From 1a2e93a5be1b9343e62b92fc9501ecc338fb9cbc Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 17 Apr 2012 20:28:43 +0200 Subject: [PATCH] The qsaratomic module is now also independent from the data module Change-Id: I63bb2315cda1d24873aa8104ba61f0f417e178ae Signed-off-by: Rajarshi Guha --- src/META-INF/qsaratomic.cdkdepends | 1 - .../descriptors/atomic/RDFProtonDescriptor_G3R.java | 10 ++++------ .../descriptors/atomic/RDFProtonDescriptor_GDR.java | 10 ++++------ .../descriptors/atomic/RDFProtonDescriptor_GHR.java | 10 ++++------ .../atomic/RDFProtonDescriptor_GHR_topol.java | 10 ++++------ .../descriptors/atomic/RDFProtonDescriptor_GSR.java | 10 ++++------ 6 files changed, 20 insertions(+), 31 deletions(-) diff --git a/src/META-INF/qsaratomic.cdkdepends b/src/META-INF/qsaratomic.cdkdepends index 183cd886f04..2c6daf8be9c 100644 --- a/src/META-INF/qsaratomic.cdkdepends +++ b/src/META-INF/qsaratomic.cdkdepends @@ -1,6 +1,5 @@ cdk-annotation.jar cdk-interfaces.jar -cdk-data.jar cdk-core.jar cdk-standard.jar cdk-valencycheck.jar diff --git a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java index 369ba090df5..657c58537a1 100644 --- a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java +++ b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java @@ -1,6 +1,4 @@ -/* $Revision$ $Author$ $Date$ - * - * Copyright (C) 2004-2007 Matteo Floris +/* Copyright (C) 2004-2007 Matteo Floris * Copyright (C) 2006-2007 Federico * * Contact: cdk-devel@lists.sourceforge.net @@ -29,7 +27,6 @@ import javax.vecmath.Vector3d; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.Ring; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; @@ -40,6 +37,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -228,7 +226,7 @@ public DescriptorValue calculate(IAtom atom, } } IRingSet rsAtom; - Ring ring; + IRing ring; IRingSet ringsWithThisBond; // SET ISINRING FLAGS FOR BONDS // org.openscience.cdk.interfaces.IBond[] bondsInContainer = varAtomContainer.getBonds(); @@ -331,7 +329,7 @@ && getIfBondIsNotRotatable(mol, thirdBond, if (!curAtomThird.equals(neighbour0)) { rsAtom = varRingSet.getRings(thirdBond); for (IAtomContainer aRsAtom : rsAtom.atomContainers()) { - ring = (Ring) aRsAtom; + ring = (IRing) aRsAtom; if (ring.getRingSize() > 4 && ring.contains(thirdBond)) { theBondIsInA6MemberedRing = true; diff --git a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java index 3be3a9da9c7..3856710ed8f 100644 --- a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java +++ b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java @@ -1,6 +1,4 @@ -/* $Revision$ $Author$ $Date$ - * - * Copyright (C) 2004-2007 Matteo Floris +/* Copyright (C) 2004-2007 Matteo Floris * Copyright (C) 2006-2007 Federico * * Contact: cdk-devel@lists.sourceforge.net @@ -29,7 +27,6 @@ import javax.vecmath.Vector3d; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.Ring; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; @@ -40,6 +37,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -219,7 +217,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing } } IRingSet rsAtom; - Ring ring; + IRing ring; IRingSet ringsWithThisBond; // SET ISINRING FLAGS FOR BONDS @@ -302,7 +300,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing if (!curAtomThird.equals(neighbour0)) { rsAtom = varRingSet.getRings(thirdBond); for (Object aRsAtom : rsAtom.atomContainers()) { - ring = (Ring) aRsAtom; + ring = (IRing) aRsAtom; if (ring.getRingSize() > 4 && ring.contains(thirdBond)) { theBondIsInA6MemberedRing = true; } diff --git a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java index 0c783df7f3c..d9ba9d242fa 100644 --- a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java +++ b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java @@ -1,6 +1,4 @@ -/* $Revision$ $Author$ $Date$ - * - * Copyright (C) 2004-2007 Matteo Floris +/* Copyright (C) 2004-2007 Matteo Floris * Copyright (C) 2006-2007 Federico * * Contact: cdk-devel@lists.sourceforge.net @@ -29,7 +27,6 @@ import javax.vecmath.Vector3d; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.Ring; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; @@ -40,6 +37,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -217,7 +215,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing } } IRingSet rsAtom; - Ring ring; + IRing ring; IRingSet ringsWithThisBond; // SET ISINRING FLAGS FOR BONDS Iterator bondsInContainer = varAtomContainer.bonds().iterator(); @@ -302,7 +300,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing if (!curAtomThird.equals(neighbour0)) { rsAtom = varRingSet.getRings(thirdBond); for (int f = 0; f < rsAtom.getAtomContainerCount(); f++) { - ring = (Ring) rsAtom.getAtomContainer(f); + ring = (IRing) rsAtom.getAtomContainer(f); if (ring.getRingSize() > 4 && ring.contains(thirdBond)) { theBondIsInA6MemberedRing = true; } diff --git a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java index 71ea6c661a1..600efed65fb 100644 --- a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java +++ b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java @@ -1,6 +1,4 @@ -/* $Revision$ $Author$ $Date$ - * - * Copyright (C) 2004-2007 Matteo Floris +/* Copyright (C) 2004-2007 Matteo Floris * Copyright (C) 2006-2007 Federico * * Contact: cdk-devel@lists.sourceforge.net @@ -30,7 +28,6 @@ import org._3pq.jgrapht.Edge; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.Ring; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; @@ -42,6 +39,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -217,7 +215,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing } } IRingSet rsAtom; - Ring ring; + IRing ring; IRingSet ringsWithThisBond; // SET ISINRING FLAGS FOR BONDS Iterator bondsInContainer = varAtomContainer.bonds().iterator(); @@ -302,7 +300,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing if (!curAtomThird.equals(neighbour0)) { rsAtom = varRingSet.getRings(thirdBond); for (Object aRsAtom : rsAtom.atomContainers()) { - ring = (Ring) aRsAtom; + ring = (IRing) aRsAtom; if (ring.getRingSize() > 4 && ring.contains(thirdBond)) { theBondIsInA6MemberedRing = true; } diff --git a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java index 8d28e8f6008..e21da803781 100644 --- a/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java +++ b/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java @@ -1,6 +1,4 @@ -/* $Revision$ $Author$ $Date$ - * - * Copyright (C) 2004-2007 Matteo Floris +/* Copyright (C) 2004-2007 Matteo Floris * Copyright (C) 2006-2007 Federico * * Contact: cdk-devel@lists.sourceforge.net @@ -29,7 +27,6 @@ import javax.vecmath.Vector3d; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.Ring; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; @@ -40,6 +37,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -218,7 +216,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing } } IRingSet rsAtom; - Ring ring; + IRing ring; IRingSet ringsWithThisBond; // SET ISINRING FLAGS FOR BONDS Iterator bondsInContainer = varAtomContainer.bonds().iterator(); @@ -301,7 +299,7 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing if (!curAtomThird.equals(neighbour0)) { rsAtom = varRingSet.getRings(thirdBond); for (int f = 0; f < rsAtom.getAtomContainerCount(); f++) { - ring = (Ring) rsAtom.getAtomContainer(f); + ring = (IRing) rsAtom.getAtomContainer(f); if (ring.getRingSize() > 4 && ring.contains(thirdBond)) { theBondIsInA6MemberedRing = true; }