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/*
* $Id: Lipinski.java 120 2011-01-18 06:24:55Z bill.smith $
*
* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * 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.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* 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 org.RDKit;
// Class attempts to provide functionality in
// RDBASE/rdkit/Chem/Lipinski.py
public class Lipinski {
static ROMol HDonorSmarts = RWMol.MolFromSmarts("[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]");
// changes log for HAcceptorSmarts:
// v2, 1-Nov-2008, GL : fix amide-N exclusion; remove Fs from definition
static ROMol HAcceptorSmarts = RWMol.MolFromSmarts("[$([O,S;H1;v2]-[!$(*=[O,N,P,S])])," +
"$([O,S;H0;v2]),$([O,S;-])," +
"$([N;v3;!$(N-*=!@[O,N,P,S])])," +
"$([nH0,o,s;+0])" +
"]");
static ROMol HeteroatomSmarts = RWMol.MolFromSmarts("[!#6;!#1]");
// NOTE: the Rotatable bond smarts here doesn"t treat deuteriums (which are left in the graph
// and therefore contribute to the degree of a carbon) the same as hydrogens (which are removed
// from the graph). So the bond in [2H]C([2H])([2H])C([2H])([2H])[2H] *is* considered
// rotatable.
static ROMol RotatableBondSmarts = RWMol.MolFromSmarts("[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]");
static ROMol NHOHSmarts = RWMol.MolFromSmarts("[#8H1,#7H1,#7H2,#7H3]");
static ROMol NOCountSmarts = RWMol.MolFromSmarts("[#7,#8]");
private static int getMatchCount(ROMol test, ROMol smarts) {
return (int) test.getSubstructMatches(smarts, true).size();
}
public static int getHDonorCount(ROMol mol) {
return getMatchCount(mol, HDonorSmarts);
}
public static int getHAcceptorCount(ROMol mol) {
return getMatchCount(mol, HAcceptorSmarts);
}
public static int getHeteroatomCount(ROMol mol) {
return getMatchCount(mol, HeteroatomSmarts);
}
public static int getRotatableBondCount(ROMol mol) {
return getMatchCount(mol, RotatableBondSmarts);
}
public static int getNHOHCount(ROMol mol) {
return getMatchCount(mol, NHOHSmarts);
}
public static int getNOCount(ROMol mol) {
return getMatchCount(mol, NOCountSmarts);
}
}
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