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* Add option to specify minimum clique size directly. * Make the minCliqueSize uint and default to 0. * Brain-fade. * Send timeout and 'too many bonds' message to BOOST_LOG rather than std::cout, std::cerr respectively. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
73 lines
3.6 KiB
C++
73 lines
3.6 KiB
C++
//
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// Copyright (C) David Cosgrove 2023
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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 <string>
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#include <RDGeneral/export.h>
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#ifndef RASCALOPTIONS_H
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#define RASCALOPTIONS_H
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namespace RDKit {
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namespace RascalMCES {
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struct RDKIT_RASCALMCES_EXPORT RascalOptions {
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double similarityThreshold =
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0.7; // if calculated below this, no MCES will be evaluated.
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bool completeAromaticRings =
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true; // if true, partial aromatic rings won't be returned
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bool ringMatchesRingOnly =
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false; // if true, ring bonds won't match non-ring bonds
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bool exactConnectionsMatch =
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false; /* if true, atoms will only match atoms if they have the same
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number of explicit connections. E.g. the central atom of
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C(C)(C) won't match either atom in CC */
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bool singleLargestFrag =
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false; /* if true, only return a single fragment for the MCES. Default
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is to produce multiple matching fragments if necessary. */
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int minFragSize =
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-1; /* minimum number of atoms in any fragment - -1 means no minimum */
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int maxFragSeparation = -1; /* biggest through-bond distance that bonds can
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match. -1 means no limit. */
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bool allBestMCESs =
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false; /* If true, all MCESs are returned, in order of diminishing score.
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This is likely to result in higher run times. */
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int timeout = 60; // max run time, in seconds. -1 means no max.
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bool doEquivBondPruning =
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false; /* This might make the code run a bit faster in some
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circumstances, but on average it is very marginal. */
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bool returnEmptyMCES = false; /* if true, if the similarity thresholds aren't
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matched still return a RascalResult with the
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tier1 and tier2 sims filled in. */
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unsigned int maxBondMatchPairs = 1000; /* Too many matching bond (vertex)
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pairs can cause it to run out of memory. This
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is a reasonable default for my Mac. */
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std::string equivalentAtoms = ""; /* SMARTS strings defining atoms that should
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be considered equivalent. e.g.
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[F,Cl,Br,I] so all halogens will match
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each other. Space-separated list allowing
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more than 1 class of equivalent atoms.*/
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bool ignoreBondOrders = false; /* If true, will treat all bonds as the same,
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irrespective of order. */
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bool ignoreAtomAromaticity = true; /* If true, atoms are matched just on
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atomic number; if false, will treat
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aromatic and aliphatic as different. */
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unsigned int minCliqueSize = 0; /* Normally, the minimum clique size is
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specified via the similarityThreshold.
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Sometimes it's more convenient to
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specify it directly. If this is > 0,
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it will over-ride the similarityThreshold.
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Note that this refers to the minimum
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number of BONDS in the MCES. */
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};
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} // namespace RascalMCES
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} // namespace RDKit
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#endif // RASCALOPTIONS_H
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