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Add graph-based model interfaces for toolkit abstraction
New model/ package with 5 toolkit-agnostic interfaces: - AtomNode: graph node representing an atom - BondEdge: graph edge representing a bond - MolecularGraph: labeled molecular graph (nodes + edges) - ReactionGraph: reaction as graph transformation - ChemToolkit: adapter interface + global registry Zero CDK imports in model/ package. Users can implement these for CDK, RDKit-via-JNI, OpenBabel, or any chemistry toolkit. Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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‎src/main/java/com/bioinceptionlabs/reactionblast/model/AtomNode.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.model;
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/**
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* Graph node representing an atom. Toolkit-agnostic — implementations
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* wrap CDK IAtom, RDKit Atom, OpenBabel OBAtom, etc.
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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 interface AtomNode {
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String getSymbol();
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int getAtomicNumber();
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Integer getFormalCharge();
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Integer getMassNumber();
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boolean isAromatic();
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void setAromatic(boolean aromatic);
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Integer getImplicitHydrogenCount();
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String getId();
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void setId(String id);
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Object getProperty(String key);
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void setProperty(String key, Object value);
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boolean getFlag(int flag);
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void setFlag(int flag, boolean value);
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}

‎src/main/java/com/bioinceptionlabs/reactionblast/model/BondEdge.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.model;
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/**
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* Graph edge representing a chemical bond. Toolkit-agnostic — implementations
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* wrap CDK IBond, RDKit Bond, OpenBabel OBBond, etc.
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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 interface BondEdge {
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AtomNode getSource();
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AtomNode getTarget();
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BondOrder getOrder();
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void setOrder(BondOrder order);
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boolean isAromatic();
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void setAromatic(boolean aromatic);
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boolean connects(AtomNode atom);
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enum BondOrder {
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SINGLE(1), DOUBLE(2), TRIPLE(3), QUADRUPLE(4), UNSET(0);
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private final int numeric;
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BondOrder(int numeric) {
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this.numeric = numeric;
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}
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public int numeric() {
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return numeric;
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}
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}
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}

‎src/main/java/com/bioinceptionlabs/reactionblast/model/ChemToolkit.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.model;
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import java.util.Map;
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/**
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* Toolkit adapter interface + global registry.
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* Implement this for CDK, RDKit, OpenBabel, etc.
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*
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* Usage:
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* <pre>
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* ChemToolkit.register(new CDKToolkit()); // once at startup
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* ReactionGraph rxn = ChemToolkit.get().parseReactionSmiles("CC>>CC");
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* </pre>
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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 interface ChemToolkit {
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// ---- Parsing ----
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ReactionGraph parseReactionSmiles(String smiles);
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MolecularGraph parseMoleculeSmiles(String smiles);
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// ---- Serialization ----
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String toSmiles(MolecularGraph mol);
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String toSmiles(ReactionGraph rxn);
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String toCanonicalSmiles(MolecularGraph mol);
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// ---- Perception ----
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void perceiveAtomTypes(MolecularGraph mol);
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void perceiveAromaticity(MolecularGraph mol);
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void addImplicitHydrogens(MolecularGraph mol);
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// ---- Substructure / MCS ----
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boolean isSubstructure(MolecularGraph query, MolecularGraph target);
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Map<AtomNode, AtomNode> findMCS(MolecularGraph mol1, MolecularGraph mol2);
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// ---- Factory methods ----
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MolecularGraph createMolecularGraph();
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AtomNode createAtomNode(String symbol);
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BondEdge createBondEdge(AtomNode source, AtomNode target, BondEdge.BondOrder order);
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ReactionGraph createReactionGraph();
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// ---- Global registry ----
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static ChemToolkit get() {
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return ChemToolkitRegistry.INSTANCE;
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}
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static void register(ChemToolkit toolkit) {
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ChemToolkitRegistry.INSTANCE = toolkit;
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}
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}
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/**
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* Internal holder for the global toolkit singleton.
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*/
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class ChemToolkitRegistry {
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static volatile ChemToolkit INSTANCE;
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}

‎src/main/java/com/bioinceptionlabs/reactionblast/model/MolecularGraph.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.model;
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import java.util.List;
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import java.util.Map;
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/**
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* Labeled molecular graph — nodes are atoms, edges are bonds.
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* Toolkit-agnostic — implementations wrap CDK IAtomContainer,
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* RDKit RWMol, OpenBabel OBMol, etc.
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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 interface MolecularGraph {
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int getNodeCount();
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int getEdgeCount();
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AtomNode getNode(int index);
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BondEdge getEdge(int index);
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int indexOf(AtomNode node);
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Iterable<AtomNode> nodes();
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Iterable<BondEdge> edges();
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List<BondEdge> getEdges(AtomNode node);
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List<AtomNode> getNeighbors(AtomNode node);
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BondEdge getEdge(AtomNode a, AtomNode b);
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String getId();
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void setId(String id);
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Object getProperty(String key);
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void setProperty(String key, Object value);
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MolecularGraph clone() throws CloneNotSupportedException;
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void addNode(AtomNode node);
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void addEdge(BondEdge edge);
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void removeNode(AtomNode node);
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void removeEdge(BondEdge edge);
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}

‎src/main/java/com/bioinceptionlabs/reactionblast/model/ReactionGraph.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
11+
* 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.model;
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import java.util.Map;
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/**
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* Reaction as a graph transformation: reactant graphs → product graphs
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* with atom-atom mapping between them. Toolkit-agnostic.
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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 interface ReactionGraph {
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int getReactantCount();
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int getProductCount();
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MolecularGraph getReactant(int index);
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MolecularGraph getProduct(int index);
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Iterable<MolecularGraph> getReactants();
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Iterable<MolecularGraph> getProducts();
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void addReactant(MolecularGraph mol);
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void addProduct(MolecularGraph mol);
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String getId();
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void setId(String id);
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Map<AtomNode, AtomNode> getAtomMapping();
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void setAtomMapping(Map<AtomNode, AtomNode> mapping);
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boolean isMapped();
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ReactionGraph clone() throws CloneNotSupportedException;
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}

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