1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
|
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: cn3dutils.c
*
* Author: Yanli Wang
*
* Initial Version Creation Date: 8/12/2002
*
* File Description:
* facility function for adding drawing-style and user annotations
*
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: cn3dutil.c,v $
* Revision 1.5 2002/12/12 15:59:45 ywang
* wording improvement
*
*
* ==========================================================================
*/
#include <ncbi.h> /* the NCBI SDK header */
#include <asn.h> /* the ASN.1 header */
#include <mmdbapi.h> /* the MMDB-API header */
#include <sequtil.h>
#include <objsset.h>
#include <mmdbdata.h>
#include <mmdblocl.h>
#include <string.h>
#include <accentr.h>
#include <saledit.h>
#include <lsqfetch.h>
#include <objseq.h>
#include <asnseq.h>
#include <objmgr.h>
#include <sequtil.h>
#include <objmime.h>
#include <blast.h>
#include <www.h>
#include <accutils.h>
#include <netentr.h>
#include <cddutil.h>
#include <objcn3d.h>
/*-------- set cn3dcolor ---------*/
void SetCn3dColor(Cn3dColorPtr ccp, Int4 scale_factor, Int4 red, Int4 green, Int4 blue, Int4 alpha)
{
ccp->scale_factor = scale_factor;
ccp->red = red;
ccp->green = green;
ccp->blue = blue;
ccp->alpha = alpha;
}
/*-------- get default style setting -----------*/
Cn3dStyleSettingsPtr GetDefaultCn3DStyleSettings()
{
Cn3dStyleSettingsPtr cssp = NULL;
Cn3dBackboneStylePtr cbsp = NULL;
Cn3dGeneralStylePtr cgsp = NULL;
Cn3dColorPtr ccp = NULL;
Cn3dBackboneLabelStylePtr cblsp = NULL;
cssp = Cn3dStyleSettingsNew();
cssp->next = NULL;
cssp->name = NULL;
cbsp = Cn3dBackboneStyleNew();
cbsp->type = Cn3d_backbone_type_trace;
/* cbsp->style = Cn3d_drawing_style_tubes; */
cbsp->style = Cn3d_drawing_style_wire;
/* cbsp->color_scheme = Cn3d_color_scheme_weighted_variety; */
cbsp->color_scheme = Cn3d_color_scheme_identity;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cbsp->user_color = ccp;
cssp->protein_backbone = cbsp;
cbsp = Cn3dBackboneStyleNew();
cbsp->type = Cn3d_backbone_type_trace;
/* cbsp->style = Cn3d_drawing_style_tubes; */
cbsp->style = Cn3d_drawing_style_wire;
cbsp->color_scheme = Cn3d_color_scheme_molecule;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cbsp->user_color = ccp;
cssp->nucleotide_backbone = cbsp;
cgsp = Cn3dGeneralStyleNew();
cgsp->is_on = TRUE;
cgsp->style = Cn3d_drawing_style_wire;
/* cgsp->color_scheme = Cn3d_color_scheme_weighted_variety; */
cgsp->color_scheme = Cn3d_color_scheme_identity;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cgsp->user_color = ccp;
cssp->protein_sidechains = cgsp;
cgsp = Cn3dGeneralStyleNew();
cgsp->is_on = TRUE;
cgsp->style = Cn3d_drawing_style_wire;
cgsp->color_scheme = Cn3d_color_scheme_molecule;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cgsp->user_color = ccp;
cssp->nucleotide_sidechains = cgsp;
cgsp = Cn3dGeneralStyleNew();
cgsp->is_on = TRUE;
cgsp->style = Cn3d_drawing_style_ball_and_stick;
cgsp->color_scheme = Cn3d_color_scheme_element;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cgsp->user_color = ccp;
cssp->heterogens = cgsp;
cgsp = Cn3dGeneralStyleNew();
cgsp->is_on = FALSE;
cgsp->style = Cn3d_drawing_style_ball_and_stick;
cgsp->color_scheme = Cn3d_color_scheme_element;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cgsp->user_color = ccp;
cssp->solvents = cgsp;
cgsp = Cn3dGeneralStyleNew();
cgsp->is_on = TRUE;
cgsp->style = Cn3d_drawing_style_tubes;
cgsp->color_scheme = Cn3d_color_scheme_user_select;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cgsp->user_color = ccp;
cssp->connections = cgsp;
cgsp = Cn3dGeneralStyleNew();
cgsp->is_on = FALSE;
cgsp->style = Cn3d_drawing_style_with_arrows;
cgsp->color_scheme = Cn3d_color_scheme_object;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cgsp->user_color = ccp;
cssp->helix_objects = cgsp;
cgsp = Cn3dGeneralStyleNew();
cgsp->is_on = FALSE;
cgsp->style = Cn3d_drawing_style_with_arrows;
cgsp->color_scheme = Cn3d_color_scheme_object;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 5000, 5000, 5000, 10000);
cgsp->user_color = ccp;
cssp->strand_objects = cgsp;
cssp->virtual_disulfides_on = TRUE;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 9300, 5500, 500, 10000);
cssp->virtual_disulfide_color = ccp;
cssp->hydrogens_on = FALSE;
ccp = Cn3dColorNew();
SetCn3dColor(ccp, 10000, 0, 0, 0, 10000);
cssp->background_color = ccp;
cssp->scale_factor = 10000;
cssp->space_fill_proportion = 10000;
cssp->ball_radius = 4000;
cssp->stick_radius = 2000;
cssp->tube_radius = 3000;
cssp->tube_worm_radius = 3000;
cssp->helix_radius = 18000;
cssp->strand_width = 20000;
cssp->strand_thickness = 5000;
cblsp = Cn3dBackboneLabelStyleNew();
cblsp->spacing = 0;
cblsp->type = Cn3d_backbone_label_style_type_three_letter;
cblsp->number = Cn3d_backbone_label_style_number_sequential;
cblsp->termini = FALSE;
cblsp->white = TRUE;
cssp->protein_labels = cblsp;
cblsp = Cn3dBackboneLabelStyleNew();
cblsp->spacing = 0;
cblsp->type = Cn3d_backbone_label_style_type_three_letter;
cblsp->number = Cn3d_backbone_label_style_number_sequential;
cblsp->termini = FALSE;
cblsp->white = TRUE;
cssp->nucleotide_labels =cblsp;
cssp->ion_labels = TRUE;
return cssp;
}
|
