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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/modeling/builder3d AtomPlacer3D.java,1.8,1.9 AtomTetrahedralLigandPlacer3D.java,1.9,1.10 ForceFieldConfigurator.java,1.11,1.12 MM2BasedAtomTypePattern.java,1.5,1.6 MM2BasedParameterSetReader.java,1.5,1.6 MMFF94BasedAtomTypePattern.java,1.5,1.6 MMFF94BasedParameterSetReader.java,1.9,1.10 MMFF94ParametersCall.java,1.1,1.2 ModelBuilder3D.java,1.16,1.17 TemplateHandler3D.java,1.13,1.14
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From: Christoph S. <ste...@us...> - 2005-08-04 14:38:12
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25886/src/org/openscience/cdk/modeling/builder3d Modified Files: AtomPlacer3D.java AtomTetrahedralLigandPlacer3D.java ForceFieldConfigurator.java MM2BasedAtomTypePattern.java MM2BasedParameterSetReader.java MMFF94BasedAtomTypePattern.java MMFF94BasedParameterSetReader.java MMFF94ParametersCall.java ModelBuilder3D.java TemplateHandler3D.java Log Message: Removed a large number of unused imports Index: AtomPlacer3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- AtomPlacer3D.java 12 Jan 2005 15:21:29 -0000 1.8 +++ AtomPlacer3D.java 4 Aug 2005 14:36:31 -0000 1.9 @@ -24,14 +24,15 @@ package org.openscience.cdk.modeling.builder3d; import java.util.Hashtable; +import java.util.Vector; -import javax.vecmath.Point3d; import javax.vecmath.Point2d; +import javax.vecmath.Point3d; import javax.vecmath.Vector3d; -import java.util.Vector; + import org.openscience.cdk.Atom; -import org.openscience.cdk.Bond; import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.geometry.GeometryTools; Index: AtomTetrahedralLigandPlacer3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- AtomTetrahedralLigandPlacer3D.java 7 Apr 2005 11:32:30 -0000 1.9 +++ AtomTetrahedralLigandPlacer3D.java 4 Aug 2005 14:36:31 -0000 1.10 @@ -28,14 +28,14 @@ */ package org.openscience.cdk.modeling.builder3d; -import java.util.Vector; -import java.util.Hashtable; import java.io.IOException; +import java.util.Hashtable; +import java.util.Vector; +import javax.vecmath.AxisAngle4d; +import javax.vecmath.Matrix3d; import javax.vecmath.Point3d; import javax.vecmath.Vector3d; -import javax.vecmath.Matrix3d; -import javax.vecmath.AxisAngle4d; import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; Index: ForceFieldConfigurator.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- ForceFieldConfigurator.java 15 Jun 2005 07:49:20 -0000 1.11 +++ ForceFieldConfigurator.java 4 Aug 2005 14:36:31 -0000 1.12 @@ -28,25 +28,28 @@ */ package org.openscience.cdk.modeling.builder3d; -import java.io.*; -import java.util.Vector; +import java.io.File; +import java.io.FileInputStream; +import java.io.InputStream; import java.util.Hashtable; -import java.util.regex.*; +import java.util.Vector; +import java.util.regex.Matcher; +import java.util.regex.Pattern; -import org.openscience.cdk.AtomType; -import org.openscience.cdk.exception.NoSuchAtomTypeException; import org.openscience.cdk.Atom; -import org.openscience.cdk.PseudoAtom; +import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.AtomType; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.ringsearch.SSSRFinder; -import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.RingSet; -import org.openscience.cdk.tools.manipulator.RingSetManipulator; import org.openscience.cdk.Molecule; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; +import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.Ring; +import org.openscience.cdk.RingSet; +import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.exception.NoSuchAtomTypeException; +import org.openscience.cdk.ringsearch.SSSRFinder; +import org.openscience.cdk.tools.HOSECodeGenerator; +import org.openscience.cdk.tools.manipulator.RingSetManipulator; /** Index: MM2BasedAtomTypePattern.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/MM2BasedAtomTypePattern.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- MM2BasedAtomTypePattern.java 12 Jan 2005 15:21:29 -0000 1.5 +++ MM2BasedAtomTypePattern.java 4 Aug 2005 14:36:31 -0000 1.6 @@ -28,8 +28,8 @@ */ package org.openscience.cdk.modeling.builder3d; -import java.util.regex.*; -import java.util.*; +import java.util.Vector; +import java.util.regex.Pattern; /** * Class stores hose code patterns to identify mm2 force field atom types. Index: MM2BasedParameterSetReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- MM2BasedParameterSetReader.java 30 Mar 2005 12:22:01 -0000 1.5 +++ MM2BasedParameterSetReader.java 4 Aug 2005 14:36:31 -0000 1.6 @@ -29,15 +29,14 @@ package org.openscience.cdk.modeling.builder3d; import java.awt.Color; +import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; -import java.util.Vector; -import java.io.BufferedReader; -import java.util.StringTokenizer; import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; -import org.openscience.cdk.tools.*; import org.openscience.cdk.AtomType; /** Index: MMFF94BasedAtomTypePattern.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/MMFF94BasedAtomTypePattern.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- MMFF94BasedAtomTypePattern.java 4 Feb 2005 12:21:04 -0000 1.5 +++ MMFF94BasedAtomTypePattern.java 4 Aug 2005 14:36:31 -0000 1.6 @@ -28,8 +28,8 @@ */ package org.openscience.cdk.modeling.builder3d; -import java.util.regex.*; -import java.util.*; +import java.util.Vector; +import java.util.regex.Pattern; /** * Class stores hose code patterns to identify mm2 force field atom types Index: MMFF94BasedParameterSetReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- MMFF94BasedParameterSetReader.java 25 Apr 2005 09:26:16 -0000 1.9 +++ MMFF94BasedParameterSetReader.java 4 Aug 2005 14:36:31 -0000 1.10 @@ -29,15 +29,14 @@ package org.openscience.cdk.modeling.builder3d; import java.awt.Color; +import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; -import java.util.Vector; -import java.io.BufferedReader; -import java.util.StringTokenizer; import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; -import org.openscience.cdk.tools.*; import org.openscience.cdk.AtomType; /** Index: MMFF94ParametersCall.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- MMFF94ParametersCall.java 17 Feb 2005 14:40:40 -0000 1.1 +++ MMFF94ParametersCall.java 4 Aug 2005 14:36:31 -0000 1.2 @@ -1,16 +1,7 @@ package org.openscience.cdk.modeling.builder3d; import java.util.Hashtable; - -import javax.vecmath.Point3d; -import javax.vecmath.Point2d; -import javax.vecmath.Vector3d; import java.util.Vector; -import org.openscience.cdk.Atom; -import org.openscience.cdk.Bond; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.geometry.GeometryTools; /** Index: ModelBuilder3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- ModelBuilder3D.java 12 May 2005 15:10:42 -0000 1.16 +++ ModelBuilder3D.java 4 Aug 2005 14:36:31 -0000 1.17 @@ -28,12 +28,12 @@ */ package org.openscience.cdk.modeling.builder3d; +import java.io.IOException; import java.util.Hashtable; +import java.util.Vector; import javax.vecmath.Point3d; import javax.vecmath.Vector3d; -import java.io.IOException; -import java.util.Vector; import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; @@ -41,11 +41,11 @@ import org.openscience.cdk.Molecule; import org.openscience.cdk.RingSet; import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.geometry.GeometryTools; import org.openscience.cdk.graph.ConnectivityChecker; -import org.openscience.cdk.tools.manipulator.RingSetManipulator; import org.openscience.cdk.layout.AtomPlacer; import org.openscience.cdk.ringsearch.RingPartitioner; -import org.openscience.cdk.geometry.GeometryTools; +import org.openscience.cdk.tools.manipulator.RingSetManipulator; /** * The main class to generate the 3D coordinates of a molecule ModelBuilder3D. Index: TemplateHandler3D.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- TemplateHandler3D.java 2 Jun 2005 19:41:04 -0000 1.13 +++ TemplateHandler3D.java 4 Aug 2005 14:36:31 -0000 1.14 @@ -28,27 +28,27 @@ package org.openscience.cdk.modeling.builder3d; import java.io.BufferedReader; -import java.io.InputStreamReader; import java.io.InputStream; -import java.util.List; -import java.util.Vector; +import java.io.InputStreamReader; import java.util.BitSet; +import java.util.List; import java.util.StringTokenizer; -import java.util.zip.*; +import java.util.Vector; +import java.util.zip.GZIPInputStream; -import org.openscience.cdk.SetOfMolecules; import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.RingSet; -import org.openscience.cdk.exception.*; -import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; -import org.openscience.cdk.isomorphism.mcss.RMap; +import org.openscience.cdk.SetOfMolecules; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.fingerprint.Fingerprinter; import org.openscience.cdk.io.iterator.IteratingMDLReader; +import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator; -import org.openscience.cdk.fingerprint.Fingerprinter; +import org.openscience.cdk.isomorphism.mcss.RMap; /** * Helper class for ModelBuilder3D. Handles templates. This is |