> edges2 = new ArrayList<>(root2.getEdges());
edges2.remove(findDoubleBond(edges2, digraph.getMol()));
removeDuplicatedEdges(edges2);
Priority priority2 = comp.sort(root2, edges2);
if (!priority2.isUnique())
return Descriptor.Unknown;
A[] carriers = getCarriers();
int config = getConfig();
// swap
if (carriers[0].equals(edges1.get(0).getEnd().getAtom()) !=
carriers[1].equals(edges2.get(0).getEnd().getAtom()))
config ^= 0x3;
Stats.INSTANCE.countRule(Math.max(priority1.getRuleIdx(), priority2.getRuleIdx()));
if (config == TOGETHER) {
if (priority1.isPseduoAsymettric() !=
priority2.isPseduoAsymettric())
return Descriptor.seqCis;
else
return Descriptor.Z;
} else if (config == OPPOSITE) {
if (priority1.isPseduoAsymettric() !=
priority2.isPseduoAsymettric())
return Descriptor.seqTrans;
else
return Descriptor.E;
}
return Descriptor.Unknown;
}
}
centres-1.4/core/src/main/java/com/simolecule/centres/config/ExtendedTetrahedral.java 0000664 0000000 0000000 00000025654 15167150676 0031051 0 ustar 00root root 0000000 0000000 /*
* Copyright (c) 2020 John Mayfield
*
* 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.
*
* 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 HOLDER 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.simolecule.centres.config;
import com.simolecule.centres.BaseMol;
import com.simolecule.centres.Descriptor;
import com.simolecule.centres.Digraph;
import com.simolecule.centres.Edge;
import com.simolecule.centres.Node;
import com.simolecule.centres.Stats;
import com.simolecule.centres.rules.Priority;
import com.simolecule.centres.rules.SequenceRule;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* This configurations is used to describe the extended tetrahedral specification
* of cumulated Sp2 bonds. It described in terms of two foci (the atoms at each
* end) and four carries (each attached to either end atom). The arrangement of the
* carriers can either be {@link #LEFT} or {@link #RIGHT}.
* Importantly carrier[0,1] should be bonded to foci[1] and carrier[1,2] to
* foci[1]. The first foci, foci[0], is used to determine where the label is
* set.
*
*
* c[0] c[2]
* \ /
* \ /
* f[1] == f[0] == f[2]
* / \
* / \
* c[1] c[3]
*
*
* The relative position of the carriers is described the same as {@link Tetrahedral}
* as if the foci where all laid on top of each other:
*
*
* c[0] c[2]
* \ /
* \ / - if the bond f[2]..c[0] pointed towards us the carriers
* f[1,0,2] c[1..3] are arranged clockwise/right-handed
* / \ - if the bond f[2]..c[0] pointed away from us the carriers
* / \ c[1..3] are arranged anti-clockwise/left-handed
* c[1] c[3]
*
*
* You can handle extended tetrahedrals > 3 atoms by only including the middle
* and end atoms.
*
*
* c[0] c[2]
* \ /
* \ /
* f[1] == x == f[0] == x == f[2]
* / \
* / \
* c[1] c[3]
*
*
* To handle implicit hydrogens you should use the "foci" of the atom the
* hydrogen is attached to. For example:
*
*
* H H
* \ /
* \ /
* f[1] == f[0] == f[2]
* / \
* / \
* c[1] c[3]
*
*
* We use the f[1] and f[2] as place holders.
*
*
* f[1] f[2]
* \ /
* \ /
* f[1] == f[0] == f[2]
* / \
* / \
* c[1] c[3]
*
*
* For this input SMILES the arguments are shown below:
*
* [CH3:1][CH:2]=[C@:3]=[CH:4][CH3:5]
* foci: [C@:3], [CH:2], [CH:4]
* carriers: [CH3:1], [CH:2] (ImplH), [CH:4] (ImplH), [CH3:5]
*
* Note the ordering is important:
*
* [CH:2]([CH3:1])=[C@:3]=[CH:4][CH3:5]
* foci: [C@:3], [CH:2], [CH:4]
* carriers: [CH:2] (ImplH), [CH3:1], [CH:4] (ImplH), [CH3:5]
*
* A longer extended tetrahedral example:
*
* [CH3:1][CH:2]=C=[C@:3]=C=[CH:4][CH3:5]
* foci: [C@:3], [CH:2], [CH:4]
* carriers: [CH3:1], [CH:2] (ImplH), [CH:4] (ImplH), [CH3:5]
*
*
*
* @param the atom class
* @param the bond class
*/
public final class ExtendedTetrahedral extends Configuration {
public static final int LEFT = 0x1;
public static final int RIGHT = 0x2;
public ExtendedTetrahedral(A[] foci, A[] carriers, int cfg)
{
super(foci, carriers, cfg);
if (foci.length != 3)
throw new IllegalArgumentException("Only X=X=X cumulenes are currently supported.");
}
@Override
public void setPrimaryLabel(BaseMol mol, Descriptor desc)
{
// we store the label on the middle atom
mol.setAtomProp(getFocus(), BaseMol.CIP_LABEL_KEY, desc);
}
private List> getEdges(Node node) {
List> edges = node.getEdges();
List> res = new ArrayList<>();
for (Edge edge : edges) {
if (!edge.getBeg().equals(node))
continue;
if (edge.getEnd().isDuplicate())
continue;
res.add(edge);
}
return res;
}
private Node findOther(Node node, Node skip) {
BaseMol mol = node.getDigraph().getMol();
for (Edge e : getEdges(node)) {
if (e.getEnd().equals(skip))
continue;
if (e.getBond() == null ||
mol.getBondOrder(e.getBond()) != 2)
continue;
return e.getEnd();
}
return null;
}
private Node[] getEnds(Node root) {
List> edges = getEdges(root);
Node pEnd1 = root;
Node pEnd2 = root;
Node end1 = edges.get(0).getEnd();
Node end2 = edges.get(1).getEnd();
Node tmp;
while (end1 != null && end2 != null) {
tmp = findOther(end1, pEnd1);
pEnd1 = end1;
end1 = tmp;
tmp = findOther(end2, pEnd2);
pEnd2 = end2;
end2 = tmp;
}
return (Node[]) new Node[]{pEnd1, pEnd2};
}
@Override
public Descriptor label(SequenceRule comp)
{
Digraph digraph = getDigraph();
Node root;
if (digraph.getRoot() == null)
root = digraph.init(getFocus());
else
root = digraph.getRoot();
digraph.changeRoot(root);
Node[] ends = getEnds(root);
Node end1 = ends[0];
Node end2 = ends[1];
A atom1 = getFoci()[1];
A atom2 = getFoci()[2];
// swap to make things easier when comparing to reference ordering
if (end1.getAtom() == atom2 && end2.getAtom() == atom1) {
A tmp = atom1;
atom1 = atom2;
atom2 = tmp;
} else if (end1.getAtom() != atom1 && end2.getAtom() != atom2) {
System.err.println("Stereo Focus mismatch!");
return Descriptor.Unknown;
}
return label2(comp, end1, end2, atom1, atom2, getEdges(end1), getEdges(end2));
}
private void removeDuplicates(List> e) {
Iterator> iter = e.iterator();
while (iter.hasNext()) {
if (iter.next().getEnd().isDuplicate())
iter.remove();
}
}
@Override
public Descriptor label(Node node,
Digraph digraph,
SequenceRule comp) {
A[] foci = getFoci();
A focus = foci[0];
if (focus != node.getAtom())
return Descriptor.Unknown;
Node root = node;
digraph.changeRoot(root);
List> edges = root.getEdges();
removeDuplicates(edges);
if (edges.size() != 2)
return Descriptor.Unknown;
Node end1 = edges.get(0).getEnd();
Node end2 = edges.get(1).getEnd();
A atom1 = getFoci()[1];
A atom2 = getFoci()[2];
// swap to make things easier when comparing to reference ordering
if (end1.getAtom() == atom2 && end2.getAtom() == atom1) {
A tmp = atom1;
atom1 = atom2;
atom2 = tmp;
} else if (end1.getAtom() != atom1 && end2.getAtom() != atom2) {
System.err.println("Stereo Focus mismatch!");
return Descriptor.Unknown;
}
List> edges1 = new ArrayList<>(end1.getEdges());
List> edges2 = new ArrayList<>(end2.getEdges());
removeDuplicates(edges1);
removeDuplicates(edges2);
edges1.remove(edges.get(0));
edges2.remove(edges.get(1));
return label2(comp, end1, end2, atom1, atom2, edges1, edges2);
}
private Descriptor label2(SequenceRule comp,
Node end1, Node end2,
A atom1, A atom2,
List> edges1,
List> edges2) {
if (edges1.size() > 2)
return Descriptor.Unknown;
if (edges2.size() > 2)
return Descriptor.Unknown;
BaseMol mol = end1.getDigraph().getMol();
end1.getDigraph().changeRoot(end1);
Priority priority1 = comp.sort(end1, edges1);
end2.getDigraph().changeRoot(end2);
Priority priority2 = comp.sort(end2, edges2);
if (!priority1.isUnique() && !priority2.isUnique() &&
mol.isInRing(edges1.get(0).getBond()) &&
mol.isInRing(edges2.get(0).getBond())) {
end1.getDigraph().setRule6Ref(edges1.get(0).getEnd().getAtom());
priority1 = comp.sort(end1, edges1);
priority2 = comp.sort(end2, edges2);
end1.getDigraph().setRule6Ref(null);
}
if (!priority1.isUnique() || !priority2.isUnique())
return Descriptor.Unknown;
Object[] ordered = new Object[4];
ordered[0] = edges1.get(0).getEnd().getAtom();
ordered[1] = edges1.size() > 1 ? edges1.get(1).getEnd().getAtom() : atom1;
ordered[2] = edges2.get(0).getEnd().getAtom();
ordered[3] = edges2.size() > 1 ? edges2.get(1).getEnd().getAtom() : atom2;
if (ordered[1] == null)
ordered[1] = atom1;
if (ordered[3] == null)
ordered[3] = atom2;
int parity = parity4(ordered, getCarriers());
if (parity == 0)
return Descriptor.Unknown;
// throw new RuntimeException("Could not calculate parity! Carrier mismatch");
int config = this.getConfig();
if (parity == 1)
config ^= 0x3;
Stats.INSTANCE.countRule(Math.max(priority1.getRuleIdx(),
priority2.getRuleIdx()));
if (config == RIGHT) {
if (priority1.isPseduoAsymettric() != priority2.isPseduoAsymettric())
return Descriptor.m;
else
return Descriptor.M;
} else if (config == LEFT) {
if (priority1.isPseduoAsymettric() != priority2.isPseduoAsymettric())
return Descriptor.p;
else
return Descriptor.P;
}
return null;
}
}
centres-1.4/core/src/main/java/com/simolecule/centres/config/Octahedral.java 0000664 0000000 0000000 00000017533 15167150676 0027174 0 ustar 00root root 0000000 0000000 /*
* Copyright (c) 2020 John Mayfield
*
* 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.
*
* 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 HOLDER 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.simolecule.centres.config;
import com.simolecule.centres.BaseMol;
import com.simolecule.centres.Descriptor;
import com.simolecule.centres.Digraph;
import com.simolecule.centres.Edge;
import com.simolecule.centres.Node;
import com.simolecule.centres.rules.Priority;
import com.simolecule.centres.rules.SequenceRule;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* An octahedral configuration is described by a focus and six carriers. The
* configuration index can be a number 1..30 and describes the relative
* arrangement of the neighbours. The configs allow any possible orderings
* but to input an octahedral we can just use 1 (OH1). It looks like this,
* the axis is made of the first and last carrier 'c[0]-f-c[5]'. The remaining
* carriers c[1..4] and then ordered anti-clockwise around the focus:
*
*