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/*
* 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.chem.AtomTypeCalculator;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import java.text.DecimalFormat;
import java.text.NumberFormat;
public class SolubilityPredictor {
public static final float cSolubilityUnknown = -999;
private static final long[] cAtomType = {
0x80002L, 0x80004L, 0x80009L, 0x8000dL,
0x90002L, 0x90003L, 0x90004L, 0x90005L,
0x90008L, 0x90009L, 0x9000dL, 0x9000eL,
0xa8002L, 0xa8003L, 0xa8004L, 0xa8009L,
0xa800dL, 0xc8002L, 0xc8003L, 0xc8004L,
0xc8005L, 0xc8008L, 0xc8009L, 0x110002L,
0x110003L, 0x110004L, 0x110008L, 0x128004L,
0x148004L, 0x148008L, 0x190002L, 0x190003L,
0x1090002L, 0x1090003L, 0x1090004L, 0x1090005L,
0x1090008L, 0x1090009L, 0x109000dL, 0x109000eL,
0x10a8002L, 0x40080004L, 0x48080002L, 0x48080004L,
0x48090002L, 0x48090003L, 0x48090004L, 0x48090008L,
0x4809000cL, 0x54080002L, 0x54090002L, 0x54090003L,
0x54090004L, 0x54090008L, 0x540a8002L, 0x540a8008L,
0x540a800cL, 0x64090002L, 0x64090003L, 0x64090004L,
0x64090008L, 0x6409000cL, 0x640a8002L, 0x640a8003L,
0x640a8004L, 0x640c8002L, 0x640c8003L, 0x640c8004L,
0x640c8008L, 0x88090002L, 0x88090003L, 0x880a8002L,
0x880a8003L, 0x880c8002L, 0x880c8003L, 0x94090002L,
0x94090003L, 0x940a8002L, 0x940a8003L, 0xa4128002L,
0xc8090002L, 0xd4090002L, 0xd40a8002L, 0xd40c8002L,
0x809010002L, 0x809010003L, 0x809010004L, 0x809010008L,
0x815010002L, 0x815010003L, 0x815010004L, 0x815010008L,
0x815028002L, 0x815028003L, 0x815028004L, 0x825010002L,
0x825010003L, 0x825028002L, 0x848090002L, 0x848090003L,
0x848090004L, 0x848090008L, 0x8480a8002L, 0x8480a8003L,
0x8480a8004L, 0x8480c8002L, 0x8480c8003L, 0x8480c8004L,
0x8480c8008L, 0x848110002L, 0x848110003L, 0x848128002L,
0x848128003L, 0x84812800eL, 0x848190002L, 0x849090002L,
0x849090003L, 0x849090004L, 0x849090008L, 0x854080002L,
0x854090002L, 0x8540a8002L, 0x8540c8002L, 0x855090002L,
0x24048090002L, 0x24048090003L, 0x2a048090002L, 0x2a048090003L,
0x2a054090002L, 0x2a054090003L, 0x2a0540a8002L, 0x32048090002L,
0x32048090003L, 0x32054090002L, 0x320540a8002L, 0x32064090002L,
0x320640c8002L, 0x320640c8003L, 0x44048090002L, 0x44054090002L,
0x44054090003L, 0x440540a8002L, 0x44064090002L, 0x440640a8002L,
0x440640c8002L, 0x4a048090002L, 0x4a048090008L, 0x4a054090002L,
0x4a054090003L, 0x4a0540a8002L, 0x4a0540a8003L, 0x4a0540a8007L,
0x4a0540a8008L, 0x4a064090002L, 0x4a064090008L, 0x4a0640a8002L,
0x4a0640c8002L, 0x52054090002L, 0x520540a8002L, 0x520640a8002L,
0x520640c8002L, 0x404808090002L, 0x404808090003L, 0x4048080a8002L,
0x4048080c8002L, 0x404809010002L, 0x404809010003L, 0x40a808090002L,
0x40a808090003L, 0x40a8080a8002L, 0x40a8080c8002L, 0x40a8080c8003L,
0x40a809010002L, 0x40a809010003L, 0x40a814090002L, 0x40a814090003L,
0x40a8140a8002L, 0x40a8140c8002L, 0x40a815010002L, 0x40a815028002L,
0x412808090002L, 0x4128080a8002L, 0x4128080c8002L, 0x412809010002L,
0x412814090002L, 0x4128140a8002L, 0x4128140c8002L, 0x412815010002L,
0x424048090002L, 0x424048090003L, 0x424054090002L, 0x424054090003L,
0x4240540a8002L, 0x424064090002L, 0x424064090003L, 0x4240640a8002L,
0x4240640c8002L, 0x4240640c8003L, 0x424088090002L, 0x4240880a8002L,
0x4240880c8002L, 0x4240880c8008L, 0x424094090002L, 0x424094090008L,
0x4240940a8002L, 0x4240940a8007L, 0x4240940c8002L, 0x42409412800eL,
0x424809010002L, 0x424815010002L, 0x424815010003L, 0x424815028002L,
0x424815028003L, 0x424848090002L, 0x424848090003L, 0x4248480a8002L,
0x4248480a8003L, 0x424848110002L, 0x424848128002L, 0x424849090002L,
0x42a048090002L, 0x42a054090002L, 0x42a088090002L, 0x42a094090002L,
0x42a0940a8002L, 0x12024048090002L, 0x15024048090002L, 0x15024048090003L,
0x1502a048090002L, 0x1502a054090002L, 0x1502a0540a8002L, 0x19024048090002L,
0x1902a048090002L, 0x1902a054090002L, 0x1902a0540a8002L, 0x19032048090002L,
0x19032054090002L, 0x190320540a8002L, 0x19032064090002L, 0x190320640a8002L,
0x190320640c8002L, 0x25024048090007L, 0x2502a048090007L, 0x2502a054090007L,
0x2502a0540a8007L, 0x25032054090007L, 0x250320540a8007L, 0x250320640a8007L,
0x250320640c8007L, 0x2504a048090008L, 0x2504a054090008L, 0x2504a0540a8008L,
0x2504a064090008L, 0x2504a0640a8008L, 0x2902a054090007L, 0x212024048090002L,
0x21202a048090002L, 0x21202a054090002L, 0x21202a0540a8002L, 0x212032048090002L,
0x2120320640c8002L, 0x21204a0540a8007L, 0x21204a094090008L, 0x21204a0940a8008L,
0x21204a0940c8008L, 0x212424048090002L, 0x212424054090002L, 0x2124240540a8002L,
0x212424848090002L, 0x2124248480a8002L, 0x2124248480c8002L };
private static final float[] cIncrement = {
-0.19f, 1.27f, -0.701f, 2.691f, -0.227f, 0.03f, 0.106f, -0.476f,
-0.447f, -0.191f, -0.333f, 0.086f, 0.247f, -0.062f, 0.016f, 0.387f,
0.235f, -0.432f, -0.903f, 0.39f, 0.581f, 4.524f, -0.635f, -0.28f,
0.77f, -0.05f, 1.087f, 0.192f, 0.196f, -0.52f, 0.542f, 0.363f,
0.792f, 0.592f, 0.964f, 0.354f, -0.685f, -0.315f, -0.413f, -0.595f,
0.22f, -1.432f, -2.254f, 0.44f, -0.27f, -0.133f, -0.269f, 0.267f,
0.572f, -0.568f, 0.174f, -0.185f, -0.235f, -0.17f, -0.181f, -0.342f,
-0.348f, -0.437f, -0.804f, -0.412f, -0.215f, -0.625f, -0.831f, 0.497f,
-0.431f, -1.331f, 0.507f, -0.632f, -0.599f, -0.156f, -0.353f, -0.164f,
-0.441f, -0.497f, -1.06f, 0.115f, -0.225f, -0.154f, -0.031f, -1.574f,
-1.093f, -0.738f, -0.45f, -0.556f, -0.181f, 2.384f, 1.75f, -1.666f,
-1.066f, 1.327f, 0.803f, -1.505f, -2.537f, -0.17f, 0.149f, 0.521f,
2.905f, -0.252f, 0.86f, 0.361f, 0.403f, 0.005f, 1.146f, 0.936f,
-0.3f, 0.209f, -0.583f, -0.024f, -0.01f, 0.611f, 0.486f, 0.862f,
-0.035f, -0.596f, 1.161f, 1.647f, 0.844f, 0.125f, 0.142f, -0.171f,
0.442f, 0.088f, 3.066f, 1.652f, -0.203f, -0.018f, 0.023f, 0.073f,
0.254f, 0.554f, 0.595f, -0.406f, -0.637f, -0.174f, -0.101f, -0.543f,
-2.406f, -3.292f, -0.053f, -0.193f, 1.85f, -1.261f, -0.656f, -0.73f,
-0.938f, 0.128f, 1.154f, 0.242f, -0.529f, -0.278f, -0.802f, 0.912f,
-1.381f, 0.463f, 1.074f, -0.628f, -0.962f, -1.832f, -1.499f, -2.116f,
-2.207f, -1.317f, 2.501f, -0.849f, -0.602f, -0.622f, 2.122f, -2.226f,
0.913f, -2.259f, -1.25f, 1.394f, -1.402f, 2.073f, -2.957f, 0.291f,
-3.476f, -2.727f, -3.132f, -2.12f, -0.725f, -0.297f, 0.083f, 0.347f,
-1.425f, -1.66f, -1.282f, -1.265f, 0.719f, 0.138f, 1.302f, 0.859f,
1.359f, 0.659f, -0.94f, 0.9f, 0.319f, -2.571f, 1.109f, 0.972f,
1.653f, 2.602f, 0.729f, 1.066f, 1.067f, -0.311f, 0.031f, -0.203f,
-0.681f, -1.258f, 1.07f, -3.096f, -0.228f, 1.933f, 0.119f, 2.108f,
0.113f, 1.628f, 1.308f, 3.336f, 0.754f, -0.465f, -0.397f, 0.077f,
-0.479f, -0.153f, 0.141f, 2.135f, 0.234f, 0.461f, 0.67f, -0.361f,
-1.039f, -0.483f, 0.137f, -0.768f, -0.511f, 3.424f, -0.855f, -0.585f,
-1.567f, 3.343f, 1.84f, 0.389f, 1.122f, 1.63f, 1.335f, 0.366f,
-0.557f, 0.432f, 0.204f, 0.882f, 0.466f, -0.458f, 0.404f, 0.657f,
1.115f, 1.976f, 1.786f, -0.036f, -1.05f, 1.045f, 0.044f, 1.033f,
-1.08f, 2.539f, 2.235f, 2.29f, 3.121f, 3.932f, 2.75f };
public SolubilityPredictor() {
}
/**
* 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.
* This method may normalize ambiguous bonds of the molecule.
* @param mol
* @return aquous solubility value estimated from atom type specific increments
*/
public float assessSolubility(StereoMolecule mol) {
float logS = -0.530f;
mol.normalizeAmbiguousBonds();
mol.ensureHelperArrays(Molecule.cHelperRings);
for (int atom=0; atom