RDKit: USRDescriptor.h Source File

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USRDescriptor.h
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1 //
2 // Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
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32
33 /*! \file USRDescriptor.h
34
35 \brief Contains the USR descriptor. Use MolDescriptors.h in client code.
36
37 */
38 #ifndef __RD_USR_H__
39 #define __RD_USR_H__
40
41 #include <Geometry/point.h>
42 #include <Numerics/Vector.h>
43
44 namespace RDKit {
45 class ROMol;
46 class Conformer;
47 namespace Descriptors {
48 /*!
49 Calculates the ultra-fast shape recognition (USR) descriptor
50
51 Reference: P. J. Ballester, W. G. Richards, JCC (2007), 28, 1711 - 1723.
52
53 Derived from RDKit Python implementation of Jan Domanski
54 who derived his code from Adrian Schreyer's code:
55 http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default
56
57 \param mol the molecule of interest
58 \param descriptor storage for the computed USR descriptor
59 \param confId the conformer Id
60
61 */
62 void USR(const ROMol &mol, std::vector<double> &descriptor, int confId = -1);
63
64 /*!
65 Calculates the ultra-fast shape recognition with CREDO atom types (USRCAT)
66 descriptor
67
68 Reference: A. M. Schreyer, T. Blundell, J. Cheminf. (2012), 4, 27.
69
70 Derived from Python implementation Adrian Schreyer:
71 http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default
72
73 \param mol the molecule of interest
74 \param descriptor storage for the computed USR descriptor
75 \param confId the conformer Id
76
77 */
78 void USRCAT(const ROMol &mol, std::vector<double> &descriptor,
79 std::vector<std::vector<unsigned int> > &atomIds, int confId = -1);
80 /*!
81 Calculates the four distance distributions for the USR descriptor
82
83 \param coords the atom coordinates
84 \param dist storage for the four distance distributions
85 \param points storage for the four points
86
87 */
88 void calcUSRDistributions(const RDGeom::Point3DConstPtrVect &coords,
89 std::vector<std::vector<double> > &dist,
90 std::vector<RDGeom::Point3D> &points);
91
92 /*!
93 Calculates the four distance distributions for the USR descriptor
94
95 \param coords the atom coordinates
96 \param points vector with the points
97 \param dist storage for the distance distributions
98
99 */
100 void calcUSRDistributionsFromPoints(const RDGeom::Point3DConstPtrVect &coords,
101 const std::vector<RDGeom::Point3D> &points,
102 std::vector<std::vector<double> > &dist);
103
104 /*!
105 Calculates the USR descriptor from the four distance distributions
106
107 \param dist vector with the four distance distributions
108 \param descriptor storage for the computed USR descriptor
109
110 */
111 void calcUSRFromDistributions(const std::vector<std::vector<double> > &dist,
112 std::vector<double> &descriptor);
113
114 /*!
115 Calculates the score between two USRCAT descriptors with weights
116
117 \param d1 descriptor 1
118 \param d2 descriptor 2
119 \param weights the weights for each subset of moments
120
121 \return the score
122 */
123 double calcUSRScore(const std::vector<double> &d1,
124 const std::vector<double> &d2,
125 const std::vector<double> &weights);
126
127 } // end of namespace Descriptors
128 } // end of namespace RDKit
129
130 #endif
RDKit::Descriptors::USRCAT
void USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1)
point.h
RDKit::Descriptors::calcUSRDistributions
void calcUSRDistributions(const RDGeom::Point3DConstPtrVect &coords, std::vector< std::vector< double > > &dist, std::vector< RDGeom::Point3D > &points)
RDKit::Descriptors::calcUSRFromDistributions
void calcUSRFromDistributions(const std::vector< std::vector< double > > &dist, std::vector< double > &descriptor)
RDGeom::Point3DConstPtrVect
std::vector< const RDGeom::Point3D * > Point3DConstPtrVect
Definition: point.h:503
RDKit::Descriptors::calcUSRDistributionsFromPoints
void calcUSRDistributionsFromPoints(const RDGeom::Point3DConstPtrVect &coords, const std::vector< RDGeom::Point3D > &points, std::vector< std::vector< double > > &dist)
RDKit::Descriptors::calcUSRScore
double calcUSRScore(const std::vector< double > &d1, const std::vector< double > &d2, const std::vector< double > &weights)
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::Descriptors::USR
void USR(const ROMol &mol, std::vector< double > &descriptor, int confId=-1)
Vector.h