| /dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ |
| H A D | ChemModelManipulator.java | 69 if (moleculeSet != null) { in getAtomCount()
92 if (moleculeSet != null) { in getBondCount()
119 if (moleculeSet != null) { in removeAtomAndConnectedElectronContainers()
144 if (moleculeSet != null) { in removeElectronContainer()
171 moleculeSet.addAtomContainer(molecule); in createNewMolecule()
174 moleculeSet.addAtomContainer(molecule); in createNewMolecule()
175 chemModel.setMoleculeSet(moleculeSet); in createNewMolecule()
192 model.setMoleculeSet(moleculeSet); in newChemModel()
311 if (moleculeSet != null) { in getAllChemObjects()
312 list.add(moleculeSet); in getAllChemObjects()
[all …]
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| H A D | MoleculeSetManipulator.java | 106 … public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet moleculeSet, IAtom atom) { in getRelevantAtomContainer() argument
107 return AtomContainerSetManipulator.getRelevantAtomContainer(moleculeSet, atom); in getRelevantAtomContainer()
110 … public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet moleculeSet, IBond bond) { in getRelevantAtomContainer() argument
111 return AtomContainerSetManipulator.getRelevantAtomContainer(moleculeSet, bond); in getRelevantAtomContainer()
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| H A D | ReactionManipulator.java | 148 IAtomContainerSet moleculeSet = reaction.getBuilder().newInstance(IAtomContainerSet.class); in getAllMolecules() local
150 moleculeSet.add(getAllReactants(reaction)); in getAllMolecules()
151 moleculeSet.add(getAllAgents(reaction)); in getAllMolecules()
152 moleculeSet.add(getAllProducts(reaction)); in getAllMolecules()
154 return moleculeSet; in getAllMolecules()
167 moleculeSet.addAtomContainer(products.getAtomContainer(i)); in getAllProducts()
169 return moleculeSet; in getAllProducts()
182 moleculeSet.addAtomContainer(reactants.getAtomContainer(i)); in getAllReactants()
184 return moleculeSet; in getAllReactants()
191 moleculeSet.addAtomContainer(agents.getAtomContainer(i)); in getAllAgents()
[all …]
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| H A D | ReactionSetManipulator.java | 80 IAtomContainerSet moleculeSet = set.getBuilder().newInstance(IAtomContainerSet.class); in getAllMolecules() local
85 for (IAtomContainer atomContainer : moleculeSet.atomContainers()) { in getAllMolecules()
91 if (!contain) moleculeSet.addAtomContainer(ac); in getAllMolecules()
95 return moleculeSet; in getAllMolecules()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/graph/ |
| H A D | ConnectivityCheckerTest.java | 75 Assert.assertNotNull(moleculeSet); in testPartitionIntoMolecules_IAtomContainer()
76 Assert.assertEquals(3, moleculeSet.getAtomContainerCount()); in testPartitionIntoMolecules_IAtomContainer()
92 Assert.assertNotNull(moleculeSet); in testPartitionIntoMoleculesKeepsAtomIDs()
93 Assert.assertEquals(2, moleculeSet.getAtomContainerCount()); in testPartitionIntoMoleculesKeepsAtomIDs()
113 Assert.assertNotNull(moleculeSet); in testPartitionIntoMolecules_IsConnected_Consistency()
114 Assert.assertEquals(3, moleculeSet.getAtomContainerCount()); in testPartitionIntoMolecules_IsConnected_Consistency()
146 Assert.assertNotNull(moleculeSet); in testDontDeleteSingleElectrons()
147 Assert.assertEquals(2, moleculeSet.getAtomContainerCount()); in testDontDeleteSingleElectrons()
159 moleculeSet.getAtomContainer(0).getAtom(0)) == 0 in testDontDeleteSingleElectrons()
161 moleculeSet.getAtomContainer(1).getAtom(0)) == 0); in testDontDeleteSingleElectrons()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/test/java/org/openscience/cdk/io/ |
| H A D | MoSSOutputReaderTest.java | 54 IAtomContainerSet moleculeSet = new AtomContainerSet(); in testExampleFile_MolReading() local
55 moleculeSet = reader.read(moleculeSet); in testExampleFile_MolReading()
56 Assert.assertEquals(19, moleculeSet.getAtomContainerCount()); in testExampleFile_MolReading()
57 for (IAtomContainer mol : moleculeSet.atomContainers()) { in testExampleFile_MolReading()
68 IAtomContainerSet moleculeSet = new AtomContainerSet(); in testExampleFile_SupportColumns() local
69 moleculeSet = reader.read(moleculeSet); in testExampleFile_SupportColumns()
71 ….valueOf(moleculeSet.getAtomContainer(0).getProperty("focusSupport").toString()).doubleValue(), 0.… in testExampleFile_SupportColumns()
73 … Double.valueOf(moleculeSet.getAtomContainer(0).getProperty("complementSupport").toString()) in testExampleFile_SupportColumns()
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| /dports/science/cdk/cdk-cdk-2.3/display/renderextra/src/main/java/org/openscience/cdk/renderer/ |
| H A D | ChemModelRenderer.java | 191 IAtomContainerSet moleculeSet = chemModel.getMoleculeSet(); in paint() local
194 if (moleculeSet == null && reactionSet != null) { in paint()
202 if (moleculeSet != null && reactionSet == null) { in paint()
203 Rectangle2D totalBounds = calculateBounds(moleculeSet); in paint()
210 if (moleculeSet != null && reactionSet != null) { in paint()
217 diagram.add(moleculeSetRenderer.generateDiagram(moleculeSet)); in paint()
278 IAtomContainerSet moleculeSet = chemModel.getMoleculeSet(); in paint() local
283 if (moleculeSet == null || reactionSet != null) { in paint()
321 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in calculateDiagramBounds() local
323 if ((moleculeSet == null && reactionSet == null)) { in calculateDiagramBounds()
[all …]
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| H A D | MoleculeSetRenderer.java | 142 public void setup(IAtomContainerSet moleculeSet, Rectangle screen) { in setup() argument
143 this.setScale(moleculeSet); in setup()
144 Rectangle2D bounds = BoundsCalculator.calculateBounds(moleculeSet); in setup()
210 public void setScale(IAtomContainerSet moleculeSet) { in setScale() argument
211 double bondLength = AverageBondLengthCalculator.calculateAverageBondLength(moleculeSet); in setScale()
220 public Rectangle paint(IAtomContainerSet moleculeSet, IDrawVisitor drawVisitor) { in paint() argument
222 Rectangle2D totalBounds = BoundsCalculator.calculateBounds(moleculeSet); in paint()
227 IRenderingElement diagram = this.generateDiagram(moleculeSet); in paint()
267 public Rectangle calculateDiagramBounds(IAtomContainerSet moleculeSet) { in calculateDiagramBounds() argument
268 if (moleculeSet == null) return this.calculateScreenBounds(new Rectangle2D.Double()); in calculateDiagramBounds()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/misc/test-extra/src/test/java/org/openscience/cdk/io/ |
| H A D | INChIPlainTextReaderTest.java | 83 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in testGuanine() local
84 Assert.assertNotNull(moleculeSet); in testGuanine()
85 IAtomContainer molecule = moleculeSet.getAtomContainer(0); in testGuanine()
107 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in testChebi26120() local
108 Assert.assertNotNull(moleculeSet); in testChebi26120()
109 IAtomContainer molecule = moleculeSet.getAtomContainer(0); in testChebi26120()
131 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in testPlatinum() local
132 Assert.assertNotNull(moleculeSet); in testPlatinum()
133 IAtomContainer molecule = moleculeSet.getAtomContainer(0); in testPlatinum()
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| H A D | INChIReaderTest.java | 79 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in testGuanine() local
80 Assert.assertNotNull(moleculeSet); in testGuanine()
81 IAtomContainer molecule = moleculeSet.getAtomContainer(0); in testGuanine()
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| /dports/science/cdk/cdk-cdk-2.3/display/renderbasic/src/main/java/org/openscience/cdk/renderer/ |
| H A D | AverageBondLengthCalculator.java | 74 public static double calculateAverageBondLength(IAtomContainerSet moleculeSet) { in calculateAverageBondLength() argument
76 for (IAtomContainer atomContainer : moleculeSet.atomContainers()) { in calculateAverageBondLength()
79 return averageBondModelLength / moleculeSet.getAtomContainerCount(); in calculateAverageBondLength()
91 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in calculateAverageBondLength() local
92 if (moleculeSet == null) { in calculateAverageBondLength()
100 return calculateAverageBondLength(moleculeSet); in calculateAverageBondLength()
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| H A D | BoundsCalculator.java | 53 IAtomContainerSet moleculeSet = chemModel.getMoleculeSet(); in calculateBounds() local
56 if (moleculeSet != null) { in calculateBounds()
57 totalBounds = totalBounds.createUnion(calculateBounds(moleculeSet)); in calculateBounds()
107 public static Rectangle2D calculateBounds(IAtomContainerSet moleculeSet) { in calculateBounds() argument
109 for (int i = 0; i < moleculeSet.getAtomContainerCount(); i++) { in calculateBounds()
110 IAtomContainer container = moleculeSet.getAtomContainer(i); in calculateBounds()
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| /dports/science/cdk/cdk-cdk-2.3/storage/io/src/test/java/org/openscience/cdk/io/ |
| H A D | CTXReaderTest.java | 80 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in testMethanol() local
81 Assert.assertNotNull(moleculeSet); in testMethanol()
82 Assert.assertEquals(1, moleculeSet.getAtomContainerCount()); in testMethanol()
84 IAtomContainer container = moleculeSet.getAtomContainer(0); in testMethanol()
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| /dports/science/cdk/cdk-cdk-2.3/storage/io/src/test/java/org/openscience/cdk/io/cml/ |
| H A D | CML25FragmentsTest.java | 96 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in checkForXMoleculeFile() local
97 Assert.assertNotNull(moleculeSet); in checkForXMoleculeFile()
99 Assert.assertEquals(moleculeSet.getAtomContainerCount(), numberOfMolecules); in checkForXMoleculeFile()
102 mol = moleculeSet.getAtomContainer(i); in checkForXMoleculeFile()
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| H A D | JChemPaintTest.java | 102 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in testWWMMOutput() local
103 Assert.assertNotNull(moleculeSet); in testWWMMOutput()
104 Assert.assertEquals(1, moleculeSet.getAtomContainerCount()); in testWWMMOutput()
107 IAtomContainer mol = moleculeSet.getAtomContainer(0); in testWWMMOutput()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ |
| H A D | ChemSequenceManipulatorTest.java | 58 IAtomContainerSet moleculeSet = null; field in ChemSequenceManipulatorTest
81 moleculeSet = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class); in setUp()
82 moleculeSet.addAtomContainer(molecule1); in setUp()
83 moleculeSet.addAtomContainer(molecule2); in setUp()
90 chemModel1.setMoleculeSet(moleculeSet); in setUp()
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| H A D | ChemFileManipulatorTest.java | 70 IAtomContainerSet moleculeSet = null; field in ChemFileManipulatorTest
94 moleculeSet = new AtomContainerSet(); in setUp()
95 moleculeSet.addAtomContainer(molecule1); in setUp()
96 moleculeSet.addAtomContainer(molecule2); in setUp()
103 chemModel.setMoleculeSet(moleculeSet); in setUp()
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| /dports/science/cdk/cdk-cdk-2.3/base/reaction/src/main/java/org/openscience/cdk/reaction/type/ |
| H A D | AdductionProtonLPReaction.java | 143 … IAtomContainerSet moleculeSet = reactant.getBuilder().newInstance(IAtomContainerSet.class); in initiate() local
144 moleculeSet.addAtomContainer(reactant); in initiate()
147 moleculeSet.addAtomContainer(adduct); in initiate()
149 IReaction reaction = mechanism.initiate(moleculeSet, atomList, null); in initiate()
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| H A D | AdductionSodiumLPReaction.java | 147 … IAtomContainerSet moleculeSet = reactant.getBuilder().newInstance(IAtomContainerSet.class); in initiate() local
148 moleculeSet.addAtomContainer(reactant); in initiate()
151 moleculeSet.addAtomContainer(adduct); in initiate()
153 IReaction reaction = mechanism.initiate(moleculeSet, atomList, null); in initiate()
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| H A D | ElectronImpactNBEReaction.java | 137 … IAtomContainerSet moleculeSet = reactant.getBuilder().newInstance(IAtomContainerSet.class); in initiate() local
138 moleculeSet.addAtomContainer(reactant); in initiate()
139 IReaction reaction = mechanism.initiate(moleculeSet, atomList, null); in initiate()
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| H A D | AdductionProtonPBReaction.java | 167 … IAtomContainerSet moleculeSet = reactant.getBuilder().newInstance(IAtomContainerSet.class); in initiate() local
168 moleculeSet.addAtomContainer(reactant); in initiate()
171 moleculeSet.addAtomContainer(adduct); in initiate()
173 IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); in initiate()
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| /dports/science/cdk/cdk-cdk-2.3/storage/libiocml/src/test/java/org/openscience/cdk/io/cml/ |
| H A D | CMLRoundTripTool.java | 79 IAtomContainerSet moleculeSet = chemModel.getMoleculeSet(); in roundTripMolecule() local
80 Assert.assertNotNull(moleculeSet); in roundTripMolecule()
81 Assert.assertEquals(1, moleculeSet.getAtomContainerCount()); in roundTripMolecule()
82 roundTrippedMol = moleculeSet.getAtomContainer(0); in roundTripMolecule()
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| /dports/science/cdk/cdk-cdk-2.3/storage/io/src/main/java/org/openscience/cdk/io/ |
| H A D | Gaussian03Reader.java | 268 IAtomContainerSet moleculeSet = model.getBuilder().newInstance(IAtomContainerSet.class); in readCoordinates() local
269 … moleculeSet.addAtomContainer(model.getBuilder().newInstance(IAtomContainer.class, container)); in readCoordinates()
270 model.setMoleculeSet(moleculeSet); in readCoordinates()
278 IAtomContainerSet moleculeSet = model.getMoleculeSet(); in readPartialCharges() local
279 IAtomContainer molecule = moleculeSet.getAtomContainer(0); in readPartialCharges()
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| /dports/science/cdk/cdk-cdk-2.3/misc/extra/src/main/java/org/openscience/cdk/io/ |
| H A D | GamessReader.java | 215 IAtomContainerSet moleculeSet = file.getBuilder().newInstance(IAtomContainerSet.class); in readChemFile() local
217 model.setMoleculeSet(moleculeSet); //TODO Answer the question : Should I do this? in readChemFile()
234 …moleculeSet.addAtomContainer(this.readCoordinates(file.getBuilder().newInstance(IAtomContainer.cla… in readChemFile()
245 …moleculeSet.addAtomContainer(this.readCoordinates(file.getBuilder().newInstance(IAtomContainer.cla… in readChemFile()
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| H A D | INChIPlainTextReader.java | 178 … IAtomContainerSet moleculeSet = cf.getBuilder().newInstance(IAtomContainerSet.class); in readChemFile() local
179 … moleculeSet.addAtomContainer(cf.getBuilder().newInstance(IAtomContainer.class, parsedContent)); in readChemFile()
181 model.setMoleculeSet(moleculeSet); in readChemFile()
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