcmp(*atoms->resinfo[resind].name,
+ *atoms->resinfo[start].name)) ||
+ (i == atoms->nr-1))
+ {
+ if (bDiff)
+ {
+ end = prev_resind;
+ }
+ else
+ {
+ end = resind;
+ }
+ if (end < start+3)
+ {
+ for (j = start; j <= end; j++)
+ {
+ printf("%4d %-5s",
+ j+1, *(atoms->resinfo[j].name));
+ }
+ }
+ else
+ {
+ printf(" %4d - %4d %-5s ",
+ start+1, end+1, *(atoms->resinfo[start].name));
+ }
+ start = resind;
+ }
+ }
+ prev_resind = resind;
+ }
+ printf("\n");
}
-static void edit_index(int natoms, t_atoms *atoms,rvec *x,t_blocka *block, char ***gn, gmx_bool bVerbose)
+static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, char ***gn, gmx_bool bVerbose)
{
- static char **atnames, *ostring;
- static gmx_bool bFirst=TRUE;
- char inp_string[STRLEN],*string;
- char gname[STRLEN],gname1[STRLEN],gname2[STRLEN];
- int i,i0,i1,sel_nr,sel_nr2,newgroup;
- atom_id nr,nr1,nr2,*index,*index1,*index2;
- gmx_bool bAnd,bOr,bPrintOnce;
-
- if (bFirst) {
- bFirst=FALSE;
- snew(atnames,MAXNAMES);
- for (i=0; i<MAXNAMES; i++)
- snew(atnames[i],NAME_LEN+1);
- }
-
- string=NULL;
-
- snew(index,natoms);
- snew(index1,natoms);
- snew(index2,natoms);
-
- newgroup=NOTSET;
- bPrintOnce = TRUE;
- do {
- gname1[0]='\0';
- if (bVerbose || bPrintOnce || newgroup!=NOTSET) {
- printf("\n");
- if (bVerbose || bPrintOnce || newgroup==NOTSET) {
- i0=0;
- i1=block->nr;
- } else {
- i0=newgroup;
- i1=newgroup+1;
- }
- for(i=i0; i<i1; i++)
- printf("%3d %-20s: %5u atoms\n",i,(*gn)[i],
- block->index[i+1]-block->index[i]);
- newgroup=NOTSET;
- }
- if (bVerbose || bPrintOnce) {
- printf("\n");
- printf(" nr : group ! 'name' nr name 'splitch' nr Enter: list groups\n");
- printf(" 'a': atom & 'del' nr 'splitres' nr 'l': list residues\n");
- printf(" 't': atom type | 'keep' nr 'splitat' nr 'h': help\n");
- printf(" 'r': residue 'res' nr 'chain' char\n");
- printf(" \"name\": group 'case': case %s 'q': save and quit\n",
- bCase ? "insensitive" : "sensitive ");
- printf(" 'ri': residue index\n");
- bPrintOnce = FALSE;
+ static char **atnames, *ostring;
+ static gmx_bool bFirst = TRUE;
+ char inp_string[STRLEN], *string;
+ char gname[STRLEN], gname1[STRLEN], gname2[STRLEN];
+ int i, i0, i1, sel_nr, sel_nr2, newgroup;
+ atom_id nr, nr1, nr2, *index, *index1, *index2;
+ gmx_bool bAnd, bOr, bPrintOnce;
+
+ if (bFirst)
+ {
+ bFirst = FALSE;
+ snew(atnames, MAXNAMES);
+ for (i = 0; i < MAXNAMES; i++)
+ {
+ snew(atnames[i], NAME_LEN+1);
+ }
}
- printf("\n");
- printf("> ");
- if(NULL==fgets(inp_string,STRLEN,stdin))
+
+ string = NULL;
+
+ snew(index, natoms);
+ snew(index1, natoms);
+ snew(index2, natoms);
+
+ newgroup = NOTSET;
+ bPrintOnce = TRUE;
+ do
{
- gmx_fatal(FARGS,"Error reading user input");
+ gname1[0] = '\0';
+ if (bVerbose || bPrintOnce || newgroup != NOTSET)
+ {
+ printf("\n");
+ if (bVerbose || bPrintOnce || newgroup == NOTSET)
+ {
+ i0 = 0;
+ i1 = block->nr;
+ }
+ else
+ {
+ i0 = newgroup;
+ i1 = newgroup+1;
+ }
+ for (i = i0; i < i1; i++)
+ {
+ printf("%3d %-20s: %5u atoms\n", i, (*gn)[i],
+ block->index[i+1]-block->index[i]);
+ }
+ newgroup = NOTSET;
+ }
+ if (bVerbose || bPrintOnce)
+ {
+ printf("\n");
+ printf(" nr : group ! 'name' nr name 'splitch' nr Enter: list groups\n");
+ printf(" 'a': atom & 'del' nr 'splitres' nr 'l': list residues\n");
+ printf(" 't': atom type | 'keep' nr 'splitat' nr 'h': help\n");
+ printf(" 'r': residue 'res' nr 'chain' char\n");
+ printf(" \"name\": group 'case': case %s 'q': save and quit\n",
+ bCase ? "insensitive" : "sensitive ");
+ printf(" 'ri': residue index\n");
+ bPrintOnce = FALSE;
+ }
+ printf("\n");
+ printf("> ");
+ if (NULL == fgets(inp_string, STRLEN, stdin))
+ {
+ gmx_fatal(FARGS, "Error reading user input");
+ }
+ inp_string[strlen(inp_string)-1] = 0;
+ printf("\n");
+ string = inp_string;
+ while (string[0] == ' ')
+ {
+ string++;
+ }
+
+ ostring = string;
+ nr = 0;
+ if (string[0] == 'h')
+ {
+ printf(" nr : selects an index group by number or quoted string.\n");
+ printf(" The string is first matched against the whole group name,\n");
+ printf(" then against the beginning and finally against an\n");
+ printf(" arbitrary substring. A multiple match is an error.\n");
+
+ printf(" 'a' nr1 [nr2 ...] : selects atoms, atom numbering starts at 1.\n");
+ printf(" 'a' nr1 - nr2 : selects atoms in the range from nr1 to nr2.\n");
+ printf(" 'a' name1[*] [name2[*] ...] : selects atoms by name(s), '?' matches any char,\n");
+ printf(" wildcard '*' allowed at the end of a name.\n");
+ printf(" 't' type1[*] [type2[*] ...] : as 'a', but for type, run input file required.\n");
+ printf(" 'r' nr1[ic1] [nr2[ic2] ...] : selects residues by number and insertion code.\n");
+ printf(" 'r' nr1 - nr2 : selects residues in the range from nr1 to nr2.\n");
+ printf(" 'r' name1[*] [name2[*] ...] : as 'a', but for residue names.\n");
+ printf(" 'ri' nr1 - nr2 : selects residue indices, 1-indexed, (as opposed to numbers) in the range from nr1 to nr2.\n");
+ printf(" 'chain' ch1 [ch2 ...] : selects atoms by chain identifier(s),\n");
+ printf(" not available with a .gro file as input.\n");
+ printf(" ! : takes the complement of a group with respect to all\n");
+ printf(" the atoms in the input file.\n");
+ printf(" & | : AND and OR, can be placed between any of the options\n");
+ printf(" above, the input is processed from left to right.\n");
+ printf(" 'name' nr name : rename group nr to name.\n");
+ printf(" 'del' nr1 [- nr2] : deletes one group or groups in the range from nr1 to nr2.\n");
+ printf(" 'keep' nr : deletes all groups except nr.\n");
+ printf(" 'case' : make all name compares case (in)sensitive.\n");
+ printf(" 'splitch' nr : split group into chains using CA distances.\n");
+ printf(" 'splitres' nr : split group into residues.\n");
+ printf(" 'splitat' nr : split group into atoms.\n");
+ printf(" 'res' nr : interpret numbers in group as residue numbers\n");
+ printf(" Enter : list the currently defined groups and commands\n");
+ printf(" 'l' : list the residues.\n");
+ printf(" 'h' : show this help.\n");
+ printf(" 'q' : save and quit.\n");
+ printf("\n");
+ printf(" Examples:\n");
+ printf(" > 2 | 4 & r 3-5\n");
+ printf(" selects all atoms from group 2 and 4 that have residue numbers 3, 4 or 5\n");
+ printf(" > a C* & !a C CA\n");
+ printf(" selects all atoms starting with 'C' but not the atoms 'C' and 'CA'\n");
+ printf(" > \"protein\" & ! \"backb\"\n");
+ printf(" selects all atoms that are in group 'protein' and not in group 'backbone'\n");
+ if (bVerbose)
+ {
+ printf("\npress Enter ");
+ getchar();
+ }
+ }
+ else if (strncmp(string, "del", 3) == 0)
+ {
+ string += 3;
+ if (parse_int(&string, &sel_nr))
+ {
+ while (string[0] == ' ')
+ {
+ string++;
+ }
+ if (string[0] == '-')
+ {
+ string++;
+ parse_int(&string, &sel_nr2);
+ }
+ else
+ {
+ sel_nr2 = NOTSET;
+ }
+ while (string[0] == ' ')
+ {
+ string++;
+ }
+ if (string[0] == '\0')
+ {
+ remove_group(sel_nr, sel_nr2, block, gn);
+ }
+ else
+ {
+ printf("\nSyntax error: \"%s\"\n", string);
+ }
+ }
+ }
+ else if (strncmp(string, "keep", 4) == 0)
+ {
+ string += 4;
+ if (parse_int(&string, &sel_nr))
+ {
+ remove_group(sel_nr+1, block->nr-1, block, gn);
+ remove_group(0, sel_nr-1, block, gn);
+ }
+ }
+ else if (strncmp(string, "name", 4) == 0)
+ {
+ string += 4;
+ if (parse_int(&string, &sel_nr))
+ {
+ if ((sel_nr >= 0) && (sel_nr < block->nr))
+ {
+ sscanf(string, "%s", gname);
+ sfree((*gn)[sel_nr]);
+ (*gn)[sel_nr] = strdup(gname);
+ }
+ }
+ }
+ else if (strncmp(string, "case", 4) == 0)
+ {
+ bCase = !bCase;
+ printf("Switched to case %s\n", bCase ? "sensitive" : "insensitive");
+ }
+ else if (string[0] == 'v')
+ {
+ bVerbose = !bVerbose;
+ printf("Turned verbose %s\n", bVerbose ? "on" : "off");
+ }
+ else if (string[0] == 'l')
+ {
+ if (check_have_atoms(atoms, ostring) )
+ {
+ list_residues(atoms);
+ }
+ }
+ else if (strncmp(string, "splitch", 7) == 0)
+ {
+ string += 7;
+ if (check_have_atoms(atoms, ostring) &&
+ parse_int(&string, &sel_nr) &&
+ (sel_nr >= 0) && (sel_nr < block->nr))
+ {
+ split_chain(atoms, x, sel_nr, block, gn);
+ }
+ }
+ else if (strncmp(string, "splitres", 8) == 0)
+ {
+ string += 8;
+ if (check_have_atoms(atoms, ostring) &&
+ parse_int(&string, &sel_nr) &&
+ (sel_nr >= 0) && (sel_nr < block->nr))
+ {
+ split_group(atoms, sel_nr, block, gn, FALSE);
+ }
+ }
+ else if (strncmp(string, "splitat", 7) == 0)
+ {
+ string += 7;
+ if (check_have_atoms(atoms, ostring) &&
+ parse_int(&string, &sel_nr) &&
+ (sel_nr >= 0) && (sel_nr < block->nr))
+ {
+ split_group(atoms, sel_nr, block, gn, TRUE);
+ }
+ }
+ else if (string[0] == '\0')
+ {
+ bPrintOnce = TRUE;
+ }
+ else if (string[0] != 'q')
+ {
+ nr1 = -1;
+ nr2 = -1;
+ if (parse_entry(&string, natoms, atoms, block, gn, &nr, index, gname))
+ {
+ do
+ {
+ while (string[0] == ' ')
+ {
+ string++;
+ }
+
+ bAnd = FALSE;
+ bOr = FALSE;
+ if (string[0] == '&')
+ {
+ bAnd = TRUE;
+ }
+ else if (string[0] == '|')
+ {
+ bOr = TRUE;
+ }
+
+ if (bAnd || bOr)
+ {
+ string++;
+ nr1 = nr;
+ for (i = 0; i < nr; i++)
+ {
+ index1[i] = index[i];
+ }
+ strcpy(gname1, gname);
+ if (parse_entry(&string, natoms, atoms, block, gn, &nr2, index2, gname2))
+ {
+ if (bOr)
+ {
+ or_groups(nr1, index1, nr2, index2, &nr, index);
+ sprintf(gname, "%s_%s", gname1, gname2);
+ }
+ else
+ {
+ and_groups(nr1, index1, nr2, index2, &nr, index);
+ sprintf(gname, "%s_&_%s", gname1, gname2);
+ }
+ }
+ }
+ }
+ while (bAnd || bOr);
+ }
+ while (string[0] == ' ')
+ {
+ string++;
+ }
+ if (string[0])
+ {
+ printf("\nSyntax error: \"%s\"\n", string);
+ }
+ else if (nr > 0)
+ {
+ copy2block(nr, index, block);
+ srenew(*gn, block->nr);
+ newgroup = block->nr-1;
+ (*gn)[newgroup] = strdup(gname);
+ }
+ else
+ {
+ printf("Group is empty\n");
+ }
+ }
}
- inp_string[strlen(inp_string)-1]=0;
- printf("\n");
- string=inp_string;
- while (string[0]==' ')
- string++;
-
- ostring = string;
- nr=0;
- if (string[0] == 'h') {
- printf(" nr : selects an index group by number or quoted string.\n");
- printf(" The string is first matched against the whole group name,\n");
- printf(" then against the beginning and finally against an\n");
- printf(" arbitrary substring. A multiple match is an error.\n");
-
- printf(" 'a' nr1 [nr2 ...] : selects atoms, atom numbering starts at 1.\n");
- printf(" 'a' nr1 - nr2 : selects atoms in the range from nr1 to nr2.\n");
- printf(" 'a' name1[*] [name2[*] ...] : selects atoms by name(s), '?' matches any char,\n");
- printf(" wildcard '*' allowed at the end of a name.\n");
- printf(" 't' type1[*] [type2[*] ...] : as 'a', but for type, run input file required.\n");
- printf(" 'r' nr1[ic1] [nr2[ic2] ...] : selects residues by number and insertion code.\n");
- printf(" 'r' nr1 - nr2 : selects residues in the range from nr1 to nr2.\n");
- printf(" 'r' name1[*] [name2[*] ...] : as 'a', but for residue names.\n");
- printf(" 'ri' nr1 - nr2 : selects residue indices, 1-indexed, (as opposed to numbers) in the range from nr1 to nr2.\n");
- printf(" 'chain' ch1 [ch2 ...] : selects atoms by chain identifier(s),\n");
- printf(" not available with a .gro file as input.\n");
- printf(" ! : takes the complement of a group with respect to all\n");
- printf(" the atoms in the input file.\n");
- printf(" & | : AND and OR, can be placed between any of the options\n");
- printf(" above, the input is processed from left to right.\n");
- printf(" 'name' nr name : rename group nr to name.\n");
- printf(" 'del' nr1 [- nr2] : deletes one group or groups in the range from nr1 to nr2.\n");
- printf(" 'keep' nr : deletes all groups except nr.\n");
- printf(" 'case' : make all name compares case (in)sensitive.\n");
- printf(" 'splitch' nr : split group into chains using CA distances.\n");
- printf(" 'splitres' nr : split group into residues.\n");
- printf(" 'splitat' nr : split group into atoms.\n");
- printf(" 'res' nr : interpret numbers in group as residue numbers\n");
- printf(" Enter : list the currently defined groups and commands\n");
- printf(" 'l' : list the residues.\n");
- printf(" 'h' : show this help.\n");
- printf(" 'q' : save and quit.\n");
- printf("\n");
- printf(" Examples:\n");
- printf(" > 2 | 4 & r 3-5\n");
- printf(" selects all atoms from group 2 and 4 that have residue numbers 3, 4 or 5\n");
- printf(" > a C* & !a C CA\n");
- printf(" selects all atoms starting with 'C' but not the atoms 'C' and 'CA'\n");
- printf(" > \"protein\" & ! \"backb\"\n");
- printf(" selects all atoms that are in group 'protein' and not in group 'backbone'\n");
- if (bVerbose) {
- printf("\npress Enter ");
- getchar();
- }
- }
- else if (strncmp(string,"del",3)==0) {
- string+=3;
- if (parse_int(&string,&sel_nr)) {
- while(string[0]==' ')
- string++;
- if (string[0]=='-') {
- string++;
- parse_int(&string,&sel_nr2);
- } else
- sel_nr2=NOTSET;
- while(string[0]==' ')
- string++;
- if (string[0]=='\0')
- remove_group(sel_nr,sel_nr2,block,gn);
- else
- printf("\nSyntax error: \"%s\"\n",string);
- }
- }
- else if (strncmp(string,"keep",4)==0) {
- string+=4;
- if (parse_int(&string,&sel_nr)) {
- remove_group(sel_nr+1,block->nr-1,block,gn);
- remove_group(0,sel_nr-1,block,gn);
- }
- }
- else if (strncmp(string,"name",4)==0) {
- string+=4;
- if (parse_int(&string,&sel_nr)) {
- if ((sel_nr>=0) && (sel_nr<block->nr)) {
- sscanf(string,"%s",gname);
- sfree((*gn)[sel_nr]);
- (*gn)[sel_nr]=strdup(gname);
- }
- }
- }
- else if (strncmp(string,"case",4)==0) {
- bCase=!bCase;
- printf("Switched to case %s\n",bCase ? "sensitive" : "insensitive");
- }
- else if (string[0] == 'v' ) {
- bVerbose=!bVerbose;
- printf("Turned verbose %s\n",bVerbose ? "on" : "off");
- }
- else if (string[0] == 'l') {
- if ( check_have_atoms(atoms, ostring) )
- list_residues(atoms);
- }
- else if (strncmp(string,"splitch",7)==0) {
- string+=7;
- if ( check_have_atoms(atoms, ostring) &&
- parse_int(&string,&sel_nr) &&
- (sel_nr>=0) && (sel_nr<block->nr))
- split_chain(atoms,x,sel_nr,block,gn);
- }
- else if (strncmp(string,"splitres",8)==0 ) {
- string+=8;
- if ( check_have_atoms(atoms, ostring) &&
- parse_int(&string,&sel_nr) &&
- (sel_nr>=0) && (sel_nr<block->nr))
- split_group(atoms,sel_nr,block,gn,FALSE);
- }
- else if (strncmp(string,"splitat",7)==0 ) {
- string+=7;
- if ( check_have_atoms(atoms, ostring) &&
- parse_int(&string,&sel_nr) &&
- (sel_nr>=0) && (sel_nr<block->nr))
- split_group(atoms,sel_nr,block,gn,TRUE);
- }
- else if (string[0] == '\0') {
- bPrintOnce = TRUE;
- }
- else if (string[0] != 'q') {
- nr1=-1;
- nr2=-1;
- if (parse_entry(&string,natoms,atoms,block,gn,&nr,index,gname)) {
- do {
- while (string[0]==' ')
- string++;
-
- bAnd=FALSE;
- bOr=FALSE;
- if (string[0]=='&')
- bAnd=TRUE;
- else if (string[0]=='|')
- bOr=TRUE;
-
- if (bAnd || bOr) {
- string++;
- nr1=nr;
- for(i=0; i<nr; i++)
- index1[i]=index[i];
- strcpy(gname1,gname);
- if (parse_entry(&string,natoms,atoms,block,gn,&nr2,index2,gname2)) {
- if (bOr) {
- or_groups(nr1,index1,nr2,index2,&nr,index);
- sprintf(gname,"%s_%s",gname1,gname2);
- }
- else {
- and_groups(nr1,index1,nr2,index2,&nr,index);
- sprintf(gname,"%s_&_%s",gname1,gname2);
- }
- }
- }
- } while (bAnd || bOr);
- }
- while(string[0]==' ')
- string++;
- if (string[0])
- printf("\nSyntax error: \"%s\"\n",string);
- else if (nr>0) {
- copy2block(nr,index,block);
- srenew(*gn,block->nr);
- newgroup = block->nr-1;
- (*gn)[newgroup]=strdup(gname);
- }
- else
- printf("Group is empty\n");
- }
- } while (string[0]!='q');
-
- sfree(index);
- sfree(index1);
- sfree(index2);
+ while (string[0] != 'q');
+
+ sfree(index);
+ sfree(index1);
+ sfree(index2);
}
static int block2natoms(t_blocka *block)
{
- int i, natoms;
-
- natoms = 0;
- for(i=0; i<block->nra; i++)
- natoms = max(natoms, block->a[i]);
- natoms++;
-
- return natoms;
+ int i, natoms;
+
+ natoms = 0;
+ for (i = 0; i < block->nra; i++)
+ {
+ natoms = max(natoms, block->a[i]);
+ }
+ natoms++;
+
+ return natoms;
}
void merge_blocks(t_blocka *dest, t_blocka *source)
{
- int i,nra0,i0;
-
- /* count groups, srenew and fill */
- i0 = dest->nr;
- nra0 = dest->nra;
- dest->nr+=source->nr;
- srenew(dest->index, dest->nr+1);
- for(i=0; i<source->nr; i++)
- dest->index[i0+i] = nra0 + source->index[i];
- /* count atoms, srenew and fill */
- dest->nra+=source->nra;
- srenew(dest->a, dest->nra);
- for(i=0; i<source->nra; i++)
- dest->a[nra0+i] = source->a[i];
-
- /* terminate list */
- dest->index[dest->nr]=dest->nra;
-
+ int i, nra0, i0;
+
+ /* count groups, srenew and fill */
+ i0 = dest->nr;
+ nra0 = dest->nra;
+ dest->nr += source->nr;
+ srenew(dest->index, dest->nr+1);
+ for (i = 0; i < source->nr; i++)
+ {
+ dest->index[i0+i] = nra0 + source->index[i];
+ }
+ /* count atoms, srenew and fill */
+ dest->nra += source->nra;
+ srenew(dest->a, dest->nra);
+ for (i = 0; i < source->nra; i++)
+ {
+ dest->a[nra0+i] = source->a[i];
+ }
+
+ /* terminate list */
+ dest->index[dest->nr] = dest->nra;
+
}
-int gmx_make_ndx(int argc,char *argv[])
+int gmx_make_ndx(int argc, char *argv[])
{
- const char *desc[] = {
- "Index groups are necessary for almost every gromacs program.",
- "All these programs can generate default index groups. You ONLY",
- "have to use [TT]make_ndx[tt] when you need SPECIAL index groups.",
- "There is a default index group for the whole system, 9 default",
- "index groups for proteins, and a default index group",
- "is generated for every other residue name.[PAR]",
- "When no index file is supplied, also [TT]make_ndx[tt] will generate the",
- "default groups.",
- "With the index editor you can select on atom, residue and chain names",
- "and numbers.",
- "When a run input file is supplied you can also select on atom type.",
- "You can use NOT, AND and OR, you can split groups",
- "into chains, residues or atoms. You can delete and rename groups.[PAR]",
- "The atom numbering in the editor and the index file starts at 1."
- };
-
- static int natoms=0;
- static gmx_bool bVerbose=FALSE;
- t_pargs pa[] = {
- { "-natoms", FALSE, etINT, {&natoms},
- "set number of atoms (default: read from coordinate or index file)" },
- { "-verbose", FALSE, etBOOL, {&bVerbose},
- "HIDDENVerbose output" }
- };
+ const char *desc[] = {
+ "Index groups are necessary for almost every gromacs program.",
+ "All these programs can generate default index groups. You ONLY",
+ "have to use [TT]make_ndx[tt] when you need SPECIAL index groups.",
+ "There is a default index group for the whole system, 9 default",
+ "index groups for proteins, and a default index group",
+ "is generated for every other residue name.[PAR]",
+ "When no index file is supplied, also [TT]make_ndx[tt] will generate the",
+ "default groups.",
+ "With the index editor you can select on atom, residue and chain names",
+ "and numbers.",
+ "When a run input file is supplied you can also select on atom type.",
+ "You can use NOT, AND and OR, you can split groups",
+ "into chains, residues or atoms. You can delete and rename groups.[PAR]",
+ "The atom numbering in the editor and the index file starts at 1."
+ };
+
+ static int natoms = 0;
+ static gmx_bool bVerbose = FALSE;
+ t_pargs pa[] = {
+ { "-natoms", FALSE, etINT, {&natoms},
+ "set number of atoms (default: read from coordinate or index file)" },
+ { "-verbose", FALSE, etBOOL, {&bVerbose},
+ "HIDDENVerbose output" }
+ };
#define NPA asize(pa)
- output_env_t oenv;
- char title[STRLEN];
- int nndxin;
- const char *stxfile;
- char **ndxinfiles;
- const char *ndxoutfile;
- gmx_bool bNatoms;
- int i,j;
- t_atoms *atoms;
- rvec *x,*v;
- int ePBC;
- matrix box;
- t_blocka *block,*block2;
- char **gnames,**gnames2;
- t_filenm fnm[] = {
- { efSTX, "-f", NULL, ffOPTRD },
- { efNDX, "-n", NULL, ffOPTRDMULT },
- { efNDX, "-o", NULL, ffWRITE }
- };
+ output_env_t oenv;
+ char title[STRLEN];
+ int nndxin;
+ const char *stxfile;
+ char **ndxinfiles;
+ const char *ndxoutfile;
+ gmx_bool bNatoms;
+ int i, j;
+ t_atoms *atoms;
+ rvec *x, *v;
+ int ePBC;
+ matrix box;
+ t_blocka *block, *block2;
+ char **gnames, **gnames2;
+ t_filenm fnm[] = {
+ { efSTX, "-f", NULL, ffOPTRD },
+ { efNDX, "-n", NULL, ffOPTRDMULT },
+ { efNDX, "-o", NULL, ffWRITE }
+ };
#define NFILE asize(fnm)
-
- parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa,asize(desc),desc,
- 0,NULL,&oenv);
-
- stxfile = ftp2fn_null(efSTX,NFILE,fnm);
- if (opt2bSet("-n",NFILE,fnm)) {
- nndxin = opt2fns(&ndxinfiles,"-n",NFILE,fnm);
- } else {
- nndxin = 0;
- }
- ndxoutfile = opt2fn("-o",NFILE,fnm);
- bNatoms = opt2parg_bSet("-natoms",NPA,pa);
-
- if (!stxfile && !nndxin)
- gmx_fatal(FARGS,"No input files (structure or index)");
-
- if (stxfile) {
- snew(atoms,1);
- get_stx_coordnum(stxfile,&(atoms->nr));
- init_t_atoms(atoms,atoms->nr,TRUE);
- snew(x,atoms->nr);
- snew(v,atoms->nr);
- fprintf(stderr,"\nReading structure file\n");
- read_stx_conf(stxfile,title,atoms,x,v,&ePBC,box);
- natoms = atoms->nr;
- bNatoms=TRUE;
- } else {
- atoms = NULL;
- x = NULL;
- }
-
- /* read input file(s) */
- block = new_blocka();
- gnames = NULL;
- printf("Going to read %d old index file(s)\n",nndxin);
- if (nndxin) {
- for(i=0; i<nndxin; i++) {
- block2 = init_index(ndxinfiles[i],&gnames2);
- srenew(gnames, block->nr+block2->nr);
- for(j=0; j<block2->nr; j++)
- gnames[block->nr+j]=gnames2[j];
- sfree(gnames2);
- merge_blocks(block, block2);
- sfree(block2->a);
- sfree(block2->index);
+
+ parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
+ 0, NULL, &oenv);
+
+ stxfile = ftp2fn_null(efSTX, NFILE, fnm);
+ if (opt2bSet("-n", NFILE, fnm))
+ {
+ nndxin = opt2fns(&ndxinfiles, "-n", NFILE, fnm);
+ }
+ else
+ {
+ nndxin = 0;
+ }
+ ndxoutfile = opt2fn("-o", NFILE, fnm);
+ bNatoms = opt2parg_bSet("-natoms", NPA, pa);
+
+ if (!stxfile && !nndxin)
+ {
+ gmx_fatal(FARGS, "No input files (structure or index)");
+ }
+
+ if (stxfile)
+ {
+ snew(atoms, 1);
+ get_stx_coordnum(stxfile, &(atoms->nr));
+ init_t_atoms(atoms, atoms->nr, TRUE);
+ snew(x, atoms->nr);
+ snew(v, atoms->nr);
+ fprintf(stderr, "\nReading structure file\n");
+ read_stx_conf(stxfile, title, atoms, x, v, &ePBC, box);
+ natoms = atoms->nr;
+ bNatoms = TRUE;
+ }
+ else
+ {
+ atoms = NULL;
+ x = NULL;
+ }
+
+ /* read input file(s) */
+ block = new_blocka();
+ gnames = NULL;
+ printf("Going to read %d old index file(s)\n", nndxin);
+ if (nndxin)
+ {
+ for (i = 0; i < nndxin; i++)
+ {
+ block2 = init_index(ndxinfiles[i], &gnames2);
+ srenew(gnames, block->nr+block2->nr);
+ for (j = 0; j < block2->nr; j++)
+ {
+ gnames[block->nr+j] = gnames2[j];
+ }
+ sfree(gnames2);
+ merge_blocks(block, block2);
+ sfree(block2->a);
+ sfree(block2->index);
/* done_block(block2); */
- sfree(block2);
- }
- }
- else {
- snew(gnames,1);
- analyse(atoms,block,&gnames,FALSE,TRUE);
- }
-
- if (!bNatoms) {
- natoms = block2natoms(block);
- printf("Counted atom numbers up to %d in index file\n", natoms);
- }
-
- edit_index(natoms,atoms,x,block,&gnames,bVerbose);
-
- write_index(ndxoutfile,block,gnames);
-
- thanx(stderr);
-
- return 0;
+ sfree(block2);
+ }
+ }
+ else
+ {
+ snew(gnames, 1);
+ analyse(atoms, block, &gnames, FALSE, TRUE);
+ }
+
+ if (!bNatoms)
+ {
+ natoms = block2natoms(block);
+ printf("Counted atom numbers up to %d in index file\n", natoms);
+ }
+
+ edit_index(natoms, atoms, x, block, &gnames, bVerbose);
+
+ write_index(ndxoutfile, block, gnames);
+
+ thanx(stderr);
+
+ return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff