- Generated by
1.9.4
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DENOPTIM
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Tool to build build three-dimensional (3D) tree-like molecular structures from DGraph.
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Public Member Functions | |
| ThreeDimTreeBuilder (Logger logger, Randomizer randomizer) | |
| Constructor providing the program-specific logger and randomizer. More... | |
| void | setAlignBBsIn3D (boolean align) |
| Sets the flag that controls whether building blocks have to be aligned according to the AP vectors or not. More... | |
| IAtomContainer | convertGraphTo3DAtomContainer (DGraph graph) throws DENOPTIMException |
Created a three-dimensional molecular representation from a given DGraph. More... | |
| IAtomContainer | convertGraphTo3DAtomContainer (DGraph graph, boolean removeUsedRCAs) throws DENOPTIMException |
Creates a three-dimensional molecular representation from a given DGraph. More... | |
| IAtomContainer | convertGraphTo3DAtomContainer (DGraph graph, boolean removeUsedRCAs, boolean setCDKRequirements, boolean rebuild) throws DENOPTIMException |
Created a three-dimensional molecular representation from a given DGraph. More... | |
Private Member Functions | |
| void | append3DFragmentsViaEdges (IAtomContainer mol, DGraph graph, int idSrcAtmA, Point3d srcApA, Point3d trgApA, Edge edge, boolean removeUsedRCAs, boolean rebuild, Map< Long, ArrayList< AttachmentPoint > > apsPerVertexId, Map< Edge, ArrayList< AttachmentPoint > > apsPerEdge, Map< IAtom, ArrayList< AttachmentPoint > > apsPerAtom, Map< IBond, ArrayList< AttachmentPoint > > apsPerBond) throws DENOPTIMException |
| Recursive method that appends branches of building blocks following the edges of the graph. More... | |
| Point3d | getRandomPoint (IAtomContainer mol) |
Private Attributes | |
| double | maxCoord = 20.0 |
| Controls the maximum distance between a random place where unanchored building blocks are placed and the system centroid. More... | |
| boolean | alignIn3D = true |
| Flag controlling whether to align building blocks according to the AP vectors or not. More... | |
| IChemObjectBuilder | builder = SilentChemObjectBuilder.getInstance() |
| Private builder of atom containers. More... | |
| Logger | logger = Logger.getLogger("3dTreeBuilderLogger") |
| Program-specific logger. More... | |
| Randomizer | randomizer = new Randomizer() |
| Program-specific randomizer. More... | |
Static Private Attributes | |
| static final String | NL = DENOPTIMConstants.EOL |
Tool to build build three-dimensional (3D) tree-like molecular structures from DGraph.
The molecular structure is assembled from the building blocks by attaching any set of atoms/pseudo-atoms contained in the building block, and (optionally) aligning each incoming building block by using the geometric parameters defined in their attachment points. By default, this builder does align building blocks, but method ThreeDimTreeBuilder#setAlignBBsIn3D(boolean) allows to configure this builder so that building blocks are not aligned during their assembly. In the latter configuration, the coordinates of atom in the resulting molecular structure will be the same as those found in the building block stored in the given library of building blocks.
Definition at line 75 of file ThreeDimTreeBuilder.java.
| denoptim.molecularmodeling.ThreeDimTreeBuilder.ThreeDimTreeBuilder | ( | Logger | logger, |
| Randomizer | randomizer | ||
| ) |
Constructor providing the program-specific logger and randomizer.
Definition at line 112 of file ThreeDimTreeBuilder.java.
References denoptim.molecularmodeling.ThreeDimTreeBuilder.logger, and denoptim.molecularmodeling.ThreeDimTreeBuilder.randomizer.
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Recursive method that appends branches of building blocks following the edges of the graph.
The connection is controlled by the geometries of the attachment point on a growing molecule and that of the attachment point of the incoming vertex, i.e., the child/target vertex connected via the edge argument. If the latter contains no atoms, then we simply return. Thus, vertexes that contain no atoms are not expected to have more than one incident edge (i.e., the edge to their parent vertex).
| mol | the container of atoms that is being built. |
| idSrcAtmA | the index of the atom holding the AP on the growing molecules, or a negative number if no such bond exists and, thus, we do not add any chemical bond between atoms of the growing molecule and the incoming building block. |
| srcApA | the point in space corresponding to the source of the attachment point vector on the growing molecule |
| trgApA | the point in space corresponding to the end of the attachment point vector on the growing molecule |
| edge | the DENOPTIMEdge corresponding to the connection this method is asked to make between 3D molecular fragments |
| removeUsedRCAs | when true this method will remove used RCAs (the content of ring-closing vertexes, RCVs) and add bonds to close the rings defined by the DENOPTIMRings in the graph (does not alter the graph). Does not change unused RCVs. Unused RCVs should have been already replaced by capping groups (or removed, if no capping needed), with the GraphConversionTool#replaceUnusedRCVsWithCapps(DGraph) method. |
| DENOPTIMException |
Definition at line 512 of file ThreeDimTreeBuilder.java.
References denoptim.molecularmodeling.ThreeDimTreeBuilder.alignIn3D, denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXPATH, denoptim.graph.Vertex.containsAtoms(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getBuildingBlockType(), denoptim.graph.Edge.BondType.getCDKOrder(), denoptim.graph.AttachmentPoint.getDirectionVector(), denoptim.graph.Vertex.getIAtomContainer(), denoptim.utils.MathUtils.getNormalDirection(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.molecularmodeling.ThreeDimTreeBuilder.getRandomPoint(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.Edge.BondType.hasCDKAnalogue(), denoptim.graph.Vertex.isRCV, denoptim.molecularmodeling.ThreeDimTreeBuilder.logger, denoptim.molecularmodeling.ThreeDimTreeBuilder.NL, denoptim.molecularmodeling.ThreeDimTreeBuilder.randomizer, denoptim.constants.DENOPTIMConstants.RCAPROPAPCTORCA, denoptim.constants.DENOPTIMConstants.RCAPROPCHORDBNDTYP, and denoptim.constants.DENOPTIMConstants.RCAPROPRINGUSER.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), and denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer().
| IAtomContainer denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer | ( | DGraph | graph | ) | throws DENOPTIMException |
Created a three-dimensional molecular representation from a given DGraph.
The conversion creates also two maps to retrace the attachment points within the final 3D structure both based on the ID of the source DENOPTIMVertex and correspondence to DENOPTIMEdge. To retrieve this information see properties DENOPTIMConstants#MOLPROPAPxATOM, DENOPTIMConstants#MOLPROPAPxBOND, DENOPTIMConstants#MOLPROPAPxVID and DENOPTIMConstants#MOLPROPAPxEDGE. In addition each atom is blended with the unique index of the DENOPTIMVertex corresponding to the molecular fragment to which the atom belongs.
This method does not remove ring-closing attractors. You can remove them by calling ThreeDimTreeBuilder#convertGraphTo3DAtomContainer(
DGraph, boolean) (with a true 2nd argument) instead of this method.
| graph | the DGraph to be transformed into a 3D molecule |
IAtomContainer representation of the molecular system represented by the DGraph. | DENOPTIMException |
Definition at line 158 of file ThreeDimTreeBuilder.java.
References denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer().
Referenced by denoptim.ga.GraphOperations.addRing(), denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.graph.DGraph.checkConsistency(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.graph.Template.getIAtomContainer(), denoptim.gui.GUIGraphHandler.importGraphsFromFile(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation(), denoptim.task.FitnessTask.runFitnessProvider(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), denoptim.programs.genetweeker.GeneOpsRunner.runXOver(), denoptim.ga.EAUtils.setupRings(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), denoptim.graph.rings.PathSubGraphTest.testMakePathSubGraph(), denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates(), denoptim.gui.GraphVertexMolViewerPanel.updateMolevularViewer(), and denoptim.io.DenoptimIO.writeGraphsToSDF().
| IAtomContainer denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer | ( | DGraph | graph, |
| boolean | removeUsedRCAs | ||
| ) | throws DENOPTIMException |
Creates a three-dimensional molecular representation from a given DGraph.
The conversion creates also two maps to retrace the attachment points within the final 3D structure both based on the ID of the source DENOPTIMVertex and correspondence to DENOPTIMEdge. To retrieve this information see properties DENOPTIMConstants#MOLPROPAPxATOM, DENOPTIMConstants#MOLPROPAPxBOND, DENOPTIMConstants#MOLPROPAPxVID and DENOPTIMConstants#MOLPROPAPxEDGE.
In addition each atom is blended with the unique index of the DENOPTIMVertex corresponding to the molecular fragment to which the atom belongs.
| graph | the DGraph to be transformed into a 3D molecule |
| removeUsedRCAs | when true this method will remove used RCAs (the content of ring-closing vertexes, RCVs) and add bonds to close the rings defined by the DENOPTIMRings in the graph (does not alter the graph). Does not change unused RCVs. Unused RCVs should have been already replaced by capping groups (or removed, if no capping needed), with the GraphConversionTool#replaceUnusedRCVsWithCapps(DGraph) method. |
AtomContainer representation | DENOPTIMException |
Definition at line 194 of file ThreeDimTreeBuilder.java.
References denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer().
| IAtomContainer denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer | ( | DGraph | graph, |
| boolean | removeUsedRCAs, | ||
| boolean | setCDKRequirements, | ||
| boolean | rebuild | ||
| ) | throws DENOPTIMException |
Created a three-dimensional molecular representation from a given DGraph.
The conversion creates also two maps to retrace the attachment points within the final 3D structure both based on the ID of the source Vertex and correspondence to Edge. To retrieve this information see properties DENOPTIMConstants#MOLPROPAPxATOM, DENOPTIMConstants#MOLPROPAPxBOND, DENOPTIMConstants#MOLPROPAPxVID and DENOPTIMConstants#MOLPROPAPxEDGE. In addition each atom is blended with the unique index of the Vertex corresponding to the molecular fragment to which the atom belongs.
| graph | the DGraph to be transformed into a 3D molecule |
| removeUsedRCAs | when true this method will remove used RCAs (the content of ring-closing vertexes, RCVs) and add bonds to close the rings defined by the Ring in the graph (does not alter the graph). Does not change unused RCVs. Unused RCVs should have been already replaced by capping groups (or removed, if no capping needed), with the GraphConversionTool#replaceUnusedRCVsWithCapps(DGraph) method. |
| setCDKRequirements | when true this method will ensure that the CDK requirements for IAtomContainers are all met. Namely, no bond order is 'undefined' and that intrinsic hydrogen is zero for all atoms (i.e., internal convention in DENOPTIM: all atoms are explicit). |
true the chemical representation of every building block is rebuilt ignoring previously available structures. AtomContainer representation | DENOPTIMException |
Definition at line 238 of file ThreeDimTreeBuilder.java.
References denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXPATH, denoptim.molecularmodeling.ThreeDimTreeBuilder.builder, denoptim.graph.Vertex.containsAtoms(), denoptim.utils.MoleculeUtils.ensureNoUnsetBondOrdersSilent(), denoptim.graph.AttachmentPoint.getAPDefinitionsForSDF(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.graph.AttachmentPoint.getDirectionVector(), denoptim.graph.Vertex.getIAtomContainer(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.molecularmodeling.ThreeDimTreeBuilder.getRandomPoint(), denoptim.graph.Vertex.getVertexId(), denoptim.molecularmodeling.ThreeDimTreeBuilder.logger, denoptim.constants.DENOPTIMConstants.MOLPROPAPxATOM, denoptim.constants.DENOPTIMConstants.MOLPROPAPxBOND, denoptim.constants.DENOPTIMConstants.MOLPROPAPxEDGE, denoptim.constants.DENOPTIMConstants.MOLPROPAPxVID, denoptim.molecularmodeling.ThreeDimTreeBuilder.NL, denoptim.molecularmodeling.ThreeDimTreeBuilder.randomizer, denoptim.utils.MoleculeUtils.removeUsedRCA(), denoptim.utils.MoleculeUtils.setZeroImplicitHydrogensToAllAtoms(), denoptim.io.DenoptimIO.writeGraphToJSON(), denoptim.utils.GraphUtils.writeSDFFields(), and denoptim.io.DenoptimIO.writeSDFFile().
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Definition at line 858 of file ThreeDimTreeBuilder.java.
References denoptim.utils.MoleculeUtils.calculateCentroid(), denoptim.molecularmodeling.ThreeDimTreeBuilder.maxCoord, denoptim.utils.Randomizer.nextInt(), and denoptim.molecularmodeling.ThreeDimTreeBuilder.randomizer.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), and denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer().
| void denoptim.molecularmodeling.ThreeDimTreeBuilder.setAlignBBsIn3D | ( | boolean | align | ) |
Sets the flag that controls whether building blocks have to be aligned according to the AP vectors or not.
| align | the new value. Use true to align building blocks (default), or false to prevent alignment. |
Definition at line 126 of file ThreeDimTreeBuilder.java.
Referenced by denoptim.ga.GraphOperations.addRing(), denoptim.combinatorial.GraphBuildingTask.call(), denoptim.graph.DGraph.checkConsistency(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), denoptim.ga.EAUtils.setupRings(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), and denoptim.graph.rings.PathSubGraphTest.testMakePathSubGraph().
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Flag controlling whether to align building blocks according to the AP vectors or not.
By default, we do align building blocks.
Definition at line 87 of file ThreeDimTreeBuilder.java.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges().
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Private builder of atom containers.
Definition at line 92 of file ThreeDimTreeBuilder.java.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer().
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Program-specific logger.
Definition at line 97 of file ThreeDimTreeBuilder.java.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), and denoptim.molecularmodeling.ThreeDimTreeBuilder.ThreeDimTreeBuilder().
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Controls the maximum distance between a random place where unanchored building blocks are placed and the system centroid.
Definition at line 81 of file ThreeDimTreeBuilder.java.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.getRandomPoint().
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Definition at line 104 of file ThreeDimTreeBuilder.java.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), and denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer().
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Program-specific randomizer.
Definition at line 102 of file ThreeDimTreeBuilder.java.
Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.molecularmodeling.ThreeDimTreeBuilder.getRandomPoint(), and denoptim.molecularmodeling.ThreeDimTreeBuilder.ThreeDimTreeBuilder().
1.9.4