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The qsaratomic module is now also independent from the data module
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Change-Id: I63bb2315cda1d24873aa8104ba61f0f417e178ae

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
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@egonw @rajarshi
egonw authored and rajarshi committed Apr 20, 2012
1 parent 646c37b commit 1a2e93a
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Showing 6 changed files with 20 additions and 31 deletions.
1 change: 0 additions & 1 deletion src/META-INF/qsaratomic.cdkdepends
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@@ -1,6 +1,5 @@
cdk-annotation.jar
cdk-interfaces.jar
cdk-data.jar
cdk-core.jar
cdk-standard.jar
cdk-valencycheck.jar
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10 changes: 4 additions & 6 deletions src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
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@@ -1,6 +1,4 @@
/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
/* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
* Copyright (C) 2006-2007 Federico
*
* Contact: cdk-devel@lists.sourceforge.net
Expand Down Expand Up @@ -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;
Expand All @@ -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;
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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;
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10 changes: 4 additions & 6 deletions src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
View file
@@ -1,6 +1,4 @@
/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
/* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
* Copyright (C) 2006-2007 Federico
*
* Contact: cdk-devel@lists.sourceforge.net
Expand Down Expand Up @@ -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;
Expand All @@ -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;
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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;
}
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10 changes: 4 additions & 6 deletions src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
View file
@@ -1,6 +1,4 @@
/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
/* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
* Copyright (C) 2006-2007 Federico
*
* Contact: cdk-devel@lists.sourceforge.net
Expand Down Expand Up @@ -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;
Expand All @@ -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;
Expand Down Expand Up @@ -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<IBond> bondsInContainer = varAtomContainer.bonds().iterator();
Expand Down Expand Up @@ -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;
}
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10 changes: 4 additions & 6 deletions src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
View file
@@ -1,6 +1,4 @@
/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
/* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
* Copyright (C) 2006-2007 Federico
*
* Contact: cdk-devel@lists.sourceforge.net
Expand Down Expand Up @@ -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;
Expand All @@ -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;
Expand Down Expand Up @@ -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<IBond> bondsInContainer = varAtomContainer.bonds().iterator();
Expand Down Expand Up @@ -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;
}
Expand Down
10 changes: 4 additions & 6 deletions src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
View file
@@ -1,6 +1,4 @@
/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
/* Copyright (C) 2004-2007 Matteo Floris <mfe4@users.sf.net>
* Copyright (C) 2006-2007 Federico
*
* Contact: cdk-devel@lists.sourceforge.net
Expand Down Expand Up @@ -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;
Expand All @@ -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;
Expand Down Expand Up @@ -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<IBond> bondsInContainer = varAtomContainer.bonds().iterator();
Expand Down Expand Up @@ -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;
}
Expand Down

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