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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

cylin_slab.c

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

cylin_slab.c

Purpose:

Check which atoms are inside the cylindrical slab. Cylindrical slab

is defined by two concentric cylinders. A given atom is inside the

slab if it is outside the inner and inside the outer cylinder. Use

this slab type to hide the inner part (the "cork") of a porin-like

protein. The y axis is a symmetry axis.

Input:

(1) Pointer to MolComplexS structure.

Output:

(1) Slab flag set for each atom. The value one is assigned to atoms

inside the slab, zero to the rest.

(2) Return value.

Return value:

The number of atoms inside the slab.

========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"

/*======cylindrical slab:====================================================*/

size_t CylinSlab_ (MolComplexS *curr_mol_complexSP)

{

size_t atoms_inside_slabN = 0;

size_t atomsN, atomI;

AtomS *curr_atomSP;

double x0, z0, rho0_squared, rho1_squared;

double x, z, rho_squared;

/* The number of atoms in a complex: */

atomsN = curr_mol_complexSP->atomsN;

/* Copy the slab center coordinates: */

x0 = curr_mol_complexSP->slab_center_vectorS.x;

z0 = curr_mol_complexSP->slab_center_vectorS.z;

rho0_squared = curr_mol_complexSP->slab_back_relative_position;

rho0_squared *= rho0_squared;

rho1_squared = curr_mol_complexSP->slab_front_relative_position;

rho1_squared *= rho1_squared;

/* Set the slab flag for each atom: */

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

{

/** Pointer to the current atom: **/

curr_atomSP = curr_mol_complexSP->atomSP + atomI;

/** Set the initial values of slab flags to one; this **/

/** will be changed later for atoms outside the slab: **/

curr_atomSP->inside_slabF = 1;

curr_atomSP->inside_projected_slabF = 1;

/** Distance between the current atom and the cylinder axis: **/

x = curr_atomSP->raw_atomS.x[0] - x0;

z = curr_atomSP->raw_atomS.z[0] - z0;

rho_squared = x * x + z * z;

/** If atom is inside the inner cylinder, set **/

/** slab flag to zero and check the next atom: **/

if (rho_squared < rho0_squared)

{

curr_atomSP->inside_slabF = 0;

curr_atomSP->inside_projected_slabF = 0;

continue;

}

/** If atom is outside the outer slab cylinder: **/

if (rho_squared > rho1_squared)

{

curr_atomSP->inside_slabF = 0;

curr_atomSP->inside_projected_slabF = 0;

continue;

}

/** If this points is reached, current atom is inside the slab: **/

atoms_inside_slabN++;

}

/* Return the number of atoms inside the slab: */

return atoms_inside_slabN;

}

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

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