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.
3// All rights reserved.
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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#include <RDGeneral/export.h>
39#ifndef __RD_USR_H__
40#define __RD_USR_H__
41
42#include <Geometry/point.h>
43#include <Numerics/Vector.h>
44
45namespace RDKit {
46class ROMol;
47class Conformer;
48namespace Descriptors {
49/*!
50 Calculates the ultra-fast shape recognition (USR) descriptor
51
52 Reference: P. J. Ballester, W. G. Richards, JCC (2007), 28, 1711 - 1723.
53
54 Derived from RDKit Python implementation of Jan Domanski
55 who derived his code from Adrian Schreyer's code:
56 http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default
57
58 \param mol the molecule of interest
59 \param descriptor storage for the computed USR descriptor
60 \param confId the conformer Id
61
62*/
63 RDKIT_DESCRIPTORS_EXPORT void USR(const ROMol &mol,
64 std::vector<double> &descriptor,
65 int confId = -1);
66
67/*!
68 Calculates the ultra-fast shape recognition with CREDO atom types (USRCAT)
69 descriptor
70
71 Reference: A. M. Schreyer, T. Blundell, J. Cheminf. (2012), 4, 27.
72
73 Derived from Python implementation Adrian Schreyer:
74 http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default
75
76 \param mol the molecule of interest
77 \param descriptor storage for the computed USR descriptor
78 \param confId the conformer Id
79
80*/
81 RDKIT_DESCRIPTORS_EXPORT void USRCAT(
82 const ROMol &mol, std::vector<double> &descriptor,
83 std::vector<std::vector<unsigned int>> &atomIds, int confId = -1);
84/*!
85 Calculates the four distance distributions for the USR descriptor
86
87 \param coords the atom coordinates
88 \param dist storage for the four distance distributions
89 \param points storage for the four points
90
91*/
92 RDKIT_DESCRIPTORS_EXPORT void calcUSRDistributions(
93 const RDGeom::Point3DConstPtrVect &coords,
94 std::vector<std::vector<double>> &dist,
95 std::vector<RDGeom::Point3D> &points);
96
97/*!
98 Calculates the four distance distributions for the USR descriptor
99
100 \param coords the atom coordinates
101 \param points vector with the points
102 \param dist storage for the distance distributions
103
104*/
105 RDKIT_DESCRIPTORS_EXPORT void calcUSRDistributionsFromPoints(
106 const RDGeom::Point3DConstPtrVect &coords,
107 const std::vector<RDGeom::Point3D> &points,
108 std::vector<std::vector<double>> &dist);
109
110/*!
111 Calculates the USR descriptor from the four distance distributions
112
113 \param dist vector with the four distance distributions
114 \param descriptor storage for the computed USR descriptor
115
116*/
117 RDKIT_DESCRIPTORS_EXPORT void calcUSRFromDistributions(
118 const std::vector<std::vector<double>> &dist,
119 std::vector<double> &descriptor);
120
121/*!
122 Calculates the score between two USRCAT descriptors with weights
123
124 \param d1 descriptor 1
125 \param d2 descriptor 2
126 \param weights the weights for each subset of moments
127
128 \return the score
129*/
130 RDKIT_DESCRIPTORS_EXPORT double calcUSRScore(
131 const std::vector<double> &d1, const std::vector<double> &d2,
132 const std::vector<double> &weights);
133
134} // end of namespace Descriptors
135} // end of namespace RDKit
136
137#endif
Vector.h
RDKit::Conformer
The class for representing 2D or 3D conformation of a molecule.
Definition Conformer.h:46
RDKit::ROMol
Definition ROMol.h:199
export.h
RDKIT_DESCRIPTORS_EXPORT
#define RDKIT_DESCRIPTORS_EXPORT
Definition export.h:113
RDGeom::Point3DConstPtrVect
std::vector< const RDGeom::Point3D * > Point3DConstPtrVect
Definition point.h:548
RDKit::Descriptors
Definition AtomFeat.h:30
RDKit::Descriptors::calcUSRScore
RDKIT_DESCRIPTORS_EXPORT double calcUSRScore(const std::vector< double > &d1, const std::vector< double > &d2, const std::vector< double > &weights)
RDKit::Descriptors::USR
RDKIT_DESCRIPTORS_EXPORT void USR(const ROMol &mol, std::vector< double > &descriptor, int confId=-1)
RDKit::Descriptors::calcUSRDistributionsFromPoints
RDKIT_DESCRIPTORS_EXPORT void calcUSRDistributionsFromPoints(const RDGeom::Point3DConstPtrVect &coords, const std::vector< RDGeom::Point3D > &points, std::vector< std::vector< double > > &dist)
RDKit::Descriptors::calcUSRFromDistributions
RDKIT_DESCRIPTORS_EXPORT void calcUSRFromDistributions(const std::vector< std::vector< double > > &dist, std::vector< double > &descriptor)
RDKit::Descriptors::USRCAT
RDKIT_DESCRIPTORS_EXPORT void USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1)
RDKit::Descriptors::calcUSRDistributions
RDKIT_DESCRIPTORS_EXPORT void calcUSRDistributions(const RDGeom::Point3DConstPtrVect &coords, std::vector< std::vector< double > > &dist, std::vector< RDGeom::Point3D > &points)
RDKit
Std stuff.
Definition Abbreviations.h:19
point.h