RDKit: Property.h Source File

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Property.h
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1 //
2 // Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
3 // All rights reserved.
4 //
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6 // modification, are permitted provided that the following conditions are
7 // met:
8 //
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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
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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
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31 //
32 #ifndef RDKIT_PROPERTIES_H
33 #define RDKIT_PROPERTIES_H
34
35 #include <GraphMol/RDKitBase.h>
36 #include <string>
37 #include <RDGeneral/BoostStartInclude.h>
38 #include <boost/shared_ptr.hpp>
39 #include <RDGeneral/BoostEndInclude.h>
40 #include <Query/Query.h>
41 #include <RDGeneral/Exceptions.h>
42
43 namespace RDKit {
44 namespace Descriptors {
45 struct PropertyFunctor {
46 // Registry of property functions
47 // See REGISTER_DESCRIPTOR
48 std::string propName;
49 std::string propVersion;
50 double (*d_dataFunc)(const ROMol&);
51
52 PropertyFunctor(const std::string &name, const std::string &version,
53 double (*func)(const ROMol&)=NULL) :
54 propName(name), propVersion(version), d_dataFunc(func) {
55 }
56 virtual ~PropertyFunctor() {};
57
58 //! Compute the value of the property
59 virtual double operator()(const RDKit::ROMol &) const = 0;
60
61 //! Return the name of the property
62 const std::string getName() const { return propName; }
63 //! Return the properties version
64 const std::string getVersion() const { return propVersion; }
65
66 };
67
68
69 //! Holds a collection of properties for computation purposes
70 class Properties {
71 protected:
72 std::vector<boost::shared_ptr<PropertyFunctor> > m_properties;
73
74 public:
75 Properties();
76 Properties(const std::vector<std::string> &propNames);
77
78 std::vector<std::string> getPropertyNames() const;
79 std::vector<double> computeProperties(const RDKit::ROMol &mol, bool annotate=false) const;
80 void annotateProperties(RDKit::ROMol& mol) const;
81
82 //! Register a property function - takes ownership
83 static int registerProperty(PropertyFunctor *ptr);
84 static boost::shared_ptr<PropertyFunctor> getProperty(const std::string &name);
85 static std::vector<std::string> getAvailableProperties();
86 static std::vector<boost::shared_ptr<PropertyFunctor> > registry;
87
88
89 };
90
91
92 typedef Queries::Query<bool, const ROMol &, true> PROP_BOOL_QUERY;
93 typedef Queries::AndQuery<int, const ROMol &, true> PROP_AND_QUERY;
94 typedef Queries::OrQuery<int, const ROMol &, true> PROP_OR_QUERY;
95 typedef Queries::XOrQuery<int, const ROMol &, true> PROP_XOR_QUERY;
96
97 typedef Queries::EqualityQuery<double, const ROMol &, true> PROP_EQUALS_QUERY;
98
99 typedef Queries::GreaterQuery<double, const ROMol &, true> PROP_GREATER_QUERY;
100
101 typedef Queries::GreaterEqualQuery<double, const ROMol &, true>
102 PROP_GREATEREQUAL_QUERY;
103
104
105 typedef Queries::LessQuery<double, const ROMol &, true> PROP_LESS_QUERY;
106
107 typedef Queries::LessEqualQuery<double, const ROMol &, true> PROP_LESSEQUAL_QUERY;
108
109 typedef Queries::RangeQuery<double, const ROMol &, true> PROP_RANGE_QUERY;
110
111
112 template<class T>
113 T* makePropertyQuery(const std::string &name, double what) {
114 T *t = new T(what);
115 t->setDataFunc( Properties::getProperty(name)->d_dataFunc );
116 return t;
117 }
118
119
120 PROP_RANGE_QUERY *makePropertyRangeQuery(const std::string &name,
121 double min,
122 double max);
123
124 }
125 }
126 #endif
RDKit::Descriptors::PropertyFunctor
Definition: Property.h:45
RDKit::Descriptors::PropertyFunctor::~PropertyFunctor
virtual ~PropertyFunctor()
Definition: Property.h:56
BoostStartInclude.h
RDKit::Descriptors::PROP_LESS_QUERY
Queries::LessQuery< double, const ROMol &, true > PROP_LESS_QUERY
Definition: Property.h:105
RDKit::Descriptors::Properties
Holds a collection of properties for computation purposes.
Definition: Property.h:70
RDKit::Descriptors::PROP_GREATEREQUAL_QUERY
Queries::GreaterEqualQuery< double, const ROMol &, true > PROP_GREATEREQUAL_QUERY
Definition: Property.h:102
RDKit::Descriptors::PROP_XOR_QUERY
Queries::XOrQuery< int, const ROMol &, true > PROP_XOR_QUERY
Definition: Property.h:95
RDKit::Descriptors::PropertyFunctor::propVersion
std::string propVersion
Definition: Property.h:49
Queries::AndQuery
a Query implementing AND: requires all children to be true
Definition: AndQuery.h:20
Queries::OrQuery
a Query implementing AND: requires any child to be true
Definition: OrQuery.h:19
RDKit::Descriptors::PropertyFunctor::PropertyFunctor
PropertyFunctor(const std::string &name, const std::string &version, double(*func)(const ROMol &)=NULL)
Definition: Property.h:52
RDKit::Descriptors::PROP_BOOL_QUERY
Queries::Query< bool, const ROMol &, true > PROP_BOOL_QUERY
Definition: Property.h:92
RDKit::Descriptors::PROP_LESSEQUAL_QUERY
Queries::LessEqualQuery< double, const ROMol &, true > PROP_LESSEQUAL_QUERY
Definition: Property.h:107
Query.h
RDKit::Descriptors::PROP_OR_QUERY
Queries::OrQuery< int, const ROMol &, true > PROP_OR_QUERY
Definition: Property.h:94
RDKit::Descriptors::PropertyFunctor::getName
const std::string getName() const
Return the name of the property.
Definition: Property.h:62
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
Exceptions.h
RDKit::Descriptors::Properties::getProperty
static boost::shared_ptr< PropertyFunctor > getProperty(const std::string &name)
RDKit::Descriptors::PROP_RANGE_QUERY
Queries::RangeQuery< double, const ROMol &, true > PROP_RANGE_QUERY
Definition: Property.h:109
Queries::RangeQuery
a Query implementing a range: arguments must fall in a particular range of values.
Definition: RangeQuery.h:26
BoostEndInclude.h
Queries::LessEqualQuery
a Query implementing <= using a particular value (and an optional tolerance)
Definition: LessEqualQuery.h:20
RDKit::Descriptors::PROP_AND_QUERY
Queries::AndQuery< int, const ROMol &, true > PROP_AND_QUERY
Definition: Property.h:93
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::Descriptors::PROP_EQUALS_QUERY
Queries::EqualityQuery< double, const ROMol &, true > PROP_EQUALS_QUERY
Definition: Property.h:97
RDKit::Descriptors::Properties::m_properties
std::vector< boost::shared_ptr< PropertyFunctor > > m_properties
Definition: Property.h:72
RDKit::Descriptors::makePropertyRangeQuery
PROP_RANGE_QUERY * makePropertyRangeQuery(const std::string &name, double min, double max)
Queries::LessQuery
a Query implementing < using a particular value (and an optional tolerance)
Definition: LessQuery.h:20
Queries::EqualityQuery
a Query implementing ==: arguments must match a particular value (within an optional tolerance) ...
Definition: EqualityQuery.h:22
RDKit::Descriptors::PropertyFunctor::d_dataFunc
double(* d_dataFunc)(const ROMol &)
Definition: Property.h:50
RDKit::Descriptors::PropertyFunctor::propName
std::string propName
Definition: Property.h:48
Queries::GreaterQuery
a Query implementing > using a particular value (and an optional tolerance)
Definition: GreaterQuery.h:20
Queries::GreaterEqualQuery
a Query implementing >= using a particular value (and an optional tolerance)
Definition: GreaterEqualQuery.h:20
RDKit::Descriptors::PropertyFunctor::operator()
virtual double operator()(const RDKit::ROMol &) const =0
Compute the value of the property.
RDKit::Descriptors::PropertyFunctor::getVersion
const std::string getVersion() const
Return the properties version.
Definition: Property.h:64
RDKit::Descriptors::Properties::registry
static std::vector< boost::shared_ptr< PropertyFunctor > > registry
Definition: Property.h:86
RDKit::Descriptors::PROP_GREATER_QUERY
Queries::GreaterQuery< double, const ROMol &, true > PROP_GREATER_QUERY
Definition: Property.h:99
Queries::Query
Base class for all queries.
Definition: Query.h:45
Queries::XOrQuery
a Query implementing XOR: requires exactly one child to be true
Definition: XOrQuery.h:20
RDKit::Descriptors::makePropertyQuery
T * makePropertyQuery(const std::string &name, double what)
Definition: Property.h:113