RDKit: FilterMatcherBase.h Source File

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FilterMatcherBase.h
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1 // Copyright (c) 2015, 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
32 #ifndef __RD_FILTER_MATCHER_BASE_H__
33 #define __RD_FILTER_MATCHER_BASE_H__
34 #include <GraphMol/RDKitBase.h>
35 #include <GraphMol/Substruct/SubstructMatch.h>
36
37 #ifdef RDK_USE_BOOST_SERIALIZATION
38 #include <RDGeneral/BoostStartInclude.h>
39 #include <boost/archive/text_oarchive.hpp>
40 #include <boost/archive/text_iarchive.hpp>
41 #include <boost/serialization/assume_abstract.hpp>
42 #include <boost/enable_shared_from_this.hpp>
43 #include <RDGeneral/BoostEndInclude.h>
44 #endif // RDK_USE_BOOST_SERIALIZATION
45
46 namespace RDKit {
47
48 class FilterMatcherBase; // Forward declaration
49
50 //! Holds the atomPairs matched by the underlying matcher
51 struct FilterMatch {
52 boost::shared_ptr<FilterMatcherBase> filterMatch;
53 MatchVectType atomPairs;
54
55 FilterMatch() : filterMatch(), atomPairs() {}
56 FilterMatch(boost::shared_ptr<FilterMatcherBase> filter,
57 MatchVectType atomPairs)
58 : filterMatch(filter), atomPairs(atomPairs) {}
59
60 FilterMatch(const FilterMatch &rhs)
61 : filterMatch(rhs.filterMatch), atomPairs(rhs.atomPairs) {}
62
63 bool operator==(const FilterMatch &rhs) const {
64 return (filterMatch.get() == rhs.filterMatch.get() &&
65 atomPairs == rhs.atomPairs);
66 }
67
68 bool operator!=(const FilterMatch &rhs) const {
69 return !(filterMatch.get() == rhs.filterMatch.get() &&
70 atomPairs == rhs.atomPairs);
71 }
72
73 };
74
75 extern const char *DEFAULT_FILTERMATCHERBASE_NAME;
76 class FilterMatcherBase
77 : public boost::enable_shared_from_this<FilterMatcherBase> {
78 //------------------------------------
79 //! Virtual API for filter matching
80 std::string d_filterName;
81
82 public:
83 FilterMatcherBase(const std::string &name = DEFAULT_FILTERMATCHERBASE_NAME)
84 : boost::enable_shared_from_this<FilterMatcherBase>(),
85 d_filterName(name) {}
86
87 FilterMatcherBase(const FilterMatcherBase &rhs)
88 : boost::enable_shared_from_this<FilterMatcherBase>(),
89 d_filterName(rhs.d_filterName) {}
90
91 virtual ~FilterMatcherBase() {}
92
93 virtual bool isValid() const = 0;
94
95 virtual std::string getName() const { return d_filterName; }
96 //------------------------------------
97 //! getMatches
98 /*!
99 Match the filter against a molecule
100
101 \param mol readonly const molecule being searched
102 \param matches output vector of atom index matches found in the molecule
103 */
104
105 virtual bool getMatches(const ROMol &mol,
106 std::vector<FilterMatch> &matchVect) const = 0;
107
108 //------------------------------------
109 //! hasMatches
110 /*!
111 Does the given molecule contain this filter pattern
112
113 \param mol readonly const molecule being searched
114 */
115
116 virtual bool hasMatch(const ROMol &mol) const = 0;
117
118 //------------------------------------
119 //! Clone - deprecated
120 // Clones the current FilterMatcherBase into one that
121 // can be passed around safely.
122 virtual boost::shared_ptr<FilterMatcherBase> Clone() const {
123 BOOST_LOG(rdWarningLog) << "FilterMatcherBase::Clone is deprecated, use copy instead" << std::endl;
124 return copy();
125 }
126
127 //------------------------------------
128 //! copy
129 // copies the current FilterMatcherBase into one that
130 // can be passed around safely.
131 virtual boost::shared_ptr<FilterMatcherBase> copy() const = 0;
132
133 private:
134 #ifdef RDK_USE_BOOST_SERIALIZATION
135 friend class boost::serialization::access;
136 template <class Archive>
137 void serialize(Archive &ar, const unsigned int version) {
138 RDUNUSED_PARAM(version);
139 ar &d_filterName;
140 }
141 #endif
142 };
143
144 #ifdef RDK_USE_BOOST_SERIALIZATION
145 BOOST_SERIALIZATION_ASSUME_ABSTRACT(FilterMatcherBase)
146 #endif
147 }
148 #endif
RDKit::FilterMatcherBase::getName
virtual std::string getName() const
Definition: FilterMatcherBase.h:95
RDKit::FilterMatcherBase::Clone
virtual boost::shared_ptr< FilterMatcherBase > Clone() const
Clone - deprecated.
Definition: FilterMatcherBase.h:122
BoostStartInclude.h
boost
Definition: RDLog.h:20
BOOST_LOG
#define BOOST_LOG(__arg__)
Definition: RDLog.h:87
RDKit::FilterMatch::FilterMatch
FilterMatch()
Definition: FilterMatcherBase.h:55
RDKit::DEFAULT_FILTERMATCHERBASE_NAME
const char * DEFAULT_FILTERMATCHERBASE_NAME
RDKit::FilterMatch::operator==
bool operator==(const FilterMatch &rhs) const
Definition: FilterMatcherBase.h:63
RDKit::FilterMatcherBase::FilterMatcherBase
FilterMatcherBase(const std::string &name=DEFAULT_FILTERMATCHERBASE_NAME)
Definition: FilterMatcherBase.h:83
RDKit::MatchVectType
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx) ...
Definition: FragFPGenerator.h:23
RDKit::FilterMatch
Holds the atomPairs matched by the underlying matcher.
Definition: FilterMatcherBase.h:51
RDKit::FilterMatch::filterMatch
boost::shared_ptr< FilterMatcherBase > filterMatch
Definition: FilterMatcherBase.h:52
SubstructMatch.h
RDKitBase.h
pulls in the core RDKit functionality
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
rdWarningLog
boost::logging::rdLogger * rdWarningLog
RDKit::FilterMatch::atomPairs
MatchVectType atomPairs
Definition: FilterMatcherBase.h:53
RDKit::FilterMatcherBase
Definition: FilterMatcherBase.h:76
BoostEndInclude.h
RDKit::FilterMatch::FilterMatch
FilterMatch(const FilterMatch &rhs)
Definition: FilterMatcherBase.h:60
RDKit::FilterMatcherBase::FilterMatcherBase
FilterMatcherBase(const FilterMatcherBase &rhs)
Definition: FilterMatcherBase.h:87
RDKit::FilterMatch::FilterMatch
FilterMatch(boost::shared_ptr< FilterMatcherBase > filter, MatchVectType atomPairs)
Definition: FilterMatcherBase.h:56
RDKit
Std stuff.
Definition: Atom.h:29
RDUNUSED_PARAM
#define RDUNUSED_PARAM(x)
Definition: Invariant.h:194
RDKit::FilterMatch::operator!=
bool operator!=(const FilterMatch &rhs) const
Definition: FilterMatcherBase.h:68
RDKit::FilterMatcherBase::~FilterMatcherBase
virtual ~FilterMatcherBase()
Definition: FilterMatcherBase.h:91