From 7acf1902c5298673585761f570de1b6f5da90ab9 Mon Sep 17 00:00:00 2001 From: John May Date: Tue, 18 Aug 2015 22:02:35 -0400 Subject: [PATCH] Include copyright statements and some cleanup after review. Signed-off-by: Egon Willighagen --- .../PartialTChargeMMFF94DescriptorTest.java | 11 ++------- .../cdk/atomtype/MMFF94AtomTypeMatcher.java | 1 + .../openscience/cdk/forcefield/mmff/Mmff.java | 22 ++++++++++++++++++ .../mmff/MmffAromaticTypeMapping.java | 1 + .../cdk/forcefield/mmff/MmffParamSet.java | 23 +++++++++++++++++++ .../cdk/forcefield/mmff/MmffParamSetTest.java | 23 +++++++++++++++++++ .../cdk/forcefield/mmff/MmffTest.java | 22 ++++++++++++++++++ 7 files changed, 94 insertions(+), 9 deletions(-) diff --git a/descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java b/descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java index 17a9715d24c..fdb41b076db 100644 --- a/descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java +++ b/descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java @@ -18,14 +18,7 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; -import org.junit.Before; -import org.openscience.cdk.DefaultChemObjectBuilder; -import org.openscience.cdk.charges.MMFF94PartialCharges; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.inchi.InChIGeneratorFactory; -import org.openscience.cdk.inchi.InChIToStructure; -import org.openscience.cdk.interfaces.IAtom; -import org.openscience.cdk.interfaces.IAtomContainer; +import org.junit.BeforeClass; /** * See tests in MmffTest. @@ -45,7 +38,7 @@ public class PartialTChargeMMFF94DescriptorTest extends AtomicDescriptorTest { */ public PartialTChargeMMFF94DescriptorTest() {} - @Before + @BeforeClass public void setUp() throws Exception { setDescriptor(PartialTChargeMMFF94Descriptor.class); } diff --git a/misc/extra/src/main/java/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java b/misc/extra/src/main/java/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java index 32ae68193d4..3491e13052b 100755 --- a/misc/extra/src/main/java/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java +++ b/misc/extra/src/main/java/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java @@ -44,6 +44,7 @@ * @cdk.module extra * @cdk.githash * @deprecated use the newer Mmff.assignAtomTypes() + * @see org.openscience.cdk.forcefield.mmff.Mmff */ @Deprecated public class MMFF94AtomTypeMatcher implements IAtomTypeMatcher { diff --git a/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/Mmff.java b/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/Mmff.java index b952bf8e7fd..0551efeeea8 100644 --- a/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/Mmff.java +++ b/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/Mmff.java @@ -1,3 +1,25 @@ +/* + * Copyright (c) 2015 John May + * + * Contact: cdk-devel@lists.sourceforge.net + * + * This program is free software; you can redistribute it and/or modify it + * under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation; either version 2.1 of the License, or (at + * your option) any later version. All we ask is that proper credit is given + * for our work, which includes - but is not limited to - adding the above + * copyright notice to the beginning of your source code files, and to any + * copyright notice that you may distribute with programs based on this work. + * + * This program is distributed in the hope that it will be useful, but WITHOUT + * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public + * License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U + */ package org.openscience.cdk.forcefield.mmff; import org.openscience.cdk.CDKConstants; diff --git a/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAromaticTypeMapping.java b/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAromaticTypeMapping.java index 0e93eee480d..a77c59827a1 100644 --- a/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAromaticTypeMapping.java +++ b/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAromaticTypeMapping.java @@ -83,6 +83,7 @@ final class MmffAromaticTypeMapping { * @param container structure representation * @param symbs vector of symbolic types for the whole structure * @param bonds edge to bond map lookup + * @param graph adjacency list graph representation of structure * @param mmffArom set of bonds that are aromatic */ void assign(IAtomContainer container, String[] symbs, EdgeToBondMap bonds, int[][] graph, Set mmffArom) { diff --git a/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffParamSet.java b/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffParamSet.java index fe5c0791055..e38162b942d 100644 --- a/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffParamSet.java +++ b/tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffParamSet.java @@ -1,3 +1,26 @@ +/* + * Copyright (c) 2015 John May + * + * Contact: cdk-devel@lists.sourceforge.net + * + * This program is free software; you can redistribute it and/or modify it + * under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation; either version 2.1 of the License, or (at + * your option) any later version. All we ask is that proper credit is given + * for our work, which includes - but is not limited to - adding the above + * copyright notice to the beginning of your source code files, and to any + * copyright notice that you may distribute with programs based on this work. + * + * This program is distributed in the hope that it will be useful, but WITHOUT + * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public + * License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U + */ + package org.openscience.cdk.forcefield.mmff; import com.google.common.base.Charsets; diff --git a/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffParamSetTest.java b/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffParamSetTest.java index fa2444d1958..f02960e7abb 100644 --- a/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffParamSetTest.java +++ b/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffParamSetTest.java @@ -1,3 +1,26 @@ +/* + * Copyright (c) 2015 John May + * + * Contact: cdk-devel@lists.sourceforge.net + * + * This program is free software; you can redistribute it and/or modify it + * under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation; either version 2.1 of the License, or (at + * your option) any later version. All we ask is that proper credit is given + * for our work, which includes - but is not limited to - adding the above + * copyright notice to the beginning of your source code files, and to any + * copyright notice that you may distribute with programs based on this work. + * + * This program is distributed in the hope that it will be useful, but WITHOUT + * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public + * License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U + */ + package org.openscience.cdk.forcefield.mmff; import org.junit.Test; diff --git a/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffTest.java b/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffTest.java index 6bc1a05efcc..b495767ec6d 100644 --- a/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffTest.java +++ b/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffTest.java @@ -1,3 +1,25 @@ +/* + * Copyright (c) 2015 John May + * + * Contact: cdk-devel@lists.sourceforge.net + * + * This program is free software; you can redistribute it and/or modify it + * under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation; either version 2.1 of the License, or (at + * your option) any later version. All we ask is that proper credit is given + * for our work, which includes - but is not limited to - adding the above + * copyright notice to the beginning of your source code files, and to any + * copyright notice that you may distribute with programs based on this work. + * + * This program is distributed in the hope that it will be useful, but WITHOUT + * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public + * License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U + */ package org.openscience.cdk.forcefield.mmff; import org.junit.AfterClass;