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Viewing changes to read_config.c

Committer: Bazaar Package Importer
Author(s): zhaoway
Date: 2001-04-24 07:09:13 UTC
Revision ID: james.westby@ubuntu.com-20010424070913-uzpupnwdfhmliebz

Tags: upstream-1.1

Import upstream version 1.1

files added:

.garlicrc

1mal.script

2fcp.script

2omf.script

2por.script

BUGS

COPYING

ENVIRONMENT

HISTORY

INSTALL

Makefile

README

TODO

absolute_value.c

add_bond.c

add_char.c

add_three_colors.c

add_two_colors.c

align_complexes.c

align_normal.c

alloc_config.c

alloc_gui.c

alloc_mol_complex.c

alloc_nearest.c

anchor.xpm

angle.c

apply_selection.c

assign_hyphob.c

assign_radii.c

atom_names.c

atoms.c

atoms.script

atoms_style1.c

atoms_style2.c

atoms_style3.c

atoms_style4.c

atoms_style5.c

atoms_style6.c

atoms_style7.c

backbone.c

background.c

balls.c

balls2.c

big2.c

big_spheres.c

bond_style1_quad1.c

bond_style1_quad2.c

bond_style1_quad3.c

bond_style1_quad4.c

bond_style2_quad1.c

bond_style2_quad2.c

bond_style2_quad3.c

bond_style2_quad4.c

bond_style3_quad1.c

bond_style3_quad2.c

bond_style3_quad3.c

bond_style3_quad4.c

bond_style4_quad1.c

bond_style4_quad2.c

bond_style4_quad3.c

bond_style4_quad4.c

bond_style5_quad1.c

bond_style5_quad2.c

bond_style5_quad3.c

bond_style5_quad4.c

bonds.c

bonds.script

bonds_style1.c

bonds_style2.c

bonds_style3.c

bonds_style4.c

bonds_style5.c

button_press.c

calc_params.c

calculate_phi.c

calculate_psi.c

catch.c

center.c

chain.c

chains.c

change_fading.c

change_slab.c

check_con.c

check_dist.c

cis_trans.c

color.c

color_hyphob.c

color_model.c

color_schemes.c

color_shifts.c

colors.script

colors2.script

comm_backbone.c

comm_fading.c

comm_move.c

comm_rotate.c

comm_slab.c

comm_translate.c

commands.h

compare.c

compare_sequences.c

comparison_mouse.c

control.xpm

control_click.c

control_refresh.c

copy_doubles.c

copy_sequence.c

copypur.c

count_nc_bonds.c

count_residues.c

cpk.c

create_log_file.c

create_windows.c

cylin_fading.c

cylin_slab.c

dance.script

defines.h

dihedral_angles.c

discard.c

disp_color_cap.c

display_init.c

disulfide_bonds.c

dock.c

docking.xpm

docking_project.c

docking_refresh.c

docking_resize.c

docking_window.c

draw_bottom.c

draw_comparison.c

draw_labels.c

draw_planes.c

draw_plots.c

draw_ramachandran.c

draw_system.c

draw_tags.c

draw_titles.c

draw_top.c

draw_venn.c

draw_wheel.c

eat_left_char.c

eat_right_char.c

errmsg.c

event_loop.c

ex2doubles.c

ex2ints.c

ex_fading_steps.c

ex_rot_steps.c

ex_slab_steps.c

ex_trans_steps.c

exclude.c

exclude_distant.c

execute_command1.c

execute_command2.c

execute_script.c

extent.c

extract_args.c

extract_double.c

extract_field.c

extract_index.c

extract_int.c

extract_ncaco.c

extract_phrase.c

extract_sequence.c

extract_serials.c

extract_token.c

fading.c

fading_shift.c

fileformat.c

flipvector.c

font.c

foreground.c

free_memory.c

free_runtime.c

full_colors.c

full_select.c

garlic.c

garlic.xpm

gen_hybonds.c

gen_plane.c

geo.script

geomcenter.c

half_cylin_fading.c

half_cylin_slab.c

half_sphere_fading.c

half_sphere_slab.c

headerline.c

hide.c

hide_backbone.c

hide_control.c

hide_no_refresh.c

hybond_style.c

hybonds.c

hydrophobicity.c

identify_button.c

include.c

init_buttons.c

init_colors.c

init_fading.c

init_header.c

init_hyphob.c

init_nearest.c

init_runtime.c

init_slab.c

input_refresh.c

insert

interpolate_color.c

is_old.c

is_pdb.c

is_polar.c

key_press.c

key_release.c

labels.c

list_exposed_polar.c

load.c

load_complex.c

load_font.c

load_sequence.c

log.c

main_refresh.c

main_resize.c

make_pixmap.c

masks.txt

mix_colors.c

mono.c

motion_notify.c

move_back_fading.c

move_back_slab.c

move_front_fading.c

move_front_slab.c

neighborhood.c

no_fading.c

no_slab.c

open_cfg_file.c

openfile_r.c

parse_color.c

parse_options.c

parse_sequence.c

pattern.c

pdb_atom.c

pdb_id.c

phe.pdb

pixel_from_rgbs.c

planar_fading.c

planar_slab.c

plane.c

plane_extent.c

plot.c

plot_mouse.c

position.c

prepare_backbone.c

prepare_color.c

prepare_cursor.c

prepare_oc.c

print_config.c

print_cursor_names.c

print_help.c

print_usage.c

print_version.c

project_atoms.c

project_planes.c

purge

quick_select.c

radius.c

rainbow.script

rama_frame.c

rama_mouse.c

ramachandran.c

read_config.c

read_fasta.c

read_file.c

read_pdb.c

realloc_pdb.c

refresh_pixmap.c

replace_command.c

representative_atoms.c

reset_pos_flag.c

residue_names.c

residue_ranges.c

rgbs_from_xcolor.c

rotate.c

rotate_plane.c

rotation_angle.c

sample.fasta

sample.script

save.c

save_seq_w_numbers.c

save_sequence.c

scalar_product.c

scale.c

select.c

select_above.c

select_alternate.c

select_below.c

select_cis_trans.c

select_complement.c

select_events.c

select_hetero.c

select_model.c

select_sequence.c

select_sphere.c

select_to_stdout.c

sequence.c

sequence_from.c

show.c

show_backbone.c

show_no_refresh.c

single_bond.pdb

size_hints.c

skip_keyword.c

slab.c

slab_shift.c

sp2.c

sp2_color.c

spacefill.c

spacefill_color.c

special_select.c

sphere_fading.c

sphere_slab.c

ssb.c

stereo.c

stereo_data.c

strong_bonds.c

system.xpm

tag.c

tag_position.c

text_background.c

text_foreground.c

title.c

translate.c

translate_complex.c

translate_plane.c

translation_shift.c

trp.pdb

truncate_comm.c

typedefs.h

vector_product.c

venn.c

warnmsg.c

weight_colors.c

wheel.c

window.c

wmhints.c

words

write_hints.c

write_line.c

zebra.c

Show diffs side-by-side

added added

removed removed

read_config.c

/*=============================================================================

read_config.c

Purpose:

Read configuration data. Configuration file is .garlicrc and up to

five directories are searched for this file. If all attempts fail,

default (hard-coded) parameters are used.

Input:

(1) Pointer to ConfigS structure, where some data will be stored.

Output:

(1) Some data stored to ConfigS structure.

(2) Return value.

Return value:

(1) Positive if configuration read from file.

(2) Zero if default values used for initialization.

Notes:

(1) This function is quite fast: on a 233 MHz Pentium MMX, it will

take few milliseconds to execute. Therefore do not be surprised

that if's are not optimized here.

========includes:============================================================*/

#include <stdio.h>

#include <string.h>

#include <math.h>

#include <X11/Xlib.h>

#include <X11/Xutil.h>

#include <X11/Xos.h>

#include <X11/Xatom.h>

#include "defines.h"

#include "typedefs.h"

/*======function prototypes:=================================================*/

FILE *OpenConfigFile_ (void);

int ExtractInteger_ (char *);

int ExtractTwoIntegers_ (int *, int *, char *);

int ExtractPhrase_ (char *, char *);

double ExtractDouble_ (char *);

int ExtractTwoDoubles_ (double *, double *, char *);

int ExtractIndex_ (char *);

int ExtractRotationSteps_ (ConfigS *, char *);

int ExtractTranslationSteps_ (ConfigS *, char *);

int ExtractSlabSteps_ (ConfigS *, char *);

int ExtractFadingSteps_ (ConfigS *, char *);

/*======read configuration data (.garlicrc file):============================*/

int ReadConfig_ (ConfigS *configSP)

{

FILE *fileP;

char s[STRINGSIZE];

int line_size;

char phraseA[SHORTSTRINGSIZE];

int n, n1, n2;

double d, d1, d2;

int surfaceI;

/* Default values; used if both attempts to find .garlicrc fail, */

/* or if the corresponding entry does not exist in .garlicrc file: */

/** Main window geometry: **/

strcpy (configSP->geometryA, "default");

/** Font name and cursor name: **/

strcpy (configSP->font_nameA, "10x20");

strcpy (configSP->cursor_nameA, "default");

/** Coordinate system in the top left corner is visible by default: **/

configSP->show_coord_systemF = 1;

/** Control window in the top right corner is visible by default: **/

configSP->show_control_windowF = 1;

/** The sequence neighborhood of the residue **/

/** under the pointer is visible by default: **/

configSP->show_sequence_neighborhoodF = 1;

/** Stereo flag (default is mono): **/

configSP->stereoF = 0;

/** Light source theta angle (with respect to z): **/

configSP->light_theta = 150.0 * DEG_TO_RAD;

/** Light source phi angle (with respect to x): **/

configSP->light_phi = 225.0 * DEG_TO_RAD;

/** Window colors: **/

strcpy (configSP->bg_colorA, "black");

100

strcpy (configSP->fg_colorA, "white");

101

strcpy (configSP->text_bg_colorA, "black");

102

strcpy (configSP->text_fg_colorA, "white");

103

104

/** Slab mode index (default is planar): **/

105

configSP->default_slab_modeI = 1;

106

107

/** Color fading mode index (default is planar): **/

108

configSP->default_fading_modeI = 1;

109

110

/** Default number of color fading surfaces (up to MAXSURFACES): **/

111

configSP->default_surfacesN = 3;

112

113

/** Color specifications: **/

114

strcpy (configSP->left_colorAA[0], "RGB:FFFF/FFFF/0000");

115

strcpy (configSP->middle_colorAA[0], "RGB:FFFF/AAAA/0000");

116

strcpy (configSP->right_colorAA[0], "RGB:FFFF/5555/0000");

117

strcpy (configSP->left_colorAA[1], "RGB:FFFF/8888/0000");

118

strcpy (configSP->middle_colorAA[1], "RGB:FFFF/0000/0000");

119

strcpy (configSP->right_colorAA[1], "RGB:AAAA/0000/0000");

120

strcpy (configSP->left_colorAA[2], "RGB:7777/0000/0000");

121

strcpy (configSP->middle_colorAA[2], "RGB:5555/0000/0000");

122

strcpy (configSP->right_colorAA[2], "RGB:4444/0000/0000");

123

for (n = 3; n < MAXSURFACES; n++)

124

{

125

strcpy (configSP->left_colorAA[n], "white");

126

strcpy (configSP->middle_colorAA[n], "gray");

127

strcpy (configSP->right_colorAA[n], "DarkGray");

128

}

129

130

/* Drawing styles for atoms, bonds and backbone: */

131

configSP->default_atom_styleI = 2;

132

configSP->default_bond_styleI = 2;

133

configSP->default_backbone_styleI = 5;

134

135

/** Bond lengths (angstroms): **/

136

configSP->max_bond_length = 2.2;

137

configSP->C_C_bond_length_min = 1.40;

138

configSP->C_C_bond_length_max = 1.70;

139

configSP->C_N_bond_length_min = 1.10;

140

configSP->C_N_bond_length_max = 1.60;

141

configSP->C_O_bond_length_min = 1.10;

142

configSP->C_O_bond_length_max = 1.40;

143

configSP->C_S_bond_length_min = 1.60;

144

configSP->C_S_bond_length_max = 2.00;

145

configSP->C_H_bond_length_min = 0.80;

146

configSP->C_H_bond_length_max = 1.20;

147

configSP->N_H_bond_length_min = 0.90;

148

configSP->N_H_bond_length_max = 1.30;

149

configSP->O_H_bond_length_min = 0.70;

150

configSP->O_H_bond_length_max = 1.30;

151

configSP->S_H_bond_length_min = 0.90;

152

configSP->S_H_bond_length_max = 1.60;

153

configSP->O_P_bond_length_min = 1.20;

154

configSP->O_P_bond_length_max = 1.80;

155

configSP->S_S_bond_length_min = 1.80;

156

configSP->S_S_bond_length_max = 2.30;

157

configSP->generic_bond_length_min = 0.8;

158

configSP->generic_bond_length_max = 2.0;

159

configSP->hydro_bond_length_min = 2.4;

160

configSP->hydro_bond_length_max = 4.1;

161

configSP->hydro_bond_angle_min = (double) 125 * DEG_TO_RAD;

162

configSP->hydro_bond_angle_max = (double) 180 * DEG_TO_RAD;

163

164

/** The maximal CA_CA distance for two neighbouring residues (angstroms): **/

165

configSP->CA_CA_dist_max = 4.1;

166

167

/** Atomic radii (in angstroms): **/

168

configSP->H_radius = 0.70;

169

configSP->C_radius = 1.20;

170

configSP->N_radius = 1.05;

171

configSP->O_radius = 1.00;

172

configSP->S_radius = 1.25;

173

configSP->P_radius = 1.25;

174

configSP->generic_radius = 1.40;

175

176

/** van der Waals radii (in angstroms): **/

177

configSP->H_van_der_Waals_radius = 1.00;

178

configSP->C_van_der_Waals_radius = 1.70;

179

configSP->N_van_der_Waals_radius = 1.50;

180

configSP->O_van_der_Waals_radius = 1.40;

181

configSP->S_van_der_Waals_radius = 1.80;

182

configSP->P_van_der_Waals_radius = 1.80;

183

configSP->generic_van_der_Waals_radius = 2.00;

184

185

/** Ball radius (used to draw balls and sticks): **/

186

configSP->ball_radius = 0.45;

187

188

/** Number of neighbors to be checked as bond candidates: **/

189

configSP->bond_candidates_backward = 50;

190

configSP->bond_candidates_forward = 50;

191

192

/** Geometric parameters: **/

193

configSP->main_margin_left = 30;

194

configSP->main_margin_right = 30;

195

configSP->main_margin_top = 60;

196

configSP->main_margin_bottom = 30;

197

configSP->max_main_win_width = MAXWINWIDTH;

198

configSP->max_main_win_height = MAXWINHEIGHT;

199

configSP->nearest_line_thickness = MAXLINES;

200

configSP->screen_real_width = SCREEN_REAL_WX;

201

configSP->screen_real_height = SCREEN_REAL_WY;

202

configSP->user_screen_real_distance = USER_SCREEN_REAL_DIST;

203

configSP->screen_atomic_width = SCREEN_ATOMIC_WX;

204

configSP->user_atomic_position = USER_ATOMIC_Z;

205

configSP->stereo_screen_margin = STEREO_MARGIN;

206

configSP->stereo_angle = STEREO_ANGLE * DEG_TO_RAD;

207

configSP->rotation_stepA[0] = 0.2 * DEG_TO_RAD;

208

configSP->rotation_stepA[1] = 1.0 * DEG_TO_RAD;

209

configSP->rotation_stepA[2] = 5.0 * DEG_TO_RAD;

210

configSP->rotation_stepA[3] = 30.0 * DEG_TO_RAD;

211

configSP->rotation_stepA[4] = 90.0 * DEG_TO_RAD;

212

configSP->translation_stepA[0] = 0.2;

213

configSP->translation_stepA[1] = 1.0;

214

configSP->translation_stepA[2] = 5.0;

215

configSP->translation_stepA[3] = 25.0;

216

configSP->translation_stepA[4] = 100.0;

217

configSP->slab_stepA[0] = 0.2;

218

configSP->slab_stepA[1] = 1.0;

219

configSP->slab_stepA[2] = 5.0;

220

configSP->slab_stepA[3] = 20.0;

221

configSP->slab_stepA[4] = 80.0;

222

configSP->fading_stepA[0] = 0.2;

223

configSP->fading_stepA[1] = 1.0;

224

configSP->fading_stepA[2] = 5.0;

225

configSP->fading_stepA[3] = 20.0;

226

configSP->fading_stepA[4] = 80.0;

227

228

/* Try to find personal or public configuration file: */

229

if ((fileP = OpenConfigFile_ ()) == NULL) return 0;

230

231

/* If this point is reached, file is available - read and parse all lines: */

232

line_size = sizeof (s);

233

while (fgets (s, line_size, fileP))

234

{

235

/* Skip comments: */

236

if (strstr (s, "#") == s) continue;

237

238

/* Skip very short lines: */

239

if (strlen (s) <= 5) continue;

240

241

/* Main window geometry: */

242

if (strstr (s, "main") && strstr (s, "window") &&

243

strstr (s, "geometry"))

244

{

245

if (ExtractPhrase_ (phraseA, s) > 0)

246

{

247

strncpy (configSP->geometryA,

248

phraseA, SHORTSTRINGSIZE - 1);

249

configSP->geometryA[SHORTSTRINGSIZE - 1] = '\0';

250

}

251

continue;

252

}

253

254

/* Main font name: */

255

if (strstr (s, "main") && strstr (s, "font"))

256

{

257

if (ExtractPhrase_ (phraseA, s) > 0)

258

{

259

strncpy (configSP->font_nameA,

260

phraseA, SHORTSTRINGSIZE - 1);

261

configSP->font_nameA[SHORTSTRINGSIZE - 1] = '\0';

262

}

263

continue;

264

}

265

266

/* Main window cursor: */

267

if (strstr (s, "main") && strstr (s, "window") && strstr (s, "cursor"))

268

{

269

if (ExtractPhrase_ (phraseA, s) > 0)

270

{

271

strncpy (configSP->cursor_nameA,

272

phraseA, SHORTSTRINGSIZE - 1);

273

configSP->cursor_nameA[SHORTSTRINGSIZE - 1] = '\0';

274

}

275

continue;

276

}

277

278

/* Coordinate system in the top left corner (yes or no): */

279

if (strstr (s, "show") && strstr (s, "coordinate") &&

280

strstr (s, "system"))

281

{

282

if (ExtractPhrase_ (phraseA, s) > 0)

283

{

284

if (strstr (phraseA, "no"))

285

{

286

configSP->show_coord_systemF = 0;

287

}

288

}

289

continue;

290

}

291

292

/* Control window in the top right corner: */

293

if (strstr (s, "show") && strstr (s, "control") &&

294

strstr (s, "window"))

295

{

296

if (ExtractPhrase_ (phraseA, s) > 0)

297

{

298

if (strstr (phraseA, "no"))

299

{

300

configSP->show_control_windowF = 0;

301

}

302

}

303

continue;

304

}

305

306

/* Sequence neighborhood of the residue under the pointer: */

307

if (strstr (s, "show") && strstr (s, "sequence") &&

308

strstr (s, "neighborhood"))

309

{

310

if (ExtractPhrase_ (phraseA, s) > 0)

311

{

312

if (strstr (phraseA, "no"))

313

{

314

configSP->show_sequence_neighborhoodF = 0;

315

}

316

}

317

continue;

318

}

319

320

/* Stereo flag (0 = mono, 1 = stereo): */

321

if (strstr (s, "display") && strstr (s, "stereo") &&

322

strstr (s, "image"))

323

{

324

if (ExtractPhrase_ (phraseA, s) > 0)

325

{

326

if (strstr (phraseA, "yes")) configSP->stereoF = 1;

327

}

328

continue;

329

}

330

331

/* Default slab mode index (see typedefs.h for available modes): */

332

if (strstr (s, "default") && strstr (s, "slab") && strstr (s, "mode"))

333

{

334

if (ExtractPhrase_ (phraseA, s) > 0)

335

{

336

if (strncmp (phraseA, "off", 50) == 0)

337

configSP->default_slab_modeI = 0;

338

else if (strncmp (phraseA, "planar", 50) == 0)

339

configSP->default_slab_modeI = 1;

340

else if (strncmp (phraseA, "sphere", 50) == 0)

341

configSP->default_slab_modeI = 2;

342

else if (strncmp (phraseA, "half-sphere", 50) == 0)

343

configSP->default_slab_modeI = 3;

344

else if (strncmp (phraseA, "cylinder", 50) == 0)

345

configSP->default_slab_modeI = 4;

346

else if (strncmp (phraseA, "half-cylinder", 50) == 0)

347

configSP->default_slab_modeI = 5;

348

else configSP->default_slab_modeI = 1; /* Default */

349

}

350

continue;

351

}

352

353

/* Default fading mode index (see typedefs.h for available modes): */

354

if (strstr (s, "default") && strstr (s, "fading") &&

355

strstr (s, "mode"))

356

{

357

if (ExtractPhrase_ (phraseA, s) > 0)

358

{

359

if (strncmp (phraseA, "off", 50) == 0)

360

configSP->default_fading_modeI = 0;

361

else if (strncmp (phraseA, "planar", 50) == 0)

362

configSP->default_fading_modeI = 1;

363

else if (strncmp (phraseA, "sphere", 50) == 0)

364

configSP->default_fading_modeI = 2;

365

else if (strncmp (phraseA, "half-sphere", 50) == 0)

366

configSP->default_fading_modeI = 3;

367

else if (strncmp (phraseA, "cylinder", 50) == 0)

368

configSP->default_fading_modeI = 4;

369

else if (strncmp (phraseA, "half-cylinder", 50) == 0)

370

configSP->default_fading_modeI = 5;

371

else configSP->default_fading_modeI = 1; /* Default */

372

}

373

continue;

374

}

375

376

/* Main window left margin: */

377

if (strstr (s, "main") && strstr (s, "window") &&

378

strstr (s, "left") && strstr (s, "margin"))

379

{

380

n = ExtractInteger_ (s);

381

if (n >= 0) configSP->main_margin_left = n;

382

continue;

383

}

384

385

/* Main window right margin: */

386

if (strstr (s, "main") && strstr (s, "window") &&

387

strstr (s, "right") && strstr (s, "margin"))

388

{

389

n = ExtractInteger_ (s);

390

if (n >= 0) configSP->main_margin_right = n;

391

continue;

392

}

393

394

/* Main window top margin: */

395

if (strstr (s, "main") && strstr (s, "window") &&

396

strstr (s, "top") && strstr (s, "margin"))

397

{

398

n = ExtractInteger_ (s);

399

if (n >= 0) configSP->main_margin_top = n;

400

continue;

401

}

402

403

/* Main window bottom margin: */

404

if (strstr (s, "main") && strstr (s, "window") &&

405

strstr (s, "bottom") && strstr (s, "margin"))

406

{

407

n = ExtractInteger_ (s);

408

if (n >= 0) configSP->main_margin_bottom = n;

409

continue;

410

}

411

412

/* Background color specification: */

413

if (strstr (s, "main") && strstr (s, "window") &&

414

strstr (s, "background") && strstr (s, "color"))

415

{

416

if (ExtractPhrase_ (phraseA, s) > 0)

417

{

418

strncpy (configSP->bg_colorA,

419

phraseA, SHORTSTRINGSIZE - 1);

420

configSP->bg_colorA[SHORTSTRINGSIZE - 1] = '\0';

421

}

422

continue;

423

}

424

425

/* Foreground color specification: */

426

if (strstr (s, "main") && strstr (s, "window") &&

427

strstr (s, "foreground") && strstr (s, "color"))

428

{

429

if (ExtractPhrase_ (phraseA, s) > 0)

430

{

431

strncpy (configSP->fg_colorA,

432

phraseA, SHORTSTRINGSIZE - 1);

433

configSP->fg_colorA[SHORTSTRINGSIZE - 1] = '\0';

434

}

435

continue;

436

}

437

438

/* Text background color: */

439

if (strstr (s, "text") && strstr (s, "background") &&

440

strstr (s, "color"))

441

{

442

if (ExtractPhrase_ (phraseA, s) > 0)

443

{

444

strncpy (configSP->text_bg_colorA,

445

phraseA, SHORTSTRINGSIZE - 1);

446

configSP->text_bg_colorA[SHORTSTRINGSIZE - 1] = '\0';

447

}

448

continue;

449

}

450

451

/* Text foreground color: */

452

if (strstr (s, "text") && strstr (s, "foreground") &&

453

strstr (s, "color"))

454

{

455

if (ExtractPhrase_ (phraseA, s) > 0)

456

{

457

strncpy (configSP->text_fg_colorA,

458

phraseA, SHORTSTRINGSIZE - 1);

459

configSP->text_fg_colorA[SHORTSTRINGSIZE - 1] = '\0';

460

}

461

continue;

462

}

463

464

/* Default number of color fading surfaces: */

465

if (strstr (s, "number") && strstr (s, "color") &&

466

strstr (s, "surfaces"))

467

{

468

n = ExtractInteger_ (s);

469

if ((n > 0) && (n <= MAXSURFACES))

470

{

471

configSP->default_surfacesN = n;

472

}

473

continue;

474

}

475

476

/* Left color: */

477

if (strstr (s, "left") && strstr (s, "color"))

478

{

479

surfaceI = ExtractIndex_ (s);

480

if ((surfaceI < 0) || (surfaceI >= MAXSURFACES)) continue;

481

if (ExtractPhrase_ (phraseA, s) > 0)

482

{

483

strncpy (configSP->left_colorAA[surfaceI],

484

phraseA, SHORTSTRINGSIZE - 1);

485

n = SHORTSTRINGSIZE - 1;

486

configSP->left_colorAA[surfaceI][n] = '\0';

487

}

488

continue;

489

}

490

491

/* Middle color: */

492

if (strstr (s, "middle") && strstr (s, "color"))

493

{

494

surfaceI = ExtractIndex_ (s);

495

if ((surfaceI < 0) || (surfaceI >= MAXSURFACES)) continue;

496

if (ExtractPhrase_ (phraseA, s) > 0)

497

{

498

strncpy (configSP->middle_colorAA[surfaceI],

499

phraseA, SHORTSTRINGSIZE - 1);

500

n = SHORTSTRINGSIZE - 1;

501

configSP->middle_colorAA[surfaceI][n] = '\0';

502

}

503

continue;

504

}

505

506

/* Right color: */

507

if (strstr (s, "right") && strstr (s, "color"))

508

{

509

surfaceI = ExtractIndex_ (s);

510

if ((surfaceI < 0) || (surfaceI >= MAXSURFACES)) continue;

511

if (ExtractPhrase_ (phraseA, s) > 0)

512

{

513

strncpy (configSP->right_colorAA[surfaceI],

514

phraseA, SHORTSTRINGSIZE - 1);

515

n = SHORTSTRINGSIZE - 1;

516

configSP->right_colorAA[surfaceI][n] = '\0';

517

}

518

continue;

519

}

520

521

/* Default drawing style for atoms: */

522

if (strstr (s, "default") && strstr (s, "atom") &&

523

strstr (s, "drawing") && strstr (s, "style"))

524

{

525

n = ExtractInteger_ (s);

526

if ((n >= 0) && (n <= MAXATOMSTYLEI))

527

{

528

configSP->default_atom_styleI = (short int) n;

529

}

530

}

531

532

/* Default drawing style for bonds: */

533

if (strstr (s, "default") && strstr (s, "bond") &&

534

strstr (s, "drawing") && strstr (s, "style"))

535

{

536

n = ExtractInteger_ (s);

537

if ((n >= 0) && (n <= MAXBONDSTYLEI))

538

{

539

configSP->default_bond_styleI = (short int) n;

540

}

541

}

542

543

/* Default drawing style for bonds: */

544

if (strstr (s, "default") && strstr (s, "backbone") &&

545

strstr (s, "drawing") && strstr (s, "style"))

546

{

547

n = ExtractInteger_ (s);

548

if ((n >= 0) && (n <= MAXBONESTYLEI))

549

{

550

configSP->default_backbone_styleI = (short int) n;

551

}

552

}

553

554

/* Maximal main window width: */

555

if (strstr (s, "maximal") && strstr (s, "window") &&

556

strstr (s, "width"))

557

{

558

n = ExtractInteger_ (s);

559

if (n >= 0) configSP->max_main_win_width = n;

560

continue;

561

}

562

563

/* Maximal main window height: */

564

if (strstr (s, "maximal") && strstr (s, "window") &&

565

strstr (s, "height"))

566

{

567

n = ExtractInteger_ (s);

568

if (n >= 0) configSP->max_main_win_height = n;

569

continue;

570

}

571

572

/* The nearest line (i.e. the nearest bond) thickness. */

573

/* Used only if line thickness is used for perspective! */

574

if (strstr (s, "nearest") && strstr (s, "line") &&

575

strstr (s, "thickness"))

576

{

577

n = ExtractInteger_ (s);

578

if (n >= 0) configSP->nearest_line_thickness = n;

579

continue;

580

}

581

582

/* Screen width in real world: */

583

if (strstr (s, "screen") && strstr (s, "real") && strstr (s, "width"))

584

{

585

d = ExtractDouble_ (s);

586

if (d > 0) configSP->screen_real_width = d;

587

continue;

588

}

589

590

/* Screen height in real world: */

591

if (strstr (s, "screen") && strstr (s, "real") && strstr (s, "height"))

592

{

593

d = ExtractDouble_ (s);

594

if (d > 0) configSP->screen_real_height = d;

595

continue;

596

}

597

598

/* Distance between user and screen in real world: */

599

if (strstr (s, "distance") && strstr (s, "user") &&

600

strstr (s, "screen") && strstr (s, "real"))

601

{

602

d = ExtractDouble_ (s);

603

if (d > 0) configSP->user_screen_real_distance = d;

604

continue;

605

}

606

607

/* Screen width in atomic world: */

608

if (strstr (s, "screen") && strstr (s, "width") &&

609

strstr (s, "atomic"))

610

{

611

d = ExtractDouble_ (s);

612

if (d > 0) configSP->screen_atomic_width = d;

613

continue;

614

}

615

616

/* User z coordinate in atomic world (must be negative!): */

617

if (strstr (s, "user") && strstr (s, "position") &&

618

strstr (s, "atomic"))

619

{

620

d = ExtractDouble_ (s);

621

if (d < 0) configSP->user_atomic_position = d; /* Negative! */

622

continue;

623

}

624

625

/* Stereo internal margin (separating left and right image): */

626

if (strstr (s, "stereo") && strstr (s, "internal") &&

627

strstr (s, "margin"))

628

{

629

n = ExtractInteger_ (s);

630

if (n > 0) configSP->stereo_screen_margin = n;

631

continue;

632

}

633

634

/* Stereo angle. The right image is rotated around y axis for that */

635

/* angle (right-handed rotation). Degrees read, radians stored: */

636

if (strstr (s, "stereo") && strstr (s, "angle"))

637

{

638

d = ExtractDouble_ (s);

639

configSP->stereo_angle = d * DEG_TO_RAD;

640

continue;

641

}

642

643

/* Light source theta angle: */

644

if (strstr (s, "light") && strstr (s, "source") &&

645

strstr (s, "theta") && strstr (s, "angle"))

646

{

647

d = ExtractDouble_ (s);

648

configSP->light_theta = d * DEG_TO_RAD;

649

continue;

650

}

651

652

/* Light source phi angle: */

653

if (strstr (s, "light") && strstr (s, "source") &&

654

strstr (s, "phi") && strstr (s, "angle"))

655

{

656

d = ExtractDouble_ (s);

657

configSP->light_phi = d * DEG_TO_RAD;

658

continue;

659

}

660

661

/* Rotation steps (very small, small, normal, large, very large): */

662

if (strstr (s, "rotation") && strstr (s, "steps"))

663

{

664

ExtractRotationSteps_ (configSP, s);

665

continue;

666

}

667

668

/* Translation steps (very small, small, normal, large, very large): */

669

if (strstr (s, "translation") && strstr (s, "steps"))

670

{

671

ExtractTranslationSteps_ (configSP, s);

672

continue;

673

}

674

675

/* Slab steps (very small, small, normal, large, very large): */

676

if (strstr (s, "slab") && strstr (s, "steps"))

677

{

678

ExtractSlabSteps_ (configSP, s);

679

continue;

680

}

681

682

/* Fading steps (very small, small, normal, large, very large): */

683

if (strstr (s, "fading") && strstr (s, "steps"))

684

{

685

ExtractFadingSteps_ (configSP, s);

686

continue;

687

}

688

689

/* Maximal bond length, used to check */

690

/* which atoms and bonds are invisible: */

691

if (strstr (s, "maximal") && strstr (s, "bond") &&

692

strstr (s, "length"))

693

{

694

d = ExtractDouble_ (s);

695

if (d > 0) configSP->max_bond_length = d;

696

continue;

697

}

698

699

/* Crude bond length limits for C-C bond: */

700

if (strstr (s, "approx") && strstr (s, "C-C") &&

701

strstr (s, "bond") && strstr (s, "length"))

702

{

703

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

704

{

705

if ((d1 > 0) && (d2 > d1))

706

{

707

configSP->C_C_bond_length_min = d1;

708

configSP->C_C_bond_length_max = d2;

709

}

710

}

711

continue;

712

}

713

714

/* Crude bond length limits for C-N bond: */

715

if (strstr (s, "approx") && strstr (s, "C-N") &&

716

strstr (s, "bond") && strstr (s, "length"))

717

{

718

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

719

{

720

if ((d1 > 0) && (d2 > d1))

721

{

722

configSP->C_N_bond_length_min = d1;

723

configSP->C_N_bond_length_max = d2;

724

}

725

}

726

continue;

727

}

728

729

/* Crude bond length limits for C-O bond: */

730

if (strstr (s, "approx") && strstr (s, "C-O") &&

731

strstr (s, "bond") && strstr (s, "length"))

732

{

733

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

734

{

735

if ((d1 > 0) && (d2 > d1))

736

{

737

configSP->C_O_bond_length_min = d1;

738

configSP->C_O_bond_length_max = d2;

739

}

740

}

741

continue;

742

}

743

744

/* Crude bond length limits for C-S bond: */

745

if (strstr (s, "approximate") && strstr (s, "C-S") &&

746

strstr (s, "bond") && strstr (s, "length"))

747

{

748

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

749

{

750

if ((d1 > 0) && (d2 > d1))

751

{

752

configSP->C_S_bond_length_min = d1;

753

configSP->C_S_bond_length_max = d2;

754

}

755

}

756

continue;

757

}

758

759

/* Crude bond length limits for C-H bond: */

760

if (strstr (s, "approximate") && strstr (s, "C-H") &&

761

strstr (s, "bond") && strstr (s, "length"))

762

{

763

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

764

{

765

if ((d1 > 0) && (d2 > d1))

766

{

767

configSP->C_H_bond_length_min = d1;

768

configSP->C_H_bond_length_max = d2;

769

}

770

}

771

continue;

772

}

773

774

/* Crude bond length limits for N-H bond: */

775

if (strstr (s, "approximate") && strstr (s, "N-H") &&

776

strstr (s, "bond") && strstr (s, "length"))

777

{

778

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

779

{

780

if ((d1 > 0) && (d2 > d1))

781

{

782

configSP->N_H_bond_length_min = d1;

783

configSP->N_H_bond_length_max = d2;

784

}

785

}

786

continue;

787

}

788

789

/* Crude bond length limits for O-H bond: */

790

if (strstr (s, "approximate") && strstr (s, "O-H") &&

791

strstr (s, "bond") && strstr (s, "length"))

792

{

793

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

794

{

795

if ((d1 > 0) && (d2 > d1))

796

{

797

configSP->O_H_bond_length_min = d1;

798

configSP->O_H_bond_length_max = d2;

799

}

800

}

801

continue;

802

}

803

804

/* Crude bond length limits for S-H bond: */

805

if (strstr (s, "approximate") && strstr (s, "S-H") &&

806

strstr (s, "bond") && strstr (s, "length"))

807

{

808

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

809

{

810

if ((d1 > 0) && (d2 > d1))

811

{

812

configSP->S_H_bond_length_min = d1;

813

configSP->S_H_bond_length_max = d2;

814

}

815

}

816

continue;

817

}

818

819

/* Crude bond length limits for O-P bond: */

820

if (strstr (s, "approximate") && strstr (s, "O-P") &&

821

strstr (s, "bond") && strstr (s, "length"))

822

{

823

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

824

{

825

if ((d1 > 0) && (d2 > d1))

826

{

827

configSP->O_P_bond_length_min = d1;

828

configSP->O_P_bond_length_max = d2;

829

}

830

}

831

continue;

832

}

833

834

/* Crude bond length limits for S-S bond: */

835

if (strstr (s, "approximate") && strstr (s, "S-S") &&

836

strstr (s, "bond") && strstr (s, "length"))

837

{

838

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

839

{

840

if ((d1 > 0) && (d2 > d1))

841

{

842

configSP->S_S_bond_length_min = d1;

843

configSP->S_S_bond_length_max = d2;

844

}

845

}

846

continue;

847

}

848

849

/* Bond length limits for unrecognized atomic pairs: */

850

if (strstr (s, "generic") && strstr (s, "bond") &&

851

strstr (s, "length"))

852

{

853

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

854

{

855

if ((d1 > 0) && (d2 > d1))

856

{

857

configSP->generic_bond_length_min = d1;

858

configSP->generic_bond_length_max = d2;

859

}

860

}

861

continue;

862

}

863

864

/* Hydrogen bond length range: */

865

if (strstr (s, "hydrogen") && strstr (s, "bond") &&

866

strstr (s, "length"))

867

{

868

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

869

{

870

if ((d1 > 0) && (d2 > d1))

871

{

872

configSP->hydro_bond_length_min = d1;

873

configSP->hydro_bond_length_max = d2;

874

}

875

}

876

continue;

877

}

878

879

/* Hydrogen bond angular range: */

880

if (strstr (s, "hydrogen") && strstr (s, "bond") &&

881

strstr (s, "angle"))

882

{

883

if (ExtractTwoDoubles_ (&d1, &d2, s) > 0)

884

{

885

if ((d1 >= 0.0) && (d1 <= 180.0) &&

886

(d2 > d1) && (d2 <= 180))

887

{

888

configSP->hydro_bond_angle_min =

889

d1 * DEG_TO_RAD;

890

configSP->hydro_bond_angle_max =

891

d2 * DEG_TO_RAD;

892

}

893

}

894

}

895

896

/* The maximal CA-CA distance for two neighbouring residues: */

897

if (strstr (s, "maximal") && strstr (s, "CA-CA") &&

898

strstr (s, "distance"))

899

{

900

d = ExtractDouble_ (s);

901

if (d > 0) configSP->CA_CA_dist_max = d;

902

continue;

903

}

904

905

/* Radius of hydrogen atom: */

906

if (strstr (s, "radius") && strstr (s, "hydrogen") &&

907

!strstr (s, "Waals"))

908

{

909

d = ExtractDouble_ (s);

910

if (d > 0) configSP->H_radius = (float) d;

911

continue;

912

}

913

914

/* Radius of carbon atom: */

915

if (strstr (s, "radius") && strstr (s, "carbon") &&

916

!strstr (s, "Waals"))

917

{

918

d = ExtractDouble_ (s);

919

if (d > 0) configSP->C_radius = (float) d;

920

continue;

921

}

922

923

/* Radius of nitrogen atom: */

924

if (strstr (s, "radius") && strstr (s, "nitrogen") &&

925

!strstr (s, "Waals"))

926

{

927

d = ExtractDouble_ (s);

928

if (d > 0) configSP->N_radius = (float) d;

929

continue;

930

}

931

932

/* Radius of oxygen atom: */

933

if (strstr (s, "radius") && strstr (s, "oxygen") &&

934

!strstr (s, "Waals"))

935

{

936

d = ExtractDouble_ (s);

937

if (d > 0) configSP->O_radius = (float) d;

938

continue;

939

}

940

941

/* Radius of sulfur atom: */

942

if (strstr (s, "radius") && strstr (s, "sulfur") &&

943

!strstr (s, "Waals"))

944

{

945

d = ExtractDouble_ (s);

946

if (d > 0) configSP->S_radius = (float) d;

947

continue;

948

}

949

950

/* Radius of phosphorus atom: */

951

if (strstr (s, "radius") && strstr (s, "phosphorus") &&

952

!strstr (s, "Waals"))

953

{

954

d = ExtractDouble_ (s);

955

if (d > 0) configSP->P_radius = (float) d;

956

continue;

957

}

958

959

/* Radius of unknown atom (generic radius): */

960

if (strstr (s, "generic") && strstr (s, "radius") &&

961

!strstr (s, "Waals"))

962

{

963

d = ExtractDouble_ (s);

964

if (d > 0) configSP->generic_radius = (float) d;

965

continue;

966

}

967

968

/* Van der Waals radius of hydrogen: */

969

if (strstr (s, "hydrogen") && strstr (s, "Waals"))

970

{

971

d = ExtractDouble_ (s);

972

if (d > 0) configSP->H_van_der_Waals_radius = (float) d;

973

continue;

974

}

975

976

/* Van der Waals radius of carbon: */

977

if (strstr (s, "carbon") && strstr (s, "Waals"))

978

{

979

d = ExtractDouble_ (s);

980

if (d > 0) configSP->C_van_der_Waals_radius = (float) d;

981

continue;

982

}

983

984

/* Van der Waals radius of nitrogen: */

985

if (strstr (s, "nitrogen") && strstr (s, "Waals"))

986

{

987

d = ExtractDouble_ (s);

988

if (d > 0) configSP->N_van_der_Waals_radius = (float) d;

989

continue;

990

}

991

992

/* Van der Waals radius of oxygen: */

993

if (strstr (s, "oxygen") && strstr (s, "Waals"))

994

{

995

d = ExtractDouble_ (s);

996

if (d > 0) configSP->O_van_der_Waals_radius = (float) d;

997

continue;

998

}

999

1000

/* Van der Waals radius of sulfur: */

1001

if (strstr (s, "sulfur") && strstr (s, "Waals"))

1002

{

1003

d = ExtractDouble_ (s);

1004

if (d > 0) configSP->S_van_der_Waals_radius = (float) d;

1005

continue;

1006

}

1007

1008

/* Van der Waals radius of phosphorus: */

1009

if (strstr (s, "phosphorus") && strstr (s, "Waals"))

1010

{

1011

d = ExtractDouble_ (s);

1012

if (d > 0) configSP->P_van_der_Waals_radius = (float) d;

1013

continue;

1014

}

1015

1016

/* Van der Waals radius of unknown atom (generic radius): */

1017

if (strstr (s, "generic") && strstr (s, "Waals"))

1018

{

1019

d = ExtractDouble_ (s);

1020

if (d > 0) configSP->generic_van_der_Waals_radius = (float) d;

1021

continue;

1022

}

1023

1024

/* Ball radius (used to draw balls and sticks): */

1025

if (strstr (s, "ball") && strstr (s, "radius"))

1026

{

1027

d = ExtractDouble_ (s);

1028

if (d > 0) configSP->ball_radius = (float) d;

1029

continue;

1030

}

1031

1032

/* The number of neighboring atoms which should be checked */

1033

/* as bond candidates, in each direction of AtomS array: */

1034

if (strstr (s, "number") && strstr (s, "bond") &&

1035

strstr (s, "candidates"))

1036

{

1037

if (ExtractTwoIntegers_ (&n1, &n2, s) > 0)

1038

{

1039

if (n1 > 0) configSP->bond_candidates_backward = n1;

1040

if (n2 > 0) configSP->bond_candidates_forward = n2;

1041

}

1042

}

1043

continue;

1044

}

1045

1046

/* Close file: */

1047

fclose (fileP);

1048

1049

return 1;

1050

}

1051

1052

/*===========================================================================*/

1053

1054

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