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79 lines
2.4 KiB
C++
79 lines
2.4 KiB
C++
// $Id$
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//
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// Copyright (C) 2005-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include "FeatTreeUtils.h"
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#include "FeatTree.h"
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#include <vector>
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#include <algorithm>
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#include <boost/graph/graph_utility.hpp>
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namespace RDKit {
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namespace FeatTrees {
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typedef boost::property_map<FeatTreeGraph, FeatTreeEdge_t>::type
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FeatTreeEdgePMap;
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FeatTreeGraphSPtr molToBaseTree(const ROMol &mol) {
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FeatTreeGraphSPtr resGraph(new FeatTreeGraph());
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// EFF: This can almost certainly be done with a single pass through
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// the atoms and rings, for now we're just trying to get it right
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// ------ ------ ------ ------
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// add a node to the initial feature tree for each of the SSSR rings:
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// ------ ------ ------ ------
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addRingsAndConnectors(mol, *resGraph);
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// ------ ------ ------ ------
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// Reduce any fused ring systems that form cycles in
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// the FeatTree to single points:
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// ------ ------ ------ ------
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replaceCycles(*resGraph);
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// ------ ------ ------ ------
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// We have not yet added bonds between ring systems, like
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// the N-N bond in:
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// C1CN1-N1CC1
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// So loop over the rings that we currently have and add
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// those bonds as appropriate:
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// ------ ------ ------ ------
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addRingRingBonds(mol, *resGraph);
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// ------ ------ ------ ------
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// Now go through the molecule and add every non-ring atom that
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// has more than one neighbor; we include Hs in the neighbor count
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// ------ ------ ------ ------
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std::vector<unsigned int> atomIndices;
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atomIndices = addNonringAtoms(mol, *resGraph);
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// ------ ------ ------ ------
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// At this point all atom and ring nodes have been added to
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// the graph.
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// Add the atom-atom and atom-ring edges:
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// ------ ------ ------ ------
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addBondsFromNonringAtoms(mol, *resGraph, atomIndices);
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// ------ ------ ------ ------
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// Go through the graph and add zero nodes
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// (points not associated with atoms that are used to
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// break cycles caused by non-ring atoms bonding to rings)
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// ------ ------ ------ ------
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addZeroNodes(*resGraph);
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return resGraph;
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}
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void baseTreeToFeatTree(FeatTreeGraph &baseTree) {}
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} // end of namespace FeatTrees
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} // namespace RDKit
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