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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.
*
*/
package com.actelion.research.chem.reaction;
import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.DrawingObjectList;
import com.actelion.research.chem.IDCodeParser;
import com.actelion.research.chem.StereoMolecule;
public class ReactionEncoder
{
public static final char MOLECULE_DELIMITER = ' ';
public static final char PRODUCT_IDENTIFIER = '!';
public static final char OBJECT_DELIMITER = '#';
public static final int INCLUDE_MAPPING = 1;
public static final int INCLUDE_COORDS = 2;
public static final int INCLUDE_DRAWING_OBJECTS = 4;
public static final int RETURN_RXN_CODE_ONLY = 0;
public static final int RETAIN_REACTANT_AND_PRODUCT_ORDER = 8;
public static final int RETURN_DEFAULT = INCLUDE_MAPPING | INCLUDE_COORDS;
private ReactionEncoder()
{}
/**
* Creates a String containing a unique reaction code by
* creating idcodes of every reactant and product and
* concatenating them in lexical order.
* If mapping information is available this will be encoded
* in a 2nd string. Otherwise this will be null.
* Coordinates, if available, will be encoded in a 3rd string.
* If there are drawing objects assigned to this reaction
* then these are encoded in a 4th string.
*
* @return String[4] with reaction code, coordinates, mapping, drawing objects
*/
public static String[] encode(Reaction reaction, boolean keepAbsoluteCoordinates) {
return encode(reaction, keepAbsoluteCoordinates, true);
}
/**
* Creates a non-unique String containing a reaction code by
* creating idcodes of every reactant and product and
* concatenating them in original order.
* If mapping information is available this will be encoded
* in a 2nd string. Otherwise this will be null.
* Coordinates, if available, will be encoded in a 3rd string.
* If there are drawing objects assigned to this reaction
* then these are encoded in a 4th string.
*
* @return String[4] with reaction code, coordinates, mapping, drawing objects
*/
private static String[] encode(Reaction reaction, boolean keepAbsoluteCoordinates, boolean sortByIDCode) {
if (reaction == null
|| reaction.getReactants() == 0
|| reaction.getProducts() == 0) {
return null;
}
String[] idcode = new String[reaction.getMolecules()];
String[] mapping = new String[reaction.getMolecules()];
String[] coords = new String[reaction.getMolecules()];
for (int i = 0; i < reaction.getMolecules(); i++) {
Canonizer canonizer = new Canonizer(reaction.getMolecule(i));
idcode[i] = canonizer.getIDCode();
if (idcode[i] == null) {
return null;
}
mapping[i] = canonizer.getEncodedMapping();
coords[i] = canonizer.getEncodedCoordinates(keepAbsoluteCoordinates);
}
StringBuilder idcodeSequence = new StringBuilder();
StringBuilder coordsSequence = new StringBuilder();
StringBuilder mappingSequence = new StringBuilder();
for (int i = 0; i < reaction.getReactants(); i++) {
int index = i;
if (sortByIDCode) {
String maxString = "";
index = -1;
for (int j = 0; j < reaction.getReactants(); j++) {
if (maxString.compareTo(idcode[j]) < 0) {
maxString = idcode[j];
index = j;
}
}
}
if (i > 0) {
idcodeSequence.append(MOLECULE_DELIMITER);
mappingSequence.append(MOLECULE_DELIMITER);
coordsSequence.append(MOLECULE_DELIMITER);
}
idcodeSequence.append(idcode[index]);
mappingSequence.append(mapping[index]);
coordsSequence.append(coords[index]);
idcode[index] = "";
}
idcodeSequence.append(PRODUCT_IDENTIFIER);
mappingSequence.append(MOLECULE_DELIMITER);
coordsSequence.append(MOLECULE_DELIMITER);
for (int i = reaction.getReactants(); i < reaction.getMolecules(); i++) {
int index = i;
if (sortByIDCode) {
String maxString = "";
index = -1;
for (int j = reaction.getReactants(); j < reaction.getMolecules(); j++) {
if (maxString.compareTo(idcode[j]) < 0) {
maxString = idcode[j];
index = j;
}
}
}
if (i > reaction.getReactants()) {
idcodeSequence.append(MOLECULE_DELIMITER);
mappingSequence.append(MOLECULE_DELIMITER);
coordsSequence.append(MOLECULE_DELIMITER);
}
idcodeSequence.append(idcode[index]);
mappingSequence.append(mapping[index]);
coordsSequence.append(coords[index]);
idcode[index] = "";
}
String[] result = new String[4];
result[0] = idcodeSequence.toString();
if (mappingSequence.length() > reaction.getMolecules() - 1) // delimiters only
{
result[1] = mappingSequence.toString();
}
if (coordsSequence.length() > reaction.getMolecules() - 1) // delimiters only
{
result[2] = coordsSequence.toString();
}
if (reaction.getDrawingObjects() != null) {
result[3] = reaction.getDrawingObjects().toString();
}
return result;
}
/**
* Creates a String containing a reaction code by creating idcodes of every reactant and product and
* concatenating them in original (if mode includes RETAIN_REACTANT_AND_PRODUCT_ORDER) or in
* lexical order. In the latter case this string is a canonical reaction encoding.
* If mapping information is available this will be encoded in a 2nd string.
* Coordinates, if available, will be encoded in a 3rd string.
* If there are drawing objects assigned to this reaction then these are encoded in a 4th string.
*
* @return One String with reaction code, coordinates, mapping, drawing objects as defined by mode.
*/
public static String encode(Reaction reaction, boolean keepAbsoluteCoordinates, int mode) {
String[] result = encode(reaction, keepAbsoluteCoordinates, (mode & RETAIN_REACTANT_AND_PRODUCT_ORDER) == 0);
if (result == null) {
return null;
}
StringBuffer buf = new StringBuffer(result[0]);
// System.out.println("Buffer: 1:" + buf);
if (mode != 0) {
buf.append(OBJECT_DELIMITER);
if ((mode & INCLUDE_MAPPING) != 0
&& result.length > 1
&& result[1] != null) {
buf.append(result[1]);
}
}
// System.out.println("Buffer: 2:" + buf);
mode &= ~INCLUDE_MAPPING;
if (mode != 0) {
buf.append(OBJECT_DELIMITER);
if ((mode & INCLUDE_COORDS) != 0
&& result.length > 2
&& result[2] != null) {
buf.append(result[2]);
}
}
// System.out.println("Buffer: 3:" + buf);
mode &= ~INCLUDE_COORDS;
if (mode != 0) {
buf.append(OBJECT_DELIMITER);
if ((mode & INCLUDE_DRAWING_OBJECTS) != 0
&& result.length > 3
&& result[3] != null) {
buf.append(result[3]);
}
}
// System.out.println("Buffer: 4:" + buf);
return buf.toString();
}
/**
* Creates a Reaction object by interpreting a reaction code,
* mapping, coordinates and drawing objects that were earlier created
* by this class.
* If rxnCoords are relative or null, and if ensureCoordinates==true
* then all reactants and products are placed automatically along a
* horizontal line. In this case providing a valid Graphics ensure a
* more accurate molecule positioning.
*
* @return Reaction
*/
public static Reaction decode(String rxnCode, String rxnMapping, String rxnCoords,
String rxnObjects, boolean ensureCoordinates) {
if (rxnCode == null || rxnCode.length() == 0) {
return null;
}
boolean isProduct = false;
int idcodeIndex = 0;
int mappingIndex = 0;
int coordsIndex = 0;
boolean reactionLayoutRequired = false;
int productIndex = rxnCode.indexOf(PRODUCT_IDENTIFIER);
if (productIndex == -1) {
return null;
}
Reaction rxn = new Reaction();
while (idcodeIndex != -1) {
if (idcodeIndex > productIndex) {
isProduct = true;
}
int delimiterIndex = rxnCode.indexOf(MOLECULE_DELIMITER, idcodeIndex);
if (!isProduct
&& (delimiterIndex > productIndex || delimiterIndex == -1)) {
delimiterIndex = productIndex;
}
String idcode = null;
if (delimiterIndex == -1) {
idcode = rxnCode.substring(idcodeIndex);
idcodeIndex = -1;
} else {
idcode = rxnCode.substring(idcodeIndex, delimiterIndex);
idcodeIndex = delimiterIndex + 1;
}
String mapping = null;
if (rxnMapping != null && rxnMapping.length() != 0) {
delimiterIndex = rxnMapping.indexOf(MOLECULE_DELIMITER, mappingIndex);
if (delimiterIndex == -1) {
mapping = rxnMapping.substring(mappingIndex);
} else {
mapping = rxnMapping.substring(mappingIndex, delimiterIndex);
mappingIndex = delimiterIndex + 1;
}
}
String coords = null;
if (rxnCoords != null && rxnCoords.length() != 0) {
delimiterIndex = rxnCoords.indexOf(MOLECULE_DELIMITER, coordsIndex);
if (delimiterIndex == -1) {
coords = rxnCoords.substring(coordsIndex);
} else {
coords = rxnCoords.substring(coordsIndex, delimiterIndex);
coordsIndex = delimiterIndex + 1;
}
}
IDCodeParser parser = new IDCodeParser(ensureCoordinates);
StereoMolecule mol = parser.getCompactMolecule(idcode, coords);
if (!reactionLayoutRequired && (coords == null || !parser.coordinatesAreAbsolute(coords)))
reactionLayoutRequired = true;
if (mapping != null) {
parser.parseMapping(mapping.getBytes());
}
if (isProduct) {
rxn.addProduct(mol);
} else {
rxn.addReactant(mol);
}
}
if (rxnObjects != null && rxnObjects.length() != 0) {
rxn.setDrawingObjects(new DrawingObjectList(rxnObjects));
}
rxn.setReactionLayoutRequired(reactionLayoutRequired);
return rxn;
}
/**
* Creates a Reaction object by interpreting a reaction code,
* mapping, coordinates and drawing objects that were earlier created
* by this class and are passed OBJECT_DELIMITER-delimited within
* one string.
* If rxnCoords are relative or null, and if ensureCoordinates==true
* then all reactants and products are placed automatically along a
* horizontal line. In this case providing a valid Graphics ensure a
* more accurate molecule positioning.
*
* @return Reaction
*/
public static Reaction decode(String s, boolean ensureCoordinates) {
if (s == null)
return null;
String rxnCode = s;
String rxnMapping = null;
String rxnCoords = null;
String rxnObjects = null;
int index1 = s.indexOf(OBJECT_DELIMITER);
if (index1 == -1) {
rxnCode = s;
} else {
rxnCode = s.substring(0, index1);
int index2 = s.indexOf(OBJECT_DELIMITER, index1 + 1);
if (index2 == -1) {
rxnMapping = s.substring(index1 + 1);
} else {
rxnMapping = s.substring(index1 + 1, index2);
int index3 = s.indexOf(OBJECT_DELIMITER, index2 + 1);
if (index3 == -1) {
rxnCoords = s.substring(index2 + 1);
} else {
rxnCoords = s.substring(index2 + 1, index3);
rxnObjects = s.substring(index3 + 1);
}
}
}
return decode(rxnCode, rxnMapping, rxnCoords, rxnObjects, ensureCoordinates);
}
public static Reaction decode(String s, int type) {
if (s == null)
return null;
String rxnCode = s;
String rxnMapping = null;
String rxnCoords = null;
String rxnObjects = null;
int index1 = s.indexOf(OBJECT_DELIMITER);
if (index1 == -1) {
rxnCode = s;
} else {
rxnCode = s.substring(0, index1);
int index2 = s.indexOf(OBJECT_DELIMITER, index1 + 1);
if (index2 == -1) {
rxnMapping = s.substring(index1 + 1);
} else {
rxnMapping = s.substring(index1 + 1, index2);
int index3 = s.indexOf(OBJECT_DELIMITER, index2 + 1);
if (index3 == -1) {
rxnCoords = s.substring(index2 + 1);
} else {
rxnCoords = s.substring(index2 + 1, index3);
rxnObjects = s.substring(index3 + 1);
}
}
}
return decode(rxnCode,
(type & INCLUDE_MAPPING) == INCLUDE_MAPPING ? rxnMapping : null,
(type & INCLUDE_COORDS) == INCLUDE_COORDS ? rxnCoords : null,
(type & INCLUDE_DRAWING_OBJECTS) == INCLUDE_DRAWING_OBJECTS ? rxnObjects : null,
false);
}
}
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