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 [THISMODULE] 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.",
"",
"When no index file is supplied, also [THISMODULE] 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 boolean operations, you can split groups",
"into chains, residues or atoms. You can delete and rename groups.",
"Type 'h' in the editor for more details.",
"",
"The atom numbering in the editor and the index file starts at 1.",
"",
"The [TT]-twin[tt] switch duplicates all index groups with an offset of",
"[TT]-natoms[tt], which is useful for Computational Electrophysiology",
"double-layer membrane setups.",
"",
"See also [gmx-select] [TT]-on[tt], which provides an alternative way",
"for constructing index groups. It covers nearly all of [THISMODULE]",
"functionality, and in many cases much more."
};
static int natoms = 0;
static gmx_bool bVerbose = FALSE;
static gmx_bool bDuplicate = FALSE;
t_pargs pa[] = {
{ "-natoms", FALSE, etINT, {&natoms},
"set number of atoms (default: read from coordinate or index file)" },
{ "-twin", FALSE, etBOOL, {&bDuplicate},
"Duplicate all index groups with an offset of -natoms" },
{ "-verbose", FALSE, etBOOL, {&bVerbose},
"HIDDENVerbose output" }
};
#define NPA asize(pa)
gmx_output_env_t *oenv;
const char *stxfile;
const char *ndxoutfile;
gmx_bool bNatoms;
int j;
t_atoms *atoms;
rvec *x, *v;
int ePBC;
matrix box;
t_blocka *block, *block2;
char **gnames, **gnames2;
t_filenm fnm[] = {
{ efSTX, "-f", nullptr, ffOPTRD },
{ efNDX, "-n", nullptr, ffOPTRDMULT },
{ efNDX, "-o", nullptr, ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
0, nullptr, &oenv))
{
return 0;
}
stxfile = ftp2fn_null(efSTX, NFILE, fnm);
gmx::ArrayRef<const std::string> ndxInFiles = opt2fnsIfOptionSet("-n", NFILE, fnm);
ndxoutfile = opt2fn("-o", NFILE, fnm);
bNatoms = opt2parg_bSet("-natoms", NPA, pa);
if (!stxfile && ndxInFiles.empty())
{
gmx_fatal(FARGS, "No input files (structure or index)");
}
if (stxfile)
{
t_topology *top;
snew(top, 1);
fprintf(stderr, "\nReading structure file\n");
read_tps_conf(stxfile, top, &ePBC, &x, &v, box, FALSE);
atoms = &top->atoms;
if (atoms->pdbinfo == nullptr)
{
snew(atoms->pdbinfo, atoms->nr);
}
natoms = atoms->nr;
bNatoms = TRUE;
}
else
{
atoms = nullptr;
x = nullptr;
}
/* read input file(s) */
block = new_blocka();
gnames = nullptr;
printf("Going to read %td old index file(s)\n", ndxInFiles.size());
if (!ndxInFiles.empty())
{
for (const std::string &ndxInFile : ndxInFiles)
{
block2 = init_index(ndxInFile.c_str(), &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, bDuplicate, natoms);
return 0;
}
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 [THISMODULE] 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 [THISMODULE] 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.[PAR]",
"The [TT]-twin[tt] switch duplicates all index groups with an offset of",
"[TT]-natoms[tt], which is useful for Computational Electrophysiology",
"double-layer membrane setups."
};
static int natoms = 0;
static gmx_bool bVerbose = FALSE;
static gmx_bool bDuplicate = FALSE;
t_pargs pa[] = {
{ "-natoms", FALSE, etINT, {&natoms},
"set number of atoms (default: read from coordinate or index file)" },
{ "-twin", FALSE, etBOOL, {&bDuplicate},
"Duplicate all index groups with an offset of -natoms" },
{ "-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 }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
0, NULL, &oenv))
{
return 0;
}
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, bDuplicate, natoms);
return 0;
}
/*
* Main command processor.
* Accept and execute commands until a quit command.
*/
void
commands(void)
{
int c = 0;
int action;
char *cbuf;
int newaction;
int save_search_type;
char *extra;
char tbuf[2];
PARG parg;
IFILE old_ifile;
IFILE new_ifile;
char *tagfile;
search_type = SRCH_FORW;
wscroll = (sc_height + 1) / 2;
newaction = A_NOACTION;
for (;;) {
mca = 0;
cmd_accept();
number = 0;
curropt = NULL;
/*
* See if any signals need processing.
*/
if (sigs) {
psignals();
if (quitting)
quit(QUIT_SAVED_STATUS);
}
/*
* Display prompt and accept a character.
*/
cmd_reset();
prompt();
if (sigs)
continue;
if (newaction == A_NOACTION)
c = getcc();
again:
if (sigs)
continue;
if (newaction != A_NOACTION) {
action = newaction;
newaction = A_NOACTION;
} else {
/*
* If we are in a multicharacter command, call mca_char.
* Otherwise we call fcmd_decode to determine the
* action to be performed.
*/
if (mca)
switch (mca_char(c)) {
case MCA_MORE:
/*
* Need another character.
*/
c = getcc();
goto again;
case MCA_DONE:
/*
* Command has been handled by mca_char.
* Start clean with a prompt.
*/
continue;
case NO_MCA:
/*
* Not a multi-char command
* (at least, not anymore).
*/
break;
}
/*
* Decode the command character and decide what to do.
*/
if (mca) {
/*
* We're in a multichar command.
* Add the character to the command buffer
* and display it on the screen.
* If the user backspaces past the start
* of the line, abort the command.
*/
if (cmd_char(c) == CC_QUIT || len_cmdbuf() == 0)
continue;
cbuf = get_cmdbuf();
} else {
/*
* Don't use cmd_char if we're starting fresh
* at the beginning of a command, because we
* don't want to echo the command until we know
* it is a multichar command. We also don't
* want erase_char/kill_char to be treated
* as line editing characters.
*/
tbuf[0] = (char)c;
tbuf[1] = '\0';
cbuf = tbuf;
}
extra = NULL;
action = fcmd_decode(cbuf, &extra);
/*
* If an "extra" string was returned,
* process it as a string of command characters.
*/
if (extra != NULL)
ungetsc(extra);
}
/*
* Clear the cmdbuf string.
* (But not if we're in the prefix of a command,
* because the partial command string is kept there.)
*/
if (action != A_PREFIX)
cmd_reset();
switch (action) {
case A_DIGIT:
/*
* First digit of a number.
*/
start_mca(A_DIGIT, ":", (void*)NULL, CF_QUIT_ON_ERASE);
goto again;
case A_F_WINDOW:
/*
* Forward one window (and set the window size).
*/
if (number > 0)
swindow = (int)number;
/* FALLTHRU */
case A_F_SCREEN:
/*
* Forward one screen.
*/
if (number <= 0)
number = get_swindow();
cmd_exec();
if (show_attn)
set_attnpos(bottompos);
forward((int)number, 0, 1);
break;
case A_B_WINDOW:
/*
* Backward one window (and set the window size).
*/
if (number > 0)
swindow = (int)number;
/* FALLTHRU */
case A_B_SCREEN:
/*
* Backward one screen.
*/
if (number <= 0)
number = get_swindow();
cmd_exec();
backward((int)number, 0, 1);
break;
case A_F_LINE:
/*
* Forward N (default 1) line.
*/
if (number <= 0)
number = 1;
cmd_exec();
if (show_attn == OPT_ONPLUS && number > 1)
set_attnpos(bottompos);
forward((int)number, 0, 0);
break;
case A_B_LINE:
/*
* Backward N (default 1) line.
*/
if (number <= 0)
number = 1;
cmd_exec();
backward((int)number, 0, 0);
break;
case A_F_SKIP:
/*
* Skip ahead one screen, and then number lines.
*/
if (number <= 0) {
number = get_swindow();
} else {
number += get_swindow();
}
cmd_exec();
if (show_attn == OPT_ONPLUS)
set_attnpos(bottompos);
forward((int)number, 0, 1);
break;
case A_FF_LINE:
/*
* Force forward N (default 1) line.
*/
if (number <= 0)
number = 1;
cmd_exec();
if (show_attn == OPT_ONPLUS && number > 1)
set_attnpos(bottompos);
forward((int)number, 1, 0);
break;
case A_BF_LINE:
/*
* Force backward N (default 1) line.
*/
if (number <= 0)
number = 1;
cmd_exec();
backward((int)number, 1, 0);
break;
case A_FF_SCREEN:
/*
* Force forward one screen.
*/
if (number <= 0)
number = get_swindow();
cmd_exec();
if (show_attn == OPT_ONPLUS)
set_attnpos(bottompos);
forward((int)number, 1, 0);
break;
case A_F_FOREVER:
/*
* Forward forever, ignoring EOF.
*/
newaction = forw_loop(0);
break;
case A_F_UNTIL_HILITE:
newaction = forw_loop(1);
break;
case A_F_SCROLL:
/*
* Forward N lines
* (default same as last 'd' or 'u' command).
*/
if (number > 0)
wscroll = (int)number;
cmd_exec();
if (show_attn == OPT_ONPLUS)
set_attnpos(bottompos);
forward(wscroll, 0, 0);
break;
case A_B_SCROLL:
/*
* Forward N lines
* (default same as last 'd' or 'u' command).
*/
if (number > 0)
wscroll = (int)number;
cmd_exec();
backward(wscroll, 0, 0);
break;
case A_FREPAINT:
/*
* Flush buffers, then repaint screen.
* Don't flush the buffers on a pipe!
*/
clear_buffers();
/* FALLTHRU */
case A_REPAINT:
/*
* Repaint screen.
*/
cmd_exec();
repaint();
break;
case A_GOLINE:
/*
* Go to line N, default beginning of file.
*/
if (number <= 0)
number = 1;
cmd_exec();
jump_back(number);
break;
case A_PERCENT:
/*
* Go to a specified percentage into the file.
*/
if (number < 0) {
number = 0;
fraction = 0;
}
if (number > 100) {
number = 100;
fraction = 0;
}
cmd_exec();
jump_percent((int)number, fraction);
break;
case A_GOEND:
/*
* Go to line N, default end of file.
*/
cmd_exec();
if (number <= 0)
jump_forw();
else
jump_back(number);
break;
case A_GOPOS:
/*
* Go to a specified byte position in the file.
*/
cmd_exec();
if (number < 0)
number = 0;
jump_line_loc((off_t) number, jump_sline);
break;
case A_STAT:
/*
* Print file name, etc.
*/
if (ch_getflags() & CH_HELPFILE)
break;
cmd_exec();
parg.p_string = eq_message();
error("%s", &parg);
break;
case A_VERSION:
/*
* Print version number, without the "@(#)".
*/
cmd_exec();
dispversion();
break;
case A_QUIT:
/*
* Exit.
*/
if (curr_ifile != NULL_IFILE &&
ch_getflags() & CH_HELPFILE) {
/*
* Quit while viewing the help file
* just means return to viewing the
* previous file.
*/
hshift = save_hshift;
if (edit_prev(1) == 0)
break;
}
if (extra != NULL)
quit(*extra);
quit(QUIT_OK);
break;
/*
* Define abbreviation for a commonly used sequence below.
*/
#define DO_SEARCH() \
if (number <= 0) number = 1; \
mca_search(); \
cmd_exec(); \
multi_search(NULL, (int)number);
case A_F_SEARCH:
/*
* Search forward for a pattern.
* Get the first char of the pattern.
*/
search_type = SRCH_FORW;
if (number <= 0)
number = 1;
mca_search();
c = getcc();
goto again;
case A_B_SEARCH:
/*
* Search backward for a pattern.
* Get the first char of the pattern.
*/
search_type = SRCH_BACK;
if (number <= 0)
number = 1;
mca_search();
c = getcc();
goto again;
case A_FILTER:
search_type = SRCH_FORW | SRCH_FILTER;
mca_search();
c = getcc();
goto again;
case A_AGAIN_SEARCH:
/*
* Repeat previous search.
*/
DO_SEARCH();
break;
case A_T_AGAIN_SEARCH:
/*
* Repeat previous search, multiple files.
*/
search_type |= SRCH_PAST_EOF;
DO_SEARCH();
break;
case A_REVERSE_SEARCH:
/*
* Repeat previous search, in reverse direction.
*/
save_search_type = search_type;
search_type = SRCH_REVERSE(search_type);
DO_SEARCH();
search_type = save_search_type;
break;
case A_T_REVERSE_SEARCH:
/*
* Repeat previous search,
* multiple files in reverse direction.
*/
save_search_type = search_type;
search_type = SRCH_REVERSE(search_type);
search_type |= SRCH_PAST_EOF;
DO_SEARCH();
search_type = save_search_type;
break;
case A_UNDO_SEARCH:
undo_search();
break;
case A_HELP:
/*
* Help.
*/
if (ch_getflags() & CH_HELPFILE)
break;
if (ungot != NULL || unget_end) {
error(less_is_more
? "Invalid option -p h"
: "Invalid option ++h",
NULL_PARG);
break;
}
cmd_exec();
save_hshift = hshift;
hshift = 0;
(void) edit(FAKE_HELPFILE);
break;
case A_EXAMINE:
/*
* Edit a new file. Get the filename.
*/
if (secure) {
error("Command not available", NULL_PARG);
break;
}
start_mca(A_EXAMINE, "Examine: ", ml_examine, 0);
c = getcc();
goto again;
case A_VISUAL:
/*
* Invoke an editor on the input file.
*/
if (secure) {
error("Command not available", NULL_PARG);
break;
}
if (ch_getflags() & CH_HELPFILE)
break;
if (strcmp(get_filename(curr_ifile), "-") == 0) {
error("Cannot edit standard input", NULL_PARG);
break;
}
if (curr_altfilename != NULL) {
error("WARNING: This file was viewed via "
"LESSOPEN", NULL_PARG);
}
start_mca(A_SHELL, "!", ml_shell, 0);
/*
* Expand the editor prototype string
* and pass it to the system to execute.
* (Make sure the screen is displayed so the
* expansion of "+%lm" works.)
*/
make_display();
cmd_exec();
lsystem(pr_expand(editproto, 0), NULL);
break;
case A_NEXT_FILE:
/*
* Examine next file.
*/
if (ntags()) {
error("No next file", NULL_PARG);
break;
}
if (number <= 0)
number = 1;
if (edit_next((int)number)) {
if (get_quit_at_eof() && eof_displayed() &&
!(ch_getflags() & CH_HELPFILE))
quit(QUIT_OK);
parg.p_string = (number > 1) ? "(N-th) " : "";
error("No %snext file", &parg);
}
break;
case A_PREV_FILE:
/*
* Examine previous file.
*/
if (ntags()) {
error("No previous file", NULL_PARG);
break;
}
if (number <= 0)
number = 1;
if (edit_prev((int)number)) {
parg.p_string = (number > 1) ? "(N-th) " : "";
error("No %sprevious file", &parg);
}
break;
case A_NEXT_TAG:
if (number <= 0)
number = 1;
tagfile = nexttag((int)number);
if (tagfile == NULL) {
error("No next tag", NULL_PARG);
break;
}
if (edit(tagfile) == 0) {
off_t pos = tagsearch();
if (pos != -1)
jump_loc(pos, jump_sline);
}
break;
case A_PREV_TAG:
if (number <= 0)
number = 1;
tagfile = prevtag((int)number);
if (tagfile == NULL) {
error("No previous tag", NULL_PARG);
break;
}
if (edit(tagfile) == 0) {
off_t pos = tagsearch();
if (pos != -1)
jump_loc(pos, jump_sline);
}
break;
case A_INDEX_FILE:
/*
* Examine a particular file.
*/
if (number <= 0)
number = 1;
if (edit_index((int)number))
error("No such file", NULL_PARG);
break;
case A_REMOVE_FILE:
if (ch_getflags() & CH_HELPFILE)
break;
old_ifile = curr_ifile;
new_ifile = getoff_ifile(curr_ifile);
if (new_ifile == NULL_IFILE) {
ring_bell();
break;
}
if (edit_ifile(new_ifile) != 0) {
reedit_ifile(old_ifile);
break;
}
del_ifile(old_ifile);
break;
case A_OPT_TOGGLE:
optflag = OPT_TOGGLE;
optgetname = FALSE;
mca_opt_toggle();
c = getcc();
goto again;
case A_DISP_OPTION:
/*
* Report a flag setting.
*/
optflag = OPT_NO_TOGGLE;
optgetname = FALSE;
mca_opt_toggle();
c = getcc();
goto again;
case A_FIRSTCMD:
/*
* Set an initial command for new files.
*/
start_mca(A_FIRSTCMD, "+", NULL, 0);
c = getcc();
goto again;
case A_SHELL:
/*
* Shell escape.
*/
if (secure) {
error("Command not available", NULL_PARG);
break;
}
start_mca(A_SHELL, "!", ml_shell, 0);
c = getcc();
goto again;
case A_SETMARK:
/*
* Set a mark.
*/
if (ch_getflags() & CH_HELPFILE)
break;
start_mca(A_SETMARK, "mark: ", (void*)NULL, 0);
c = getcc();
if (c == erase_char || c == erase2_char ||
c == kill_char || c == '\n' || c == '\r')
break;
setmark(c);
break;
case A_GOMARK:
/*
* Go to a mark.
*/
start_mca(A_GOMARK, "goto mark: ", (void*)NULL, 0);
c = getcc();
if (c == erase_char || c == erase2_char ||
c == kill_char || c == '\n' || c == '\r')
break;
cmd_exec();
gomark(c);
break;
case A_PIPE:
if (secure) {
error("Command not available", NULL_PARG);
break;
}
start_mca(A_PIPE, "|mark: ", (void*)NULL, 0);
c = getcc();
if (c == erase_char || c == erase2_char ||
c == kill_char)
break;
if (c == '\n' || c == '\r')
c = '.';
if (badmark(c))
break;
pipec = c;
start_mca(A_PIPE, "!", ml_shell, 0);
c = getcc();
goto again;
case A_B_BRACKET:
case A_F_BRACKET:
start_mca(action, "Brackets: ", (void*)NULL, 0);
c = getcc();
goto again;
case A_LSHIFT:
if (number > 0)
shift_count = number;
else
number = (shift_count > 0) ?
shift_count : sc_width / 2;
if (number > hshift)
number = hshift;
hshift -= number;
screen_trashed = 1;
break;
case A_RSHIFT:
if (number > 0)
shift_count = number;
else
number = (shift_count > 0) ?
shift_count : sc_width / 2;
hshift += number;
screen_trashed = 1;
break;
case A_PREFIX:
/*
* The command is incomplete (more chars are needed).
* Display the current char, so the user knows
* what's going on, and get another character.
*/
if (mca != A_PREFIX) {
cmd_reset();
start_mca(A_PREFIX, " ", (void*)NULL,
CF_QUIT_ON_ERASE);
(void) cmd_char(c);
}
c = getcc();
goto again;
case A_NOACTION:
break;
default:
ring_bell();
break;
}
}
}