RDKit: ReactionFingerprints.h Source File

| RDKit Open-source cheminformatics and machine learning.

Loading...
Searching...
No Matches
ReactionFingerprints.h
Go to the documentation of this file.
1//
2// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
3// All rights reserved.
4//
5// Redistribution and use in source and binary forms, with or without
6// modification, are permitted provided that the following conditions are
7// met:
8//
9// * Redistributions of source code must retain the above copyright
10// notice, this list of conditions and the following disclaimer.
11// * Redistributions in binary form must reproduce the above
12// copyright notice, this list of conditions and the following
13// disclaimer in the documentation and/or other materials provided
14// with the distribution.
15// * Neither the name of Novartis Institutes for BioMedical Research Inc.
16// nor the names of its contributors may be used to endorse or promote
17// products derived from this software without specific prior written
18// permission.
19//
20// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
21// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
22// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
23// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
24// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
25// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
26// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
27// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
28// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
29// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31//
32#include <RDGeneral/export.h>
33#ifndef RD_REACTIONFINGERPRINTS_H
34#define RD_REACTIONFINGERPRINTS_H
35
36#include <DataStructs/SparseIntVect.h>
37#include <DataStructs/ExplicitBitVect.h>
38
39namespace RDKit {
40
41class ChemicalReaction;
42
43 enum class FingerprintType {
44 AtomPairFP = 1,
45 TopologicalTorsionFP,
46 MorganFP,
47 RDKitFP,
48 PatternFP
49};
50
51//! A struct for storing parameters to manipulate
52//! the calculation of fingerprints of chemical reactions
53/*!
54 Different parameters can be chosen to influence the generation
55 of chemical reaction fingerprints. Generally different setting
56 should be used for structural or difference fingerprints.
57
58 \param includeAgents include the agents of a reaction for fingerprint
59 generation
60 \param bitRatioAgents in structural fingerprints it determines the
61 ratio of bits of
62 the agents in the fingerprint
63 \param nonAgentWeight in difference fingerprints weight factor for
64 reactants and products
65 compared to agents
66 \param agentWeight if agents are included, agents could be weighted
67 compared to reactants
68 and products in difference fingerprints
69 \param fpSize number of bits of the fingerprint
70 \param fpType kind of fingerprint used, e.g AtompairFP. Be
71 aware that only AtompairFP,
72 TopologicalTorsion and MorganFP were supported in
73 the difference fingerprint.
74 */
75 struct RDKIT_CHEMREACTIONS_EXPORT ReactionFingerprintParams {
76 ReactionFingerprintParams() {}
77
78 ReactionFingerprintParams(bool includeAgents, double bitRatioAgents,
79 unsigned int nonAgentWeight, int agentWeight,
80 unsigned int fpSize, FingerprintType fpType)
81 : includeAgents(includeAgents),
82 bitRatioAgents(bitRatioAgents),
83 nonAgentWeight(nonAgentWeight),
84 agentWeight(agentWeight),
85 fpSize(fpSize),
86 fpType(fpType) {}
87
88 bool includeAgents{false};
89 double bitRatioAgents{0.2};
90 unsigned int nonAgentWeight{10};
91 int agentWeight{1};
92 unsigned int fpSize{2048};
93 FingerprintType fpType{FingerprintType::AtomPairFP};
94};
95
96 RDKIT_CHEMREACTIONS_EXPORT extern const ReactionFingerprintParams
97 DefaultStructuralFPParams;
98 RDKIT_CHEMREACTIONS_EXPORT extern const ReactionFingerprintParams
99 DefaultDifferenceFPParams;
100
101//! Generates a structural fingerprint for a reaction
102//! to use in screening
103/*!
104 A structural fingerprint is generated as an ExplicitBitVect to use for
105 searching
106 e.g. substructure in reactions. By default the fingerprint is generated as
107 4096 BitVect
108 using a PatternFP for reactants and products and tentatively agents which
109 were finally concatenated
110
111 \param rxn: the reaction to be fingerprinted
112 \param params: specific settings to manipulate fingerprint generation
113
114 \return the reaction fingerprint, as an ExplicitBitVect
115
116 <b>Notes:</b>
117 - the caller is responsible for <tt>delete</tt>ing the result
118*/
119 RDKIT_CHEMREACTIONS_EXPORT ExplicitBitVect *StructuralFingerprintChemReaction(
120 const ChemicalReaction &rxn,
121 const ReactionFingerprintParams &params = DefaultStructuralFPParams);
122
123//! Generates a difference fingerprint for a reaction
124//! to use in similarity search of reactions
125/*!
126 A difference fingerprint is generated as a SparseIntVect to use for
127 similarity search of reactions. By default the fingerprint is generated as
128 2048 bit
129 hashed fingerprint subtracting AtompairFP of the reactants from the products'
130 AtompairFP
131 and tentatively the agent AtompairFP is added
132
133 \param rxn: the reaction to be fingerprinted
134 \param params: specific settings to manipulate fingerprint generation
135
136 \return the reaction fingerprint, as an SparseIntVec
137
138 <b>Notes:</b>
139 - the caller is responsible for <tt>delete</tt>ing the result
140*/
141 RDKIT_CHEMREACTIONS_EXPORT SparseIntVect<std::uint32_t> *
142DifferenceFingerprintChemReaction(
143 const ChemicalReaction &rxn,
144 const ReactionFingerprintParams &params = DefaultDifferenceFPParams);
145} // namespace RDKit
146
147#endif
ExplicitBitVect.h
SparseIntVect.h
ExplicitBitVect
a class for bit vectors that are densely occupied
Definition ExplicitBitVect.h:29
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:121
RDKit::SparseIntVect
a class for efficiently storing sparse vectors of ints
Definition SparseIntVect.h:28
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition export.h:57
RDKit::RDKitFP
Definition RDKitFPGenerator.h:18
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::StructuralFingerprintChemReaction
RDKIT_CHEMREACTIONS_EXPORT ExplicitBitVect * StructuralFingerprintChemReaction(const ChemicalReaction &rxn, const ReactionFingerprintParams &params=DefaultStructuralFPParams)
RDKit::DifferenceFingerprintChemReaction
RDKIT_CHEMREACTIONS_EXPORT SparseIntVect< std::uint32_t > * DifferenceFingerprintChemReaction(const ChemicalReaction &rxn, const ReactionFingerprintParams &params=DefaultDifferenceFPParams)
RDKit::DefaultStructuralFPParams
RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams DefaultStructuralFPParams
RDKit::DefaultDifferenceFPParams
RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams DefaultDifferenceFPParams
RDKit::FingerprintType
FingerprintType
Definition ReactionFingerprints.h:43
RDKit::FingerprintType::TopologicalTorsionFP
@ TopologicalTorsionFP
Definition ReactionFingerprints.h:45
RDKit::FingerprintType::MorganFP
@ MorganFP
Definition ReactionFingerprints.h:46
RDKit::FingerprintType::PatternFP
@ PatternFP
Definition ReactionFingerprints.h:48
RDKit::FingerprintType::AtomPairFP
@ AtomPairFP
Definition ReactionFingerprints.h:44
RDKit::ReactionFingerprintParams
Definition ReactionFingerprints.h:75
RDKit::ReactionFingerprintParams::bitRatioAgents
double bitRatioAgents
Definition ReactionFingerprints.h:89
RDKit::ReactionFingerprintParams::ReactionFingerprintParams
ReactionFingerprintParams()
Definition ReactionFingerprints.h:76
RDKit::ReactionFingerprintParams::includeAgents
bool includeAgents
Definition ReactionFingerprints.h:88
RDKit::ReactionFingerprintParams::ReactionFingerprintParams
ReactionFingerprintParams(bool includeAgents, double bitRatioAgents, unsigned int nonAgentWeight, int agentWeight, unsigned int fpSize, FingerprintType fpType)
Definition ReactionFingerprints.h:78
RDKit::ReactionFingerprintParams::fpType
FingerprintType fpType
Definition ReactionFingerprints.h:93
RDKit::ReactionFingerprintParams::fpSize
unsigned int fpSize
Definition ReactionFingerprints.h:92
RDKit::ReactionFingerprintParams::nonAgentWeight
unsigned int nonAgentWeight
Definition ReactionFingerprints.h:90
RDKit::ReactionFingerprintParams::agentWeight
int agentWeight
Definition ReactionFingerprints.h:91