org.openscience.cdk.io.MDLValence Maven / Gradle / Ivy
/*
* Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
* John May
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or (at
* your option) any later version. All we ask is that proper credit is given
* for our work, which includes - but is not limited to - adding the above
* copyright notice to the beginning of your source code files, and to any
* copyright notice that you may distribute with programs based on this work.
*
* This program is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
*
* Additionally the 'MDLValence' method has the following licence/copyright.
*
* Copyright (C) 2012 NextMove Software
*
* @@ All Rights Reserved @@ This file is part of the RDKit. The contents
* are covered by the terms of the BSD license which is included in the file
* license.txt, found at the root of the RDKit source tree.
*/
package org.openscience.cdk.io;
import com.google.common.collect.Maps;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import java.util.Map;
/**
* Adds implicit hydrogens and specifies valency using the MDL valence model.
*
* @author John May
* @cdk.module io
* @see Explicit
* and Implicit Hydrogens: taking liberties with valence
*/
final class MDLValence {
private MDLValence() {}
/**
* Apply the MDL valence model to the provided atom container.
*
* @param container an atom container loaded from an MDL format
* @return the container (for convenience)
*/
static IAtomContainer apply(IAtomContainer container) {
int n = container.getAtomCount();
int[] valences = new int[n];
Map atomToIndex = Maps.newHashMapWithExpectedSize(n);
for (IAtom atom : container.atoms())
atomToIndex.put(atom, atomToIndex.size());
// compute the bond order sums
for (IBond bond : container.bonds()) {
int u = atomToIndex.get(bond.getAtom(0));
int v = atomToIndex.get(bond.getAtom(1));
int bondOrder = bond.getOrder().numeric();
valences[u] += bondOrder;
valences[v] += bondOrder;
}
for (int i = 0; i < n; i++) {
IAtom atom = container.getAtom(i);
Integer charge = atom.getFormalCharge();
Integer element = atom.getAtomicNumber();
if (element == null) continue;
// unset = 0 in this case
charge = charge == null ? 0 : charge;
int explicit = valences[i];
// if there was a valence read from the mol file use that otherwise
// use the default value from the valence model to set the correct
// number of implied hydrogens
if (atom.getValency() != null) {
atom.setImplicitHydrogenCount(atom.getValency() - explicit);
} else {
int implicit = implicitValence(element, charge, valences[i]);
atom.setImplicitHydrogenCount(implicit - explicit);
atom.setValency(implicit);
}
}
return container;
}
/**
* Given an element (atomic number) its charge and the explicit valence
* (bond order sum) return the implicit valence for that atom. This valence
* is from the MDL valence model which was decoded by NextMove Software and
* licenced as below.
*
* $Id: MDLValence.h 2288 2012-11-26 03:39:27Z glandrum $
*
* Copyright (C) 2012 NextMove Software
*
* @@ All Rights Reserved @@ This file is part of the RDKit. The contents
* are covered by the terms of the BSD license which is included in the file
* license.txt, found at the root of the RDKit source tree.
* @see Explicit
* and Implicit Hydrogens taking liberties with valence
*/
static int implicitValence(int elem, int q, int val) {
switch (elem) {
case 1: // H
case 3: // Li
case 11: // Na
case 19: // K
case 37: // Rb
case 55: // Cs
case 87: // Fr
if (q == 0 && val <= 1) return 1;
break;
case 4: // Be
case 12: // Mg
case 20: // Ca
case 38: // Sr
case 56: // Ba
case 88: // Ra
switch (q) {
case 0:
if (val <= 2) return 2;
break;
case 1:
if (val <= 1) return 1;
break;
}
break;
case 5: // B
switch (q) {
case -4:
if (val <= 1) return 1;
break;
case -3:
if (val <= 2) return 2;
break;
case -2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case -1:
if (val <= 4) return 4;
break;
case 0:
if (val <= 3) return 3;
break;
case 1:
if (val <= 2) return 2;
break;
case 2:
if (val <= 1) return 1;
break;
}
break;
case 6: // C
switch (q) {
case -3:
if (val <= 1) return 1;
break;
case -2:
if (val <= 2) return 2;
break;
case -1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 0:
if (val <= 4) return 4;
break;
case 1:
if (val <= 3) return 3;
break;
case 2:
if (val <= 2) return 2;
break;
case 3:
if (val <= 1) return 1;
break;
}
break;
case 7: // N
switch (q) {
case -2:
if (val <= 1) return 1;
break;
case -1:
if (val <= 2) return 2;
break;
case 0:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 1:
if (val <= 4) return 4;
break;
case 2:
if (val <= 3) return 3;
break;
case 3:
if (val <= 2) return 2;
break;
case 4:
if (val <= 1) return 1;
break;
}
break;
case 8: // O
switch (q) {
case -1:
if (val <= 1) return 1;
break;
case 0:
if (val <= 2) return 2;
break;
case 1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 2:
if (val <= 4) return 4;
break;
case 3:
if (val <= 3) return 3;
break;
case 4:
if (val <= 2) return 2;
break;
case 5:
if (val <= 1) return 1;
break;
}
break;
case 9: // F
switch (q) {
case 0:
if (val <= 1) return 1;
break;
case 1:
if (val <= 2) return 2;
break;
case 2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 3:
if (val <= 4) return 4;
break;
case 4:
if (val <= 3) return 3;
break;
case 5:
if (val <= 2) return 2;
break;
case 6:
if (val <= 1) return 1;
break;
}
break;
case 13: // Al
switch (q) {
case -4:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -3:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case -2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case -1:
if (val <= 4) return 4;
break;
case 0:
if (val <= 3) return 3;
break;
case 1:
if (val <= 2) return 2;
break;
case 2:
if (val <= 1) return 1;
break;
}
break;
case 14: // Si
switch (q) {
case -3:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -2:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case -1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 0:
if (val <= 4) return 4;
break;
case 1:
if (val <= 3) return 3;
break;
case 2:
if (val <= 2) return 2;
break;
case 3:
if (val <= 1) return 1;
break;
}
break;
case 15: // P
switch (q) {
case -2:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -1:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 0:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 1:
if (val <= 4) return 4;
break;
case 2:
if (val <= 3) return 3;
break;
case 3:
if (val <= 2) return 2;
break;
case 4:
if (val <= 1) return 1;
break;
}
break;
case 16: // S
switch (q) {
case -1:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case 0:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 2:
if (val <= 4) return 4;
break;
case 3:
if (val <= 3) return 3;
break;
case 4:
if (val <= 2) return 2;
break;
case 5:
if (val <= 1) return 1;
break;
}
break;
case 17: // Cl
switch (q) {
case 0:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case 1:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 3:
if (val <= 4) return 4;
break;
case 4:
if (val <= 3) return 3;
break;
case 5:
if (val <= 2) return 2;
break;
case 6:
if (val <= 1) return 1;
break;
}
break;
case 31: // Ga
switch (q) {
case -4:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -3:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case -2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case -1:
if (val <= 4) return 4;
break;
case 0:
if (val <= 3) return 3;
break;
case 2:
if (val <= 1) return 1;
break;
}
break;
case 32: // Ge
switch (q) {
case -3:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -2:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case -1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 0:
if (val <= 4) return 4;
break;
case 1:
if (val <= 3) return 3;
break;
case 3:
if (val <= 1) return 1;
break;
}
break;
case 33: // As
switch (q) {
case -2:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -1:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 0:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 1:
if (val <= 4) return 4;
break;
case 2:
if (val <= 3) return 3;
break;
case 4:
if (val <= 1) return 1;
break;
}
break;
case 34: // Se
switch (q) {
case -1:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case 0:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 2:
if (val <= 4) return 4;
break;
case 3:
if (val <= 3) return 3;
break;
case 5:
if (val <= 1) return 1;
break;
}
break;
case 35: // Br
switch (q) {
case 0:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case 1:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 3:
if (val <= 4) return 4;
break;
case 4:
if (val <= 3) return 3;
break;
case 6:
if (val <= 1) return 1;
break;
}
break;
case 49: // In
switch (q) {
case -4:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -3:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case -2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case -1:
if (val <= 2) return 2;
if (val <= 4) return 4;
break;
case 0:
if (val <= 3) return 3;
break;
case 2:
if (val <= 1) return 1;
break;
}
break;
case 50: // Sn
case 82: // Pb
switch (q) {
case -3:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -2:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case -1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 0:
if (val <= 2) return 2;
if (val <= 4) return 4;
break;
case 1:
if (val <= 3) return 3;
break;
case 3:
if (val <= 1) return 1;
break;
}
break;
case 51: // Sb
case 83: // Bi
switch (q) {
case -2:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -1:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 0:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 1:
if (val <= 2) return 2;
if (val <= 4) return 4;
break;
case 2:
if (val <= 3) return 3;
break;
case 4:
if (val <= 1) return 1;
break;
}
break;
case 52: // Te
case 84: // Po
switch (q) {
case -1:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case 0:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 1:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 2:
if (val <= 2) return 2;
if (val <= 4) return 4;
break;
case 3:
if (val <= 3) return 3;
break;
case 5:
if (val <= 1) return 1;
break;
}
break;
case 53: // I
case 85: // At
switch (q) {
case 0:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case 1:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case 2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case 3:
if (val <= 2) return 2;
if (val <= 4) return 4;
break;
case 4:
if (val <= 3) return 3;
break;
case 6:
if (val <= 1) return 1;
break;
}
break;
case 81: // Tl
switch (q) {
case -4:
if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7;
break;
case -3:
if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6;
break;
case -2:
if (val <= 3) return 3;
if (val <= 5) return 5;
break;
case -1:
if (val <= 2) return 2;
if (val <= 4) return 4;
break;
case 0:
if (val <= 1) return 1;
if (val <= 3) return 3;
break;
}
break;
}
return val;
}
}
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