com.actelion.research.chem.prediction.CLogPPredictor Maven / Gradle / Ivy
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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 com.actelion.research.util.SortedList;
import java.util.TreeMap;
public class CLogPPredictor {
private static final int ATOM_TYPE_MODE = AtomTypeCalculator.cPropertiesForCLogPCharges;
protected static final long[] ATOM_TYPE = {
0x40002L, 0x40004L, 0x40802L, 0x40803L,
0x40804L, 0x40805L, 0x40808L, 0x40809L,
0x4080dL, 0x4080eL, 0x41402L, 0x41403L,
0x41404L, 0x41409L, 0x4140eL, 0x42402L,
0x42403L, 0x42404L, 0x42405L, 0x4240eL,
0x60802L, 0x60803L, 0x60804L, 0x60805L,
0x60808L, 0x60809L, 0x6080dL, 0x6080eL,
0x61402L, 0x61404L, 0x61409L, 0x80004L,
0x80802L, 0x80803L, 0x80804L, 0x80808L,
0x81404L, 0x82404L, 0x82408L, 0xc0802L,
0xc0803L, 0x8220842L, 0x8220843L, 0x8220844L,
0x8220848L, 0x8520842L, 0x8520843L, 0x8520844L,
0x8520848L, 0x8521442L, 0x8521443L, 0x8521444L,
0x8521448L, 0x8920842L, 0x8920843L, 0x8921442L,
0x8921443L, 0x8921444L, 0x10240002L, 0x10240008L,
0x10240048L, 0x10240802L, 0x10240803L, 0x10240804L,
0x10240808L, 0x1024080cL, 0x10240842L, 0x10240843L,
0x10240844L, 0x10240848L, 0x10540802L, 0x10540803L,
0x10540804L, 0x10540808L, 0x10540842L, 0x10540843L,
0x10540844L, 0x10540848L, 0x10541402L, 0x10541408L,
0x10541442L, 0x10940004L, 0x10940802L, 0x10940803L,
0x10940804L, 0x10940808L, 0x10940842L, 0x10940843L,
0x10940844L, 0x10940848L, 0x10941402L, 0x10941403L,
0x10941404L, 0x10941442L, 0x10942402L, 0x10942408L,
0x1094240aL, 0x10942442L, 0x18240802L, 0x18240803L,
0x18240804L, 0x18240808L, 0x1824080cL, 0x18240842L,
0x18240843L, 0x18240844L, 0x18240848L, 0x1824084cL,
0x18241402L, 0x18241403L, 0x18241404L, 0x18241442L,
0x18241448L, 0x18242402L, 0x18242403L, 0x18242404L,
0x18242408L, 0x18242442L, 0x18242443L, 0x18242444L,
0x18242448L, 0x18260802L, 0x18260803L, 0x18260804L,
0x18260808L, 0x18260842L, 0x18260843L, 0x18260844L,
0x18260848L, 0x18540802L, 0x18540804L, 0x18540842L,
0x18541402L, 0x18560802L, 0x18560803L, 0x20240802L,
0x20240803L, 0x20240842L, 0x20240843L, 0x20241402L,
0x20241403L, 0x20241442L, 0x20241443L, 0x20241444L,
0x20242402L, 0x20242403L, 0x20242442L, 0x20242443L,
0x20260802L, 0x20260803L, 0x20260842L, 0x20260843L,
0x20261402L, 0x20540802L, 0x20540803L, 0x20540842L,
0x20540843L, 0x20540844L, 0x20540848L, 0x20541402L,
0x20541403L, 0x20541442L, 0x20541443L, 0x20560802L,
0x20560803L, 0x20560843L, 0x20561402L, 0x20981402L,
0x30240802L, 0x30260802L, 0x30540802L, 0x30541402L,
0x30542402L, 0x30560802L, 0x2088220842L, 0x2088220843L,
0x2148220842L, 0x2148220843L, 0x2148520842L, 0x2148520848L,
0x2148521442L, 0x2248220842L, 0x2248520842L, 0x2248920842L,
0x4088220842L, 0x4088220843L, 0x4088520842L, 0x4088520843L,
0x4088521442L, 0x4088521443L, 0x4088920842L, 0x4088921442L,
0x4090240043L, 0x4090240802L, 0x4090240803L, 0x4090240842L,
0x4090240843L, 0x4148220842L, 0x4148220843L, 0x4148520842L,
0x4148520843L, 0x4148521442L, 0x4148920842L, 0x4148921442L,
0x4150240802L, 0x4150240803L, 0x4150240842L, 0x4150240843L,
0x4150540802L, 0x4150540803L, 0x4150540842L, 0x4150541402L,
0x4150541442L, 0x4248220842L, 0x4248520842L, 0x4248521442L,
0x4248920842L, 0x4248921442L, 0x4250240802L, 0x4250240803L,
0x4250240842L, 0x4250240843L, 0x4250540802L, 0x4250540803L,
0x4250540842L, 0x4250541402L, 0x4250940802L, 0x4250942402L,
0x6088220842L, 0x6088220843L, 0x6088520842L, 0x6088520843L,
0x6088521442L, 0x6088521443L, 0x6088920842L, 0x6088921442L,
0x6090240802L, 0x6090240803L, 0x6090240842L, 0x6090240843L,
0x6090540802L, 0x6090540803L, 0x6090540842L, 0x6090540843L,
0x6090541402L, 0x6090541442L, 0x6090940802L, 0x6090940803L,
0x6090940842L, 0x6090940843L, 0x6090941403L, 0x6090941442L,
0x6090942403L, 0x6098240802L, 0x6098240803L, 0x6098240842L,
0x6098240843L, 0x6098241402L, 0x6098241442L, 0x6098260802L,
0x6148220842L, 0x6148520842L, 0x6148521442L, 0x6150240802L,
0x6150240842L, 0x6150540802L, 0x6150540842L, 0x6150940842L,
0x6158240802L, 0x6158260802L, 0x8090240802L, 0x8090240842L,
0x8090240843L, 0x8090540802L, 0x8090540842L, 0x8090540843L,
0x8090541402L, 0x8090541442L, 0x8090940802L, 0x8090940842L,
0x8090941442L, 0x8090942402L, 0x8090942442L, 0x8098240802L,
0x8098240842L, 0x8098241402L, 0x8098241442L, 0x8098242402L,
0x8098242408L, 0x8098242442L, 0x8098260802L, 0x8098260842L,
0x8098560842L, 0x8150240802L, 0x8150240808L, 0x8150240842L,
0x8150240843L, 0x8150240848L, 0x8150540802L, 0x8150540842L,
0x8150541402L, 0x8150541407L, 0x8150541442L, 0x8150541448L,
0x8150940802L, 0x8150940842L, 0x8150941402L, 0x8150941442L,
0x8150942442L, 0x8158240802L, 0x8158240808L, 0x8158240842L,
0x8158240843L, 0x8158240848L, 0x8158241402L, 0x8158241408L,
0x8158241442L, 0x8158242402L, 0x8158242442L, 0x8158260802L,
0x8158260808L, 0x8158260842L, 0x8158540802L, 0x8158541402L,
0x8158560802L, 0x8250240842L, 0x8250540802L, 0x8250540842L,
0x8250541402L, 0x8250541442L, 0x8250940842L, 0x8250941402L,
0x8250941442L, 0x8258241402L, 0x8258241442L, 0x8258541402L,
0x1024090240043L, 0x1024090240801L, 0x1024090240802L, 0x1024090240842L,
0x1054090240802L, 0x1054090240842L, 0x1054150240802L, 0x1054150240842L,
0x1054150540802L, 0x1054150540842L, 0x1054150541402L, 0x1094088220843L,
0x1094090240802L, 0x1094090240803L, 0x1094090240842L, 0x1094090240843L,
0x1094150240802L, 0x1094150540802L, 0x1094150541402L, 0x1094250240802L,
0x1094250240842L, 0x1094250540802L, 0x1094250940802L, 0x1094250941402L,
0x1094250942402L, 0x1824090240802L, 0x1824090240842L, 0x1824150240802L,
0x1824150240842L, 0x1824150540802L, 0x1824150540842L, 0x1824150541402L,
0x1824250942402L, 0x1826090240802L, 0x1826090240842L, 0x1826090540802L,
0x1826090540842L, 0x1826098241402L, 0x1826098241442L, 0x1854090240802L,
0x1854090240842L, 0x2024250240803L, 0x2054150240807L, 0x2054150540807L,
0x2054150541407L, 0x2054150541447L, 0x2054250540807L, 0x2054250541407L,
0x2054250941407L, 0x205425094144aL, 0x2056090541407L, 0x2058150240808L,
0x2058150240848L, 0x2058150540808L, 0x2058150541408L, 0x2058150541448L,
0x2058158240808L, 0x2058158240848L, 0x2058158241408L, 0x2058158241448L,
0x2058158260808L, 0x2058158260848L, 0x2094150540807L, 0x2094150541407L,
0x2094250541407L, 0x2096090541407L, 0x4000000040803L, 0x4000000040804L,
0x4000000040808L, 0x4000000041404L, 0x4000000042404L, 0x4000000060804L,
0x4000000061404L, 0x4000000081403L, 0x4000008220843L, 0x4000010240803L,
0x4000010540803L, 0x4000020580803L, 0x4000020581403L, 0x4000030241403L,
0x4004088220843L, 0x4004088520843L, 0x4004090240803L, 0x4004090240843L,
0x4004148220843L, 0x4004148520843L, 0x4006088520843L, 0x4008090240803L,
0x4008090540803L, 0x4008090540843L, 0x4008098241403L, 0x4008150540803L,
0x4008150541403L, 0x4008158241403L, 0x5024090240803L, 0x5024090240843L,
0x5054090240803L, 0x5054090240843L, 0x5824090240803L, 0x8000000040803L,
0x8000008220843L, 0x8000010240803L, 0x8000010240843L, 0x8000020242443L,
0x8004090240803L, 0x8004090240843L };
protected static final float[] INCREMENT = {
0.6967f, 0.0000f, 0.4886f, -0.4727f, -0.0749f, 0.6262f, 0.2735f, 0.5700f,
0.7010f, 0.9534f, -0.2809f, -0.8260f, -0.1785f, -1.6203f, -1.0960f, 0.1395f,
-0.2975f, -1.2908f, 1.0162f, -1.3825f, 0.5111f, -0.4357f, -0.1041f, 0.3424f,
-0.0615f, 0.6035f, 0.7227f, 0.4346f, -0.3310f, -0.4980f, -1.4915f, 0.3317f,
0.4292f, -0.5824f, -0.1834f, 0.1306f, -0.5015f, -0.5258f, 0.4244f, -0.1610f,
-0.2778f, 0.2766f, 0.3593f, 0.7715f, 0.3150f, -0.2652f, -0.0965f, 0.4202f,
0.1871f, -0.3684f, -0.0778f, 0.8943f, 0.3694f, 0.2879f, 0.4489f, -0.2601f,
0.4771f, 0.1923f, 0.4597f, 0.3384f, 0.6633f, 0.4544f, 0.1597f, 0.6339f,
0.3504f, 0.0449f, 0.3420f, 0.2611f, 0.4046f, 0.5219f, -0.3632f, -0.4108f,
0.3057f, -0.1456f, -0.2713f, -0.5193f, 0.4526f, 0.5539f, -0.7070f, -0.4881f,
-0.4100f, 0.0000f, 0.1479f, 0.3448f, 0.4298f, 0.5579f, -0.1265f, -0.0425f,
0.0767f, 0.6635f, -0.3812f, -0.8368f, 1.0287f, -0.1021f, 0.3587f, -0.5945f,
0.1692f, -0.1218f, 0.4381f, 0.1695f, 0.4525f, 0.3352f, 0.1583f, 0.4036f,
-0.0480f, 0.5023f, -0.2649f, 0.7691f, -0.3552f, 1.0301f, -0.1141f, -0.5932f,
0.1749f, 0.1313f, -0.1804f, 0.3994f, 0.2291f, 0.3169f, 0.3599f, -0.0039f,
-0.2956f, 0.4907f, 0.3540f, 0.2192f, 0.1565f, 0.6935f, 0.3618f, 0.6735f,
0.5778f, -0.5636f, 0.5569f, 0.3038f, -0.3276f, -0.4659f, 0.3818f, 0.3283f,
0.2239f, 0.2043f, 0.0590f, -0.4835f, 0.6165f, -0.4011f, 0.5578f, -0.2164f,
-0.0175f, 0.2981f, 0.1100f, 0.2715f, 0.4409f, -0.1609f, 0.3775f, -0.1346f,
-0.6992f, -0.4670f, 0.1566f, 0.0468f, -0.1321f, 1.3686f, 0.0000f, -0.4116f,
1.0186f, -0.3935f, 0.5223f, 0.2839f, 0.5129f, 0.1266f, 0.0103f, 1.5193f,
0.2705f, 0.4294f, 0.0120f, -0.3397f, 0.1483f, 0.2806f, 0.3206f, 0.5662f,
-0.0987f, -0.1005f, -0.3576f, 0.0961f, -0.6401f, 0.1921f, -0.1533f, -0.4170f,
0.1094f, 0.8231f, -0.3784f, 0.4032f, -0.6461f, 0.8035f, 0.2029f, -0.3745f,
0.3317f, 0.1841f, 0.7071f, 0.1227f, 0.7949f, 0.0350f, 0.3818f, -0.1554f,
0.3785f, -0.2405f, 0.2359f, 0.3463f, -0.4925f, -0.0929f, -0.4352f, -0.2207f,
-0.9960f, -0.7238f, -0.5469f, -1.2939f, -0.0136f, 0.2791f, -0.1653f, -0.1238f,
0.4951f, 0.2899f, 0.0657f, 0.7189f, 0.0570f, 0.6619f, -0.6381f, -0.8073f,
0.2355f, 0.3048f, -0.0199f, -0.0752f, 0.2764f, 0.8011f, -0.1744f, 0.1581f,
-0.3848f, 0.5993f, 0.5268f, -0.0417f, 0.3770f, 0.6998f, 0.5940f, 0.5912f,
-0.5571f, 0.0238f, -0.2475f, 0.0307f, -0.3875f, -0.7437f, 0.5144f, 0.0057f,
0.7655f, 0.1720f, -2.5624f, -0.3066f, 0.3647f, 0.4733f, -0.3401f, -0.1450f,
0.7088f, -0.1318f, 0.0426f, -0.1203f, -0.3624f, 0.5358f, -0.3701f, -0.5648f,
-0.1972f, -0.8769f, -0.3675f, -0.2004f, 0.1336f, -0.1699f, 0.4461f, 0.1559f,
1.1168f, 0.2365f, -0.2206f, 0.4480f, -0.4053f, -0.1361f, 0.2199f, 0.0536f,
-0.0210f, 0.6985f, 0.9643f, 0.1727f, -0.0329f, -0.1893f, 0.0702f, 0.1496f,
-1.3825f, 0.4146f, -0.5028f, 0.3832f, 0.9545f, -0.4152f, -1.0369f, -0.1830f,
0.5883f, -0.2918f, -0.5294f, -0.6541f, -0.1906f, -0.8484f, -0.3457f, 0.9541f,
-0.7924f, -0.6020f, 0.0800f, -0.2596f, 0.8382f, -0.2668f, -0.1106f, 0.0362f,
-0.3189f, -0.7278f, -0.0894f, -0.2277f, -0.2394f, -0.2962f, 0.7776f, -0.0118f,
-0.4358f, 0.3749f, -0.6070f, -0.1857f, 0.1139f, -0.4416f, -0.3704f, -0.7487f,
-0.1079f, -0.2992f, -0.3277f, 0.0251f, -0.9188f, 0.2945f, -0.2234f, 0.3468f,
0.3317f, 0.2891f, 0.2613f, -0.0344f, -0.6005f, -0.6258f, -0.5434f, -0.7712f,
-0.9057f, -0.1668f, -0.9905f, -1.4915f, -0.0372f, -1.1638f, 0.1262f, -0.5248f,
-0.1538f, -0.3682f, 0.3249f, 0.0650f, 0.0511f, -0.4607f, 0.2231f, 0.2822f,
0.1397f, 0.2833f, -0.1226f, -0.4592f, -0.3435f, -0.6654f, -0.5056f, -0.8631f,
0.1536f, -0.4051f, 0.0891f, -0.6972f, -0.4699f, -0.6774f, -0.0622f, -0.9300f,
0.1337f, -0.4938f, 0.3948f, -0.4075f, -0.6411f, -0.0091f, -0.1333f, -0.5192f,
-0.1661f, 0.3317f, -0.6427f, -0.0707f, 0.4806f, 0.3828f, 0.2229f, 0.6160f,
-0.0884f, -0.0471f, 0.1106f, 0.3821f, 0.0922f, 0.0806f, 0.3371f, 0.1884f,
0.1381f, -0.2392f, -3.6435f, -2.1509f, 0.4975f, -0.3620f, -2.5384f, -1.6821f,
-0.3651f, 0.6262f, -1.6185f, -1.0650f, 0.8374f, 0.3685f, 0.2577f, 0.3791f,
-3.2333f, -1.7948f, -0.6592f, -1.3148f, -0.7380f, 0.0534f, -1.7552f, -1.8039f,
-1.1340f, -0.5653f, -1.2454f, 0.9473f, 1.4231f, 1.0112f, -1.9498f, -2.0249f,
-1.2349f, 0.3280f, -3.9189f, -2.1995f, 0.1889f, -1.2314f, -1.8023f, -0.2995f,
-0.4067f, -0.1316f };
public static final float cCLogPUnknown = -999f;
private static SortedList sSortedTypeList;
public CLogPPredictor() {
if (sSortedTypeList == null) {
synchronized(CLogPPredictor.class) {
if (sSortedTypeList == null) {
sSortedTypeList = new SortedList();
for (Long l:ATOM_TYPE)
sSortedTypeList.add(l);
}
}
}
}
/**
* Ambiguous bonds are normalized.
* @param mol
* @return
*/
public float assessCLogP(StereoMolecule mol) {
float cLogP = 0.0f;
mol.normalizeAmbiguousBonds();
mol.ensureHelperArrays(Molecule.cHelperRings);
for (int atom=0; atom countMap = new TreeMap();
for (int atom=0; atom © 2015 - 2025 Weber Informatics LLC | Privacy Policy