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
|
import java.util.List;
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;
Rectangle drawArea;
IMolecule molecule = new Molecule();
IMoleculeSet moleculeSet;
IMolecule[] coordinated_mols;
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
Vector<Integer> idlist = new Vector<Integer>();
List generators = new ArrayList();
Renderer renderer;
BufferedImage image;
Graphics2D g2;
MoleculeSet highBSet = new MoleculeSet();
ChemModel chemModel = new ChemModel();
LogicalSelection selection = new LogicalSelection(LogicalSelection.Type.ALL);
ByteArrayOutputStream out = new ByteArrayOutputStream();
public Structure (String smiles, int s) {
size = s;
// generators make the image elements
generators.add(new BasicSceneGenerator());
generators.add(new RingGenerator());
generators.add(new BasicBondGenerator());
generators.add(new BasicAtomGenerator());
//generators.add(new AtomNumberGenerator());
generators.add(new SelectBondGenerator());
generators.add(new SelectAtomGenerator());
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.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
last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last,2);
coordinated_mols[i] = (IMolecule) mol;
}
moleculeSet.setMolecules(coordinated_mols);
} catch (Exception ex) {
ex.printStackTrace();
}
}
public void match_activating(String[] smarts) {
Color color = Color.RED;
for (int i = 0; i < smarts.length; i++) {
match(smarts[i], color);
}
}
public void match_deactivating(String[] smarts) {
Color color = Color.GREEN;
for (int i = 0; i < smarts.length; i++) {
match(smarts[i], color);
}
}
public void match(String smarts, Color color) {
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);
for (int j = 0; j < matches.size(); j++) {
IAtomContainer highB = new AtomContainer();
List atomIndices = (List) matches.get(j);
for (int k = 0; k < atomIndices.size(); k++) {
IAtom a1 = mol.getAtom( (Integer) atomIndices.get(k));
if (!highB.contains(a1)) { highB.addAtom(a1); }
for (int l = k + 1; l < atomIndices.size(); l++) {
IAtom a2 = mol.getAtom( (Integer) atomIndices.get(l));
IBond bond = mol.getBond(a1,a2);
if (bond != null) { highB.addBond(bond); }
}
}
highBSet.addMolecule(new Molecule(highB));
}
}
}
chemModel.setMoleculeSet(highBSet);
selection.select(chemModel);
renderer.getRenderer2DModel().setSelection(selection);
renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,color);
} catch (Exception exc) {
exc.printStackTrace();
}
}
}
|
