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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/modeling/builder3d AtomPlacer3D.java,1.10,1.11 AtomTetrahedralLigandPlacer3D.java,1.11,1.12 ForceFieldConfigurator.java,1.12,1.13 ModelBuilder3D.java,1.19,1.20 TemplateHandler3D.java,1.14,1.15
Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8380/src/org/openscience/cdk/modeling/builder3d Modified Files: AtomPlacer3D.java AtomTetrahedralLigandPlacer3D.java ForceFieldConfigurator.java ModelBuilder3D.java TemplateHandler3D.java Log Message: Final tweaks to get CVS compiling again. Transition of cdk.interfaces.SetOfAtomContainers() to return an interface. What a hell that was. Index: AtomPlacer3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- AtomPlacer3D.java 29 Aug 2005 19:50:17 -0000 1.10 +++ AtomPlacer3D.java 30 Aug 2005 19:55:47 -0000 1.11 @@ -31,7 +31,7 @@ import javax.vecmath.Vector3d; import org.openscience.cdk.interfaces.Atom; -import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.interfaces.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.geometry.GeometryTools; @@ -559,7 +559,7 @@ public AtomContainer getPlacedHeavyAtoms(AtomContainer molecule, Atom atom) { Bond[] bonds = molecule.getConnectedBonds(atom); - AtomContainer connectedAtoms = new AtomContainer(); + AtomContainer connectedAtoms = new org.openscience.cdk.AtomContainer(); Atom connectedAtom = null; for (int i = 0; i < bonds.length; i++) { connectedAtom = bonds[i].getConnectedAtom(atom); @@ -580,7 +580,7 @@ public AtomContainer getUnplacedAtoms(AtomContainer molecule, Atom atom) { Bond[] bonds = molecule.getConnectedBonds(atom); - AtomContainer connectedAtoms = new AtomContainer(); + AtomContainer connectedAtoms = new org.openscience.cdk.AtomContainer(); Atom connectedAtom = null; for (int i = 0; i < bonds.length; i++) { connectedAtom = bonds[i].getConnectedAtom(atom); @@ -613,7 +613,7 @@ * @return The allPlacedAtoms value */ public AtomContainer getAllPlacedAtoms(AtomContainer molecule) { - AtomContainer placedAtoms = new AtomContainer(); + AtomContainer placedAtoms = new org.openscience.cdk.AtomContainer(); for (int i = 0; i < molecule.getAtomCount(); i++) { if (molecule.getAtomAt(i).getFlag(CDKConstants.ISPLACED)) { placedAtoms.addAtom(molecule.getAtomAt(i)); Index: AtomTetrahedralLigandPlacer3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- AtomTetrahedralLigandPlacer3D.java 29 Aug 2005 19:50:17 -0000 1.11 +++ AtomTetrahedralLigandPlacer3D.java 30 Aug 2005 19:55:47 -0000 1.12 @@ -38,8 +38,8 @@ import javax.vecmath.Vector3d; import org.openscience.cdk.interfaces.Atom; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Bond; +import org.openscience.cdk.interfaces.AtomContainer; +import org.openscience.cdk.interfaces.Bond; import org.openscience.cdk.CDKConstants; /** @@ -97,8 +97,8 @@ *@cdk.keyword 3D model */ public void add3DCoordinatesForSinglyBondedLigands(AtomContainer atomContainer) throws Exception { - AtomContainer noCoords = new AtomContainer(); - AtomContainer withCoords = new AtomContainer(); + AtomContainer noCoords = new org.openscience.cdk.AtomContainer(); + AtomContainer withCoords = new org.openscience.cdk.AtomContainer(); Atom refAtom = null; Atom atomC = null; int nwanted = 0; @@ -856,7 +856,7 @@ public AtomContainer getPlacedAtomsInAtomContainer(Atom atom, AtomContainer ac) { Bond[] bonds = ac.getConnectedBonds(atom); - AtomContainer connectedAtoms = new AtomContainer(); + AtomContainer connectedAtoms = new org.openscience.cdk.AtomContainer(); Atom connectedAtom = null; for (int i = 0; i < bonds.length; i++) { connectedAtom = bonds[i].getConnectedAtom(atom); @@ -878,7 +878,7 @@ */ public AtomContainer getUnsetAtomsInAtomContainer(Atom atom, AtomContainer ac) { Atom[] atoms = ac.getConnectedAtoms(atom); - AtomContainer connectedAtoms = new AtomContainer(); + AtomContainer connectedAtoms = new org.openscience.cdk.AtomContainer(); for (int i = 0; i < atoms.length; i++) { if (!atoms[i].getFlag(CDKConstants.ISPLACED)){//&& atoms[i].getPoint3d() == null) { connectedAtoms.addAtom(atoms[i]); Index: ForceFieldConfigurator.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- ForceFieldConfigurator.java 4 Aug 2005 14:36:31 -0000 1.12 +++ ForceFieldConfigurator.java 30 Aug 2005 19:55:47 -0000 1.13 @@ -37,7 +37,7 @@ import java.util.regex.Pattern; import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.interfaces.AtomContainer; import org.openscience.cdk.AtomType; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; Index: ModelBuilder3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- ModelBuilder3D.java 29 Aug 2005 19:50:17 -0000 1.19 +++ ModelBuilder3D.java 30 Aug 2005 19:55:47 -0000 1.20 @@ -36,7 +36,7 @@ import javax.vecmath.Vector3d; import org.openscience.cdk.interfaces.Atom; -import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.interfaces.AtomContainer; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.RingSet; @@ -311,7 +311,7 @@ setAtomsToUnVisited(); atom = ap3d.getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(molecule); if (atom != null) { - ac = new AtomContainer(); + ac = new org.openscience.cdk.AtomContainer(); ac.addAtom(atom); searchAndPlaceBranches(ac); ac = null; @@ -409,7 +409,7 @@ */ public void setBranchAtom(Atom unplacedAtom, Atom atomA, AtomContainer atomNeighbours) throws Exception { //System.out.println("****** SET Branch Atom ****** >"+molecule.getAtomNumber(unplacedAtom)); - AtomContainer noCoords = new AtomContainer(); + AtomContainer noCoords = new org.openscience.cdk.AtomContainer(); noCoords.addAtom(unplacedAtom); Point3d centerPlacedMolecule = ap3d.geometricCenterAllPlacedAtoms(molecule); Atom atomB = atomNeighbours.getAtomAt(0); @@ -466,8 +466,8 @@ public void searchAndPlaceBranches(AtomContainer chain) throws Exception { //System.out.println("****** SEARCH AND PLACE ****** Chain length: "+chain.getAtomCount()); Atom[] atoms = null; - AtomContainer branchAtoms = new AtomContainer(); - AtomContainer connectedAtoms = new AtomContainer(); + AtomContainer branchAtoms = new org.openscience.cdk.AtomContainer(); + AtomContainer connectedAtoms = new org.openscience.cdk.AtomContainer(); for (int i = 0; i < chain.getAtomCount(); i++) { atoms = molecule.getConnectedAtoms(chain.getAtomAt(i)); for (int j = 0; j < atoms.length; j++) { @@ -508,7 +508,7 @@ //System.out.println("****** PLACE LINEAR CHAINS ******"); Atom dihPlacedAtom = null; Atom thirdPlacedAtom = null; - AtomContainer longestUnplacedChain = new AtomContainer(); + AtomContainer longestUnplacedChain = new org.openscience.cdk.AtomContainer(); if (startAtoms.getAtomCount() == 0) { //no branch points ->linear chain //System.out.println("------ LINEAR CHAIN - FINISH ------"); Index: TemplateHandler3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- TemplateHandler3D.java 4 Aug 2005 14:36:31 -0000 1.14 +++ TemplateHandler3D.java 30 Aug 2005 19:55:47 -0000 1.15 @@ -37,7 +37,7 @@ import java.util.zip.GZIPInputStream; import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.interfaces.AtomContainer; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.RingSet; @@ -164,8 +164,8 @@ } if (Fingerprinter.isSubset(ringSystemFingerprint,(BitSet)fingerprintData.get(i))){ query=QueryAtomContainerCreator.createAnyAtomContainer(template,true); - if (UniversalIsomorphismTester.isSubgraph(ringSystems,query)){ - List list = UniversalIsomorphismTester.getSubgraphAtomsMap(ringSystems,query); + if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ringSystems,query)){ + List list = UniversalIsomorphismTester.getSubgraphAtomsMap((org.openscience.cdk.AtomContainer)ringSystems,query); //System.out.println("Found a subgraph mapping of size " + list.size()+" Position:"+i+" RingSize:"+NumberOfRingAtoms); if ((NumberOfRingAtoms)/list.size()==1){ flagMaxSubstructure=true; |