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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.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
/**
* This class predicts the topological polar surface area (TPSA) of a molecule as a sum of
* contributions of its polar atom-types. The method was published by
* Peter Ertl, Bernhard Rohde and Paul Selzer in J. Med. Chem. 2000, 43, 3714-3717.
*/
public class PolarSurfaceAreaPredictor {
public static final float cPSAUnknown = -1.0f;
protected static final String[] cPolarAtomTypeName = {
"[N](-*)(-*)-*",
"[N](-*)=*",
"[N]#*",
"[N](-*)(=*)=* as in nitro",
"[N](=*)#* middle atom of azide",
"[N]1(-*)-*-*-1 3-membered ring",
"[NH](-*)-*",
"[NH]1-*-*-1 3-membered ring",
"[NH]=*",
"[NH2]-*",
"[N+](-*)(-*)(-*)-*",
"[N+](-*)(-*)=*",
"[N+](-*)#* N in isocyano",
"[NH+](-*)(-*)-*",
"[NH+](-*)=*",
"[NH2+](-*)-*",
"[NH2+]=*",
"[NH3+]-*",
"[n](:*):*",
"[n](:*)(:*):*",
"[n](-*)(:*):*",
"[n](=*)(:*):* as in pyridine-N-oxid",
"[nH](:*):*",
"[n+](:*)(:*):*",
"[n+](-*)(:*):*",
"[nH+](:*):*",
"[O](-*)-*",
"[O]1-*-*-1 3-membered ring",
"[O]=*",
"[OH]-*",
"[O-]-*",
"[o](:*):*",
"[S](-*)-*",
"[S]=*",
"[S](-*)(-*)=*",
"[S](-*)(-*)(=*)=*",
"[SH]-*",
"[s](:*):*",
"[s](=*)(:*):*",
"[P](-*)(-*)-*",
"[P](-*)=*",
"[P](-*)(-*)(-*)=*",
"[PH](-*)(-*)=*"
};
private static final float[] cTPSAIncrement = {
3.24f, 12.36f, 23.79f, 11.68f, 13.60f, 3.01f, 12.03f, 21.94f,
23.85f, 26.02f, 0.00f, 3.01f, 4.36f, 4.44f, 13.97f, 16.61f,
25.59f, 27.64f, 12.89f, 4.41f, 4.93f, 8.39f, 15.79f, 4.10f,
3.88f, 14.14f, 9.23f, 12.53f, 17.07f, 20.23f, 23.06f, 13.14f,
25.30f, 32.09f, 19.21f, 8.38f, 38.80f, 28.24f, 21.70f, 13.59f,
34.14f, 9.81f, 23.47f };
public PolarSurfaceAreaPredictor() {
}
public static int getPolarAtomTypeCount() {
return cPolarAtomTypeName.length;
}
/**
* Calculates the topological polar surface area (TPSA) of a molecule as a sum of
* contributions of its polar atom-types. This method uses the polar atom contributions
* originally published by Peter Ertl et al. in J. Med. Chem. 2000, 43, 3714-3717.
* 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 topological polar surface area estimated from atom type specific increments
*/
public float assessPSA(StereoMolecule mol) {
int[] count = getPolarAtomTypeCounts(mol);
float psa = 0.0f;
for (int i=0; i 0
return 22;
}
else if (mol.getAtomCharge(atom) == 1) {
if (mol.getAllHydrogens(atom) == 0) {
for (int i=0; i 0
return 25;
}
}
else { // not aromatic
if (mol.getAtomCharge(atom) == 0) {
switch (mol.getAllHydrogens(atom)) {
case 0: // hydrogens
switch (mol.getAtomPi(atom)) {
case 0: // pi
if (mol.getAtomRingSize(atom) == 3)
return 5;
else
return 0;
case 1: // pi
return 1;
case 2: // pi
return 2;
}
break;
case 1: // hydrogens
switch (mol.getAtomPi(atom)) {
case 0: // pi
if (mol.getAtomRingSize(atom) == 3)
return 7;
else
return 6;
case 1: // pi
return 8;
}
break;
case 2: // hydrogens
return 9;
}
}
else if (mol.getAtomCharge(atom) == 1) {
switch (mol.getAllHydrogens(atom)) {
case 0: // hydrogens
switch (mol.getAtomPi(atom)) {
case 0: // pi
return 10;
case 1: // pi
return hasNegativeNeighbour(mol, atom) ? 3 : 11;
case 2: // pi
if (mol.getConnBondOrder(atom, 0) == 2)
return hasNegativeNeighbour(mol, atom) ? 4 : cTPSAIncrement.length+1;
else
return 12;
}
break;
case 1: // hydrogens
switch (mol.getAtomPi(atom)) {
case 0: // pi
return 13;
case 1: // pi
return 14;
}
break;
case 2: // hydrogens
return (mol.getAtomPi(atom) == 0) ? 15 : 16;
case 3: // hydrogens
return 17;
}
}
}
return cTPSAIncrement.length+1; // unrecognized N
case 8:
if (mol.isAromaticAtom(atom)) {
if (mol.getAtomCharge(atom) == 0)
return 31;
}
else {
if (mol.getAtomCharge(atom) == 0) {
if (mol.getAtomPi(atom) > 0)
return 28;
if (mol.getNonHydrogenNeighbourCount(atom) == 1)
return 29;
if (mol.getAtomRingSize(atom) == 3)
return 27;
return 26;
}
else if (mol.getAtomCharge(atom) == -1) {
if (mol.getNonHydrogenNeighbourCount(atom) == 1
&& mol.getAtomCharge(mol.getConnAtom(atom, 0)) > 0)
return 28; // return -[O-] of nitro as =O
return 30;
}
}
return cTPSAIncrement.length+1; // unrecognized O
case 15:
if (mol.getAtomCharge(atom) == 0) {
if (mol.getAllHydrogens(atom) == 0) {
if (mol.getNonHydrogenNeighbourCount(atom) == 3
&& mol.getAtomPi(atom) == 0)
return 39;
if (mol.getNonHydrogenNeighbourCount(atom) == 2
&& mol.getAtomPi(atom) == 1)
return 40;
if (mol.getNonHydrogenNeighbourCount(atom) == 4
&& mol.getAtomPi(atom) == 1)
return 41;
}
else if (mol.getAllHydrogens(atom) == 1) {
if (mol.getNonHydrogenNeighbourCount(atom) == 3
&& mol.getAtomPi(atom) == 1)
return 42;
}
}
return cTPSAIncrement.length+1; // unrecognized P
case 16:
if (mol.getAtomCharge(atom) == 0) {
if (mol.isAromaticAtom(atom)) {
if (mol.getNonHydrogenNeighbourCount(atom) == 2)
return 37;
else
return 38;
}
else {
if (mol.getAllHydrogens(atom) == 0) {
if (mol.getNonHydrogenNeighbourCount(atom) == 2
&& mol.getAtomPi(atom) == 0)
return 32;
if (mol.getNonHydrogenNeighbourCount(atom) == 1
&& mol.getAtomPi(atom) == 1)
return 33;
if (mol.getNonHydrogenNeighbourCount(atom) == 3
&& mol.getAtomPi(atom) == 1)
return 34;
if (mol.getNonHydrogenNeighbourCount(atom) == 4
&& mol.getAtomPi(atom) == 2)
return 35;
}
else if (mol.getAllHydrogens(atom) == 1) {
if (mol.getNonHydrogenNeighbourCount(atom) == 1)
return 36;
}
}
}
return cTPSAIncrement.length+1; // unrecognized S
}
return cTPSAIncrement.length; // undefined type
}
private boolean hasNegativeNeighbour(StereoMolecule mol, int atom) {
for (int i=0; i