Package org.openscience.cdk.interfaces

Examples of org.openscience.cdk.interfaces.IAtom

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
     */
    @Test public void testGetInchiEandZ12Dichloroethene2D() throws Exception {

        // (E)-1,2-dichloroethene
        IAtomContainer acE = new AtomContainer();
        IAtom a1E = new Atom("C", new Point2d(2.866, -0.250));
        IAtom a2E = new Atom("C", new Point2d(3.732, 0.250));
        IAtom a3E = new Atom("Cl", new Point2d(2.000, 2.500));
        IAtom a4E = new Atom("Cl", new Point2d(4.598, -0.250));
        a1E.setImplicitHydrogenCount(1);
        a2E.setImplicitHydrogenCount(1);
        acE.addAtom(a1E);
        acE.addAtom(a2E);
        acE.addAtom(a3E);
        acE.addAtom(a4E);

        acE.addBond(new Bond(a1E, a2E, CDKConstants.BONDORDER_DOUBLE));
        acE.addBond(new Bond(a1E, a3E, CDKConstants.BONDORDER_SINGLE));
        acE.addBond(new Bond(a2E, a4E, CDKConstants.BONDORDER_SINGLE));
       
        Assert.assertEquals(gen.generateInchi(acE).getInChI(), "InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+");
       
        // (Z)-1,2-dichloroethene
        IAtomContainer acZ = new AtomContainer();
        IAtom a1Z = new Atom("C", new Point2d(2.866, -0.440));
        IAtom a2Z = new Atom("C", new Point2d(3.732, 0.060));
        IAtom a3Z = new Atom("Cl", new Point2d(2.000, 0.060));
        IAtom a4Z = new Atom("Cl", new Point2d(3.732, 1.060));
        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);
View Full Code Here
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
    @Test
    public void testGetInchiFromLandDAlanine3D() throws Exception {
       
        // L-Alanine
        IAtomContainer acL = new AtomContainer();
        IAtom a1L = new Atom("C", new Point3d(-0.358, 0.819, 20.655));
        IAtom a2L = new Atom("C", new Point3d(-1.598, -0.032, 20.905));
        IAtom a3L = new Atom("N", new Point3d(-0.275, 2.014, 21.574));
        IAtom a4L = new Atom("C", new Point3d(0.952, 0.043, 20.838));
        IAtom a5L = new Atom("O", new Point3d(-2.678, 0.479, 21.093));
        IAtom a6L = new Atom("O", new Point3d(-1.596, -1.239, 20.958));
        a1L.setImplicitHydrogenCount(1);
        a3L.setImplicitHydrogenCount(2);
        a4L.setImplicitHydrogenCount(3);
        a5L.setImplicitHydrogenCount(1);
        acL.addAtom(a1L);
        acL.addAtom(a2L);
        acL.addAtom(a3L);
        acL.addAtom(a4L);
        acL.addAtom(a5L);
        acL.addAtom(a6L);
       
        acL.addBond(new Bond(a1L, a2L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a1L, a3L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a1L, a4L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a2L, a5L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a2L, a6L, CDKConstants.BONDORDER_DOUBLE));
       
        Assert.assertEquals(gen.generateInchi(acL).getInChI(), "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1");
       
       
        // D-Alanine
        IAtomContainer acD = new AtomContainer();
        IAtom a1D = new Atom("C", new Point3d(0.358, 0.819, 20.655));
        IAtom a2D = new Atom("C", new Point3d(1.598, -0.032, 20.905));
        IAtom a3D = new Atom("N", new Point3d(0.275, 2.014, 21.574));
        IAtom a4D = new Atom("C", new Point3d(-0.952, 0.043, 20.838));
        IAtom a5D = new Atom("O", new Point3d(2.678, 0.479, 21.093));
        IAtom a6D = new Atom("O", new Point3d(1.596, -1.239, 20.958));
        a1D.setImplicitHydrogenCount(1);
        a3D.setImplicitHydrogenCount(2);
        a4D.setImplicitHydrogenCount(3);
        a5D.setImplicitHydrogenCount(1);
        acD.addAtom(a1D);
View Full Code Here
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
        if(symbol!=null && symbol.length()>0){

            jcpPanel.get2DHub().setActiveDrawModule(newActiveModule);
            if(atomsInRange!=null){
                while(atomsInRange.hasNext()){
                    IAtom atom = atomsInRange.next();
                    jcpPanel.get2DHub().setSymbol(atom,symbol);
                    //TODO still needed? should this go in hub?
                    // configure the atom, so that the atomic number matches the symbol
                    try
                    {
                        XMLIsotopeFactory.getInstance(atom.getBuilder()).configure(atom);
                    } catch (Exception exception)
                    {
                        logger.error("Error while configuring atom");
                        logger.debug(exception);
                    }
View Full Code Here
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
      atomsInRange = atoms.iterator();
    }
    if(atomsInRange==null)
      return;
    while(atomsInRange.hasNext()){
            IAtom atom = atomsInRange.next();
            int isotopeNumber = 0;
            try {
                IIsotope isotope =
                    XMLIsotopeFactory.getInstance(
                                atom.getBuilder()).getMajorIsotope(
                                atom.getSymbol());
                isotopeNumber = isotope.getMassNumber();
            } catch (Exception exception) {
                logger.error("Error while configuring atom");
                logger.debug(exception);
            }
            // adapt for menu chosen
            if (type.equals("major")) {
                // that's the default
            } else if (type.equals("majorPlusOne")) {
                isotopeNumber += 1;
            } else if (type.equals("majorPlusTwo")) {
                isotopeNumber += 2;
            } else if (type.equals("majorPlusThree")) {
                isotopeNumber += 3;
            } else if (type.equals("majorMinusOne")) {
                isotopeNumber -= 1;
            } else if (type.equals("majorMinusTwo")) {
                isotopeNumber -= 2;
            } else if (type.equals("majorMinusThree")) {
                isotopeNumber -= 3;
            } else if (type.indexOf("specific")==0) {
              isotopeNumber = Integer.parseInt(type.substring(8));
      }
            jcpPanel.get2DHub().setMassNumber(atom,isotopeNumber);
            jcpPanel.get2DHub().updateView();
            newActiveModule.setID(atom.getSymbol());
            jcpPanel.get2DHub().getController2DModel().setDrawElement(atom.getSymbol());
            jcpPanel.get2DHub().getController2DModel().setDrawIsotopeNumber(isotopeNumber);
            jcpPanel.get2DHub().getController2DModel().setDrawPseudoAtom(false);
        }
        jcpPanel.get2DHub().setActiveDrawModule(newActiveModule);
    }
View Full Code Here
71
72
73
74
75
76
77
78
79
80
81
    for (int i = 0; i < undoRedoContainer.getBondCount(); i++) {
      IBond bond = undoRedoContainer.getBond(i);
      container.removeBond(bond);
    }
    for (int i = 0; i < undoRedoContainer.getAtomCount(); i++) {
      IAtom atom = undoRedoContainer.getAtom(i);
      container.removeAtom(atom);
    }
    chemModelRelay.updateAtoms(container, container.atoms());
    IAtomContainer molecule = container.getBuilder().newInstance(IAtomContainer.class,container);
    IAtomContainerSet moleculeSet = ConnectivityChecker
View Full Code Here
95
96
97
98
99
100
101
102
103
104
105
    for (int i = 0; i < undoRedoContainer.getBondCount(); i++) {
      IBond bond = undoRedoContainer.getBond(i);
      container.addBond(bond);
    }
    for (int i = 0; i < undoRedoContainer.getAtomCount(); i++) {
      IAtom atom = undoRedoContainer.getAtom(i);
      container.addAtom(atom);
    }
    chemModelRelay.updateAtoms(container, container.atoms());
    IAtomContainer molecule = container.getBuilder().newInstance(IAtomContainer.class,container);
    IAtomContainerSet moleculeSet = ConnectivityChecker
View Full Code Here
48
49
50
51
52
53
54
55
56
57
    this.type=type;
  }

  public void redo() {
    for (int i = 0; i < undoRedoContainer.getAtomCount(); i++) {
      IAtom atom=undoRedoContainer.getAtom(i);
      atom.getPoint2d().x+=offset.x;
      atom.getPoint2d().y+=offset.y;
    }
  }
View Full Code Here
56
57
58
59
60
61
62
63
64
65
    }
  }

  public void undo() {
    for (int i = 0; i < undoRedoContainer.getAtomCount(); i++) {
      IAtom atom=undoRedoContainer.getAtom(i);
      atom.getPoint2d().x-=offset.x;
      atom.getPoint2d().y-=offset.y;
    }
  }
View Full Code Here
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
    IRGroupQuery rgrpQ= rgrpHandler.getrGroupQuery();

    if (type.equals("setSubstitute")||type.equals("setRoot")) {
      this.redoRootAttachmentPoints=rgrpHandler.getrGroupQuery().getRootAttachmentPoints();
      for (Iterator<IAtom> atItr = existingAtomDistr.keySet().iterator(); atItr.hasNext();) {
        IAtom atom = atItr.next();
        existingAtomDistr.get(atom).addAtom(atom);
      }
      for (Iterator<IBond> bndItr = existingBondDistr.keySet().iterator(); bndItr.hasNext();) {
        IBond bond = bndItr.next();
        existingBondDistr.get(bond).addBond(bond);
      }
        hub.getChemModel().getMoleculeSet().removeAtomContainer(userSelection);
     
      if (type.equals("setRoot")) {
        if (isNewRgrp) {
          rgrpQ.setRootStructure(null);
          rgrpQ.setRootAttachmentPoints(null);
          for (IAtomContainer atc: hub.getIChemModel().getMoleculeSet().atomContainers()) {
            atc.removeProperty(CDKConstants.TITLE); 
          }
          hub.unsetRGroupHandler();
        }
        else {
          existingRoot.setProperty(CDKConstants.TITLE,RGroup.ROOT_LABEL); 
          rgrpQ.setRootStructure(existingRoot);
          rgrpQ.setRootAttachmentPoints(existingRootAttachmentPoints);
        }
      }
 
      else if (type.equals("setSubstitute")) {
        if  (existingRgroupLists !=null) {
          for(Iterator<Integer> rNums=existingRgroupLists.keySet().iterator(); rNums.hasNext();){
            int rNum= rNums.next();
            rgrpQ.getRGroupDefinitions().put(rNum, existingRgroupLists.get(rNum));
          }
        }
      }
    }

    else if (type.startsWith("setAtomApoAction")) {
      RGroup undoRGroup=existingRGroupApo.keySet().iterator().next();     
        for (Iterator<Integer> rnumItr= hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) {
          for (RGroup rgrp:  hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().get(rnumItr.next()).getRGroups()) {
            if(rgrp.equals(undoRGroup)) {
              IAtom apo1=existingRGroupApo.get(undoRGroup).get(1);
              IAtom apo2=existingRGroupApo.get(undoRGroup).get(2);
              rgrp.setFirstAttachmentPoint(apo1);
              rgrp.setSecondAttachmentPoint(apo2);
            }
          }
        }
    }
    else if (type.startsWith("setBondApoAction")) {
      for(Iterator<IAtom> atItr=existingRootAttachmentPoints.keySet().iterator(); atItr.hasNext();) {
        IAtom rAtom= atItr.next();
        Map<Integer,IBond> undoApo = existingRootAttachmentPoints.get(rAtom);
        Map<Integer,IBond> apoBonds = rgrpQ.getRootAttachmentPoints().get(rAtom);

        redoRootAttachmentPoints= new HashMap<IAtom, Map<Integer, IBond>>();
        Map<Integer,IBond> redoApo = new HashMap<Integer,IBond>();
View Full Code Here
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
        hub.setRGroupHandler(rgrpHandler);
      }
 
      IRGroupQuery rgrpQ= rgrpHandler.getrGroupQuery();
      for (Iterator<IAtom> atItr = existingAtomDistr.keySet().iterator(); atItr.hasNext();) {
        IAtom atom = atItr.next();
        existingAtomDistr.get(atom).removeAtom(atom);
      }
      for (Iterator<IBond> bndItr = existingBondDistr.keySet().iterator(); bndItr.hasNext();) {
        IBond bond = bndItr.next();
        existingBondDistr.get(bond).removeBond(bond);
      }
      hub.getChemModel().getMoleculeSet().addAtomContainer(userSelection);
 
      if (type.equals("setRoot")) {
        rgrpQ.setRootStructure(redoRootStructure);
        rgrpQ.getRootStructure().setProperty(CDKConstants.TITLE,RGroup.ROOT_LABEL); 
        rgrpQ.setRootAttachmentPoints(redoRootAttachmentPoints);
      }
      else if (type.equals("setSubstitute")) {
        if  (redoRgroupLists !=null) {
          for(Iterator<Integer> rNums=redoRgroupLists.keySet().iterator(); rNums.hasNext();){
            int rNum= rNums.next();
            rgrpQ.getRGroupDefinitions().put(rNum, redoRgroupLists.get(rNum));
          }
        }
      }
    }
    else if (type.startsWith("setAtomApoAction")) {
      RGroup redoRGroup=redoRGroupApo.keySet().iterator().next();     
        for (Iterator<Integer> rnumItr= hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) {
          for (RGroup rgrp:  hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().get(rnumItr.next()).getRGroups()) {
            if(rgrp.equals(redoRGroup)) {
              IAtom apo1=redoRGroupApo.get(redoRGroup).get(1);
              IAtom apo2=redoRGroupApo.get(redoRGroup).get(2);
              rgrp.setFirstAttachmentPoint(apo1);
              rgrp.setSecondAttachmentPoint(apo2);
            }
          }
        }
    }
    else if (type.startsWith("setBondApoAction")) {
      for(Iterator<IAtom> atItr=redoRootAttachmentPoints.keySet().iterator(); atItr.hasNext();) {
        IAtom rAtom= atItr.next();
        Map<Integer,IBond> apoBonds = hub.getRGroupHandler().getrGroupQuery().getRootAttachmentPoints().get(rAtom);

        apoBonds.remove(1); apoBonds.remove(2);
        Map<Integer,IBond> redoApo = redoRootAttachmentPoints.get(rAtom);
View Full Code Here
TOP

Related Classes of org.openscience.cdk.interfaces.IAtom

  • org.bmdrc.nmr.tool.DescriptorGenerator
  • org.openscience.cdk.CDKTestCase
  • org.openscience.jchempaint.AbstractAppletTest
  • org.openscience.jchempaint.action.ChangeAtomSymbolAction
  • org.openscience.jchempaint.action.ChangeIsotopeAction
  • org.openscience.jchempaint.action.ChangeSingleElectronAction
  • org.openscience.jchempaint.action.ChangeValenceAction
  • org.openscience.jchempaint.action.ChargeAction
  • org.openscience.jchempaint.action.ConvertToPseudoAtomAction
  • org.openscience.jchempaint.action.CopyPasteAction
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.