Merge pull request #328 from cdk/patch/stereoapi

The minor issues I've spotted can be addressed later.
cdk · Jun 24, 2017 · 851842c · 851842c
2 parents 3ef62c1 + 253820a
commit 851842c
Show file tree

Hide file tree

Showing 20 changed files with 1,589 additions and 350 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java b/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java
@@ -0,0 +1,173 @@
+/*
+ * Copyright (c) 2017 John Mayfield <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 USA
+ */
+
+package org.openscience.cdk.stereo;
+
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IStereoElement;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+abstract class AbstractStereo<F extends IChemObject, C extends IChemObject>
+    implements IStereoElement<F, C> {
+
+    private int     value;
+    private F       focus;
+    private List<C> carriers;
+    private IChemObjectBuilder builder;
+
+    AbstractStereo(F focus, C[] carriers, int value) {
+        if (focus == null)
+            throw new NullPointerException("Focus of stereochemistry can not be null!");
+        if (carriers == null)
+            throw new NullPointerException("Carriers of the configuration can not be null!");
+        if (carriers.length != ((value >>> 12) & 0xf))
+            throw new IllegalArgumentException("Unexpected number of stereo carriers! expected " + ((value >>> 12) & 0xf) + " was " + carriers.length);
+        for (C carrier : carriers) {
+            if (carrier == null)
+                throw new NullPointerException("A carrier was undefined!");
+        }
+        this.value    = value;
+        this.focus    = focus;
+        this.carriers = new ArrayList<>();
+        Collections.addAll(this.carriers, carriers);
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public F getFocus() {
+        return focus;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public List<C> getCarriers() {
+        return carriers;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public int getConfigClass() {
+        return value & CLS_MASK;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public int getConfig() {
+        return value & CFG_MASK;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void setConfig(int cfg) {
+        value = getConfigClass() | cfg;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public boolean contains(IAtom atom) {
+        if (focus.equals(atom) || (focus instanceof IBond && ((IBond) focus).contains(atom)))
+            return true;
+        for (C carrier : carriers) {
+            if (carrier.equals(atom) ||
+                (carrier instanceof IBond && ((IBond) carrier).contains(atom)))
+                return true;
+        }
+        return false;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IStereoElement<F,C> map(Map<IAtom, IAtom> atoms,
+                                   Map<IBond, IBond> bonds) {
+        if (atoms == null)
+            throw new IllegalArgumentException("Atom map should be non-null");
+        if (bonds == null)
+            throw new IllegalArgumentException("Bond map should be non-null");
+        Map<IChemObject,IChemObject> map = new HashMap<>(atoms.size() + bonds.size());
+        map.putAll(atoms);
+        map.putAll(bonds);
+        return map(map);
+    }
+
+    @Override
+    @SuppressWarnings("unchecked")
+    public IStereoElement<F, C> map(Map<IChemObject, IChemObject> chemobjs) {
+        if (chemobjs == null)
+            throw new NullPointerException("chemobj map was not provided!");
+        F newfocus = (F) chemobjs.get(focus);
+        if (newfocus == null)
+            newfocus = focus;
+        List<C> newcarriers = carriers;
+        for (int i = 0; i < newcarriers.size(); i++) {
+            C newcarrier = (C) chemobjs.get(newcarriers.get(i));
+            if (newcarrier != null) {
+                // make a copy if this is the first change
+                if (newcarriers == carriers)
+                    newcarriers = new ArrayList<>(carriers);
+                newcarriers.set(i, newcarrier);
+            }
+        }
+        // no change, return self
+        if (newfocus == focus && newcarriers == carriers)
+            return this;
+        return create(newfocus, newcarriers, value);
+    }
+
+    protected abstract IStereoElement<F,C> create(F focus, List<C> carriers, int cfg);
+
+    /**
+     *{@inheritDoc}
+     */
+    @Override
+    public IChemObjectBuilder getBuilder() {
+        if (builder == null)
+            throw new UnsupportedOperationException("Non-domain object!");
+        return this.builder;
+    }
+
+    protected void setBuilder(IChemObjectBuilder builder) {
+        this.builder = builder;
+    }
+}
diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/Atropisomeric.java b/base/core/src/main/java/org/openscience/cdk/stereo/Atropisomeric.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright (c) 2017 John Mayfield <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 USA
+ */
+
+package org.openscience.cdk.stereo;
+
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IStereoElement;
+
+import java.util.List;
+
+/**
+ * Restricted axial rotation around Aryl-Aryl bonds. The atropisomer is
+ * stored in a similar manner to {@link ExtendedTetrahedral} (and
+ * {@link TetrahedralChirality}) except instead of storing the central atom
+ * we store the sigma bond around which the rotation is restricted and the
+ * four carriers are connect to either end atom of the 'focus' bond.
+ * <br>
+ * <pre>
+ *      a     b'
+ *     /       \
+ *    Ar --f-- Ar
+ *     \      /
+ *      a'   b
+ * f: focus
+ * Ar: Aryl (carriers connected to either end of 'f')
+ * a,a',b,b': ortho substituted on the Aryl
+ * </pre>
+ * <br>
+ * Typical examples include <a href="https://en.wikipedia.org/wiki/BINOL">
+ * BiNOL</a>, and <a href="https://en.wikipedia.org/wiki/BINAP">BiNAP</a>.
+ *
+ * @see <a href="https://en.wikipedia.org/wiki/Atropisomer">Atropisomer (Wikipedia)</a>
+ */
+public class Atropisomeric extends AbstractStereo<IBond,IAtom> {
+
+    public Atropisomeric(IBond focus, IAtom[] carriers, int value) {
+        super(focus, carriers, IStereoElement.AT | value);
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    protected IStereoElement<IBond, IAtom> create(IBond focus,
+                                                  List<IAtom> carriers,
+                                                  int cfg) {
+        return new Atropisomeric(focus, carriers.toArray(new IAtom[4]), cfg);
+    }
+}
diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java b/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java
@@ -26,7 +26,9 @@
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
+import org.openscience.cdk.interfaces.IStereoElement;
 
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -38,87 +40,53 @@
  *
  * @see org.openscience.cdk.interfaces.IDoubleBondStereochemistry
  */
-public class DoubleBondStereochemistry implements IDoubleBondStereochemistry {
-
-    private Conformation       stereo;
-    private IBond[]            ligandBonds;
-    private IBond              stereoBond;
-    private IChemObjectBuilder builder;
+public class DoubleBondStereochemistry
+    extends AbstractStereo<IBond,IBond>
+    implements IDoubleBondStereochemistry {
 
     /**
      * Creates a new double bond stereo chemistry. The path of length three is defined by
      * <code>ligandBonds[0]</code>, <code>stereoBonds</code>, and <code>ligandBonds[1]</code>.
      */
     public DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, Conformation stereo) {
-        if (ligandBonds.length > 2) throw new IllegalArgumentException("expected two ligand bonds");
-        this.stereoBond = stereoBond;
-        this.ligandBonds = ligandBonds;
-        this.stereo = stereo;
+        this(stereoBond, ligandBonds, Conformation.toConfig(stereo));
     }
 
-    /**
-     * Sets a new {@link IChemObjectBuilder}.
-     *
-     * @param builder the new {@link IChemObjectBuilder} to be returned
-     * @see #getBuilder()
-     */
-    public void setBuilder(IChemObjectBuilder builder) {
-        this.builder = builder;
+    public DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, int config) {
+        super(stereoBond, ligandBonds, CT | (CFG_MASK & config));
     }
 
-    /** {@inheritDoc} */
-    @Override
-    public IChemObjectBuilder getBuilder() {
-        return this.builder;
+    public void setBuilder(IChemObjectBuilder builder) {
+        super.setBuilder(builder);
     }
 
     /** {@inheritDoc} */
     @Override
     public IBond[] getBonds() {
-        IBond[] arrayCopy = new IBond[2];
-        System.arraycopy(ligandBonds, 0, arrayCopy, 0, 2);
-        return arrayCopy;
+        return getCarriers().toArray(new IBond[0]);
     }
 
     /** {@inheritDoc} */
     @Override
     public IBond getStereoBond() {
-        return this.stereoBond;
+        return getFocus();
     }
 
     /** {@inheritDoc} */
     @Override
     public Conformation getStereo() {
-        return this.stereo;
+        return Conformation.toConformation(getConfig());
     }
 
-    /**
-     *{@inheritDoc}
-     */
     @Override
-    public boolean contains(IAtom atom) {
-        return stereoBond.contains(atom) || ligandBonds[0].contains(atom) || ligandBonds[1].contains(atom);
+    public IDoubleBondStereochemistry map(Map<IAtom, IAtom> atoms,
+                                            Map<IBond, IBond> bonds) {
+        return (IDoubleBondStereochemistry) super.map(atoms, bonds);
     }
 
     @Override
-    public IDoubleBondStereochemistry map(Map<IAtom, IAtom> atoms, Map<IBond, IBond> bonds) {
-
-        if (bonds == null) throw new IllegalArgumentException("null bond mapping provided");
-
-        // map the double bond and the connected ligand bonds
-        IBond doubleBond = bonds.containsKey(stereoBond) ? bonds.get(stereoBond) : stereoBond;
-        IBond[] connected = new IBond[ligandBonds.length];
-
-        for (int i = 0; i < connected.length; i++) {
-            if (ligandBonds[i] != null) {
-                IBond bond = bonds.get(ligandBonds[i]);
-                if (bond != null)
-                    connected[i] = bond;
-                else
-                    connected[i] = ligandBonds[i];
-            }
-        }
-
-        return new DoubleBondStereochemistry(doubleBond, connected, stereo);
+    protected IStereoElement<IBond, IBond> create(IBond focus, List<IBond> carriers,
+                                                  int cfg) {
+        return new DoubleBondStereochemistry(focus, carriers.toArray(new IBond[2]), cfg);
     }
 }