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: %5d 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] = gmx_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] = gmx_strdup(gname);
}
else
{
printf("Group is empty\n");
}
}
}
while (string[0] != 'q');
sfree(index);
sfree(index1);
sfree(index2);
}
static 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 bool bFirst=TRUE;
int j,n_names,sel_nr1;
atom_id i,nr1,*index1;
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 ((*string)[0]=='r') {
(*string)++;
if (check_have_atoms(atoms, ostring)) {
if (parse_int(string,&sel_nr1)) {
bRet=select_residuenumbers(string,atoms,sel_nr1,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;
}
