gint reaxmd_output_coords_read(gpointer import)
{
gchar *fullname, *line;
FILE *fp;
#if DEBUG_READ_DCD
printf("Adding [dcd] data to file: %s\n", import_fullpath(import));
#endif
fullname = parse_extension_set(import_fullpath(import), "dcd");
if (!g_file_test(fullname, G_FILE_TEST_EXISTS))
{
gui_text_show(ERROR, "Failed to find associated .dcd file.\n");
g_free(fullname);
return(1);
}
// TODO - if existing frames - assume replace mode
// otherwise create new frame at each step
/* NB: binary file data */
fp = fopen(fullname, "rb");
while (fp)
{
line = file_read_line(fp);
if (!line)
break;
g_free(line);
}
return(1);
}
void gui_animate_movie_type_change(GtkWidget *type, gpointer name)
{
gchar *movie;
const gchar *text, *ext;
text = gtk_entry_get_text(GTK_ENTRY(type));
//printf("type = %s\n", text);
if (g_strncasecmp(text, "avi", 3) == 0)
ext = "avi";
if (g_strncasecmp(text, "flv", 3) == 0)
ext = "flv";
if (g_strncasecmp(text, "mp4", 3) == 0)
ext = "mp4";
if (g_strncasecmp(text, "mpg", 3) == 0)
ext = "mpg";
text = gtk_entry_get_text(GTK_ENTRY(name));
movie = parse_extension_set(text, ext);
//printf("movie = %s\n", movie);
gtk_entry_set_text(GTK_ENTRY(name), movie);
g_free(movie);
}
gint write_gromacs(gchar *filename, struct model_pak *model)
{
gchar *temp;
temp = parse_extension_set(filename, "top");
write_gromacs_gro(filename, model);
write_gromacs_top(temp, model);
g_free(temp);
return(0);
}
gint reaxmd_output_import(gpointer import)
{
gint status=0;
gchar *fullname_model, *fullname_energy, *fullname_coords, *fullname_velos;
struct model_pak *model=NULL;
FILE *fp_m, *fp_c, *fp_e, *fp_v;
if (!import)
return(1);
fullname_model = parse_extension_set(import_fullpath(import), "pdb");
fullname_coords = parse_extension_set(import_fullpath(import), "dcd");
fullname_energy = parse_extension_set(import_fullpath(import), "erx");
fullname_velos = parse_extension_set(import_fullpath(import), "vrx");
fp_m = fopen(fullname_model, "rt");
fp_e = fopen(fullname_energy, "rt");
fp_c = fopen(fullname_coords, "rb");
fp_v = fopen(fullname_velos, "rb");
// bare minimum parse
if (fp_m)
{
model = model_new();
read_pdb_block(fp_m, model);
fclose(fp_m);
}
else
{
status = 1;
gui_text_show(ERROR, "Failed to open reference PDB model for ReaxMD.\n");
goto reaxmd_output_import_cleanup;
}
// main extra data (coords)
if (fp_c)
{
reaxmd_parse_coordinates(fp_c, model);
fclose(fp_c);
}
// optional extra data (velocities)
if (fp_v)
{
reaxmd_parse_velocities(fp_v, model);
fclose(fp_v);
}
// optional extra data (energy, temp, etc)
// CURRENT - only read corresponding values for which we have coord frames
if (fp_e)
{
reaxmd_parse_properties(fp_e, model, import);
fclose(fp_e);
}
// init
if (model)
import_object_add(IMPORT_MODEL, model, import);
import_init(import);
#if DEBUG_REAXMD_OUTPUT
animate_debug(model);
#endif
// done
reaxmd_output_import_cleanup:
g_free(fullname_model);
g_free(fullname_coords);
g_free(fullname_energy);
g_free(fullname_velos);
return(status);
}
// no coords - just control data for the run
// coords - .pdb file
// topology - .frx file
gint reaxmd_input_import(gpointer import)
{
gint *symbols, num_symbols, unknown;
gchar *line, *fullname_model;
gchar *filename, *filepath;
gpointer scan, config;
GString *unparsed;
struct reaxmd_pak *reaxmd;
struct model_pak *model;
FILE *fp;
scan = scan_new(import_fullpath(import));
if (!scan)
return(1);
/* populate symbol table */
reaxmd_symbols_init(scan);
config = config_new(REAXMD, NULL);
reaxmd = config_data(config);
unparsed = g_string_new(NULL);
while (!scan_complete(scan))
{
symbols = scan_get_symbols(scan, &num_symbols);
if (num_symbols)
{
unknown = FALSE;
/* process first recognized symbol */
switch (symbols[0])
{
case REAXMD_NSTEPS:
reaxmd->total_steps = parse_nth_token_dup(1, scan_cur_line(scan));
break;
case REAXMD_TIMESTEP:
case REAXMD_TEMPERATURE:
case REAXMD_THERMOSTAT:
case REAXMD_BAROSTAT:
case REAXMD_CUTOFF:
case REAXMD_UPDATE:
case REAXMD_NWRITE:
case REAXMD_GRID:
break;
case REAXMD_PLUMED_FILE:
filename = parse_nth_token_dup(1, scan_cur_line(scan));
filepath = g_build_filename(import_path(import), filename, NULL);
//printf("Looking for: %s\n", filepath);
if (g_file_test(filepath, G_FILE_TEST_EXISTS))
project_job_file_append(NULL, filepath, sysenv.workspace);
else
gui_text_show(ERROR, "REAXMD plumed file was not found!\n");
g_free(filename);
g_free(filepath);
break;
default:
unknown = TRUE;
}
g_free(symbols);
}
else
unknown=TRUE;
if (unknown)
{
line = scan_cur_line(scan);
if (line)
g_string_append(unparsed, line);
}
}
config_unparsed_set(g_string_free(unparsed, FALSE), config);
/* CURRENT - free this, until we add a GUI */
//import_object_add(IMPORT_CONFIG, config, import);
config_free(config);
/* done irx parse */
scan_free(scan);
/* NEW - attempt to load reference coordinates */
fullname_model = parse_extension_set(import_fullpath(import), "pdb");
fp = fopen(fullname_model, "rt");
if (fp)
{
model = model_new();
read_pdb_block(fp, model);
fclose(fp);
import_object_add(IMPORT_MODEL, model, import);
}
else
{
gui_text_show(WARNING, "Failed to open reference PDB model for ReaxMD.\n");
}
g_free(fullname_model);
/* init */
import_init(import);
return(0);
}
