RDKit
Open-source cheminformatics and machine learning.
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RascalOptions.h
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1//
2// Copyright (C) David Cosgrove 2023
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10#include <string>
11#include <RDGeneral/export.h>
12
13#ifndef RASCALOPTIONS_H
14#define RASCALOPTIONS_H
15
16namespace RDKit {
17
18namespace RascalMCES {
19
21 double similarityThreshold =
22 0.7; // if calculated below this, no MCES will be evaluated.
23 bool completeAromaticRings =
24 true; // if true, partial aromatic rings won't be returned
25 bool ringMatchesRingOnly =
26 false; // if true, ring bonds won't match non-ring bonds
27 bool exactConnectionsMatch =
28 false; /* if true, atoms will only match atoms if they have the same
29 number of explicit connections. E.g. the central atom of
30 C(C)(C) won't match either atom in CC */
31 bool singleLargestFrag =
32 false; /* if true, only return a single fragment for the MCES. Default
33 is to produce multiple matching fragments if necessary. */
34 int minFragSize =
35 -1; /* minimum number of atoms in any fragment - -1 means no minimum */
36 int maxFragSeparation = -1; /* biggest through-bond distance that bonds can
37 match. -1 means no limit. */
38 bool allBestMCESs =
39 false; /* If true, all MCESs are returned, in order of diminishing score.
40 This is likely to result in higher run times. */
41 int timeout = 60; // max run time, in seconds. -1 means no max.
42 bool doEquivBondPruning =
43 false; /* This might make the code run a bit faster in some
44 circumstances, but on average it is very marginal. */
45 bool returnEmptyMCES = false; /* if true, if the similarity thresholds aren't
46 matched still return a RascalResult with the
47 tier1 and tier2 sims filled in. */
48 unsigned int maxBondMatchPairs = 1000; /* Too many matching bond (vertex)
49 pairs can cause it to run out of memory. This
50 is a reasonable default for my Mac. */
51 std::string equivalentAtoms = ""; /* SMARTS strings defining atoms that should
52 be considered equivalent. e.g.
53 [F,Cl,Br,I] so all halogens will match
54 each other. Space-separated list allowing
55 more than 1 class of equivalent atoms.*/
56 bool ignoreBondOrders = false; /* If true, will treat all bonds as the same,
57 irrespective of order. */
58 bool ignoreAtomAromaticity = true; /* If true, atoms are matched just on
59 atomic number; if false, will treat
60 aromatic and aliphatic as different. */
61};
62} // namespace RascalMCES
63} // namespace RDKit
64
65#endif // RASCALOPTIONS_H
#define RDKIT_RASCALMCES_EXPORT
Definition export.h:449
Std stuff.