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base/core/src/main/java/org/openscience/cdk/stereo/Octahedral.java
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base/core/src/main/java/org/openscience/cdk/stereo/SquarePlanar.java
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| /* | ||
| * 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.IStereoElement; | ||
|
|
||
| import java.util.List; | ||
|
|
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| /** | ||
| * Describes square planar configuration. The configuration around a square | ||
| * planar is described by 3 possible values (1:U, 2:4, or 3:Z) based on the | ||
| * ordering of the planar carries around the focus: | ||
| * <pre>{@code | ||
| * Configurations: | ||
| * | ||
| * a a a | ||
| * | | | | ||
| * d--f--b = U c--f--d = 4 b--f--c = Z | ||
| * | | | | ||
| * c b d | ||
| * | ||
| * SP1 SP2 SP3 | ||
| * }</pre> | ||
| * cis-platin can be represented as any of the following: | ||
| * <pre> | ||
| * [NH3][Pt@SP1]([NH3])(Cl)Cl | ||
| * [NH3][Pt@SP3]([NH3])(Cl)Cl | ||
| * [NH3][Pt@SP2](Cl)([NH3])Cl | ||
| * [NH3][Pt@SP1](Cl)(Cl)[NH3] | ||
| * </pre> | ||
| * trans-platin can be represented as any of the following: | ||
| * <pre> | ||
| * [NH3][Pt@SP2]([NH3])(Cl)Cl | ||
| * [NH3][Pt@SP1](Cl)([NH3])Cl | ||
| * [NH3][Pt@SP1](Cl)([NH3])Cl | ||
| * [NH3][Pt@SP3](Cl)(Cl)[NH3] | ||
| * </pre> | ||
| * | ||
| * The normalize function ({@link #normalize()}) create a new | ||
| * <pre>IStereoElement</pre> where the carriers have been reorder such that the | ||
| * configuration is in a <code>U</code> shape (order=1). | ||
| * | ||
| * @see <a href="http://opensmiles.org/opensmiles.html#_square_planar_centers"> | ||
| * Square Planar Centers, OpenSMILES</a> | ||
| * @see TrigonalBipyramidal | ||
| * @see Octahedral | ||
| */ | ||
| public final class SquarePlanar extends AbstractStereo<IAtom,IAtom> { | ||
|
|
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| private static final int[][] PERMUTATIONS = new int[][]{ | ||
| {A, B, C, D, A, D, C, B, | ||
| B, C, D, A, B, A, D, C, | ||
| C, D, A, B, C, B, A, D, | ||
| D, C, B, A, D, A, B, C}, // SP1 (U) | ||
| {A, C, B, D, A, D, B, C, | ||
| B, D, A, C, B, C, A, D, | ||
| C, A, D, B, C, B, D, A, | ||
| D, B, C, A, D, A, C, B}, // SP2 (4) | ||
| {A, B, D, C, A, C, D, B, | ||
| B, A, C, D, B, D, C, A, | ||
| C, D, B, A, C, A, B, D, | ||
| D, C, A, B, D, B, A, C} // SP3 (Z) | ||
| }; | ||
|
|
||
| /** | ||
| * Create a square-planar configuration around a provided focus atom. The | ||
| * carriers are flat in the plane and their arrangement is either, U-shape, | ||
| * 4-shape, or Z-shape. | ||
| * | ||
| * @param focus the focus | ||
| * @param carriers the carriers | ||
| * @param order the configuration order, 1-3 | ||
| */ | ||
| public SquarePlanar(IAtom focus, IAtom[] carriers, int order) { | ||
| super(focus, carriers, IStereoElement.SP | order & 0xff); | ||
| if (getConfigOrder() < 0 || getConfigOrder() > 3) | ||
| throw new IllegalArgumentException("Invalid configuration order," | ||
| + "should be between 1-3"); | ||
| } | ||
|
|
||
| /** | ||
| * Normalize the configuration to the lowest configuration order (1) - | ||
| * U-shaped. | ||
| * @return the normalized configuration | ||
| */ | ||
| public SquarePlanar normalize() { | ||
| int cfg = getConfigOrder(); | ||
| if (cfg == 1) | ||
| return this; | ||
| IAtom[] carriers = invapply(getCarriers().toArray(new IAtom[4]), | ||
| PERMUTATIONS[cfg-1]); | ||
| return new SquarePlanar(getFocus(), | ||
| carriers, | ||
| SPU); | ||
| } | ||
|
|
||
| /** | ||
| * {@inheritDoc} | ||
| */ | ||
| @Override | ||
| protected SquarePlanar create(IAtom focus, List<IAtom> carriers, int cfg) { | ||
| return new SquarePlanar(focus, carriers.toArray(new IAtom[4]), cfg); | ||
| } | ||
| } |
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base/core/src/main/java/org/openscience/cdk/stereo/TrigonalBipyramidal.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| /* | ||
| * 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 java.util.List; | ||
|
|
||
| /** | ||
| * Describes a trigonal-bipyramidal configuration. The configuration carriers | ||
| * are arranged with two co-linear on an axis and three equatorial. The | ||
| * configuration order is between 1 and 20 and follows the same meaning as | ||
| * SMILES. | ||
| * <pre> | ||
| * d c TB1 | ||
| * \ / | ||
| * a---x---e where a: first carrier, b: second carrier, ... * | ||
| * | x: focus | ||
| * b 'c' is in front of 'x', 'd' is behind | ||
| * </pre> | ||
| * | ||
| * The configuration can be normalized to the lowest order (1) using the | ||
| * {@link #normalize()} function. | ||
| * | ||
| * @see <a href="http://opensmiles.org/opensmiles.html#_trigonal_bipyramidal_centers"> | ||
| * Trigonal Bipyramidal, OpenSMILES</a> | ||
| * @see Octahedral | ||
| * @see SquarePlanar | ||
| */ | ||
| public final class TrigonalBipyramidal extends AbstractStereo<IAtom,IAtom> { | ||
|
|
||
| private static final int[][] PERMUTATIONS = new int[][]{ | ||
| {A, B, C, D, E, A, C, D, B, E, A, D, B, C, E, | ||
| E, D, C, B, A, E, B, D, C, A, E, C, B, D, A }, // TB1 a -> e @ | ||
| {A, D, C, B, E, A, C, B, D, E, A, B, D, C, E, | ||
| E, B, C, D, A, E, D, B, C, A, E, C, D, B, A }, // TB2 a -> e @@ | ||
| {A, B, C, E, D, A, C, E, B, D, A, E, B, C, D, | ||
| D, E, C, B, A, D, B, E, C, A, D, C, B, E, A }, // TB3 a -> d @ | ||
| {A, E, C, B, D, A, C, B, E, D, A, B, E, C, D, | ||
| D, B, C, E, A, D, E, B, C, A, D, C, E, B, A }, // TB4 a -> d @@ | ||
| {A, B, D, E, C, A, D, E, B, C, A, E, B, D, C, | ||
| C, E, D, B, A, C, B, E, D, A, C, D, B, E, A }, // TB5 a -> c @ | ||
| {A, E, D, B, C, A, D, B, E, C, A, B, E, D, C, | ||
| C, B, D, E, A, C, E, B, D, A, C, D, E, B, A }, // TB6 a -> c @@ | ||
| {A, C, D, E, B, A, D, E, C, B, A, E, C, D, B, | ||
| B, E, D, C, A, B, C, E, D, A, B, D, C, E, A }, // TB7 a -> b @ | ||
| {A, E, D, C, B, A, D, C, E, B, A, C, E, D, B, | ||
| B, C, D, E, A, B, E, C, D, A, B, D, E, C, A }, // TB8 a -> b @@ | ||
| {B, A, C, D, E, B, C, D, A, E, B, D, A, C, E, | ||
| E, D, C, A, B, E, A, D, C, B, E, C, A, D, B }, // TB9 b -> e @ | ||
| {B, A, C, E, D, B, C, E, A, D, B, E, A, C, D, | ||
| D, E, C, A, B, D, A, E, C, B, D, C, A, E, B }, // TB10 b -> d @ | ||
| {B, D, C, A, E, B, C, A, D, E, B, A, D, C, E, | ||
| E, A, C, D, B, E, D, A, C, B, E, C, D, A, B }, // TB11 b -> e @@ | ||
| {B, E, C, A, D, B, C, A, E, D, B, A, E, C, D, | ||
| D, A, C, E, B, D, E, A, C, B, D, C, E, A, B }, // TB12 b -> d @@ | ||
| {B, A, D, E, C, B, D, E, A, C, B, E, A, D, C, | ||
| C, E, D, A, B, C, A, E, D, B, C, D, A, E, B }, // TB13 b -> c @ | ||
| {B, E, D, A, C, B, D, A, E, C, B, A, E, D, C, | ||
| C, A, D, E, B, C, E, A, D, B, C, D, E, A, B }, // TB14 b -> c @@ | ||
| {C, A, B, D, E, C, B, D, A, E, C, D, A, B, E, | ||
| E, D, B, A, C, E, A, D, B, C, E, B, A, D, C }, // TB15 c -> e @ | ||
| {C, A, B, E, D, C, B, E, A, D, C, E, A, B, D, | ||
| D, E, B, A, C, D, A, E, B, C, D, B, A, E, C }, // TB16 c -> d @ | ||
| {D, A, B, C, E, D, B, C, A, E, D, C, A, B, E, | ||
| E, C, B, A, D, E, A, C, B, D, E, B, A, C, D }, // TB17 d -> e @ | ||
| {D, C, B, A, E, D, B, A, C, E, D, A, C, B, E, | ||
| E, A, B, C, D, E, C, A, B, D, E, B, C, A, D }, // TB18 d -> e @@ | ||
| {C, E, B, A, D, C, B, A, E, D, C, A, E, B, D, | ||
| D, A, B, E, C, D, E, A, B, C, D, B, E, A, C }, // TB19 c -> d @@ | ||
| {C, D, B, A, E, C, B, A, D, E, C, A, D, B, E, | ||
| E, A, B, D, C, E, D, A, B, C, E, B, D, A, C }, // TB20 c -> e @@ | ||
| }; | ||
|
|
||
| /** | ||
| * Create a new trigonal bipyramidal configuration. | ||
| * @param focus the focus | ||
| * @param carriers the carriers | ||
| * @param order the order (1-20) | ||
| */ | ||
| public TrigonalBipyramidal(IAtom focus, IAtom[] carriers, int order) { | ||
| super(focus, carriers, TrigonalBipyramidal | order & 0xff); | ||
| if (getConfigOrder() < 0 || getConfigOrder() > 20) | ||
| throw new IllegalArgumentException("Invalid configuration order," | ||
| + "should be between 1-20"); | ||
| } | ||
|
|
||
| /** | ||
| * Normalize the configuration to the lowest configuration order (1) - | ||
| * the axis goes from the first to last carrier, the three middle carriers | ||
| * are anti-clockwise looking from the first carrier. | ||
| * @return the normalized configuration | ||
| */ | ||
| public TrigonalBipyramidal normalize() { | ||
| int cfg = getConfigOrder(); | ||
| if (cfg == 1) | ||
| return this; | ||
| IAtom[] carriers = invapply(getCarriers().toArray(new IAtom[5]), | ||
| PERMUTATIONS[cfg-1]); | ||
| return new TrigonalBipyramidal(getFocus(), | ||
| carriers, | ||
| 1); | ||
|
|
||
| } | ||
|
|
||
| /** | ||
| * {@inheritDoc} | ||
| */ | ||
| @Override | ||
| protected TrigonalBipyramidal create(IAtom focus, List<IAtom> carriers, int cfg) { | ||
| return new TrigonalBipyramidal(focus, carriers.toArray(new IAtom[5]), cfg); | ||
| } | ||
| } |
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