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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.prediction;
import com.actelion.research.calc.ThreadMaster;
import com.actelion.research.chem.IDCodeParser;
import com.actelion.research.chem.SSSearcher;
import com.actelion.research.chem.StereoMolecule;
public class DruglikenessPredictor {
public static final double cDruglikenessUnknown = -999;
private static boolean sInitialized = false;
private static IncrementTable sIncrementTable;
private ParameterizedStringList mDetail;
public DruglikenessPredictor() {
synchronized(DruglikenessPredictor.class) {
if (!sInitialized) {
try {
sIncrementTable = new IncrementTable("/resources/druglikenessNoIndex.txt");
sInitialized = true;
}
catch (Exception e) {
System.out.println("Unable to initialize DruglikenessPredictor");
}
}
}
}
/**
* Before calculating any kind of property, make sure that the molecule's structure is standardized.
* Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
* SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
* MoleculeStandardizer.
* @param mol
* @return druglikeness value estimated from atom type specific increments
*/
public double assessDruglikeness(StereoMolecule mol, ThreadMaster threadMaster) {
ParameterizedStringList detail = new ParameterizedStringList();
if (!sInitialized) {
detail.add("Druglikeness predictor not properly initialized.",
ParameterizedStringList.cStringTypeText);
return cDruglikenessUnknown;
}
detail.add("Found sub-structure fragments and their contributions:",
ParameterizedStringList.cStringTypeText);
detail.add("(yellow atoms carry at least one more substituent)",
ParameterizedStringList.cStringTypeText);
double nastyIncrementSum = 0.0;
double incrementSum = 0.0;
int fragmentCount = 0;
SSSearcher sss = new SSSearcher(SSSearcher.cMatchAtomCharge);
StereoMolecule fragment = new StereoMolecule();
for (int i=0; i