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
211
212
213
214
215
216
217
218
219
220
221

<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet
 version="1.0"
 xmlns:c="http://www.ncbi.nlm.nih.gov"
 xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
 xmlns:svg="http://www.w3.org/2000/svg"
 xmlns:xlink="http://www.w3.org/1999/xlink"
 xmlns:h="http://www.w3.org/1999/xhtml"
 >
 
 <!--

Motivation:
	transforms a pubchem 3D xml result to Processing
Author
	Pierre Lindenbaum PhD plindenbaum@yahoo.fr
	http://plindenbaum.blogspot.com
	http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/pubchem2processing.xsl 


-->

<!-- ========================================================================= -->
<xsl:output method='text' omit-xml-declaration="yes"/>



<!-- array of atoms -->
<xsl:variable name="a_array" select="/c:PC-Compound/c:PC-Compound_atoms/c:PC-Atoms/c:PC-Atoms_element"/>
<xsl:variable name="conformers" select="/c:PC-Compound/c:PC-Compound_coords/c:PC-Coordinates/c:PC-Coordinates_conformers/c:PC-Conformer"/>

<xsl:variable name="x_array" select="$conformers/c:PC-Conformer_x"/>
<xsl:variable name="y_array" select="$conformers/c:PC-Conformer_y"/>
<xsl:variable name="z_array" select="$conformers/c:PC-Conformer_z"/>

<!-- array of bound -->
<xsl:variable name="b_array" select="/c:PC-Compound/c:PC-Compound_bonds/c:PC-Bonds"/>
<xsl:variable name="bound1_array" select="$b_array/c:PC-Bonds_aid1"/>
<xsl:variable name="bound2_array" select="$b_array/c:PC-Bonds_aid2"/>




<xsl:template match="/">
<xsl:apply-templates select="c:PC-Compound"/>
</xsl:template>


<xsl:template match="c:PC-Compound">
/**
 *	Made with http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/pubchem2processing.xsl 	
 *	Author: Pierre Lindenbaum PhD plindenbaum@yahoo.fr
 *	http://plindenbaum.blogspot.com
 */
 
//number of atoms
static final int ATOM_COUNT=<xsl:value-of select="count($a_array/c:PC-Element)"/>;

//array of X positions
static final float array_x[]=new float[]{<xsl:for-each select="$x_array/c:PC-Conformer_x_E">
		<xsl:if test="position() != 1"><xsl:text>f,</xsl:text></xsl:if>
		<xsl:value-of select="." />
	</xsl:for-each>};

//array of Y positions
static final float array_y[]=new float[]{<xsl:for-each select="$y_array/c:PC-Conformer_y_E">
		<xsl:if test="position() != 1"><xsl:text>f,</xsl:text></xsl:if>
		<xsl:value-of select="." />
	</xsl:for-each>};
	
//array of Z positions
static final float array_z[]=new float[]{<xsl:for-each select="$z_array/c:PC-Conformer_z_E">
		<xsl:if test="position() != 1"><xsl:text>f,</xsl:text></xsl:if>
		<xsl:value-of select="." />
	</xsl:for-each>};

//array of atom names
static final char array_c[]=new char[]{<xsl:for-each select="$a_array/c:PC-Element">
	<xsl:if test="position() != 1"><xsl:text>,</xsl:text></xsl:if>
		<xsl:text>&apos;</xsl:text><xsl:value-of select="@value" /><xsl:text>&apos;</xsl:text>
	</xsl:for-each>};

//number of bounds
static final int BOUND_COUNT=<xsl:value-of select="count($bound1_array/c:PC-Bonds_aid1_E)"/>;

//bound start index
static final int bound_start[]=new int[]{<xsl:for-each select="$bound1_array/c:PC-Bonds_aid1_E">
		<xsl:if test="position() != 1"><xsl:text>,</xsl:text></xsl:if>
		<xsl:value-of select="number(.)-1" />
	</xsl:for-each>};
	
//bound end index
static final int bound_end[]=new int[]{<xsl:for-each select="$bound2_array/c:PC-Bonds_aid2_E">
		<xsl:if test="position() != 1"><xsl:text>,</xsl:text></xsl:if>
		<xsl:value-of select="number(.)-1" />
	</xsl:for-each>};
	
//Name of this product
static final String title= "<xsl:value-of select="c:PC-Compound_id/c:PC-CompoundType/c:PC-CompoundType_id/c:PC-CompoundType_id_cid"/>";


float mid_x=0f;
float mid_y=0f;
float mid_z=0f;
float alpha=150;
float zoom=10f;
float zoomAtom=1.0f;
boolean drawBounds=true;

void setup()
  {
 
  size(
  	500,
  	500,
  	P3D);
  mid_x= center(array_x);
  mid_y= center(array_y);
  mid_z= center(array_z);
 }

void draw()
  {
 lights();
  background(0);

  translate(width / 2, height / 2,0);
  rotateY(map(mouseX, 0, width, 0, TWO_PI));
  rotateZ(map(mouseY, 0, height, 0, -TWO_PI));
 stroke(170, 0, 0);
  for(int i=0;drawBounds &amp;&amp; i&lt; BOUND_COUNT;++i)
        {
        line(
                xAngstrom(array_x[bound_start[i]] -mid_x ),
                xAngstrom(array_y[bound_start[i]] -mid_y),
                xAngstrom(array_z[bound_start[i]] -mid_z),
                xAngstrom(array_x[bound_end[i]] -mid_x ),
                xAngstrom(array_y[bound_end[i]] -mid_y ),
                xAngstrom(array_z[bound_end[i]] -mid_z )
                );
        }
 noStroke();
  for(int i=0;i &lt; ATOM_COUNT;++i)
        {
         pushMatrix();
        translate(
                xAngstrom(array_x[i] -mid_x ),
                xAngstrom(array_y[i] -mid_y ),
                xAngstrom(array_z[i] -mid_z )
                );
        fillAtom(array_c[i]);
        sphere(zoomAtom*radiusOf(array_c[i]));
        popMatrix();
        }
  
  }
   
float xAngstrom(float x)
	{
	return x*zoom;
	}

int radiusOf(char c)
	{
	switch(c)
		{
		case 'o':case 'O': return 14;
		case 'c':case 'C': return 12;
		case 'h':case 'H': return 6;
		default: return 10;
		}
	}

void fillAtom(char c)
	{
	switch(c)
		{
		case 'o':case 'O': fill(0,0,200,alpha); break;
		case 'c':case 'C': fill(100,100,100,alpha); break;
		case 'h':case 'H': fill(200,200,200,alpha); break;
		case 'n':case 'N': fill(142,142,0,alpha); break;
		case 's':case 'S': fill(142,0,142,alpha); break;
		default: fill(142,142,142,alpha);break;
		}
	}

static float center(final float array[])
 {
   float t=0f;
   for(int i=0;i&lt;  array.length;++i)
     {
     t+=array[i];
     }
   return t/float(array.length);
 }

void keyPressed()
  {
  final float alphaShift=5;
  final float zoomShift=0.5;
  final float zoomAtomShift=0.1;
  switch(key)
        {
        case 'a':case 'A': if(alpha-alphaShift &gt;=0) this.alpha-=alphaShift; break;
        case 'z':case 'Z': if(alpha+alphaShift &lt;=255) this.alpha+=alphaShift; break;
        case 'q':case 'Q': zoom+=zoomShift; break;
        case 's':case 'S':  if(zoom-zoomShift&gt;0) zoom-=zoomShift; break;
        case 'w':case 'W': zoomAtom+=zoomAtomShift; break;
        case 'x':case 'X':  if(zoomAtom-zoomAtomShift &gt;0) zoomAtom-=zoomAtomShift; break;
        case 'd': drawBounds=!drawBounds;break;
        default:break;
        }
  }

</xsl:template>





</xsl:stylesheet>