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