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Viewing changes to disulfide_bonds.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

disulfide_bonds.c

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

disulfide_bonds.c

Purpose:

Prepare disulfide bonds. Only the distance between two sulfur

atoms is checked; the angle between two methylene groups is not

checked.

Input:

(1) Pointer to MolComplexS structure, with macromolecular data.

(2) The array index of a given macromolecular complex.

(3) Pointer to ConfigS structure, with configuration data.

Output:

(1) Information about dusulfide bonds added.

(2) Return value.

Return value:

(1) The total number of bonds on success.

(2) Zero if there are no atoms.

(3) Negative, if there are some atoms but there are no bonds.

Notes:

(1) If some atoms are deleted or inserted, all bonds have to be

updated. Note that array indices are shifted after addition

or deletion of atoms; that's the most important reason for

thorough revision of bonds.

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

#include <stdio.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:=================================================*/

short int CheckDistance_ (double *, AtomS *, AtomS *, ConfigS *);

short int AddBond_ (AtomS *, short int, unsigned char,

int, size_t, double, short int);

/*======prepare disulfide bonds:=============================================*/

size_t DisulfideBonds_ (MolComplexS *mol_complexSP,

int mol_complexI, ConfigS *configSP)

{

size_t total_bondsN = 0;

short int styleI;

size_t atomsN, atom1I, atom2I;

/* Use signed int to store the following indices: */

AtomS *atom1SP, *atom2SP;

short int pairID;

unsigned char bond_typeI;

double distance;

char alt_location1, alt_location2;

/* Initialize the styleI: */

styleI = 1;

/* Return zero if there are no atoms: */

atomsN = mol_complexSP->atomsN;

if (atomsN == 0) return 0;

/* Disulfide bonds are treated as type 2: */

bond_typeI = 2;

/* The outer atomic loop: */

for (atom1I = 0; atom1I < atomsN; atom1I++)

{

/* Pointer to atom 1: */

atom1SP = mol_complexSP->atomSP + atom1I;

/* Check is this sulfur: */

if (strcmp (atom1SP->raw_atomS.chemical_symbolA, " S") != 0) continue;

/* The inner atomic loop: */

for (atom2I = 0; atom2I < atomsN; atom2I++)

{

/* Atom is not bound to itself: */

if (atom2I == atom1I) continue;

/* Pointer to atom 2: */

atom2SP = mol_complexSP->atomSP + atom2I;

/* Both atoms should be sulfur atoms: */

if (strcmp (atom1SP->raw_atomS.chemical_symbolA, " S") != 0)

continue;

if (strcmp (atom2SP->raw_atomS.chemical_symbolA, " S") != 0)

continue;

/* Check is there a chemical bond: */

100

pairID = CheckDistance_ (&distance,

101

atom1SP, atom2SP, configSP);

102

103

/* If bond is bad, check the next atom 2: */

104

if (pairID <= 0) continue;

105

106

/* Compare the alternate location indicators; */

107

/* if both indicators are different from ' ' */

108

/* and mutually different, the bond is bad! */

109

alt_location1 = atom1SP->raw_atomS.alt_location;

110

alt_location2 = atom2SP->raw_atomS.alt_location;

111

if ((alt_location1 != alt_location2) &&

112

(alt_location1 != ' ') && (alt_location2 != ' '))

113

{

114

continue;

115

}

116

117

/* If this point is reached, the bond does exist! */

118

119

/* Add bond to atom 1: */

120

AddBond_ (atom1SP,

121

pairID, bond_typeI,

122

mol_complexI, atom2I,

123

distance, styleI);

124

125

/* Update the number of bonds in a macromolecular complex: */

126

total_bondsN++;

127

}

128

}

129

130

/* If this point is reached, return the total number of bonds: */

131

return total_bondsN;

132

}

133

134

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

135

136

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