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