static void analyse_prot(const char ** restype,t_atoms *atoms,
t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
{
/* atomnames to be used in constructing index groups: */
static const char *pnoh[] = { "H" };
static const char *pnodum[] = { "MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
"MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2" };
static const char *calpha[] = { "CA" };
static const char *bb[] = { "N","CA","C" };
static const char *mc[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT" };
static const char *mcb[] = { "N","CA","CB","C","O","O1","O2","OC1","OC2","OT","OXT" };
static const char *mch[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT",
"H1","H2","H3","H" };
/* array of arrays of atomnames: */
static const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
#define NCH asize(chains)
/* array of sizes of arrays of atomnames: */
const int sizes[NCH] = {
0, asize(pnoh), asize(calpha), asize(bb),
asize(mc), asize(mcb), asize(mch), asize(mch), asize(mch), asize(pnodum)
};
/* descriptive names of index groups */
const char *ch_name[NCH] = {
"Protein", "Protein-H", "C-alpha", "Backbone",
"MainChain", "MainChain+Cb", "MainChain+H", "SideChain", "SideChain-H",
"Prot-Masses"
};
/* construct index group containing (TRUE) or excluding (FALSE)
given atom names */
const gmx_bool complement[NCH] = {
TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE
};
const int wholename[NCH] = { -1, 0,-1,-1,-1,-1,-1,-1, 11,-1 };
/* the index in wholename gives the first item in the arrays of
* atomtypes that should be tested with 'gmx_strncasecmp' in stead of
* gmx_strcasecmp, or -1 if all items should be tested with strcasecmp
* This is comparable to using a '*' wildcard at the end of specific
* atom names, but that is more involved to implement...
*/
/* only add index group if it differs from the specified one,
specify -1 to always add group */
const int compareto[NCH] = { -1,-1,-1,-1,-1,-1,-1,-1,-1, 0 };
int n,j;
atom_id *aid;
int nra,nnpres,npres;
gmx_bool match;
char ndx_name[STRLEN],*atnm;
int i;
if (bVerb)
{
printf("Analysing Protein...\n");
}
snew(aid,atoms->nr);
/* calculate the number of protein residues */
npres=0;
for(i=0; (i<atoms->nres); i++)
if (!gmx_strcasecmp(restype[i],"Protein"))
{
npres++;
}
/* find matching or complement atoms */
for(i=0; (i<(int)NCH); i++) {
nra=0;
for(n=0; (n<atoms->nr); n++) {
if (!gmx_strcasecmp(restype[atoms->atom[n].resind],"Protein")) {
match=FALSE;
for(j=0; (j<sizes[i]); j++) {
/* skip digits at beginning of atomname, e.g. 1H */
atnm=*atoms->atomname[n];
while (isdigit(atnm[0]))
atnm++;
if ( (wholename[i]==-1) || (j<wholename[i]) ) {
if (gmx_strcasecmp(chains[i][j],atnm) == 0)
match=TRUE;
} else {
if (gmx_strncasecmp(chains[i][j],atnm,strlen(chains[i][j])) == 0)
match=TRUE;
}
}
if (match != complement[i])
aid[nra++]=n;
}
}
/* if we want to add this group always or it differs from previous
group, add it: */
if ( compareto[i] == -1 || !grp_cmp(gb,nra,aid,compareto[i]-i) )
add_grp(gb,gn,nra,aid,ch_name[i]);
}
if (bASK) {
for(i=0; (i<(int)NCH); i++) {
printf("Split %12s into %5d residues (y/n) ? ",ch_name[i],npres);
if (gmx_ask_yesno(bASK)) {
int resind;
nra = 0;
for(n=0;((atoms->atom[n].resind < npres) && (n<atoms->nr));) {
resind = atoms->atom[n].resind;
for(;((atoms->atom[n].resind==resind) && (n<atoms->nr));n++) {
match=FALSE;
for(j=0;(j<sizes[i]); j++)
if (gmx_strcasecmp(chains[i][j],*atoms->atomname[n]) == 0)
match=TRUE;
if (match != complement[i])
aid[nra++]=n;
}
/* copy the residuename to the tail of the groupname */
if (nra > 0) {
t_resinfo *ri;
ri = &atoms->resinfo[resind];
sprintf(ndx_name,"%s_%s%d%c",
ch_name[i],*ri->name,ri->nr,ri->ic==' ' ? '\0' : ri->ic);
add_grp(gb,gn,nra,aid,ndx_name);
nra = 0;
}
}
}
}
printf("Make group with sidechain and C=O swapped (y/n) ? ");
if (gmx_ask_yesno(bASK)) {
/* Make swap sidechain C=O index */
int resind,hold;
nra = 0;
for(n=0;((atoms->atom[n].resind < npres) && (n<atoms->nr));) {
resind = atoms->atom[n].resind;
hold = -1;
for(;((atoms->atom[n].resind==resind) && (n<atoms->nr));n++)
if (strcmp("CA",*atoms->atomname[n]) == 0) {
aid[nra++]=n;
hold=nra;
nra+=2;
} else if (strcmp("C",*atoms->atomname[n]) == 0) {
if (hold == -1)
gmx_incons("Atom naming problem");
aid[hold]=n;
} else if (strcmp("O",*atoms->atomname[n]) == 0) {
if (hold == -1)
gmx_incons("Atom naming problem");
aid[hold+1]=n;
} else if (strcmp("O1",*atoms->atomname[n]) == 0) {
if (hold == -1)
gmx_incons("Atom naming problem");
aid[hold+1]=n;
} else
aid[nra++]=n;
}
/* copy the residuename to the tail of the groupname */
if (nra > 0) {
add_grp(gb,gn,nra,aid,"SwapSC-CO");
nra = 0;
}
}
}
sfree(aid);
}
static void analyse_prot(const char ** restype, t_atoms *atoms,
t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
{
/* lists of atomnames to be used in constructing index groups: */
static const char *pnoh[] = { "H", "HN" };
static const char *pnodum[] = {
"MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
"MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2"
};
static const char *calpha[] = { "CA" };
static const char *bb[] = { "N", "CA", "C" };
static const char *mc[] = { "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
static const char *mcb[] = { "N", "CA", "CB", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
static const char *mch[] = {
"N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT",
"H1", "H2", "H3", "H", "HN"
};
static const t_gmx_help_make_index_group constructing_data[] =
{{ NULL, 0, "Protein", TRUE, -1, -1},
{ pnoh, asize(pnoh), "Protein-H", TRUE, 0, -1},
{ calpha, asize(calpha), "C-alpha", FALSE, -1, -1},
{ bb, asize(bb), "Backbone", FALSE, -1, -1},
{ mc, asize(mc), "MainChain", FALSE, -1, -1},
{ mcb, asize(mcb), "MainChain+Cb", FALSE, -1, -1},
{ mch, asize(mch), "MainChain+H", FALSE, -1, -1},
{ mch, asize(mch), "SideChain", TRUE, -1, -1},
{ mch, asize(mch), "SideChain-H", TRUE, 11, -1},
{ pnodum, asize(pnodum), "Prot-Masses", TRUE, -1, 0}, };
const int num_index_groups = asize(constructing_data);
int n, j;
atom_id *aid;
int nra, nnpres, npres;
gmx_bool match;
char ndx_name[STRLEN], *atnm;
int i;
if (bVerb)
{
printf("Analysing Protein...\n");
}
snew(aid, atoms->nr);
/* calculate the number of protein residues */
npres = 0;
for (i = 0; (i < atoms->nres); i++)
{
if (0 == gmx_strcasecmp(restype[i], "Protein"))
{
npres++;
}
}
/* find matching or complement atoms */
for (i = 0; (i < (int)num_index_groups); i++)
{
nra = 0;
for (n = 0; (n < atoms->nr); n++)
{
if (0 == gmx_strcasecmp(restype[atoms->atom[n].resind], "Protein"))
{
match = FALSE;
for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
{
/* skip digits at beginning of atomname, e.g. 1H */
atnm = *atoms->atomname[n];
while (isdigit(atnm[0]))
{
atnm++;
}
if ( (constructing_data[i].wholename == -1) || (j < constructing_data[i].wholename) )
{
if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], atnm))
{
match = TRUE;
}
}
else
{
if (0 == gmx_strncasecmp(constructing_data[i].defining_atomnames[j], atnm, strlen(constructing_data[i].defining_atomnames[j])))
{
match = TRUE;
}
}
}
if (constructing_data[i].bTakeComplement != match)
{
aid[nra++] = n;
}
}
}
/* if we want to add this group always or it differs from previous
group, add it: */
if (-1 == constructing_data[i].compareto || !grp_cmp(gb, nra, aid, constructing_data[i].compareto-i) )
{
add_grp(gb, gn, nra, aid, constructing_data[i].group_name);
}
}
if (bASK)
{
for (i = 0; (i < (int)num_index_groups); i++)
{
printf("Split %12s into %5d residues (y/n) ? ", constructing_data[i].group_name, npres);
if (gmx_ask_yesno(bASK))
{
int resind;
nra = 0;
for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
{
resind = atoms->atom[n].resind;
for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
{
match = FALSE;
for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
{
if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], *atoms->atomname[n]))
{
match = TRUE;
}
}
if (constructing_data[i].bTakeComplement != match)
{
aid[nra++] = n;
}
}
/* copy the residuename to the tail of the groupname */
if (nra > 0)
{
t_resinfo *ri;
ri = &atoms->resinfo[resind];
sprintf(ndx_name, "%s_%s%d%c",
constructing_data[i].group_name, *ri->name, ri->nr, ri->ic == ' ' ? '\0' : ri->ic);
add_grp(gb, gn, nra, aid, ndx_name);
nra = 0;
}
}
}
}
printf("Make group with sidechain and C=O swapped (y/n) ? ");
if (gmx_ask_yesno(bASK))
{
/* Make swap sidechain C=O index */
int resind, hold;
nra = 0;
for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
{
resind = atoms->atom[n].resind;
hold = -1;
for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
{
if (strcmp("CA", *atoms->atomname[n]) == 0)
{
aid[nra++] = n;
hold = nra;
nra += 2;
}
else if (strcmp("C", *atoms->atomname[n]) == 0)
{
if (hold == -1)
{
gmx_incons("Atom naming problem");
}
aid[hold] = n;
}
else if (strcmp("O", *atoms->atomname[n]) == 0)
{
if (hold == -1)
{
gmx_incons("Atom naming problem");
}
aid[hold+1] = n;
}
else if (strcmp("O1", *atoms->atomname[n]) == 0)
{
if (hold == -1)
{
gmx_incons("Atom naming problem");
}
aid[hold+1] = n;
}
else
{
aid[nra++] = n;
}
}
}
/* copy the residuename to the tail of the groupname */
if (nra > 0)
{
add_grp(gb, gn, nra, aid, "SwapSC-CO");
nra = 0;
}
}
}
sfree(aid);
}
