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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* @author Thomas Sander
*/
package com.actelion.research.chem;
import com.actelion.research.util.DoubleFormat;
public class Mutation {
public static final int MUTATION_ADD_ATOM = 1;
public static final int MUTATION_INSERT_ATOM = 2;
public static final int MUTATION_CHANGE_ATOM = 4;
public static final int MUTATION_CUTOUT_ATOM = 8;
public static final int MUTATION_DELETE_ATOM = 16;
public static final int MUTATION_CLOSE_RING = 32;
public static final int MUTATION_CHANGE_BOND = 64;
public static final int MUTATION_DELETE_BOND = 128;
public static final int MUTATION_CHANGE_RING = 256;
public static final int MUTATION_CLOSE_RING_AND_AROMATIZE = 512;
public static final int MUTATION_TOGGLE_AMID_SULFONAMID = 1024;
public static final int MUTATION_MIGRATE = 2048;
public static final int MUTATION_SWAP_SUBSTITUENT = 4096;
public static final int MUTATION_DELETE_SUBSTITUENT = 8192;
public static final int MUTATION_CUTOUT_SFRAGMENT = 16384;
public static final int MUTATION_INVERT_PARITY = 32768;
public static final int[][] cAllowedAtomicNo =
{ { 5, 6, 7, 8, 9, 15, 16, 17, 35, 53 },
{ 6, 7, 8, 15, 16 },
{ 6, 7 } };
public int mMutationType;
public int mWhere1;
public int mWhere2;
public int mSpecifier1;
public int mSpecifier2;
public int[] mAtomList;
public double mProbability;
public Mutation() {
}
public Mutation(int mutationType,
int where1, int where2,
int specifier1, int specifier2,
double probability) {
mMutationType = mutationType;
mWhere1 = where1;
mWhere2 = where2;
mSpecifier1 = specifier1;
mSpecifier2 = specifier2;
mProbability = probability;
}
public Mutation(int mutationType, int where1, int where2, int specifier1, int[] atomList,
double probability) {
mMutationType = mutationType;
mWhere1 = where1;
mWhere2 = where2;
mSpecifier1 = specifier1;
mAtomList = atomList;
mProbability = probability;
}
public String toString() {
switch (mMutationType) {
case MUTATION_ADD_ATOM:
return "Atom Addition; AtAtom:"+mWhere1
+" AtomicNo:"+mSpecifier1
+" BondType:"+mSpecifier2
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_INSERT_ATOM:
return "Atom Insertion; AtBond:"+mWhere1
+" AtomicNo:"+mSpecifier1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_CHANGE_ATOM:
return "Atom Change; Atom:"+mWhere1
+" AtomicNo:"+mSpecifier1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_DELETE_ATOM:
return "Atom Deletion; Atom:"+mWhere1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_CUTOUT_ATOM:
return "Atom CutOut; Atom:"+mWhere1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_CLOSE_RING:
return "Bond Addition; FromAtom:"+mWhere1
+" ToAtom:"+mWhere2
+" BondType:"+mSpecifier1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_CHANGE_BOND:
return "Bond Change; Bond:"+mWhere1
+" BondType:"+mSpecifier1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_DELETE_BOND:
return "Bond Deletion; Bond:"+mWhere1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_CHANGE_RING:
return "Ring Change; Ring:"+mWhere1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_CLOSE_RING_AND_AROMATIZE:
return "Close Ring And Aromatize; FromAtom:"+mWhere1
+" ToAtom:"+mWhere2
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_TOGGLE_AMID_SULFONAMID:
return "Toggle Amid-Sulfonamid; Atom:"+mWhere1
+" Oxygen:"+mWhere1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_MIGRATE:
return "Group Migration; Bond:"+mWhere1
+" originalAtom:"+mSpecifier1
+" newAtom:"+mSpecifier2
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_SWAP_SUBSTITUENT:
return "Swap Substituent; coreAtom1:"+mWhere1
+" firstAtom1:"+mSpecifier1
+" coreAtom2:"+mWhere2
+" firstAtom2:"+mSpecifier2
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_DELETE_SUBSTITUENT:
return "Delete Substituent; coreAtom:"+mWhere1
+" firstAtom:"+mSpecifier1
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_CUTOUT_SFRAGMENT:
return "CutOut Fragment; rootAtom:"+mWhere1
+" new bond from atom1:"+mSpecifier1+" to atom2:"+mSpecifier2
+" Probability:"+DoubleFormat.toString(mProbability);
case MUTATION_INVERT_PARITY:
return "Invert Parity; "
+(mWhere1 != -1 ? "atom:"+mWhere1 : "bond:"+mWhere2)
+" Probability:"+DoubleFormat.toString(mProbability);
}
return "Unknown Mutation";
}
}