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 completeSmallestRings =
28 false; // if true, only complete rings present in both input molecule's
29 // RingInfo will be returned. Implies completeAromaticRings and
30 // ringMatchesRingOnly.
31 bool exactConnectionsMatch =
32 false; /* if true, atoms will only match atoms if they have the same
33 number of explicit connections. E.g. the central atom of
34 C(C)(C) won't match either atom in CC */
35 bool singleLargestFrag =
36 false; /* if true, only return a single fragment for the MCES. Default
37 is to produce multiple matching fragments if necessary. */
38 int minFragSize =
39 -1; /* minimum number of atoms in any fragment - -1 means no minimum */
40 int maxFragSeparation = -1; /* biggest through-bond distance that bonds can
41 match. -1 means no limit. */
42 bool allBestMCESs =
43 false; /* If true, all MCESs are returned, in order of diminishing score.
44 This is likely to result in higher run times. */
45 int timeout = 60; // max run time, in seconds. -1 means no max.
46 bool doEquivBondPruning =
47 false; /* This might make the code run a bit faster in some
48 circumstances, but on average it is very marginal. */
49 bool returnEmptyMCES = false; /* if true, if the similarity thresholds aren't
50 matched still return a RascalResult with the
51 tier1 and tier2 sims filled in. */
52 unsigned int maxBondMatchPairs = 1000; /* Too many matching bond (vertex)
53 pairs can cause it to run out of memory. This
54 is a reasonable default for my Mac. */
55 std::string equivalentAtoms = ""; /* SMARTS strings defining atoms that should
56 be considered equivalent. e.g.
57 [F,Cl,Br,I] so all halogens will match
58 each other. Space-separated list allowing
59 more than 1 class of equivalent atoms.*/
60 bool ignoreBondOrders = false; /* If true, will treat all bonds as the same,
61 irrespective of order. */
62 bool ignoreAtomAromaticity = true; /* If true, atoms are matched just on
63 atomic number; if false, will treat
64 aromatic and aliphatic as different. */
65 unsigned int minCliqueSize = 0; /* Normally, the minimum clique size is
66 specified via the similarityThreshold.
67 Sometimes it's more convenient to
68 specify it directly. If this is > 0,
69 it will over-ride the similarityThreshold.
70 Note that this refers to the minimum
71 number of BONDS in the MCES. */
72};
73} // namespace RascalMCES
74} // namespace RDKit
75
76#endif // RASCALOPTIONS_H
#define RDKIT_RASCALMCES_EXPORT
Definition export.h:449
Std stuff.