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13bb831dd5
Code/ForceField/MMFF/Params.h, Code/ForceField/UFF/Params.h, Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp and Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h (I realized their uselessness thanks to a warning issued by Intel C++ compiler) - refactored O3A code - added the possibility to set weighted constraints on selected atom pairs - added an option to carry out local-only optimization
1209 lines
80 KiB
C++
1209 lines
80 KiB
C++
// $Id$
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//
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// Copyright (C) 2013-2014 Paolo Tosco
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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 "O3AAlignMolecules.h"
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#include <RDGeneral/utils.h>
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#include <Numerics/Vector.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/Conformer.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/AtomIterators.h>
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#include <Numerics/Alignment/AlignPoints.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <boost/dynamic_bitset.hpp>
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#include <boost/algorithm/string.hpp>
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#include <boost/math/special_functions/round.hpp>
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#define square(x) ((x) * (x))
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namespace RDKit {
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namespace MolAlign {
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static boost::uint8_t mmffSimMatrix[99][99] = {
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{ 1, 3, 4, 3, 0, 4, 6, 7, 5, 6, 7, 4, 5, 7, 3, 5, 6, 7, 3, 2, 0, 2, 0, 0, 6, 7, 0, 0, 0, 3, 0, 10, 0, 10, 10, 0, 3, 6, 7, 6, 8, 7, 8, 4, 7, 6, 8, 7, 10, 0, 10, 0, 6, 10, 12, 14, 12, 10, 4, 4, 6, 10, 3, 3, 6, 6, 8, 8, 8, 8, 0, 10, 10, 4, 5, 10, 10, 3, 6, 10, 12, 8, 0, 0, 0, 0, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 },
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{ 3, 1, 2, 2, 0, 5, 6, 7, 3, 5, 7, 4, 5, 7, 3, 4, 5, 6, 3, 2, 0, 2, 0, 0, 5, 8, 0, 0, 0, 2, 0, 10, 0, 8, 10, 0, 2, 4, 5, 5, 6, 4, 7, 4, 6, 5, 7, 6, 10, 0, 8, 0, 4, 10, 12, 14, 12, 10, 4, 3, 5, 10, 2, 2, 4, 4, 7, 7, 7, 8, 0, 10, 8, 3, 4, 10, 10, 2, 4, 10, 12, 7, 0, 0, 0, 0, 8, 8, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8 },
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{ 4, 2, 1, 2, 0, 7, 7, 8, 2, 5, 7, 4, 5, 7, 5, 5, 3, 4, 4, 4, 0, 4, 0, 0, 4, 8, 0, 0, 0, 2, 0, 10, 0, 8, 12, 0, 2, 4, 6, 6, 4, 8, 8, 6, 6, 3, 8, 7, 8, 0, 6, 0, 6, 8, 10, 12, 10, 8, 6, 6, 3, 12, 2, 2, 6, 6, 4, 4, 4, 10, 0, 12, 5, 3, 6, 12, 12, 2, 4, 7, 10, 5, 0, 0, 0, 0, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6 },
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{ 3, 2, 2, 1, 0, 5, 6, 7, 4, 5, 7, 4, 5, 7, 3, 4, 5, 6, 3, 2, 0, 2, 0, 0, 5, 8, 0, 0, 0, 2, 0, 10, 0, 8, 10, 0, 2, 4, 5, 5, 6, 4, 7, 4, 6, 5, 7, 6, 10, 0, 8, 0, 4, 10, 12, 14, 12, 10, 4, 3, 5, 10, 2, 2, 4, 4, 7, 7, 7, 8, 0, 10, 8, 3, 4, 10, 10, 2, 4, 10, 12, 7, 0, 0, 0, 0, 8, 8, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8 },
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{ 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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{ 4, 5, 7, 5, 0, 1, 3, 5, 4, 5, 6, 5, 5, 6, 2, 4, 7, 7, 5, 4, 0, 4, 0, 0, 7, 6, 0, 0, 0, 4, 0, 5, 0, 12, 5, 0, 6, 6, 4, 4, 6, 4, 4, 4, 7, 6, 6, 6, 4, 0, 6, 0, 5, 12, 14, 16, 14, 12, 2, 4, 8, 6, 6, 6, 4, 4, 8, 8, 8, 3, 0, 6, 6, 7, 6, 6, 8, 5, 4, 12, 10, 8, 0, 0, 0, 0, 14, 14, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14 },
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{ 6, 6, 7, 6, 0, 3, 1, 6, 3, 5, 6, 5, 5, 6, 4, 2, 7, 7, 7, 6, 0, 6, 0, 0, 7, 6, 0, 0, 0, 4, 0, 4, 0, 12, 4, 0, 6, 6, 4, 4, 7, 4, 4, 5, 10, 8, 6, 5, 10, 0, 10, 0, 5, 12, 14, 16, 14, 12, 3, 4, 8, 6, 6, 6, 4, 4, 8, 8, 8, 4, 0, 6, 6, 8, 5, 6, 8, 6, 6, 12, 10, 8, 0, 0, 0, 0, 14, 14, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14 },
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{ 7, 7, 8, 7, 0, 5, 6, 1, 2, 6, 8, 7, 7, 8, 6, 7, 7, 7, 7, 7, 0, 7, 0, 0, 7, 5, 0, 0, 0, 7, 0, 12, 0, 4, 12, 0, 7, 2, 4, 2, 12, 3, 6, 7, 8, 8, 7, 7, 10, 0, 10, 0, 5, 4, 5, 5, 8, 4, 6, 6, 6, 5, 7, 7, 4, 4, 7, 7, 7, 6, 0, 10, 10, 10, 6, 6, 10, 7, 4, 7, 5, 7, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
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{ 5, 3, 2, 4, 0, 4, 3, 2, 1, 5, 8, 7, 7, 8, 6, 6, 7, 7, 7, 5, 0, 5, 0, 0, 7, 6, 0, 0, 0, 5, 0, 10, 0, 5, 10, 0, 5, 2, 4, 2, 10, 2, 5, 6, 8, 7, 5, 4, 10, 0, 8, 0, 4, 3, 3, 3, 6, 3, 5, 5, 5, 4, 5, 5, 4, 4, 7, 7, 7, 7, 0, 10, 10, 10, 3, 7, 10, 5, 4, 6, 4, 7, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
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{ 6, 5, 5, 5, 0, 5, 5, 6, 5, 1, 8, 7, 7, 8, 5, 7, 8, 8, 8, 6, 0, 6, 0, 0, 8, 6, 0, 0, 0, 6, 0, 6, 0, 8, 6, 0, 6, 3, 3, 5, 8, 3, 2, 6, 8, 7, 4, 5, 12, 0, 10, 0, 5, 6, 6, 8, 10, 5, 6, 6, 6, 3, 6, 6, 4, 4, 7, 7, 7, 8, 0, 8, 8, 10, 6, 4, 10, 6, 4, 8, 6, 7, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
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{ 7, 7, 7, 7, 0, 6, 6, 8, 8, 8, 1, 3, 4, 6, 6, 6, 10, 10, 10, 8, 0, 8, 0, 0, 8, 10, 0, 0, 0, 8, 0, 3, 0, 12, 3, 0, 7, 7, 7, 8, 4, 5, 6, 6, 10, 8, 8, 6, 12, 0, 12, 0, 10, 12, 12, 14, 12, 12, 5, 6, 8, 5, 7, 7, 6, 6, 10, 10, 10, 5, 0, 4, 6, 10, 6, 3, 5, 7, 6, 12, 14, 10, 0, 0, 0, 0, 14, 14, 3, 4, 5, 14, 14, 14, 14, 14, 14, 14, 14 },
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{ 4, 4, 4, 4, 0, 5, 5, 7, 7, 7, 3, 1, 2, 3, 4, 4, 8, 8, 6, 6, 0, 6, 0, 0, 7, 8, 0, 0, 0, 6, 0, 4, 0, 10, 4, 0, 5, 5, 5, 6, 5, 4, 5, 4, 8, 7, 7, 6, 10, 0, 10, 0, 10, 12, 12, 14, 12, 12, 4, 5, 8, 6, 5, 5, 5, 5, 10, 10, 10, 6, 0, 4, 6, 10, 6, 4, 4, 5, 5, 12, 14, 10, 0, 0, 0, 0, 12, 12, 4, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12 },
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{ 5, 5, 5, 5, 0, 5, 5, 7, 7, 7, 4, 2, 1, 2, 4, 4, 8, 8, 6, 6, 0, 6, 0, 0, 7, 8, 0, 0, 0, 6, 0, 4, 0, 10, 4, 0, 5, 5, 5, 6, 5, 4, 5, 4, 8, 7, 7, 6, 10, 0, 10, 0, 10, 12, 12, 14, 12, 12, 4, 5, 8, 6, 5, 5, 5, 5, 10, 10, 10, 6, 0, 4, 6, 10, 6, 4, 4, 5, 5, 12, 14, 10, 0, 0, 0, 0, 12, 12, 5, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12 },
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{ 7, 7, 7, 7, 0, 6, 6, 8, 8, 8, 6, 3, 2, 1, 4, 4, 7, 7, 8, 8, 0, 8, 0, 0, 8, 10, 0, 0, 0, 8, 0, 6, 0, 12, 6, 0, 7, 7, 7, 8, 5, 6, 6, 4, 10, 8, 8, 6, 10, 0, 10, 0, 10, 12, 12, 14, 14, 14, 6, 6, 10, 6, 7, 7, 7, 7, 10, 10, 10, 10, 0, 5, 7, 8, 8, 5, 5, 7, 7, 12, 14, 10, 0, 0, 0, 0, 14, 14, 8, 5, 4, 14, 14, 14, 14, 14, 14, 14, 14 },
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{ 3, 3, 5, 3, 0, 2, 4, 6, 6, 5, 6, 4, 4, 4, 1, 2, 5, 4, 5, 4, 0, 4, 0, 0, 7, 6, 0, 0, 0, 4, 0, 6, 0, 12, 6, 0, 6, 6, 5, 5, 6, 6, 5, 2, 10, 8, 6, 6, 5, 0, 7, 0, 8, 12, 12, 14, 12, 12, 3, 5, 7, 5, 6, 6, 5, 5, 10, 10, 10, 5, 0, 3, 5, 3, 6, 7, 7, 6, 5, 12, 14, 10, 0, 0, 0, 0, 14, 14, 10, 8, 7, 14, 14, 14, 14, 14, 14, 14, 14 },
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{ 5, 4, 5, 4, 0, 4, 2, 7, 6, 7, 6, 4, 4, 4, 2, 1, 5, 5, 5, 5, 0, 5, 0, 0, 7, 6, 0, 0, 0, 4, 0, 5, 0, 12, 5, 0, 5, 6, 5, 5, 3, 5, 6, 3, 10, 8, 6, 4, 10, 0, 8, 0, 8, 12, 12, 14, 12, 12, 4, 4, 8, 7, 5, 5, 5, 5, 10, 10, 10, 6, 0, 4, 7, 5, 6, 7, 8, 5, 5, 12, 14, 10, 0, 0, 0, 0, 14, 14, 10, 8, 7, 14, 14, 14, 14, 14, 14, 14, 14 },
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{ 6, 5, 3, 5, 0, 7, 7, 7, 7, 8, 10, 8, 8, 7, 5, 5, 1, 2, 5, 5, 0, 5, 0, 0, 4, 5, 0, 0, 0, 4, 0, 10, 0, 8, 12, 0, 5, 6, 7, 7, 5, 8, 8, 4, 6, 4, 8, 7, 7, 0, 6, 0, 6, 8, 10, 12, 10, 8, 6, 7, 4, 10, 5, 5, 7, 7, 6, 6, 6, 8, 0, 10, 3, 2, 6, 12, 12, 5, 7, 7, 8, 5, 0, 0, 0, 0, 6, 6, 12, 12, 12, 10, 8, 8, 8, 8, 8, 8, 8 },
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{ 7, 6, 4, 6, 0, 7, 7, 7, 7, 8, 10, 8, 8, 7, 4, 5, 2, 1, 5, 6, 0, 6, 0, 0, 3, 7, 0, 0, 0, 5, 0, 12, 0, 7, 12, 0, 5, 6, 8, 8, 3, 10, 10, 5, 3, 4, 8, 8, 6, 0, 4, 0, 4, 10, 12, 14, 6, 7, 7, 8, 5, 12, 5, 5, 8, 8, 3, 3, 3, 10, 0, 10, 2, 2, 7, 12, 12, 5, 8, 6, 8, 3, 0, 0, 0, 0, 5, 5, 12, 12, 12, 10, 8, 8, 8, 8, 8, 8, 8 },
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{ 3, 3, 4, 3, 0, 5, 7, 7, 7, 8, 10, 6, 6, 8, 5, 5, 5, 5, 1, 3, 0, 3, 0, 0, 5, 6, 0, 0, 0, 3, 0, 10, 0, 10, 10, 0, 4, 6, 7, 7, 8, 8, 10, 4, 8, 7, 8, 8, 10, 0, 10, 0, 6, 10, 12, 14, 12, 10, 4, 6, 8, 12, 4, 4, 7, 7, 8, 8, 8, 8, 0, 10, 8, 5, 5, 10, 10, 4, 7, 10, 12, 8, 0, 0, 0, 0, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 },
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{ 2, 2, 4, 2, 0, 4, 6, 7, 5, 6, 8, 6, 6, 8, 4, 5, 5, 6, 3, 1, 0, 2, 0, 0, 6, 7, 0, 0, 0, 3, 0, 10, 0, 10, 10, 0, 3, 6, 7, 6, 8, 7, 8, 4, 7, 6, 8, 7, 10, 0, 10, 0, 6, 10, 12, 14, 12, 10, 4, 4, 6, 10, 3, 3, 6, 6, 8, 8, 8, 8, 0, 10, 10, 4, 5, 10, 10, 3, 6, 10, 12, 8, 0, 0, 0, 0, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 },
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{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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{ 2, 2, 4, 2, 0, 4, 6, 7, 5, 6, 8, 6, 6, 8, 4, 5, 5, 6, 3, 2, 0, 1, 0, 0, 6, 7, 0, 0, 0, 3, 0, 10, 0, 10, 10, 0, 3, 6, 7, 6, 8, 7, 8, 4, 7, 6, 8, 7, 10, 0, 10, 0, 6, 10, 12, 14, 12, 10, 4, 4, 6, 10, 3, 3, 6, 6, 8, 8, 8, 8, 0, 10, 10, 4, 5, 10, 10, 3, 6, 10, 12, 8, 0, 0, 0, 0, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 },
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{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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{ 6, 5, 4, 5, 0, 7, 7, 7, 7, 8, 8, 7, 7, 8, 7, 7, 4, 3, 5, 6, 0, 6, 0, 0, 1, 3, 0, 0, 0, 4, 0, 10, 0, 6, 12, 0, 4, 4, 6, 5, 4, 5, 7, 7, 4, 4, 8, 6, 8, 0, 7, 0, 5, 8, 10, 12, 10, 7, 7, 7, 5, 12, 4, 4, 6, 6, 4, 4, 4, 10, 0, 12, 5, 4, 3, 12, 12, 4, 6, 6, 8, 4, 0, 0, 0, 0, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6 },
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{ 7, 8, 8, 8, 0, 6, 6, 5, 6, 6, 10, 8, 8, 10, 6, 6, 5, 7, 6, 7, 0, 7, 0, 0, 3, 1, 0, 0, 0, 8, 0, 10, 0, 8, 10, 0, 7, 7, 6, 7, 12, 4, 7, 7, 10, 8, 5, 10, 12, 0, 12, 0, 7, 6, 7, 7, 10, 6, 6, 6, 8, 7, 7, 7, 6, 6, 8, 8, 8, 7, 0, 10, 10, 7, 4, 6, 8, 7, 6, 8, 6, 8, 0, 0, 0, 0, 12, 12, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12 },
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{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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{ 3, 2, 2, 2, 0, 4, 4, 7, 5, 6, 8, 6, 6, 8, 4, 4, 4, 5, 3, 3, 0, 3, 0, 0, 4, 8, 0, 0, 0, 1, 0, 10, 0, 8, 10, 0, 2, 4, 5, 5, 6, 4, 7, 4, 6, 5, 7, 7, 10, 0, 8, 0, 4, 10, 12, 14, 12, 10, 4, 3, 5, 10, 2, 2, 4, 4, 7, 7, 7, 8, 0, 10, 8, 3, 4, 10, 10, 2, 4, 10, 12, 7, 0, 0, 0, 0, 8, 8, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8 },
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|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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|
{ 10, 10, 10, 10, 0, 5, 4, 12, 10, 6, 3, 4, 4, 6, 6, 5, 10, 12, 10, 10, 0, 10, 0, 0, 10, 10, 0, 0, 0, 10, 0, 1, 0, 20, 2, 0, 10, 12, 8, 10, 10, 4, 6, 8, 16, 14, 6, 6, 20, 0, 20, 0, 12, 20, 20, 20, 20, 20, 7, 8, 14, 2, 10, 10, 8, 8, 16, 16, 16, 5, 0, 2, 10, 8, 10, 2, 8, 10, 8, 20, 20, 16, 0, 0, 0, 0, 20, 20, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20 },
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|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
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|
{ 10, 8, 8, 8, 0, 12, 12, 4, 5, 8, 12, 10, 10, 12, 12, 12, 8, 7, 10, 10, 0, 10, 0, 0, 6, 8, 0, 0, 0, 8, 0, 20, 0, 1, 20, 0, 14, 4, 7, 5, 16, 12, 12, 16, 6, 7, 10, 12, 3, 0, 4, 0, 4, 2, 2, 2, 4, 2, 12, 14, 6, 20, 14, 14, 16, 16, 6, 6, 6, 12, 0, 20, 16, 10, 8, 20, 20, 14, 16, 4, 2, 6, 0, 0, 0, 0, 4, 4, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4 },
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{ 10, 10, 12, 10, 0, 5, 4, 12, 10, 6, 3, 4, 4, 6, 6, 5, 12, 12, 10, 10, 0, 10, 0, 0, 12, 10, 0, 0, 0, 10, 0, 2, 0, 20, 1, 0, 10, 12, 8, 10, 10, 4, 6, 8, 16, 14, 6, 8, 20, 0, 20, 0, 12, 20, 20, 20, 20, 20, 7, 10, 14, 2, 10, 10, 8, 8, 16, 16, 16, 5, 0, 2, 10, 8, 10, 2, 8, 10, 8, 20, 20, 16, 0, 0, 0, 0, 20, 20, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20 },
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|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 3, 2, 2, 2, 0, 6, 6, 7, 5, 6, 7, 5, 5, 7, 6, 5, 5, 5, 4, 3, 0, 3, 0, 0, 4, 7, 0, 0, 0, 2, 0, 10, 0, 14, 10, 0, 1, 3, 5, 5, 5, 5, 7, 4, 7, 5, 6, 8, 14, 0, 8, 0, 7, 8, 10, 12, 10, 8, 4, 7, 7, 10, 1, 1, 5, 5, 7, 7, 7, 12, 0, 10, 6, 6, 7, 10, 10, 1, 5, 7, 12, 7, 0, 0, 0, 0, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 6, 4, 4, 4, 0, 6, 6, 2, 2, 3, 7, 5, 5, 7, 6, 6, 6, 6, 6, 6, 0, 6, 0, 0, 4, 7, 0, 0, 0, 4, 0, 12, 0, 4, 12, 0, 3, 1, 5, 3, 8, 3, 8, 6, 7, 6, 7, 7, 7, 0, 6, 0, 4, 4, 5, 8, 8, 2, 6, 8, 6, 12, 3, 3, 6, 6, 6, 6, 6, 6, 0, 12, 8, 8, 6, 12, 12, 3, 5, 8, 6, 6, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
|
|
{ 7, 5, 6, 5, 0, 4, 4, 4, 4, 3, 7, 5, 5, 7, 5, 5, 7, 8, 7, 7, 0, 7, 0, 0, 6, 6, 0, 0, 0, 5, 0, 8, 0, 7, 8, 0, 5, 5, 1, 3, 10, 5, 5, 4, 8, 7, 5, 10, 12, 0, 12, 0, 10, 12, 12, 14, 14, 12, 4, 8, 8, 8, 4, 4, 2, 2, 8, 8, 8, 10, 0, 10, 10, 10, 6, 8, 10, 12, 4, 7, 4, 8, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
|
|
{ 6, 5, 6, 5, 0, 4, 4, 2, 2, 5, 8, 6, 6, 8, 5, 5, 7, 8, 7, 6, 0, 6, 0, 0, 5, 7, 0, 0, 0, 5, 0, 10, 0, 5, 10, 0, 5, 3, 3, 1, 10, 8, 8, 8, 10, 8, 5, 8, 10, 0, 10, 0, 8, 6, 5, 7, 8, 5, 8, 10, 8, 8, 7, 7, 5, 5, 7, 7, 7, 8, 0, 10, 10, 10, 8, 10, 12, 7, 5, 6, 5, 7, 0, 0, 0, 0, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12 },
|
|
{ 8, 6, 4, 6, 0, 6, 7, 12, 10, 8, 4, 5, 5, 5, 6, 3, 5, 3, 8, 8, 0, 8, 0, 0, 4, 12, 0, 0, 0, 6, 0, 10, 0, 16, 10, 0, 5, 8, 10, 10, 1, 8, 8, 10, 4, 5, 8, 10, 12, 0, 12, 0, 8, 12, 12, 14, 10, 12, 10, 8, 8, 10, 5, 5, 8, 8, 4, 4, 4, 8, 0, 8, 3, 6, 10, 4, 4, 5, 8, 10, 12, 4, 0, 0, 0, 0, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 7, 4, 8, 4, 0, 4, 4, 3, 2, 3, 5, 4, 4, 6, 6, 5, 8, 10, 8, 7, 0, 7, 0, 0, 5, 4, 0, 0, 0, 4, 0, 4, 0, 12, 4, 0, 5, 3, 5, 8, 8, 1, 6, 7, 8, 7, 4, 6, 12, 0, 12, 0, 7, 8, 12, 12, 14, 12, 7, 5, 7, 8, 5, 5, 4, 4, 10, 10, 10, 5, 0, 5, 8, 8, 3, 4, 8, 5, 4, 14, 12, 10, 0, 0, 0, 0, 14, 14, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 8, 7, 8, 7, 0, 4, 4, 6, 5, 2, 6, 5, 5, 6, 5, 6, 8, 10, 10, 8, 0, 8, 0, 0, 7, 7, 0, 0, 0, 7, 0, 6, 0, 12, 6, 0, 7, 8, 5, 8, 8, 6, 1, 8, 8, 8, 6, 8, 10, 0, 8, 0, 7, 7, 8, 10, 12, 7, 8, 8, 10, 3, 5, 5, 4, 4, 10, 10, 10, 6, 0, 7, 10, 10, 6, 4, 10, 5, 4, 12, 10, 10, 0, 0, 0, 0, 12, 12, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12 },
|
|
{ 4, 4, 6, 4, 0, 4, 5, 7, 6, 6, 6, 4, 4, 4, 2, 3, 4, 5, 4, 4, 0, 4, 0, 0, 7, 7, 0, 0, 0, 4, 0, 8, 0, 16, 8, 0, 4, 6, 4, 8, 10, 7, 8, 1, 10, 8, 6, 8, 5, 0, 7, 0, 8, 10, 10, 12, 12, 10, 2, 7, 10, 8, 4, 4, 3, 3, 10, 10, 10, 6, 0, 6, 8, 8, 7, 7, 10, 4, 3, 12, 12, 10, 0, 0, 0, 0, 14, 14, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 7, 6, 6, 6, 0, 7, 10, 8, 8, 8, 10, 8, 8, 10, 10, 10, 6, 3, 8, 7, 0, 7, 0, 0, 4, 10, 0, 0, 0, 6, 0, 16, 0, 6, 16, 0, 7, 7, 8, 10, 4, 8, 8, 10, 1, 3, 10, 10, 4, 0, 4, 0, 4, 8, 10, 12, 12, 8, 10, 12, 8, 12, 7, 7, 8, 8, 4, 4, 4, 10, 0, 12, 4, 5, 7, 10, 8, 7, 8, 12, 12, 4, 0, 0, 0, 0, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 6, 5, 3, 5, 0, 6, 8, 8, 7, 7, 8, 7, 7, 8, 8, 8, 4, 4, 7, 6, 0, 6, 0, 0, 4, 8, 0, 0, 0, 5, 0, 14, 0, 7, 14, 0, 5, 6, 7, 8, 5, 7, 8, 8, 3, 1, 8, 8, 8, 0, 7, 0, 6, 6, 8, 10, 10, 8, 6, 8, 6, 8, 5, 5, 8, 8, 3, 3, 3, 10, 0, 12, 3, 4, 7, 10, 8, 5, 8, 10, 10, 3, 0, 0, 0, 0, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 8, 7, 8, 7, 0, 6, 6, 7, 5, 4, 8, 7, 7, 8, 6, 6, 8, 8, 8, 8, 0, 8, 0, 0, 8, 5, 0, 0, 0, 7, 0, 6, 0, 10, 6, 0, 6, 7, 5, 5, 8, 4, 6, 6, 10, 8, 1, 4, 10, 0, 10, 0, 5, 8, 8, 10, 12, 8, 6, 5, 8, 5, 6, 6, 5, 5, 8, 8, 8, 6, 0, 6, 8, 8, 5, 4, 8, 6, 5, 12, 10, 8, 0, 0, 0, 0, 14, 14, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 7, 6, 7, 6, 0, 6, 5, 7, 4, 5, 6, 6, 6, 6, 6, 4, 7, 8, 8, 7, 0, 7, 0, 0, 6, 10, 0, 0, 0, 7, 0, 6, 0, 12, 8, 0, 8, 7, 10, 8, 10, 6, 8, 8, 10, 8, 4, 1, 10, 0, 10, 0, 8, 10, 10, 12, 14, 10, 6, 7, 10, 7, 8, 8, 6, 6, 10, 10, 10, 8, 0, 6, 10, 10, 4, 7, 10, 8, 6, 14, 12, 10, 0, 0, 0, 0, 14, 14, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 10, 10, 8, 10, 0, 4, 10, 10, 10, 12, 12, 10, 10, 10, 5, 10, 7, 6, 10, 10, 0, 10, 0, 0, 8, 12, 0, 0, 0, 10, 0, 20, 0, 3, 20, 0, 14, 7, 12, 10, 12, 12, 10, 5, 4, 8, 10, 10, 1, 0, 2, 0, 8, 4, 4, 5, 6, 3, 4, 8, 6, 20, 14, 14, 16, 16, 4, 4, 4, 3, 0, 20, 8, 7, 10, 20, 16, 14, 16, 6, 5, 4, 0, 0, 0, 0, 6, 6, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6 },
|
|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 10, 8, 6, 8, 0, 6, 10, 10, 8, 10, 12, 10, 10, 10, 7, 8, 6, 4, 10, 10, 0, 10, 0, 0, 7, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 8, 6, 12, 10, 12, 12, 8, 7, 4, 7, 10, 10, 2, 0, 1, 0, 6, 2, 5, 7, 8, 5, 8, 8, 12, 20, 8, 8, 10, 10, 7, 7, 7, 6, 0, 20, 10, 10, 8, 20, 16, 8, 10, 8, 7, 7, 0, 0, 0, 0, 6, 6, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6 },
|
|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 6, 4, 6, 4, 0, 5, 5, 5, 4, 5, 10, 10, 10, 10, 8, 8, 6, 4, 6, 6, 0, 6, 0, 0, 5, 7, 0, 0, 0, 4, 0, 12, 0, 4, 12, 0, 7, 4, 10, 8, 8, 7, 7, 8, 4, 6, 5, 8, 8, 0, 6, 0, 1, 4, 6, 8, 10, 4, 10, 8, 5, 14, 7, 7, 8, 8, 4, 4, 4, 10, 0, 12, 6, 6, 8, 12, 10, 7, 8, 10, 8, 4, 0, 0, 0, 0, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 10, 10, 8, 10, 0, 12, 12, 4, 3, 6, 12, 12, 12, 12, 12, 12, 8, 10, 10, 10, 0, 10, 0, 0, 8, 6, 0, 0, 0, 10, 0, 20, 0, 2, 20, 0, 8, 4, 12, 6, 12, 8, 7, 10, 8, 6, 8, 10, 4, 0, 2, 0, 4, 1, 2, 2, 4, 2, 10, 10, 6, 20, 8, 8, 10, 10, 4, 4, 4, 10, 0, 20, 10, 10, 8, 20, 16, 8, 10, 4, 2, 4, 0, 0, 0, 0, 5, 5, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5 },
|
|
{ 12, 12, 10, 12, 0, 14, 14, 5, 3, 6, 12, 12, 12, 12, 12, 12, 10, 12, 12, 12, 0, 12, 0, 0, 10, 7, 0, 0, 0, 12, 0, 20, 0, 2, 20, 0, 10, 5, 12, 5, 12, 12, 8, 10, 10, 8, 8, 10, 4, 0, 5, 0, 6, 2, 1, 2, 4, 2, 10, 10, 6, 20, 8, 8, 10, 10, 4, 4, 4, 10, 0, 20, 10, 10, 8, 20, 16, 8, 10, 4, 2, 4, 0, 0, 0, 0, 5, 5, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5 },
|
|
{ 14, 14, 12, 14, 0, 16, 16, 5, 3, 8, 14, 14, 14, 14, 14, 14, 12, 14, 14, 14, 0, 14, 0, 0, 12, 7, 0, 0, 0, 14, 0, 20, 0, 2, 20, 0, 12, 8, 14, 7, 14, 12, 10, 12, 12, 10, 10, 12, 5, 0, 7, 0, 8, 2, 2, 1, 3, 3, 12, 12, 8, 20, 10, 10, 12, 12, 8, 8, 8, 12, 0, 20, 14, 14, 12, 20, 20, 10, 12, 4, 2, 8, 0, 0, 0, 0, 8, 8, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 12, 12, 10, 12, 0, 14, 14, 8, 6, 10, 12, 12, 12, 14, 12, 12, 10, 6, 12, 12, 0, 12, 0, 0, 10, 10, 0, 0, 0, 12, 0, 20, 0, 4, 20, 0, 10, 8, 14, 8, 10, 14, 12, 12, 12, 10, 12, 14, 6, 0, 8, 0, 10, 4, 4, 3, 1, 5, 12, 12, 10, 20, 8, 8, 14, 14, 10, 10, 10, 12, 0, 20, 12, 12, 12, 20, 20, 8, 14, 2, 4, 10, 0, 0, 0, 0, 8, 8, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 10, 10, 8, 10, 0, 12, 12, 4, 3, 5, 12, 12, 12, 14, 12, 12, 8, 7, 10, 10, 0, 10, 0, 0, 7, 6, 0, 0, 0, 10, 0, 20, 0, 2, 20, 0, 8, 2, 12, 5, 12, 12, 7, 10, 8, 8, 8, 10, 3, 0, 5, 0, 4, 2, 2, 3, 5, 1, 10, 12, 6, 20, 8, 8, 12, 12, 8, 8, 8, 12, 0, 20, 12, 12, 10, 20, 20, 8, 12, 5, 3, 8, 0, 0, 0, 0, 10, 10, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 4, 4, 6, 4, 0, 2, 3, 6, 5, 6, 5, 4, 4, 6, 3, 4, 6, 7, 4, 4, 0, 4, 0, 0, 7, 6, 0, 0, 0, 4, 0, 7, 0, 12, 7, 0, 4, 6, 4, 8, 10, 7, 8, 2, 10, 6, 6, 6, 4, 0, 8, 0, 10, 10, 10, 12, 12, 10, 1, 7, 10, 8, 4, 4, 3, 3, 10, 10, 10, 4, 0, 7, 10, 10, 7, 7, 10, 4, 3, 12, 12, 10, 0, 0, 0, 0, 14, 14, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 4, 3, 6, 3, 0, 4, 4, 6, 5, 6, 6, 5, 5, 6, 5, 4, 7, 8, 6, 4, 0, 4, 0, 0, 7, 6, 0, 0, 0, 3, 0, 8, 0, 14, 10, 0, 7, 8, 8, 10, 8, 5, 8, 7, 12, 8, 5, 7, 8, 0, 8, 0, 8, 10, 10, 12, 12, 12, 7, 1, 5, 7, 7, 7, 7, 7, 12, 12, 12, 8, 0, 8, 10, 10, 7, 6, 10, 7, 7, 8, 12, 12, 0, 0, 0, 0, 14, 14, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 6, 5, 3, 5, 0, 8, 8, 6, 5, 6, 8, 8, 8, 10, 7, 8, 4, 5, 8, 6, 0, 6, 0, 0, 5, 8, 0, 0, 0, 5, 0, 14, 0, 6, 14, 0, 7, 6, 8, 8, 8, 7, 10, 10, 8, 6, 8, 10, 6, 0, 12, 0, 5, 6, 6, 8, 10, 6, 10, 5, 1, 10, 7, 7, 8, 8, 3, 3, 3, 8, 0, 14, 5, 5, 10, 10, 10, 7, 8, 10, 8, 10, 0, 0, 0, 0, 8, 8, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 10, 10, 12, 10, 0, 6, 6, 5, 4, 3, 5, 6, 6, 6, 5, 7, 10, 12, 12, 10, 0, 10, 0, 0, 12, 7, 0, 0, 0, 10, 0, 2, 0, 20, 2, 0, 10, 12, 8, 8, 10, 8, 3, 8, 12, 8, 5, 7, 20, 0, 20, 0, 14, 20, 20, 20, 20, 20, 8, 7, 10, 1, 10, 10, 8, 8, 20, 20, 20, 5, 0, 2, 10, 10, 7, 2, 6, 10, 8, 20, 20, 20, 0, 0, 0, 0, 20, 20, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20 },
|
|
{ 3, 2, 2, 2, 0, 6, 6, 7, 5, 6, 7, 5, 5, 7, 6, 5, 5, 5, 4, 3, 0, 3, 0, 0, 4, 7, 0, 0, 0, 2, 0, 10, 0, 14, 10, 0, 1, 3, 4, 7, 5, 5, 5, 4, 7, 5, 6, 8, 14, 0, 8, 0, 7, 8, 8, 10, 8, 8, 4, 7, 7, 10, 1, 2, 5, 5, 7, 7, 7, 12, 0, 10, 6, 6, 7, 10, 10, 2, 5, 10, 12, 7, 0, 0, 0, 0, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 3, 2, 2, 2, 0, 6, 6, 7, 5, 6, 7, 5, 5, 7, 6, 5, 5, 5, 4, 3, 0, 3, 0, 0, 4, 7, 0, 0, 0, 2, 0, 10, 0, 14, 10, 0, 1, 3, 4, 7, 5, 5, 5, 4, 7, 5, 6, 8, 14, 0, 8, 0, 7, 8, 8, 10, 8, 8, 4, 7, 7, 10, 2, 1, 5, 5, 7, 7, 7, 12, 0, 10, 6, 6, 7, 10, 10, 2, 5, 10, 12, 7, 0, 0, 0, 0, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 6, 4, 6, 4, 0, 4, 4, 4, 4, 4, 6, 5, 5, 7, 5, 5, 7, 8, 7, 6, 0, 6, 0, 0, 6, 6, 0, 0, 0, 4, 0, 8, 0, 16, 8, 0, 5, 6, 2, 5, 8, 4, 4, 3, 8, 8, 5, 6, 16, 0, 10, 0, 8, 10, 10, 12, 14, 12, 3, 7, 8, 8, 5, 5, 1, 2, 6, 6, 6, 10, 0, 8, 6, 6, 6, 8, 10, 5, 2, 6, 4, 6, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
|
|
{ 6, 4, 6, 4, 0, 4, 4, 4, 4, 4, 6, 5, 5, 7, 5, 5, 7, 8, 7, 6, 0, 6, 0, 0, 6, 6, 0, 0, 0, 4, 0, 8, 0, 16, 8, 0, 5, 6, 2, 5, 8, 4, 4, 3, 8, 8, 5, 6, 16, 0, 10, 0, 8, 10, 10, 12, 14, 12, 3, 7, 8, 8, 5, 5, 2, 1, 6, 6, 6, 10, 0, 8, 6, 6, 6, 8, 10, 5, 2, 6, 4, 6, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
|
|
{ 8, 7, 4, 7, 0, 8, 8, 7, 7, 7, 10, 10, 10, 10, 10, 10, 6, 3, 8, 8, 0, 8, 0, 0, 4, 8, 0, 0, 0, 7, 0, 16, 0, 6, 16, 0, 7, 6, 8, 7, 4, 10, 10, 10, 4, 3, 8, 10, 4, 0, 7, 0, 4, 4, 4, 8, 10, 8, 10, 12, 3, 20, 7, 7, 6, 6, 1, 2, 2, 10, 0, 20, 5, 5, 10, 20, 16, 7, 6, 8, 6, 2, 0, 0, 0, 0, 10, 10, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 8, 7, 4, 7, 0, 8, 8, 7, 7, 7, 10, 10, 10, 10, 10, 10, 6, 3, 8, 8, 0, 8, 0, 0, 4, 8, 0, 0, 0, 7, 0, 16, 0, 6, 16, 0, 7, 6, 8, 7, 4, 10, 10, 10, 4, 3, 8, 10, 4, 0, 7, 0, 4, 4, 4, 8, 10, 8, 10, 12, 3, 20, 7, 7, 6, 6, 2, 1, 2, 10, 0, 20, 5, 5, 10, 20, 16, 7, 6, 8, 6, 2, 0, 0, 0, 0, 10, 10, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 8, 7, 4, 7, 0, 8, 8, 7, 7, 7, 10, 10, 10, 10, 10, 10, 6, 3, 8, 8, 0, 8, 0, 0, 4, 8, 0, 0, 0, 7, 0, 16, 0, 6, 16, 0, 7, 6, 8, 7, 4, 10, 10, 10, 4, 3, 8, 10, 4, 0, 7, 0, 4, 4, 4, 8, 10, 8, 10, 12, 3, 20, 7, 7, 6, 6, 2, 2, 1, 10, 0, 20, 5, 5, 10, 20, 16, 7, 6, 8, 6, 2, 0, 0, 0, 0, 10, 10, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 8, 8, 10, 8, 0, 3, 4, 6, 7, 8, 5, 6, 6, 10, 5, 6, 8, 10, 8, 8, 0, 8, 0, 0, 10, 7, 0, 0, 0, 8, 0, 5, 0, 12, 5, 0, 12, 6, 10, 8, 8, 5, 6, 6, 10, 10, 6, 8, 3, 0, 6, 0, 10, 10, 10, 12, 12, 12, 4, 8, 8, 5, 12, 12, 10, 10, 10, 10, 10, 1, 0, 4, 7, 7, 6, 5, 8, 12, 10, 12, 14, 10, 0, 0, 0, 0, 10, 10, 5, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 10, 10, 12, 10, 0, 6, 6, 10, 10, 8, 4, 4, 4, 5, 3, 4, 10, 10, 10, 10, 0, 10, 0, 0, 12, 10, 0, 0, 0, 10, 0, 2, 0, 20, 2, 0, 10, 12, 10, 10, 8, 5, 7, 6, 12, 12, 6, 6, 20, 0, 20, 0, 12, 20, 20, 20, 20, 20, 7, 8, 14, 2, 10, 10, 8, 8, 20, 20, 20, 4, 0, 1, 6, 6, 8, 2, 6, 10, 10, 20, 20, 20, 0, 0, 0, 0, 20, 20, 4, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20 },
|
|
{ 10, 8, 5, 8, 0, 6, 6, 10, 10, 8, 6, 6, 6, 7, 5, 7, 3, 2, 8, 10, 0, 10, 0, 0, 5, 10, 0, 0, 0, 8, 0, 10, 0, 16, 10, 0, 6, 8, 10, 10, 3, 8, 10, 8, 4, 3, 8, 10, 8, 0, 10, 0, 6, 10, 10, 14, 12, 12, 10, 10, 5, 10, 6, 6, 6, 6, 5, 5, 5, 7, 0, 6, 1, 3, 8, 7, 5, 6, 10, 12, 14, 5, 0, 0, 0, 0, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 4, 3, 3, 3, 0, 7, 8, 10, 10, 10, 10, 10, 10, 8, 3, 5, 2, 2, 5, 4, 0, 4, 0, 0, 4, 7, 0, 0, 0, 3, 0, 8, 0, 10, 8, 0, 6, 8, 10, 10, 6, 8, 10, 8, 5, 4, 8, 10, 7, 0, 10, 0, 6, 10, 10, 14, 12, 12, 10, 10, 5, 10, 6, 6, 6, 6, 5, 5, 5, 7, 0, 6, 3, 1, 7, 10, 7, 6, 10, 7, 8, 5, 0, 0, 0, 0, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 5, 4, 6, 4, 0, 6, 5, 6, 3, 6, 6, 6, 6, 8, 6, 6, 6, 7, 5, 5, 0, 5, 0, 0, 3, 4, 0, 0, 0, 4, 0, 10, 0, 8, 10, 0, 7, 6, 6, 8, 10, 3, 6, 7, 7, 7, 5, 4, 10, 0, 8, 0, 8, 8, 8, 12, 12, 10, 7, 7, 10, 7, 7, 7, 6, 6, 10, 10, 10, 6, 0, 8, 8, 7, 1, 7, 8, 7, 6, 10, 8, 10, 0, 0, 0, 0, 10, 10, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 10, 10, 12, 10, 0, 6, 6, 6, 7, 4, 3, 4, 4, 5, 7, 7, 12, 12, 10, 10, 0, 10, 0, 0, 12, 6, 0, 0, 0, 10, 0, 2, 0, 20, 2, 0, 10, 12, 8, 10, 4, 4, 4, 7, 10, 10, 4, 7, 20, 0, 20, 0, 12, 20, 20, 20, 20, 20, 7, 6, 10, 2, 10, 10, 8, 8, 20, 20, 20, 5, 0, 2, 7, 10, 7, 1, 8, 10, 8, 20, 20, 20, 0, 0, 0, 0, 20, 20, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20 },
|
|
{ 10, 10, 12, 10, 0, 8, 8, 10, 10, 10, 5, 4, 4, 5, 7, 8, 12, 12, 10, 10, 0, 10, 0, 0, 12, 8, 0, 0, 0, 10, 0, 8, 0, 20, 8, 0, 10, 12, 10, 12, 4, 8, 10, 10, 8, 8, 8, 10, 16, 0, 16, 0, 10, 16, 16, 20, 20, 20, 10, 10, 10, 6, 10, 10, 10, 10, 16, 16, 16, 8, 0, 6, 5, 7, 8, 8, 1, 10, 10, 20, 20, 16, 0, 0, 0, 0, 10, 10, 8, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 3, 2, 2, 2, 0, 5, 6, 7, 5, 6, 7, 5, 5, 7, 6, 5, 5, 5, 4, 3, 0, 3, 0, 0, 4, 7, 0, 0, 0, 2, 0, 10, 0, 14, 10, 0, 1, 3, 12, 7, 5, 5, 5, 4, 7, 5, 6, 8, 14, 0, 8, 0, 7, 8, 8, 10, 8, 8, 4, 7, 7, 10, 2, 2, 5, 5, 7, 7, 7, 12, 0, 10, 6, 6, 7, 10, 10, 1, 5, 3, 6, 7, 0, 0, 0, 0, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14 },
|
|
{ 6, 4, 4, 4, 0, 4, 6, 4, 4, 4, 6, 5, 5, 7, 5, 5, 7, 8, 7, 6, 0, 6, 0, 0, 6, 6, 0, 0, 0, 4, 0, 8, 0, 16, 8, 0, 5, 5, 4, 5, 8, 4, 4, 3, 8, 8, 5, 6, 16, 0, 10, 0, 8, 10, 10, 12, 14, 12, 3, 7, 8, 8, 5, 5, 2, 2, 6, 6, 6, 10, 0, 10, 10, 10, 6, 8, 10, 5, 1, 6, 4, 6, 0, 0, 0, 0, 12, 12, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12 },
|
|
{ 10, 10, 7, 10, 0, 12, 12, 7, 6, 8, 12, 12, 12, 12, 12, 12, 7, 6, 10, 10, 0, 10, 0, 0, 6, 8, 0, 0, 0, 10, 0, 20, 0, 4, 20, 0, 7, 8, 7, 6, 10, 14, 12, 12, 12, 10, 12, 14, 6, 0, 8, 0, 10, 4, 4, 4, 2, 5, 12, 8, 10, 20, 10, 10, 6, 6, 8, 8, 8, 12, 0, 20, 12, 7, 10, 20, 20, 3, 6, 1, 3, 8, 0, 0, 0, 0, 8, 8, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8 },
|
|
{ 12, 12, 10, 12, 0, 10, 10, 5, 4, 6, 14, 14, 14, 14, 14, 14, 8, 8, 12, 12, 0, 12, 0, 0, 8, 6, 0, 0, 0, 12, 0, 20, 0, 2, 20, 0, 12, 6, 4, 5, 12, 12, 10, 12, 12, 10, 10, 12, 5, 0, 7, 0, 8, 2, 2, 2, 4, 3, 12, 12, 8, 20, 12, 12, 4, 4, 6, 6, 6, 14, 0, 20, 14, 8, 8, 20, 20, 6, 4, 3, 1, 6, 0, 0, 0, 0, 5, 5, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5 },
|
|
{ 8, 7, 5, 7, 0, 8, 8, 7, 7, 7, 10, 10, 10, 10, 10, 10, 5, 3, 8, 8, 0, 8, 0, 0, 4, 8, 0, 0, 0, 7, 0, 16, 0, 6, 16, 0, 7, 6, 8, 7, 4, 10, 10, 10, 4, 3, 8, 10, 4, 0, 7, 0, 4, 4, 4, 8, 10, 8, 10, 12, 10, 20, 7, 7, 6, 6, 2, 2, 2, 10, 0, 20, 5, 5, 10, 20, 16, 7, 6, 8, 6, 1, 0, 0, 0, 0, 10, 10, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10 },
|
|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 6, 5, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 1, 2, 20, 20, 20, 6, 5, 4, 4, 4, 4, 4, 4 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 6, 5, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 2, 1, 20, 20, 20, 7, 6, 5, 5, 5, 5, 5, 5 },
|
|
{ 10, 10, 12, 10, 0, 8, 8, 10, 10, 10, 3, 4, 5, 8, 10, 10, 12, 12, 10, 10, 0, 10, 0, 0, 12, 8, 0, 0, 0, 10, 0, 4, 0, 20, 4, 0, 14, 10, 10, 12, 12, 6, 8, 8, 12, 14, 8, 8, 20, 0, 20, 0, 14, 20, 20, 20, 20, 20, 7, 8, 16, 4, 14, 14, 10, 10, 20, 20, 20, 5, 0, 4, 14, 14, 7, 4, 8, 14, 10, 20, 20, 20, 0, 0, 0, 0, 20, 20, 1, 3, 4, 20, 20, 20, 20, 20, 20, 20, 20 },
|
|
{ 10, 10, 12, 10, 0, 8, 8, 10, 10, 10, 4, 3, 3, 5, 8, 8, 12, 12, 10, 10, 0, 10, 0, 0, 12, 8, 0, 0, 0, 10, 0, 4, 0, 20, 4, 0, 14, 10, 10, 12, 12, 6, 8, 8, 12, 14, 8, 8, 20, 0, 20, 0, 14, 20, 20, 20, 20, 20, 7, 8, 16, 4, 14, 14, 10, 10, 20, 20, 20, 4, 0, 3, 14, 14, 7, 4, 6, 14, 10, 20, 20, 20, 0, 0, 0, 0, 20, 20, 3, 1, 2, 20, 20, 20, 20, 20, 20, 20, 20 },
|
|
{ 10, 10, 12, 10, 0, 8, 8, 10, 10, 10, 5, 3, 3, 4, 7, 7, 12, 12, 10, 10, 0, 10, 0, 0, 12, 8, 0, 0, 0, 10, 0, 4, 0, 20, 4, 0, 14, 10, 10, 12, 12, 6, 8, 8, 12, 14, 8, 8, 20, 0, 20, 0, 14, 20, 20, 20, 20, 20, 7, 8, 16, 4, 14, 14, 10, 10, 20, 20, 20, 4, 0, 3, 14, 14, 7, 4, 7, 14, 10, 20, 20, 20, 0, 0, 0, 0, 20, 20, 4, 2, 1, 20, 20, 20, 20, 20, 20, 20, 20 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 10, 10, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 6, 7, 20, 20, 20, 1, 2, 3, 5, 5, 5, 5, 5 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 8, 8, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 5, 6, 20, 20, 20, 2, 1, 2, 4, 4, 4, 4, 4 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 8, 8, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 4, 5, 20, 20, 20, 3, 2, 1, 4, 4, 4, 4, 4 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 8, 8, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 4, 5, 20, 20, 20, 5, 4, 4, 1, 3, 3, 3, 3 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 8, 8, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 4, 5, 20, 20, 20, 5, 4, 4, 3, 1, 5, 4, 2 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 8, 8, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 4, 5, 20, 20, 20, 5, 4, 4, 3, 5, 1, 3, 4 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 8, 8, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 4, 5, 20, 20, 20, 5, 4, 4, 3, 4, 3, 1, 3 },
|
|
{ 10, 8, 6, 8, 0, 14, 14, 12, 12, 12, 14, 12, 12, 14, 14, 14, 8, 8, 10, 10, 0, 10, 0, 0, 6, 12, 0, 0, 0, 8, 0, 20, 0, 4, 20, 0, 14, 12, 12, 12, 8, 14, 12, 14, 8, 8, 14, 14, 6, 0, 6, 0, 8, 5, 5, 8, 8, 10, 14, 14, 8, 20, 14, 14, 12, 12, 10, 10, 10, 10, 0, 20, 8, 8, 10, 20, 10, 14, 12, 8, 5, 10, 0, 0, 0, 0, 4, 5, 20, 20, 20, 5, 4, 4, 3, 2, 4, 3, 1 },
|
|
};
|
|
|
|
|
|
MolHistogram::MolHistogram(const ROMol &mol, const double *dmat) :
|
|
d_h(boost::extents[mol.getNumHeavyAtoms()][O3_MAX_H_BINS]) {
|
|
PRECONDITION(dmat,"empty distance matrix");
|
|
unsigned int nAtoms = mol.getNumAtoms();
|
|
unsigned int y = 0;
|
|
for (unsigned int i = 0; i < nAtoms; ++i) {
|
|
// skip hydrogens
|
|
if ((mol.getAtomWithIdx(i))->getAtomicNum() == 1) {
|
|
continue;
|
|
}
|
|
// initialize h row(y) to all zeros
|
|
for (unsigned int j = 0; j < O3_MAX_H_BINS; ++j) {
|
|
d_h[y][j] = 0;
|
|
}
|
|
for (unsigned int j = 0; j < nAtoms; ++j) {
|
|
unsigned int dist = static_cast<unsigned int>(floor(dmat[i * nAtoms + j]));
|
|
if (dist < O3_MAX_H_BINS) {
|
|
++d_h[y][dist];
|
|
}
|
|
}
|
|
++y;
|
|
}
|
|
}
|
|
|
|
|
|
int o3aMMFFCostFunc(const unsigned int prbIdx,
|
|
const unsigned int refIdx, double hSum, void *data)
|
|
{
|
|
boost::uint8_t mmffSim = mmffSimMatrix
|
|
[(static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->refProp))->getMMFFAtomType(refIdx) - 1]
|
|
[(static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp))->getMMFFAtomType(prbIdx) - 1];
|
|
|
|
return boost::math::iround
|
|
((static_cast<double>(((O3AFuncData *)data)->coeff) * O3_CHARGE_WEIGHT
|
|
* fabs((static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->refProp))->getMMFFPartialCharge(refIdx)
|
|
- (static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp))->getMMFFPartialCharge(prbIdx))
|
|
+ (((O3AFuncData *)data)->useMMFFSim
|
|
? static_cast<double>(O3_MAX_WEIGHT_COEFF - ((O3AFuncData *)data)->coeff)
|
|
* static_cast<double>(mmffSim) : 0.0) + hSum) * 1.0e03);
|
|
}
|
|
|
|
|
|
int o3aCrippenCostFunc(const unsigned int prbIdx,
|
|
const unsigned int refIdx, double hSum, void *data)
|
|
{
|
|
return boost::math::iround
|
|
((static_cast<double>((static_cast<O3AFuncData *>(data))->coeff)
|
|
* O3_CHARGE_WEIGHT * fabs((*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->refProp)))[refIdx]
|
|
- (*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp)))[prbIdx])
|
|
+ hSum) * 1.0e03);
|
|
}
|
|
|
|
|
|
void LAP::computeCostMatrix(const ROMol &prbMol, const MolHistogram &prbHist,
|
|
const ROMol &refMol, const MolHistogram &refHist, O3AConstraintVect *o3aConstraintVect,
|
|
int (*costFunc)(const unsigned int, const unsigned int, double, void *),
|
|
void *data, const unsigned int n_bins)
|
|
{
|
|
unsigned int i;
|
|
unsigned int j;
|
|
unsigned int k;
|
|
unsigned int x;
|
|
unsigned int y;
|
|
unsigned int largestNHeavyAtoms =
|
|
std::max(refMol.getNumHeavyAtoms(), prbMol.getNumHeavyAtoms());
|
|
unsigned int mapIdx = 0;
|
|
double hSum = 0.0;
|
|
|
|
|
|
// ref is on rows, prb is on columns
|
|
for (i = 0; i < largestNHeavyAtoms; ++i) {
|
|
for (j = 0; j < largestNHeavyAtoms; ++j) {
|
|
d_cost[i][j] = O3_DUMMY_COST;
|
|
}
|
|
}
|
|
for (i = 0, y = 0; i < refMol.getNumAtoms(); ++i) {
|
|
if (refMol[i]->getAtomicNum() == 1) {
|
|
continue;
|
|
}
|
|
for (j = 0, x = 0; j < prbMol.getNumAtoms(); ++j) {
|
|
if (prbMol[j]->getAtomicNum() == 1) {
|
|
continue;
|
|
}
|
|
// if this pair is constrained, make sure that it is
|
|
// associated with a low cost so it is picked up
|
|
// in the minimum cost path
|
|
// first pair element is prb, second is ref
|
|
if (o3aConstraintVect && (mapIdx < o3aConstraintVect->size())
|
|
&& (j == (*o3aConstraintVect)[mapIdx]->getPrbIdx())
|
|
&& (i == (*o3aConstraintVect)[mapIdx]->getRefIdx())) {
|
|
d_cost[y][x] = O3_LARGE_NEGATIVE_WEIGHT;
|
|
++mapIdx;
|
|
}
|
|
else {
|
|
for (k = 0, hSum = 0.0; k < n_bins; ++k) {
|
|
int rhyk = refHist.get(y,k);
|
|
int phxk = prbHist.get(x,k);
|
|
if ((!rhyk) && (!phxk)) continue;
|
|
hSum += (double)square(rhyk - phxk) / (double)(rhyk + phxk);
|
|
}
|
|
d_cost[y][x] = (*costFunc)(j, i, hSum, data);
|
|
}
|
|
++x;
|
|
}
|
|
++y;
|
|
}
|
|
}
|
|
|
|
|
|
//----------------------------------------------------
|
|
// Taken from Jonker, R.; Volgenant, A.
|
|
// A Shortest Augmenting Path Algorithm for Dense
|
|
// and Sparse Linear Assignment Problems
|
|
// Computing 1987, 38, 325-340
|
|
//----------------------------------------------------
|
|
void LAP::computeMinCostPath(const int dim)
|
|
{
|
|
// input:
|
|
// dim - problem size
|
|
// cost - cost matrix
|
|
|
|
// output:
|
|
// rowsol - column assigned to row in solution
|
|
// colsol - row assigned to column in solution
|
|
// v - dual variables, column reduction numbers
|
|
|
|
int loopCnt;
|
|
int unassignedFound;
|
|
// row vars
|
|
int i;
|
|
int imin;
|
|
int numFree = 0;
|
|
int prvNumFree;
|
|
int f;
|
|
int i0;
|
|
int k;
|
|
int freeRow;
|
|
// col vars
|
|
int j;
|
|
int j1;
|
|
int j2 = 0;
|
|
int endOfPath;
|
|
int last = 0;
|
|
int low;
|
|
int up;
|
|
// cost vars
|
|
int min = 0;
|
|
int h;
|
|
int uMin;
|
|
int uSubMin;
|
|
int v2;
|
|
|
|
// init how many times a row will be assigned in the column reduction
|
|
for (int n = 0; n < dim; ++n) {
|
|
d_matches[n] = 0;
|
|
}
|
|
// COLUMN REDUCTION
|
|
// reverse order gives better results
|
|
for (j = dim - 1; j >= 0; --j) {
|
|
// find minimum cost over rows
|
|
min = d_cost[0][j];
|
|
imin = 0;
|
|
for (i = 1; i < dim; ++i) {
|
|
if (d_cost[i][j] < min) {
|
|
min = d_cost[i][j];
|
|
imin = i;
|
|
}
|
|
}
|
|
d_v[j] = min;
|
|
|
|
if (++(d_matches[imin]) == 1) {
|
|
// init assignment if minimum row assigned for first time
|
|
d_rowSol[imin] = j;
|
|
d_colSol[j] = imin;
|
|
}
|
|
else {
|
|
// row already assigned, column not assigned
|
|
d_colSol[j] = -1;
|
|
}
|
|
}
|
|
// REDUCTION TRANSFER
|
|
for (i = 0; i < dim; ++i) {
|
|
if (!(d_matches[i])) {
|
|
// fill list of unassigned 'd_free' rows
|
|
d_free[numFree++] = i;
|
|
}
|
|
else {
|
|
if (d_matches[i] == 1) {
|
|
// transfer reduction from rows that are assigned once
|
|
j1 = d_rowSol[i];
|
|
min = O3_DUMMY_COST;
|
|
for (j = 0; j < dim; ++j) {
|
|
if ((j != j1) && (d_cost[i][j] - d_v[j] < min)) {
|
|
min = d_cost[i][j] - d_v[j];
|
|
}
|
|
}
|
|
d_v[j1] -= min;
|
|
}
|
|
}
|
|
}
|
|
// AUGMENTING ROW REDUCTION
|
|
// do-loop to be done twice
|
|
for (loopCnt = 0; loopCnt < 2; ++loopCnt) {
|
|
// scan all d_free rows
|
|
// in some cases, a d_free row may be replaced
|
|
// with another one to be scanned next
|
|
k = 0;
|
|
prvNumFree = numFree;
|
|
numFree = 0;
|
|
// start list of rows still d_free after augmenting row reduction
|
|
while (k < prvNumFree) {
|
|
i = d_free[k];
|
|
++k;
|
|
// find minimum and second minimum reduced cost over columns
|
|
uMin = d_cost[i][0] - d_v[0];
|
|
j1 = 0;
|
|
uSubMin = O3_DUMMY_COST;
|
|
for (j = 1; j < dim; ++j) {
|
|
h = d_cost[i][j] - d_v[j];
|
|
if (h < uSubMin) {
|
|
if (h >= uMin) {
|
|
uSubMin = h;
|
|
j2 = j;
|
|
}
|
|
else {
|
|
uSubMin = uMin;
|
|
uMin = h;
|
|
j2 = j1;
|
|
j1 = j;
|
|
}
|
|
}
|
|
}
|
|
i0 = d_colSol[j1];
|
|
if (uMin < uSubMin) {
|
|
// change the reduction of the minimum column to increase
|
|
// the minimum reduced cost in the row to the subminimum
|
|
d_v[j1] -= (uSubMin - uMin);
|
|
}
|
|
else {
|
|
// minimum and subminimum equal
|
|
if (i0 >= 0) {
|
|
// minimum column j1 is assigned
|
|
// swap columns j1 and j2, as j2 may be unassigned
|
|
j1 = j2;
|
|
i0 = d_colSol[j2];
|
|
}
|
|
}
|
|
// (re-)assign i to j1, possibly de-assigning an i0
|
|
d_rowSol[i] = j1;
|
|
d_colSol[j1] = i;
|
|
|
|
if (i0 >= 0) {
|
|
// minimum column j1 assigned earlier
|
|
if (uMin < uSubMin) {
|
|
// put in current k, and go back to that k
|
|
// continue augmenting path i - j1 with i0
|
|
d_free[--k] = i0;
|
|
}
|
|
else {
|
|
// no further augmenting reduction possible
|
|
// store i0 in list of d_free rows for next phase
|
|
d_free[numFree++] = i0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
// AUGMENT SOLUTION for each d_free row
|
|
for (f = 0; f < numFree; ++f) {
|
|
// start row of augmenting path
|
|
freeRow = d_free[f];
|
|
// Dijkstra shortest path algorithm
|
|
// runs until unassigned column added to shortest path tree
|
|
for (j = 0; j < dim; ++j) {
|
|
d_d[j] = d_cost[freeRow][j] - d_v[j];
|
|
d_pred[j] = freeRow;
|
|
// init column list
|
|
d_colList[j] = j;
|
|
}
|
|
// columns in 0..low-1 are ready, now none
|
|
low = 0;
|
|
// columns in low..up-1 are to be scanned for current minimum, now none
|
|
up = 0;
|
|
// columns in up..dim-1 are to be considered later to find new minimum,
|
|
// at this stage the list simply contains all columns
|
|
unassignedFound = 0;
|
|
while (!unassignedFound) {
|
|
if (up == low) {
|
|
// no more columns to be scanned for current minimum
|
|
last = low - 1;
|
|
// scan columns for up..dim-1 to find all indices for which new minimum occurs
|
|
// store these indices between low..up-1 (increasing up)
|
|
min = d_d[d_colList[up++]];
|
|
for (k = up; k < dim; ++k) {
|
|
j = d_colList[k];
|
|
h = d_d[j];
|
|
if (h <= min) {
|
|
if (h < min) {
|
|
// new minimum
|
|
// restart list at index low
|
|
up = low;
|
|
min = h;
|
|
}
|
|
// new index with same minimum, put on undex up, and extend list
|
|
d_colList[k] = d_colList[up];
|
|
d_colList[up++] = j;
|
|
}
|
|
}
|
|
// check if any of the minimum columns happens to be unassigned
|
|
// if so, we have an augmenting path right away
|
|
for (k = low; k < up; ++k) {
|
|
if (d_colSol[d_colList[k]] < 0) {
|
|
endOfPath = d_colList[k];
|
|
unassignedFound = 1;
|
|
break;
|
|
}
|
|
}
|
|
}
|
|
if (!unassignedFound) {
|
|
// update 'distances' between freeRow and
|
|
// all unscanned columns, via next scanned column
|
|
j1 = d_colList[low];
|
|
++low;
|
|
i = d_colSol[j1];
|
|
h = d_cost[i][j1] - d_v[j1] - min;
|
|
for (k = up; k < dim; ++k) {
|
|
j = d_colList[k];
|
|
v2 = d_cost[i][j] - d_v[j] - h;
|
|
if (v2 < d_d[j]) {
|
|
d_pred[j] = i;
|
|
if (v2 == min) {
|
|
// new column found at same minimum value
|
|
if (d_colSol[j] < 0) {
|
|
// if unassigned, shortest augmenting path is complete
|
|
endOfPath = j;
|
|
unassignedFound = 1;
|
|
break;
|
|
}
|
|
else {
|
|
// else add to list to be scanned right away
|
|
d_colList[k] = d_colList[up];
|
|
d_colList[up++] = j;
|
|
}
|
|
}
|
|
d_d[j] = v2;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
// update column prices
|
|
for (k = 0; k <= last; ++k) {
|
|
j1 = d_colList[k];
|
|
d_v[j1] += (d_d[j1] - min);
|
|
}
|
|
// reset row and column assignments along the alternating path
|
|
do {
|
|
i = d_pred[endOfPath];
|
|
d_colSol[endOfPath] = i;
|
|
j1 = endOfPath;
|
|
endOfPath = d_rowSol[i];
|
|
d_rowSol[i] = j1;
|
|
} while (i != freeRow);
|
|
}
|
|
}
|
|
|
|
|
|
void SDM::fillFromLAP(LAP &lap)
|
|
{
|
|
unsigned int i;
|
|
unsigned int j;
|
|
unsigned int k;
|
|
unsigned int n;
|
|
unsigned int n_atoms;
|
|
unsigned int n_equiv;
|
|
const RDGeom::POINT3D_VECT &refPos = d_refConf->getPositions();
|
|
const RDGeom::POINT3D_VECT &prbPos = d_prbConf->getPositions();
|
|
const ROMol *mol[2] = { &(d_refConf->getOwningMol()), &(d_prbConf->getOwningMol()) };
|
|
|
|
|
|
// filter out atom equivalences whose cost is > O3_DUMMY_COST
|
|
for (i = 0, n_equiv = 0; i < mol[0]->getNumHeavyAtoms(); ++i) {
|
|
if (lap.getCost(i, lap.getRowSol(i)) >= O3_DUMMY_COST) {
|
|
continue;
|
|
}
|
|
SDMElement *sdmElement = new SDMElement;
|
|
sdmElement->idx[0] = i;
|
|
sdmElement->idx[1] = lap.getRowSol(i);
|
|
sdmElement->cost = lap.getCost(i, lap.getRowSol(i));
|
|
d_SDMPtrVect.push_back(boost::shared_ptr<SDMElement>(sdmElement));
|
|
++n_equiv;
|
|
}
|
|
boost::multi_array<double, 2> diff(boost::extents[n_equiv][n_equiv]);
|
|
// find out correspondences between heavy atom indexes
|
|
// in the original molecule and heavy atoms in the sdm matrix
|
|
// (the sdm matrix is rebuilt using original molecule
|
|
// heavy atom indexes)
|
|
for (n = 0; n < 2; ++n) {
|
|
for (i = 0; i < n_equiv; ++i) {
|
|
j = 0;
|
|
n_atoms = 0;
|
|
k = d_SDMPtrVect[i]->idx[n];
|
|
while ((n_atoms < mol[n]->getNumAtoms()) && (j <= k)) {
|
|
if (mol[n]->getAtomWithIdx(n_atoms)->getAtomicNum() > 1) {
|
|
++j;
|
|
d_SDMPtrVect[i]->idx[n] = n_atoms;
|
|
}
|
|
++n_atoms;
|
|
}
|
|
}
|
|
}
|
|
// loop over n_equiv rows
|
|
for (i = 0; i < n_equiv; ++i) {
|
|
d_SDMPtrVect[i]->o3aConstraint = NULL;
|
|
if (d_SDMPtrVect[i]->cost < 0) {
|
|
// this is one of the constrained atom pairs, so assign it
|
|
// a pointer to the relevant O3AConstraint object
|
|
if (d_o3aConstraintVect) {
|
|
for (j = 0; j < (*d_o3aConstraintVect).size(); ++j) {
|
|
if (((*d_o3aConstraintVect)[j]->getPrbIdx() == d_SDMPtrVect[i]->idx[1])
|
|
&& ((*d_o3aConstraintVect)[j]->getRefIdx() == d_SDMPtrVect[i]->idx[0])) {
|
|
d_SDMPtrVect[i]->o3aConstraint = (*d_o3aConstraintVect)[j];
|
|
break;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
// initialize to 0 the i-th row of the diff matrix
|
|
for (j = 0; j < n_equiv; ++j) {
|
|
diff[i][j] = 0.0;
|
|
}
|
|
for (j = 0; j < n_equiv; ++j) {
|
|
// if i == j then the distance will be 0,
|
|
// no need to spend time computing it
|
|
if (i == j) {
|
|
continue;
|
|
}
|
|
// - the euclidean distance between atoms i,j is computed for ref_conf
|
|
// - the euclidean distance between the corresponding atoms is computed for moved_conf
|
|
// - the absolute value of the difference between the two distances is computed
|
|
// and placed in diff[i][j]
|
|
diff[i][j] = fabs((refPos[d_SDMPtrVect[i]->idx[0]] - refPos[d_SDMPtrVect[j]->idx[0]]).length()
|
|
- (prbPos[d_SDMPtrVect[i]->idx[1]] - prbPos[d_SDMPtrVect[j]->idx[1]]).length());
|
|
}
|
|
}
|
|
for (i = 0; i < n_equiv; ++i) {
|
|
for (j = 0, d_SDMPtrVect[i]->score = 0; j < n_equiv; ++j) {
|
|
if ((diff[i][j] > O3_THRESHOLD_DIFF_DISTANCE) && (d_SDMPtrVect[i]->cost >= 0)) {
|
|
++(d_SDMPtrVect[i]->score);
|
|
}
|
|
}
|
|
}
|
|
// sort the SDM matrix by increasing scores
|
|
std::sort(d_SDMPtrVect.begin(), d_SDMPtrVect.end(), this->compareSDMScore);
|
|
}
|
|
|
|
|
|
void SDM::fillFromDist(double threshold,const boost::dynamic_bitset<> &refHvyAtoms,
|
|
const boost::dynamic_bitset<> &prbHvyAtoms)
|
|
{
|
|
unsigned int n = 0;
|
|
unsigned int pairs = 0;
|
|
const RDGeom::POINT3D_VECT &refPos = d_refConf->getPositions();
|
|
const RDGeom::POINT3D_VECT &prbPos = d_prbConf->getPositions();
|
|
unsigned int mapIdx = 0;
|
|
|
|
|
|
d_SDMPtrVect.clear();
|
|
double sqThreshold = square(threshold);
|
|
unsigned int refNAtoms = d_refConf->getNumAtoms();
|
|
unsigned int prbNAtoms = d_prbConf->getNumAtoms();
|
|
unsigned int largestNAtoms = std::max(prbNAtoms, refNAtoms);
|
|
boost::dynamic_bitset<> refUsed(largestNAtoms);
|
|
boost::dynamic_bitset<> prbUsed(largestNAtoms);
|
|
// loop over ref atoms
|
|
for (unsigned int i = 0; i < refNAtoms; ++i) {
|
|
if (!refHvyAtoms[i]) continue;
|
|
// loop over prb atoms
|
|
for (unsigned int j = 0; j < prbNAtoms; ++j) {
|
|
if (!prbHvyAtoms[j]) continue;
|
|
double sqDist = (refPos[i] - prbPos[j]).lengthSq();
|
|
// if the distance between these two atoms is lower
|
|
// than threshold, then include this pair in the SDM matrix
|
|
bool isConstraint = (d_o3aConstraintVect
|
|
&& (mapIdx < (*d_o3aConstraintVect).size())
|
|
&& (j == (*d_o3aConstraintVect)[mapIdx]->getPrbIdx())
|
|
&& (i == (*d_o3aConstraintVect)[mapIdx]->getRefIdx()));
|
|
if ((sqDist < sqThreshold) || isConstraint) {
|
|
SDMElement *sdmElement = new SDMElement();
|
|
sdmElement->idx[0] = i;
|
|
sdmElement->idx[1] = j;
|
|
sdmElement->sqDist = sqDist;
|
|
sdmElement->o3aConstraint = NULL;
|
|
if (isConstraint) {
|
|
sdmElement->o3aConstraint = (*d_o3aConstraintVect)[mapIdx];
|
|
//in case there are duplicate constraints referring to the same
|
|
//atom pair, apply only the one with the highest weight
|
|
while ((mapIdx < (*d_o3aConstraintVect).size())
|
|
&& (j == (*d_o3aConstraintVect)[mapIdx]->getPrbIdx())
|
|
&& (i == (*d_o3aConstraintVect)[mapIdx]->getRefIdx())) {
|
|
++mapIdx;
|
|
}
|
|
}
|
|
d_SDMPtrVect.push_back(boost::shared_ptr<SDMElement>(sdmElement));
|
|
++n;
|
|
}
|
|
}
|
|
}
|
|
// sort the SDM matrix by decreasing constraint weights and,
|
|
// as a second criterion, increasing distances
|
|
std::sort(d_SDMPtrVect.begin(), d_SDMPtrVect.end(), this->compareSDMDist);
|
|
// increase the number of pairs which will be used
|
|
// by rmsAlgorithm until an atom which has been
|
|
// included in a previous pair is found
|
|
for (unsigned int i = 0; (i < n) && (!(refUsed[d_SDMPtrVect[i]->idx[0]]))
|
|
&& (!(prbUsed[d_SDMPtrVect[i]->idx[1]])); ++i) {
|
|
++pairs;
|
|
refUsed[d_SDMPtrVect[i]->idx[0]] = 1;
|
|
prbUsed[d_SDMPtrVect[i]->idx[1]] = 1;
|
|
}
|
|
d_SDMPtrVect.resize(pairs);
|
|
}
|
|
|
|
|
|
double o3aMMFFWeightFunc(const unsigned int prbIdx, const unsigned int refIdx, void *data)
|
|
{
|
|
boost::uint8_t mmffSim = mmffSimMatrix
|
|
[(static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->refProp))->getMMFFAtomType(refIdx) - 1]
|
|
[(static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp))->getMMFFAtomType(prbIdx) - 1];
|
|
|
|
return static_cast<double>(O3_MAX_WEIGHT_COEFF
|
|
- (static_cast<O3AFuncData *>(data))->weight) * ((1.0 + O3_CHARGE_COEFF
|
|
* fabs((static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->refProp))->getMMFFPartialCharge(refIdx)
|
|
+ (static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp))->getMMFFPartialCharge(prbIdx)))
|
|
/ (1.0 + fabs((static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->refProp))->getMMFFPartialCharge(refIdx)
|
|
- (static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp))->getMMFFPartialCharge(prbIdx))))
|
|
+ (double)((static_cast<O3AFuncData *>(data))->weight) / static_cast<double>(mmffSim);
|
|
}
|
|
|
|
|
|
double o3aCrippenWeightFunc(const unsigned int prbIdx, const unsigned int refIdx, void *data)
|
|
{
|
|
return (0.01 + fabs((*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->refProp)))[refIdx]
|
|
+ (*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp)))[prbIdx])
|
|
/ (1.0 + fabs((*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->refProp)))[refIdx]
|
|
- (*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp)))[prbIdx])));
|
|
}
|
|
|
|
|
|
void SDM::prepareMatchWeightsVect(RDKit::MatchVectType &matchVect,
|
|
RDNumeric::DoubleVector &weights, double (*weightFunc)
|
|
(const unsigned int, const unsigned int, void *), void *data) {
|
|
PRECONDITION(matchVect.size() == weights.size(), "matchVect/weights size mismatch");
|
|
double min;
|
|
for (unsigned int i = 0; i < matchVect.size(); ++i) {
|
|
// first pair element is prb, second is ref
|
|
matchVect[i].first = d_SDMPtrVect[i]->idx[1];
|
|
matchVect[i].second = d_SDMPtrVect[i]->idx[0];
|
|
weights[i] = (weightFunc ? weightFunc(d_SDMPtrVect[i]->idx[1],
|
|
d_SDMPtrVect[i]->idx[0], data) : 1.0);
|
|
if (d_SDMPtrVect[i]->o3aConstraint) {
|
|
weights[i] += d_SDMPtrVect[i]->o3aConstraint->getWeight();
|
|
}
|
|
if ((!i) || (weights[i] < min)) {
|
|
min = weights[i];
|
|
}
|
|
}
|
|
for (unsigned int i = 0; i < weights.size(); ++i) {
|
|
weights[i] /= min;
|
|
}
|
|
}
|
|
|
|
|
|
double o3aMMFFScoringFunc(const unsigned int prbIdx,
|
|
const unsigned int refIdx, void *data)
|
|
{
|
|
const RDGeom::POINT3D_VECT &refPos =
|
|
(static_cast<O3AFuncData *>(data))->refConf->getPositions();
|
|
const RDGeom::POINT3D_VECT &prbPos =
|
|
(static_cast<O3AFuncData *>(data))->prbConf->getPositions();
|
|
|
|
double sqDist = (refPos[refIdx] - prbPos[prbIdx]).lengthSq();
|
|
double chargeDiff = fabs((static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->refProp))->getMMFFPartialCharge(refIdx)
|
|
- (static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp))->getMMFFPartialCharge(prbIdx));
|
|
double chargeSum = fabs((static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->refProp))->getMMFFPartialCharge(refIdx)
|
|
+ (static_cast<MMFF::MMFFMolProperties *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp))->getMMFFPartialCharge(prbIdx));
|
|
|
|
return ((O3_SCORING_FUNCTION_ALPHA + (1.0 + O3_CHARGE_COEFF * chargeSum)
|
|
/ (1.0 + chargeDiff)) * exp(-O3_SCORING_FUNCTION_BETA * sqDist));
|
|
}
|
|
|
|
|
|
double o3aCrippenScoringFunc(const unsigned int prbIdx,
|
|
const unsigned int refIdx, void *data)
|
|
{
|
|
const RDGeom::POINT3D_VECT &refPos =
|
|
(static_cast<O3AFuncData *>(data))->refConf->getPositions();
|
|
const RDGeom::POINT3D_VECT &prbPos =
|
|
(static_cast<O3AFuncData *>(data))->prbConf->getPositions();
|
|
|
|
double sqDist = (refPos[refIdx] - prbPos[prbIdx]).lengthSq();
|
|
double logpDiff = fabs((*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->refProp)))[refIdx]
|
|
- (*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp)))[prbIdx]);
|
|
double logpSum = fabs((*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->refProp)))[refIdx]
|
|
+ (*(static_cast<std::vector<double> *>
|
|
((static_cast<O3AFuncData *>(data))->prbProp)))[prbIdx]);
|
|
|
|
return ((O3_SCORING_FUNCTION_ALPHA + (1.0 + O3_CRIPPEN_COEFF * logpSum)
|
|
/ (1.0 + logpDiff)) * exp(-O3_SCORING_FUNCTION_BETA * sqDist));
|
|
}
|
|
|
|
|
|
double SDM::scoreAlignment(double (*scoringFunc)
|
|
(const unsigned int, const unsigned int, void *), void *data)
|
|
{
|
|
double score = 0.0;
|
|
|
|
for (unsigned int i = 0; i < d_SDMPtrVect.size(); ++i) {
|
|
score += scoringFunc(d_SDMPtrVect[i]->idx[1], d_SDMPtrVect[i]->idx[0], data);
|
|
}
|
|
|
|
return score;
|
|
}
|
|
|
|
|
|
O3A::O3A(int (*costFunc)(const unsigned int, const unsigned int, double, void *),
|
|
double (*weightFunc)(const unsigned int, const unsigned int, void *),
|
|
double (*scoringFunc)(const unsigned int, const unsigned int, void *),
|
|
void *data, ROMol &prbMol, const ROMol &refMol,
|
|
const int prbCid, const int refCid,
|
|
boost::dynamic_bitset<> *prbHvyAtoms,
|
|
boost::dynamic_bitset<> *refHvyAtoms,
|
|
const bool reflect, const unsigned int maxIters, unsigned int options,
|
|
O3AConstraintVect *o3aConstraintVect, ROMol *extWorkPrbMol,
|
|
LAP *extLAP, MolHistogram *extPrbHist, MolHistogram *extRefHist) :
|
|
d_prbMol(&prbMol),
|
|
d_refMol(&refMol),
|
|
d_prbCid(prbCid),
|
|
d_refCid(refCid),
|
|
d_reflect(reflect),
|
|
d_maxIters(maxIters)
|
|
{
|
|
ROMol *workPrbMol = (extWorkPrbMol ? extWorkPrbMol : new ROMol(prbMol));
|
|
Conformer &prbConf = workPrbMol->getConformer();
|
|
const Conformer &refConf = refMol.getConformer();
|
|
unsigned int accuracy = options & O3_ACCURACY_MASK;
|
|
bool local = options & O3_LOCAL_ONLY;
|
|
unsigned int refNAtoms = refMol.getNumAtoms();
|
|
unsigned int prbNAtoms = prbMol.getNumAtoms();
|
|
unsigned int refNHeavyAtoms = refMol.getNumHeavyAtoms();
|
|
unsigned int prbNHeavyAtoms = prbMol.getNumHeavyAtoms();
|
|
unsigned int largestNHeavyAtoms = std::max(refNHeavyAtoms, prbNHeavyAtoms);
|
|
unsigned int i;
|
|
if (!refHvyAtoms) {
|
|
refHvyAtoms = new boost::dynamic_bitset<>(refNAtoms);
|
|
for (i = 0; i < refNAtoms; ++i) {
|
|
if (refMol[i]->getAtomicNum() != 1) {
|
|
refHvyAtoms->set(i);
|
|
}
|
|
}
|
|
}
|
|
if (!prbHvyAtoms) {
|
|
for (i = 0; i < prbNAtoms; ++i) {
|
|
if (prbMol[i]->getAtomicNum() != 1) {
|
|
prbHvyAtoms->set(i);
|
|
}
|
|
}
|
|
}
|
|
std::vector<unsigned int> pairs(4, 0);
|
|
std::vector<double> score(3, 0.0);
|
|
std::vector<double> pairsRMSD(2, 0.0);
|
|
std::vector<SDM *> bestSDM((unsigned int)3, NULL);
|
|
SDM startSDM(&prbConf, &refConf, o3aConstraintVect);
|
|
MolHistogram *refHist = NULL;
|
|
MolHistogram *prbHist = NULL;
|
|
LAP *lap = NULL;
|
|
if (local) {
|
|
startSDM.fillFromDist(O3_SDM_THRESHOLD_START, *refHvyAtoms, *prbHvyAtoms);
|
|
}
|
|
else {
|
|
refHist = (extRefHist ? extRefHist
|
|
: new MolHistogram(refMol, MolOps::get3DDistanceMat(refMol, refCid)));
|
|
prbHist = (extPrbHist ? extPrbHist
|
|
: new MolHistogram(prbMol, MolOps::get3DDistanceMat(prbMol, prbCid)));
|
|
lap = (extLAP ? extLAP : new LAP(largestNHeavyAtoms));
|
|
lap->computeCostMatrix(prbMol, *prbHist,
|
|
refMol, *refHist, o3aConstraintVect, costFunc, data);
|
|
lap->computeMinCostPath(largestNHeavyAtoms);
|
|
startSDM.fillFromLAP(*lap);
|
|
}
|
|
for (pairs[0] = 0, score[0] = 0.0, i = 3; i < startSDM.size(); ++i) {
|
|
RDKit::MatchVectType startMatchVect(i);
|
|
RDNumeric::DoubleVector startWeights(i);
|
|
startSDM.prepareMatchWeightsVect(startMatchVect,
|
|
startWeights, weightFunc, data);
|
|
alignMol(*workPrbMol, refMol, prbCid, refCid,
|
|
&startMatchVect, &startWeights, reflect, maxIters);
|
|
unsigned int sdmThresholdIt;
|
|
for (sdmThresholdIt = ((accuracy < 1) ? 0 : O3_MAX_SDM_THRESHOLD_ITER - 1),
|
|
pairs[1] = 0, score[1] = 0.0; sdmThresholdIt < O3_MAX_SDM_THRESHOLD_ITER;
|
|
++sdmThresholdIt) {
|
|
pairs[2] = 0;
|
|
bool flag = true;
|
|
unsigned int iter = 0;
|
|
double sdmThresholdDist = O3_SDM_THRESHOLD_START
|
|
+ (double)sdmThresholdIt * O3_SDM_THRESHOLD_STEP;
|
|
while (flag && (iter < O3_MAX_SDM_ITERATIONS)) {
|
|
SDM progressSDM(&prbConf, &refConf, o3aConstraintVect);
|
|
progressSDM.fillFromDist(sdmThresholdDist, *refHvyAtoms, *prbHvyAtoms);
|
|
pairs[3] = progressSDM.size();
|
|
if (pairs[3] < 3) {
|
|
break;
|
|
}
|
|
RDKit::MatchVectType progressMatchVect(pairs[3]);
|
|
RDNumeric::DoubleVector progressWeights(pairs[3]);
|
|
progressSDM.prepareMatchWeightsVect(progressMatchVect,
|
|
progressWeights, weightFunc, data);
|
|
RDGeom::Transform3D trans;
|
|
pairsRMSD[1] = getAlignmentTransform(*workPrbMol, refMol,
|
|
trans, prbCid, refCid, &progressMatchVect, &progressWeights,
|
|
reflect, maxIters);
|
|
flag = ((pairs[3] > pairs[2]) || ((pairs[3] == pairs[2])
|
|
&& ((!iter) || ((pairsRMSD[0] - pairsRMSD[1]) > O3_RMSD_THRESHOLD))));
|
|
if (flag) {
|
|
pairs[2] = pairs[3];
|
|
pairsRMSD[0] = pairsRMSD[1];
|
|
if (bestSDM[2]) {
|
|
delete bestSDM[2];
|
|
}
|
|
bestSDM[2] = new SDM();
|
|
*(bestSDM[2]) = progressSDM;
|
|
MolTransforms::transformConformer(prbConf, trans);
|
|
}
|
|
++iter;
|
|
}
|
|
score[2] = ((pairs[2] >= 3)
|
|
? bestSDM[2]->scoreAlignment(scoringFunc, data) : 0.0);
|
|
if ((score[2] - score[1]) > O3_SCORE_THRESHOLD) {
|
|
pairs[1] = pairs[2];
|
|
score[1] = score[2];
|
|
if (bestSDM[1]) {
|
|
delete bestSDM[1];
|
|
}
|
|
bestSDM[1] = new SDM();
|
|
*(bestSDM[1]) = *(bestSDM[2]);
|
|
}
|
|
}
|
|
if ((score[1] - score[0]) > O3_SCORE_THRESHOLD) {
|
|
pairs[0] = pairs[1];
|
|
score[0] = score[1];
|
|
if (bestSDM[0]) {
|
|
delete bestSDM[0];
|
|
}
|
|
bestSDM[0] = new SDM();
|
|
*(bestSDM[0]) = *(bestSDM[1]);
|
|
}
|
|
}
|
|
if ((pairs[0] < 3) && (startSDM.size() >= 3)) {
|
|
pairs[0] = startSDM.size();
|
|
if (bestSDM[0]) {
|
|
delete bestSDM[0];
|
|
}
|
|
bestSDM[0] = new SDM();
|
|
*(bestSDM[0]) = startSDM;
|
|
score[0] = bestSDM[0]->scoreAlignment(scoringFunc, data);
|
|
}
|
|
RDKit::MatchVectType *o3aMatchVect = new RDKit::MatchVectType(pairs[0]);
|
|
RDNumeric::DoubleVector *o3aWeights = new RDNumeric::DoubleVector(pairs[0]);
|
|
d_o3aMatchVect = o3aMatchVect;
|
|
d_o3aWeights = o3aWeights;
|
|
if (pairs[0] >= 3) {
|
|
bestSDM[0]->prepareMatchWeightsVect(*o3aMatchVect, *o3aWeights, weightFunc, data);
|
|
d_o3aScore = score[0];
|
|
}
|
|
else {
|
|
d_o3aScore = 0.0;
|
|
}
|
|
for (i = 0; i < 3; ++i) {
|
|
if (bestSDM[i]) {
|
|
delete bestSDM[i];
|
|
}
|
|
}
|
|
if ((!extLAP) && lap) {
|
|
delete lap;
|
|
}
|
|
if ((!extRefHist) && refHist) {
|
|
delete refHist;
|
|
}
|
|
if ((!extPrbHist) && prbHist) {
|
|
delete prbHist;
|
|
}
|
|
if ((!extWorkPrbMol) && workPrbMol) {
|
|
delete workPrbMol;
|
|
}
|
|
}
|
|
|
|
|
|
O3A::O3A(ROMol &prbMol, const ROMol &refMol, void *prbProp, void *refProp,
|
|
AtomTypeScheme atomTypes, const int prbCid, const int refCid,
|
|
const bool reflect, const unsigned int maxIters, unsigned int options,
|
|
const MatchVectType *constraintMap, const RDNumeric::DoubleVector *constraintWeights,
|
|
LAP *extLAP, MolHistogram *extPrbHist, MolHistogram *extRefHist) :
|
|
d_prbMol(&prbMol),
|
|
d_refMol(&refMol),
|
|
d_prbCid(prbCid),
|
|
d_refCid(refCid),
|
|
d_reflect(reflect),
|
|
d_maxIters(maxIters)
|
|
{
|
|
int (*costFunc)(const unsigned int, const unsigned int, double, void *) = o3aMMFFCostFunc;
|
|
double (*weightFunc)(const unsigned int, const unsigned int, void *) = o3aMMFFWeightFunc;
|
|
double (*scoringFunc)(const unsigned int, const unsigned int, void *) = o3aMMFFScoringFunc;
|
|
if (atomTypes == CRIPPEN) {
|
|
costFunc = o3aCrippenCostFunc;
|
|
weightFunc = o3aCrippenWeightFunc;
|
|
scoringFunc = o3aCrippenScoringFunc;
|
|
}
|
|
O3AFuncData data;
|
|
ROMol extWorkPrbMol(prbMol);
|
|
data.prbConf = &(extWorkPrbMol.getConformer());
|
|
data.refConf = &(refMol.getConformer());
|
|
data.prbProp = prbProp;
|
|
data.refProp = refProp;
|
|
unsigned int refNAtoms = refMol.getNumAtoms();
|
|
unsigned int prbNAtoms = prbMol.getNumAtoms();
|
|
boost::dynamic_bitset<> refHvyAtoms(refNAtoms);
|
|
boost::dynamic_bitset<> prbHvyAtoms(prbNAtoms);
|
|
unsigned int i;
|
|
for (i = 0; i < refNAtoms; ++i) {
|
|
if (refMol[i]->getAtomicNum() != 1) {
|
|
refHvyAtoms.set(i);
|
|
}
|
|
}
|
|
for (i = 0; i < prbNAtoms; ++i) {
|
|
if (prbMol[i]->getAtomicNum() != 1) {
|
|
prbHvyAtoms.set(i);
|
|
}
|
|
}
|
|
unsigned int refNHeavyAtoms = refMol.getNumHeavyAtoms();
|
|
unsigned int prbNHeavyAtoms = prbMol.getNumHeavyAtoms();
|
|
unsigned int largestNHeavyAtoms = std::max(refNHeavyAtoms, prbNHeavyAtoms);
|
|
unsigned int accuracy = options & O3_ACCURACY_MASK;
|
|
bool local = options & O3_LOCAL_ONLY;
|
|
O3AConstraintVect o3aConstraintVect;
|
|
if (constraintMap) {
|
|
if (constraintWeights) {
|
|
if ((*constraintMap).size() != (*constraintWeights).size()) {
|
|
throw MolAlignException("The number of weights should match the number of constraints");
|
|
}
|
|
}
|
|
for (i = 0; i < (*constraintMap).size(); ++i) {
|
|
if (((*constraintMap)[i].first < 0) || ((*constraintMap)[i].first >= prbNAtoms)
|
|
|| ((*constraintMap)[i].second < 0) || ((*constraintMap)[i].second >= refNAtoms)) {
|
|
throw MolAlignException("Constrained atom idx out of range");
|
|
}
|
|
if ((!prbHvyAtoms[(*constraintMap)[i].first]) || (!refHvyAtoms[(*constraintMap)[i].second])) {
|
|
throw MolAlignException("Constrained atoms must be heavy atoms");
|
|
}
|
|
o3aConstraintVect.append((*constraintMap)[i].first, (*constraintMap)[i].second,
|
|
constraintWeights ? (*constraintWeights)[i] : O3_DEFAULT_CONSTRAINT_WEIGHT);
|
|
}
|
|
}
|
|
int c;
|
|
int l;
|
|
std::vector<double> score(2, 0.0);
|
|
O3A *bestO3A = NULL;
|
|
MolHistogram *refHist = NULL;
|
|
MolHistogram *prbHist = NULL;
|
|
LAP *lap = NULL;
|
|
if (!local) {
|
|
refHist = (extRefHist ? extRefHist
|
|
: new MolHistogram(refMol, MolOps::get3DDistanceMat(refMol, refCid)));
|
|
prbHist = (extPrbHist ? extPrbHist
|
|
: new MolHistogram(prbMol, MolOps::get3DDistanceMat(prbMol, prbCid)));
|
|
lap = (extLAP ? extLAP : new LAP(largestNHeavyAtoms));
|
|
}
|
|
for (l = 0, score[0] = 0.0;
|
|
l <= (((accuracy < 2) && (atomTypes == MMFF94)) ? 1 : 0); ++l) {
|
|
data.useMMFFSim = (bool)l;
|
|
for (c = 0; c <= O3_MAX_WEIGHT_COEFF;
|
|
c += ((accuracy < 3) ? 1 : (O3_MAX_WEIGHT_COEFF + 1))) {
|
|
data.weight = (l ? c : 0);
|
|
data.coeff = c;
|
|
O3A *o3a = new O3A(costFunc, weightFunc, scoringFunc,
|
|
&data, prbMol, refMol, prbCid, refCid, &prbHvyAtoms, &refHvyAtoms,
|
|
reflect, maxIters, options, &o3aConstraintVect, &extWorkPrbMol,
|
|
lap, prbHist, refHist);
|
|
score[1] = o3a->score();
|
|
if (((score[1] - score[0]) > O3_SCORE_THRESHOLD)
|
|
|| isDoubleZero(score[0])) {
|
|
if (bestO3A) {
|
|
delete bestO3A;
|
|
}
|
|
bestO3A = o3a;
|
|
score[0] = score[1];
|
|
}
|
|
else {
|
|
delete o3a;
|
|
}
|
|
}
|
|
}
|
|
unsigned int pairs = bestO3A->matches()->size();
|
|
RDKit::MatchVectType *bestO3AMatchVect = new RDKit::MatchVectType(pairs);
|
|
RDNumeric::DoubleVector *bestO3AWeights = new RDNumeric::DoubleVector(pairs);
|
|
d_o3aMatchVect = bestO3AMatchVect;
|
|
d_o3aWeights = bestO3AWeights;
|
|
if (pairs >= 3) {
|
|
for (i = 0; i < pairs; ++i) {
|
|
(*bestO3AMatchVect)[i].first = (*(bestO3A->matches()))[i].first;
|
|
(*bestO3AMatchVect)[i].second = (*(bestO3A->matches()))[i].second;
|
|
(*bestO3AWeights)[i] = (*(bestO3A->weights()))[i];
|
|
}
|
|
d_o3aScore = bestO3A->score();
|
|
}
|
|
else {
|
|
d_o3aScore = 0.0;
|
|
}
|
|
delete bestO3A;
|
|
if (!extLAP) {
|
|
delete lap;
|
|
}
|
|
if (!extRefHist) {
|
|
delete refHist;
|
|
}
|
|
if (!extPrbHist) {
|
|
delete prbHist;
|
|
}
|
|
}
|
|
|
|
|
|
double _rmsdMatchVect(ROMol *d_prbMol, const ROMol *d_refMol,
|
|
const RDGeom::POINT3D_VECT &prbPos, const RDGeom::POINT3D_VECT &refPos,
|
|
const RDKit::MatchVectType *matchVect)
|
|
{
|
|
double rmsd = 0.0;
|
|
if (matchVect) {
|
|
for (unsigned int i = 0; i < (*matchVect).size(); ++i) {
|
|
//first pair element is prb, second is ref
|
|
rmsd += (prbPos[(*matchVect)[i].first]
|
|
- refPos[(*matchVect)[i].second]).lengthSq();
|
|
}
|
|
rmsd = sqrt(rmsd / (*matchVect).size());
|
|
}
|
|
else {
|
|
RDGeom::Point3D refCtd;
|
|
RDGeom::Point3D prbCtd;
|
|
unsigned int i;
|
|
unsigned int j;
|
|
unsigned int nHeavy;
|
|
for (i = 0, nHeavy = 0; i < refPos.size(); ++i) {
|
|
if (d_refMol->getAtomWithIdx(i)->getAtomicNum() == 1) {
|
|
continue;
|
|
}
|
|
refCtd[0] += refPos[i][0];
|
|
refCtd[1] += refPos[i][1];
|
|
refCtd[2] += refPos[i][2];
|
|
++nHeavy;
|
|
}
|
|
refCtd[0] /= (double)nHeavy;
|
|
refCtd[1] /= (double)nHeavy;
|
|
refCtd[2] /= (double)nHeavy;
|
|
for (i = 0, nHeavy = 0; i < prbPos.size(); ++i) {
|
|
if (d_prbMol->getAtomWithIdx(i)->getAtomicNum() == 1) {
|
|
continue;
|
|
}
|
|
prbCtd[0] += prbPos[i][0];
|
|
prbCtd[1] += prbPos[i][1];
|
|
prbCtd[2] += prbPos[i][2];
|
|
++nHeavy;
|
|
}
|
|
prbCtd[0] /= (double)nHeavy;
|
|
prbCtd[1] /= (double)nHeavy;
|
|
prbCtd[2] /= (double)nHeavy;
|
|
rmsd = (refCtd - prbCtd).length();
|
|
}
|
|
|
|
return rmsd;
|
|
};
|
|
|
|
|
|
double O3A::align() {
|
|
double rmsd = 0.0;
|
|
const RDKit::MatchVectType *matchVectPtr = NULL;
|
|
|
|
if (d_o3aMatchVect && (d_o3aMatchVect->size() >= 3)) {
|
|
alignMol(*d_prbMol, *d_refMol, d_prbCid, d_refCid,
|
|
d_o3aMatchVect, d_o3aWeights, d_reflect, d_maxIters);
|
|
matchVectPtr = d_o3aMatchVect;
|
|
}
|
|
rmsd = _rmsdMatchVect(d_prbMol, d_refMol,
|
|
d_prbMol->getConformer(d_prbCid).getPositions(),
|
|
d_refMol->getConformer(d_refCid).getPositions(), matchVectPtr);
|
|
|
|
return rmsd;
|
|
}
|
|
|
|
|
|
double O3A::trans(RDGeom::Transform3D &trans) {
|
|
double rmsd = 0.0;
|
|
const RDKit::MatchVectType *matchVectPtr = NULL;
|
|
Conformer transConf(d_prbMol->getConformer(d_prbCid));
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if (d_o3aMatchVect && (d_o3aMatchVect->size() >= 3)) {
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getAlignmentTransform(*d_prbMol, *d_refMol,
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trans, d_prbCid, d_refCid, d_o3aMatchVect, d_o3aWeights,
|
|
d_reflect, d_maxIters);
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MolTransforms::transformConformer(transConf, trans);
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matchVectPtr = d_o3aMatchVect;
|
|
}
|
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rmsd = _rmsdMatchVect(d_prbMol, d_refMol, transConf.getPositions(),
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d_refMol->getConformer(d_refCid).getPositions(), d_o3aMatchVect);
|
|
|
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return rmsd;
|
|
};
|
|
|
|
|
|
void randomTransform(ROMol &mol, const int cid, const int seed)
|
|
{
|
|
if (seed > 0) {
|
|
rng_type &generator = getRandomGenerator();
|
|
generator.seed(seed);
|
|
}
|
|
Conformer &conf = mol.getConformer(cid);
|
|
RDGeom::POINT3D_VECT &pos = conf.getPositions();
|
|
double maxCoord[3];
|
|
double minCoord[3];
|
|
RDGeom::Point3D rndTrans;
|
|
double rndRot[3];
|
|
for (unsigned int j = 0; j < 3; ++j) {
|
|
for (unsigned int i = 0; i < pos.size(); ++i) {
|
|
if ((!i) || (pos[i][j] > maxCoord[j])) {
|
|
maxCoord[j] = pos[i][j];
|
|
}
|
|
if ((!i) || (pos[i][j] < minCoord[j])) {
|
|
minCoord[j] = pos[i][j];
|
|
}
|
|
}
|
|
rndTrans[j] = (maxCoord[j] - minCoord[j])
|
|
* O3_RANDOM_TRANS_COEFF * (getRandomVal() - 0.5);
|
|
rndRot[j] = getRandomVal() * 2.0 * M_PI;
|
|
}
|
|
RDGeom::Point3D ctd = MolTransforms::computeCentroid(conf, false);
|
|
RDGeom::Transform3D transToOrigin;
|
|
RDGeom::Transform3D xRot;
|
|
RDGeom::Transform3D yRot;
|
|
RDGeom::Transform3D zRotAndTrans;
|
|
transToOrigin.SetTranslation(-ctd);
|
|
xRot.SetRotation(rndRot[0], RDGeom::X_Axis);
|
|
yRot.SetRotation(rndRot[1], RDGeom::Y_Axis);
|
|
zRotAndTrans.SetRotation(rndRot[2], RDGeom::Z_Axis);
|
|
zRotAndTrans.SetTranslation(ctd + rndTrans);
|
|
MolTransforms::transformConformer(conf,
|
|
zRotAndTrans * yRot * xRot * transToOrigin);
|
|
}
|
|
}
|
|
}
|