RDKit: SubstructLibrarySerialization.h Source File

| RDKit Open-source cheminformatics and machine learning.

Loading...
Searching...
No Matches
SubstructLibrarySerialization.h
Go to the documentation of this file.
1// Copyright (c) 2019, Novartis Institutes for BioMedical Research Inc.
2// All rights reserved.
3//
4// Redistribution and use in source and binary forms, with or without
5// modification, are permitted provided that the following conditions are
6// met:
7//
8// * Redistributions of source code must retain the above copyright
9// notice, this list of conditions and the following disclaimer.
10// * Redistributions in binary form must reproduce the above
11// copyright notice, this list of conditions and the following
12// disclaimer in the documentation and/or other materials provided
13// with the distribution.
14// * Neither the name of Novartis Institutes for BioMedical Research Inc.
15// nor the names of its contributors may be used to endorse or promote
16// products derived from this software without specific prior written
17// permission.
18//
19// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
20// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
21// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
22// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
23// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
24// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
25// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
26// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
27// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
28// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
29// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
30//
31// n.b. must be included at the END of SubstructLibrary.h
32#ifndef RDK_SUBSTRUCT_LIBRARY_SERIALIZATION
33#define RDK_SUBSTRUCT_LIBRARY_SERIALIZATION
34
35#ifdef RDK_USE_BOOST_SERIALIZATION
36#include <RDGeneral/BoostStartInclude.h>
37#include <boost/archive/text_oarchive.hpp>
38#include <boost/archive/text_iarchive.hpp>
39#include <boost/serialization/vector.hpp>
40#include <boost/serialization/shared_ptr.hpp>
41#include <boost/archive/archive_exception.hpp>
42#include <RDGeneral/BoostEndInclude.h>
43
44BOOST_SERIALIZATION_ASSUME_ABSTRACT(RDKit::MolHolderBase)
45BOOST_SERIALIZATION_ASSUME_ABSTRACT(RDKit::FPHolderBase)
46
47namespace boost {
48namespace serialization {
49
50template <class Archive>
51void serialize(Archive &, RDKit::MolHolderBase &, const unsigned int) {}
52
53template <class Archive>
54void save(Archive &ar, const RDKit::MolHolder &molholder,
55 const unsigned int version) {
56 ar &boost::serialization::base_object<RDKit::MolHolderBase>(molholder);
57
58 if (version < 2) {
59 std::int64_t pkl_count = molholder.getMols().size();
60 ar & pkl_count;
61
62 for (auto &mol : molholder.getMols()) {
63 std::string pkl;
64 RDKit::MolPickler::pickleMol(*mol.get(), pkl);
65 ar << pkl;
66 }
67 } else {
68 ar & molholder.getMols();
69 }
70}
71
72template <class Archive>
73void load(Archive &ar, RDKit::MolHolder &molholder,
74 const unsigned int version) {
75 ar &boost::serialization::base_object<RDKit::MolHolderBase>(molholder);
76
77 std::vector<boost::shared_ptr<RDKit::ROMol>> &mols = molholder.getMols();
78 mols.clear();
79
80 if (version < 2) {
81 std::int64_t pkl_count = -1;
82 ar & pkl_count;
83
84 for (std::int64_t i = 0; i < pkl_count; ++i) {
85 std::string pkl;
86 ar >> pkl;
87 mols.push_back(boost::make_shared<RDKit::ROMol>(pkl));
88 }
89 } else {
90 ar & mols;
91 }
92}
93
94template <class Archive, class MolHolder>
95void serialize_strings(Archive &ar, MolHolder &molholder,
96 const unsigned int version) {
97 RDUNUSED_PARAM(version);
98 ar &boost::serialization::base_object<RDKit::MolHolderBase>(molholder);
99 ar & molholder.getMols();
100}
101
102template <class Archive>
103void serialize(Archive &ar, RDKit::CachedMolHolder &molholder,
104 const unsigned int version) {
105 serialize_strings(ar, molholder, version);
106}
107
108template <class Archive>
109void serialize(Archive &ar, RDKit::CachedSmilesMolHolder &molholder,
110 const unsigned int version) {
111 serialize_strings(ar, molholder, version);
112}
113
114template <class Archive>
115void serialize(Archive &ar, RDKit::CachedTrustedSmilesMolHolder &molholder,
116 const unsigned int version) {
117 serialize_strings(ar, molholder, version);
118}
119
120template <class Archive>
121void save(Archive &ar, const RDKit::FPHolderBase &fpholder,
122 const unsigned int version) {
123 RDUNUSED_PARAM(version);
124 std::vector<std::string> pickles;
125 for (auto &fp : fpholder.getFingerprints()) {
126 pickles.push_back(fp->toString());
127 }
128 ar & pickles;
129}
130
131template <class Archive>
132void load(Archive &ar, RDKit::FPHolderBase &fpholder,
133 const unsigned int version) {
134 RDUNUSED_PARAM(version);
135 std::vector<std::string> pickles;
136 std::vector<ExplicitBitVect *> &fps = fpholder.getFingerprints();
137
138 ar & pickles;
139 for (size_t i = 0; i < fps.size(); ++i) {
140 delete fps[i];
141 }
142 fps.clear();
143
144 for (auto &pkl : pickles) {
145 fps.push_back(new ExplicitBitVect(pkl));
146 }
147}
148
149template <class Archive>
150void serialize(Archive &ar, RDKit::PatternHolder &pattern_holder,
151 const unsigned int version) {
152 RDUNUSED_PARAM(version);
153 ar &boost::serialization::base_object<RDKit::FPHolderBase>(pattern_holder);
154 if (Archive::is_saving::value &&
155 pattern_holder.getNumBits() != RDKit::PatternHolder::defaultNumBits()) {
156 ar & pattern_holder.getNumBits();
157 } else if (Archive::is_loading::value) {
158 try {
159 ar & pattern_holder.getNumBits();
160 } catch (boost::archive::archive_exception &) {
161 pattern_holder.getNumBits() = RDKit::PatternHolder::defaultNumBits();
162 }
163 }
164}
165
166template <class Archive>
167void serialize(Archive &ar, RDKit::TautomerPatternHolder &pattern_holder,
168 const unsigned int version) {
169 RDUNUSED_PARAM(version);
170 ar &boost::serialization::base_object<RDKit::FPHolderBase>(pattern_holder);
171 ar & pattern_holder.getNumBits();
172}
173
174template <class Archive>
175void serialize(Archive &, RDKit::KeyHolderBase &, const unsigned int) {}
176
177template <class Archive>
178void serialize(Archive &ar, RDKit::KeyFromPropHolder &key_holder,
179 const unsigned int) {
180 ar &boost::serialization::base_object<RDKit::KeyHolderBase>(key_holder);
181 ar & key_holder.getPropName();
182 ar & key_holder.getKeys();
183}
184
185template <class Archive>
186void registerSubstructLibraryTypes(Archive &ar) {
187 ar.register_type(static_cast<RDKit::MolHolder *>(nullptr));
188 ar.register_type(static_cast<RDKit::CachedMolHolder *>(nullptr));
189 ar.register_type(static_cast<RDKit::CachedSmilesMolHolder *>(nullptr));
190 ar.register_type(static_cast<RDKit::CachedTrustedSmilesMolHolder *>(nullptr));
191 ar.register_type(static_cast<RDKit::PatternHolder *>(nullptr));
192 ar.register_type(static_cast<RDKit::TautomerPatternHolder *>(nullptr));
193 ar.register_type(static_cast<RDKit::KeyFromPropHolder *>(nullptr));
194}
195
196template <class Archive>
197void save(Archive &ar, const RDKit::SubstructLibrary &slib,
198 const unsigned int version) {
199 RDUNUSED_PARAM(version);
200 registerSubstructLibraryTypes(ar);
201 ar & slib.getSearchOrder();
202 ar & slib.getKeyHolder();
203 ar & slib.getMolHolder();
204 ar & slib.getFpHolder();
205}
206
207template <class Archive>
208void load(Archive &ar, RDKit::SubstructLibrary &slib,
209 const unsigned int version) {
210 RDUNUSED_PARAM(version);
211 registerSubstructLibraryTypes(ar);
212 if (version > 1) {
213 ar & slib.getSearchOrder();
214 ar & slib.getKeyHolder();
215 }
216 ar & slib.getMolHolder();
217 ar & slib.getFpHolder();
218 slib.resetHolders();
219}
220
221} // end namespace serialization
222} // end namespace boost
223
224BOOST_CLASS_VERSION(RDKit::MolHolder, 2);
225BOOST_CLASS_VERSION(RDKit::CachedMolHolder, 1);
226BOOST_CLASS_VERSION(RDKit::CachedSmilesMolHolder, 1);
227BOOST_CLASS_VERSION(RDKit::CachedTrustedSmilesMolHolder, 1);
228BOOST_CLASS_VERSION(RDKit::PatternHolder, 1);
229BOOST_CLASS_VERSION(RDKit::TautomerPatternHolder, 1);
230BOOST_CLASS_VERSION(RDKit::SubstructLibrary, 2);
231
232BOOST_SERIALIZATION_SPLIT_FREE(RDKit::MolHolder);
233BOOST_SERIALIZATION_SPLIT_FREE(RDKit::FPHolderBase);
234BOOST_SERIALIZATION_SPLIT_FREE(RDKit::SubstructLibrary);
235
236#endif
237#endif
BoostEndInclude.h
BoostStartInclude.h
RDUNUSED_PARAM
#define RDUNUSED_PARAM(x)
Definition Invariant.h:196
RDKit::CachedMolHolder
Concrete class that holds binary cached molecules in memory.
Definition SubstructLibrary.h:121
RDKit::CachedSmilesMolHolder
Concrete class that holds smiles strings in memory.
Definition SubstructLibrary.h:167
RDKit::CachedTrustedSmilesMolHolder
Concrete class that holds trusted smiles strings in memory.
Definition SubstructLibrary.h:218
RDKit::FPHolderBase
Base FPI for the fingerprinter used to rule out impossible matches.
Definition SubstructLibrary.h:258
RDKit::FPHolderBase::getFingerprints
std::vector< ExplicitBitVect * > & getFingerprints()
Definition SubstructLibrary.h:313
RDKit::KeyFromPropHolder::getKeys
std::vector< std::string > & getKeys()
Definition SubstructLibrary.h:385
RDKit::KeyFromPropHolder::getPropName
std::string & getPropName()
Definition SubstructLibrary.h:382
RDKit::MolHolderBase
Base class API for holding molecules to substructure search.
Definition SubstructLibrary.h:67
RDKit::MolHolder
Concrete class that holds molecules in memory.
Definition SubstructLibrary.h:87
RDKit::MolHolder::getMols
std::vector< boost::shared_ptr< ROMol > > & getMols()
Definition SubstructLibrary.h:109
RDKit::MolPickler::pickleMol
static void pickleMol(const ROMol *mol, std::ostream &ss)
pickles a molecule and sends the results to stream ss
RDKit::PatternHolder
Definition SubstructLibrary.h:319
RDKit::PatternHolder::getNumBits
const unsigned int & getNumBits() const
Definition SubstructLibrary.h:329
RDKit::PatternHolder::defaultNumBits
static unsigned int defaultNumBits()
Definition SubstructLibrary.h:331
RDKit::SubstructLibrary
Substructure Search a library of molecules.
Definition SubstructLibrary.h:519
RDKit::SubstructLibrary::getMolHolder
boost::shared_ptr< MolHolderBase > & getMolHolder()
Get the underlying molecule holder implementation.
Definition SubstructLibrary.h:596
RDKit::SubstructLibrary::getFpHolder
boost::shared_ptr< FPHolderBase > & getFpHolder()
Get the underlying molecule holder implementation.
Definition SubstructLibrary.h:603
RDKit::SubstructLibrary::getKeyHolder
boost::shared_ptr< KeyHolderBase > & getKeyHolder()
Get the underlying molecule holder implementation.
Definition SubstructLibrary.h:611
RDKit::SubstructLibrary::getSearchOrder
const std::vector< unsigned int > & getSearchOrder() const
Definition SubstructLibrary.h:943
RDKit::SubstructLibrary::resetHolders
void resetHolders()
access required for serialization
Definition SubstructLibrary.h:949
RDKit::TautomerPatternHolder
Definition SubstructLibrary.h:338
RDKit::MolStandardize::Operations::serialize
RDKIT_MOLSTANDARDIZE_EXPORT void serialize(RWMOL_SPTR_PAIR output, PipelineResult &result, const PipelineOptions &options)
boost
Definition RDLog.h:24