1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
//
// 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. This
works by finding the largest MCES and keeping just the largest
fragment. It is equivalent to running a normal MCES search
and using the largestFragOnly() method on the results. This
option may not produce the largest possible single fragment
that the molecules have in common. If you definitely want that
you may be better off using rdFMCS. */
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. */
unsigned int maxBestMCESs = 10000; /* Some pathological cases produce huge
numbers of equivalent solutions that
can crash the program due to memory
depletion. This caps the number of
such solutions to prevent this
happening. */
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
|
