Include copyright statements and some cleanup after review.

cdk · Aug 19, 2015 · 9272268 · 9272268
1 parent a5cb8ee
commit 9272268
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Showing 7 changed files with 94 additions and 9 deletions.
diff --git a/.../java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java b/.../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
@@ -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
@@ -1,3 +1,25 @@
+/*
+ * Copyright (c) 2015 John May <jwmay@users.sf.net>
+ *
+ * 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/...forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAromaticTypeMapping.java b/...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<IBond> 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
@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2015 John May <jwmay@users.sf.net>
+ *
+ * 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
@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2015 John May <jwmay@users.sf.net>
+ *
+ * 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
@@ -1,3 +1,25 @@
+/*
+ * Copyright (c) 2015 John May <jwmay@users.sf.net>
+ *
+ * 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;