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Add CDK adapter layer for toolkit-agnostic graph model
New cdk/ package with 6 files implementing graph model interfaces: - CDKToolkit: ChemToolkit implementation (parsing, SMILES, MCS, aromaticity) - CDKAtomNode: AtomNode wrapping CDK IAtom - CDKBondEdge: BondEdge wrapping CDK IBond - CDKMolecularGraph: MolecularGraph wrapping CDK IAtomContainer - CDKReactionGraph: ReactionGraph wrapping CDK IReaction - CDKAdapter: bidirectional conversion bridge (fromCDK/toCDK) Users can now write adapters for RDKit, OpenBabel, etc. by implementing AtomNode, BondEdge, MolecularGraph, ReactionGraph, and ChemToolkit. Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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‎src/main/java/com/bioinceptionlabs/reactionblast/cdk/CDKAdapter.java‎

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/*
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* Copyright (C) 2007-2026 Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>.
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 2.1 of the License, or (at your option) any later version.
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*
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* This library is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with this library; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package com.bioinceptionlabs.reactionblast.cdk;
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import org.openscience.cdk.interfaces.IAtom;
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import org.openscience.cdk.interfaces.IAtomContainer;
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import org.openscience.cdk.interfaces.IBond;
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import org.openscience.cdk.interfaces.IReaction;
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import com.bioinceptionlabs.reactionblast.model.AtomNode;
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import com.bioinceptionlabs.reactionblast.model.BondEdge;
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import com.bioinceptionlabs.reactionblast.model.MolecularGraph;
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import com.bioinceptionlabs.reactionblast.model.ReactionGraph;
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/**
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* Bidirectional conversion between CDK types and graph model types.
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* Use during the Strangler Fig migration: existing CDK code wraps/unwraps
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* through this adapter as it's gradually refactored to use graph model types.
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*
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* @author Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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*/
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public final class CDKAdapter {
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private CDKAdapter() {}
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// ---- CDK → Graph Model ----
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public static MolecularGraph fromCDK(IAtomContainer mol) {
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return new CDKMolecularGraph(mol);
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}
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public static ReactionGraph fromCDK(IReaction rxn) {
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return new CDKReactionGraph(rxn);
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}
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public static AtomNode fromCDK(IAtom atom) {
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return new CDKAtomNode(atom);
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}
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public static BondEdge fromCDK(IBond bond) {
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return new CDKBondEdge(bond);
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}
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// ---- Graph Model → CDK ----
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public static IAtomContainer toCDK(MolecularGraph graph) {
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if (graph instanceof CDKMolecularGraph) {
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return ((CDKMolecularGraph) graph).getCDKContainer();
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}
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throw new IllegalArgumentException(
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"Cannot convert non-CDK MolecularGraph to IAtomContainer. "
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+ "Use CDKToolkit for CDK-based operations.");
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}
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public static IReaction toCDK(ReactionGraph rxn) {
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if (rxn instanceof CDKReactionGraph) {
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return ((CDKReactionGraph) rxn).getCDKReaction();
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}
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throw new IllegalArgumentException(
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"Cannot convert non-CDK ReactionGraph to IReaction. "
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+ "Use CDKToolkit for CDK-based operations.");
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}
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public static IAtom toCDK(AtomNode node) {
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if (node instanceof CDKAtomNode) {
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return ((CDKAtomNode) node).getCDKAtom();
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}
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throw new IllegalArgumentException(
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"Cannot convert non-CDK AtomNode to IAtom.");
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}
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public static IBond toCDK(BondEdge edge) {
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if (edge instanceof CDKBondEdge) {
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return ((CDKBondEdge) edge).getCDKBond();
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}
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throw new IllegalArgumentException(
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"Cannot convert non-CDK BondEdge to IBond.");
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}
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// ---- Type checking ----
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public static boolean isCDK(MolecularGraph graph) {
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return graph instanceof CDKMolecularGraph;
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}
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public static boolean isCDK(ReactionGraph rxn) {
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return rxn instanceof CDKReactionGraph;
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}
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}

‎src/main/java/com/bioinceptionlabs/reactionblast/cdk/CDKAtomNode.java‎

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/*
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* Copyright (C) 2007-2026 Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>.
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 2.1 of the License, or (at your option) any later version.
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*
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* This library is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with this library; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package com.bioinceptionlabs.reactionblast.cdk;
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import org.openscience.cdk.interfaces.IAtom;
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import com.bioinceptionlabs.reactionblast.model.AtomNode;
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/**
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* CDK adapter for AtomNode. Wraps a CDK IAtom as a graph node.
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*
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* @author Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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*/
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public class CDKAtomNode implements AtomNode {
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private final IAtom cdkAtom;
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public CDKAtomNode(IAtom cdkAtom) {
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if (cdkAtom == null) throw new IllegalArgumentException("CDK atom cannot be null");
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this.cdkAtom = cdkAtom;
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}
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public IAtom getCDKAtom() {
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return cdkAtom;
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}
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@Override public String getSymbol() { return cdkAtom.getSymbol(); }
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@Override public int getAtomicNumber() { return cdkAtom.getAtomicNumber() != null ? cdkAtom.getAtomicNumber() : 0; }
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@Override public Integer getFormalCharge() { return cdkAtom.getFormalCharge(); }
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@Override public Integer getMassNumber() { return cdkAtom.getMassNumber(); }
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@Override public boolean isAromatic() { return cdkAtom.isAromatic(); }
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@Override public void setAromatic(boolean aromatic) { cdkAtom.setIsAromatic(aromatic); }
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@Override public Integer getImplicitHydrogenCount() { return cdkAtom.getImplicitHydrogenCount(); }
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@Override public String getId() { return cdkAtom.getID(); }
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@Override public void setId(String id) { cdkAtom.setID(id); }
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@Override public Object getProperty(String key) { return cdkAtom.getProperty(key); }
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@Override public void setProperty(String key, Object value) { cdkAtom.setProperty(key, value); }
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@Override public boolean getFlag(int flag) { return cdkAtom.getFlag(flag); }
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@Override public void setFlag(int flag, boolean value) { cdkAtom.setFlag(flag, value); }
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@Override
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public boolean equals(Object o) {
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if (this == o) return true;
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if (o instanceof CDKAtomNode) return cdkAtom == ((CDKAtomNode) o).cdkAtom;
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return false;
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}
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@Override
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public int hashCode() {
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return System.identityHashCode(cdkAtom);
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}
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@Override
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public String toString() {
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return getSymbol() + (getId() != null ? ":" + getId() : "");
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}
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}

‎src/main/java/com/bioinceptionlabs/reactionblast/cdk/CDKBondEdge.java‎

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/*
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* Copyright (C) 2007-2026 Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>.
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 2.1 of the License, or (at your option) any later version.
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*
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* This library is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with this library; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package com.bioinceptionlabs.reactionblast.cdk;
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import org.openscience.cdk.interfaces.IBond;
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import com.bioinceptionlabs.reactionblast.model.AtomNode;
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import com.bioinceptionlabs.reactionblast.model.BondEdge;
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/**
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* CDK adapter for BondEdge. Wraps a CDK IBond as a graph edge.
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*
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* @author Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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*/
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public class CDKBondEdge implements BondEdge {
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private final IBond cdkBond;
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private final CDKAtomNode source;
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private final CDKAtomNode target;
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public CDKBondEdge(IBond cdkBond) {
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if (cdkBond == null) throw new IllegalArgumentException("CDK bond cannot be null");
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this.cdkBond = cdkBond;
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this.source = new CDKAtomNode(cdkBond.getBegin());
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this.target = new CDKAtomNode(cdkBond.getEnd());
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}
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public IBond getCDKBond() {
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return cdkBond;
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}
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@Override public AtomNode getSource() { return source; }
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@Override public AtomNode getTarget() { return target; }
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@Override
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public BondOrder getOrder() {
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if (cdkBond.getOrder() == null) return BondOrder.UNSET;
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switch (cdkBond.getOrder()) {
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case SINGLE: return BondOrder.SINGLE;
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case DOUBLE: return BondOrder.DOUBLE;
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case TRIPLE: return BondOrder.TRIPLE;
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case QUADRUPLE: return BondOrder.QUADRUPLE;
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default: return BondOrder.UNSET;
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}
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}
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@Override
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public void setOrder(BondOrder order) {
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switch (order) {
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case SINGLE: cdkBond.setOrder(IBond.Order.SINGLE); break;
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case DOUBLE: cdkBond.setOrder(IBond.Order.DOUBLE); break;
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case TRIPLE: cdkBond.setOrder(IBond.Order.TRIPLE); break;
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case QUADRUPLE: cdkBond.setOrder(IBond.Order.QUADRUPLE); break;
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default: cdkBond.setOrder(IBond.Order.UNSET); break;
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}
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}
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@Override public boolean isAromatic() { return cdkBond.isAromatic(); }
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@Override public void setAromatic(boolean aromatic) { cdkBond.setIsAromatic(aromatic); }
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@Override
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public boolean connects(AtomNode atom) {
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if (atom instanceof CDKAtomNode) {
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return cdkBond.contains(((CDKAtomNode) atom).getCDKAtom());
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}
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return false;
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}
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@Override
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public boolean equals(Object o) {
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if (this == o) return true;
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if (o instanceof CDKBondEdge) return cdkBond == ((CDKBondEdge) o).cdkBond;
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return false;
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}
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@Override
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public int hashCode() {
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return System.identityHashCode(cdkBond);
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}
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}

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