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
|
import java.util.List;
import java.util.HashMap;
import java.util.Map;
import java.util.*;
import java.io.*;
import java.awt.*;
import java.awt.image.*;
import java.awt.geom.*;
import javax.imageio.*;
import org.openscience.cdk.*;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.layout.*;
import org.openscience.cdk.renderer.*;
import org.openscience.cdk.renderer.font.*;
import org.openscience.cdk.renderer.generators.*;
import org.openscience.cdk.renderer.visitor.*;
import org.openscience.cdk.renderer.selection.*;
import org.openscience.cdk.templates.*;
import org.openscience.cdk.smiles.*;
import org.openscience.cdk.smiles.smarts.*;
import org.openscience.cdk.graph.*;
import org.openscience.cdk.geometry.*;
public class Structure{
int size;
List generators = new ArrayList();
IMolecule molecule = new Molecule();
IMoleculeSet moleculeSet;
IMolecule[] coordinated_mols;
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
Map<IChemObject,Color> coloredMatches = new HashMap<IChemObject,Color>();
Renderer renderer;
BufferedImage image;
Rectangle drawArea;
Graphics2D g2;
ByteArrayOutputStream out = new ByteArrayOutputStream();
public Structure (String smiles, int imageSize) {
size = imageSize;
// generators make the image elements
generators.add(new BasicSceneGenerator());
generators.add(new RingGenerator());
generators.add(new BasicBondGenerator());
generators.add(new BasicAtomGenerator());
renderer = new Renderer(generators, new AWTFontManager());
try { molecule = sp.parseSmiles(smiles); }
catch (Exception ex) { ex.printStackTrace(); }
moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule);
coordinated_mols = new IMolecule[moleculeSet.getMoleculeCount()];
drawArea = new Rectangle(size, size);
image = new BufferedImage(size, size , BufferedImage.TYPE_INT_RGB);
g2 = (Graphics2D)image.getGraphics();
g2.setColor(Color.WHITE);
g2.fillRect(0, 0, size, size);
layout();
}
public byte[] show() {
try {
renderer.getRenderer2DModel().set( RendererModel.ColorHash.class, coloredMatches );
renderer.paintMoleculeSet(moleculeSet, new AWTDrawVisitor(g2), drawArea, true);
ImageIO.write(image, "png", out);
}
catch (Exception ex) { ex.printStackTrace(); }
return out.toByteArray();
}
private void layout() {
try {
Rectangle2D last = new Rectangle(0,0);
for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
IAtomContainer mol = moleculeSet.getMolecule(i);
sdg.setMolecule((IMolecule) mol);
sdg.generateCoordinates();
mol = sdg.getMolecule();
GeometryTools.translateAllPositive(mol);
// get size of previous mol and shift to the right
last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last, 5);
coordinated_mols[i] = (IMolecule) mol;
}
moleculeSet.setMolecules(coordinated_mols);
}
catch (Exception ex) { ex.printStackTrace(); }
}
public void match_activating(String[] smarts) {
for (int i = 0; i < smarts.length; i++) {
match(smarts[i],Color.RED);
}
}
public void match_deactivating(String[] smarts) {
for (int i = 0; i < smarts.length; i++) {
match(smarts[i],Color.GREEN);
}
}
public void match(String smarts) { match(smarts, Color.BLUE); }
public void match(String smarts, Color color) {
IAtom a1 = new Atom();
IAtom a2 = new Atom();
IBond bond = new Bond();
try {
SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
// iterate over molecule set
for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
IAtomContainer mol = moleculeSet.getMolecule(i);
ChemModel fragment = new ChemModel();
// match smarts
boolean status = querytool.matches(mol);
if (status) {
List matches = querytool.getUniqueMatchingAtoms();
//System.out.print("Matches: ");
//System.out.println(matches);
// iterate over all matches
for (int j = 0; j < matches.size(); j++) {
List atomIndices = (List) matches.get(j);
// itrate over all atoms
for (int k = 0; k < atomIndices.size(); k++) {
a1 = mol.getAtom( (Integer) atomIndices.get(k));
// find bonds
for (int l = k + 1; l < atomIndices.size(); l++) {
a2 = mol.getAtom( (Integer) atomIndices.get(l));
bond = mol.getBond(a1,a2);
if (bond != null) { coloredMatches.put((IChemObject) bond , color); }
}
}
}
}
}
}
catch (Exception exc) { exc.printStackTrace(); }
}
}
|
