RDKit
Open-source cheminformatics and machine learning.
PMI.h
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1 //
2 // Copyright (C) 2016 Greg Landrum
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 
11 #ifndef PMI_H_SEPT2016
12 #define PMI_H_SEPT2016
13 
14 #ifdef RDK_BUILD_DESCRIPTORS3D
15 namespace RDKit {
16 class ROMol;
17 namespace Descriptors {
18 //! Normalized principal moments ratio 1 (=I1/I3)
19 //! from Sauer and Schwarz JCIM 43:987-1003 (2003)
20 //! https://dx.doi.org/10.1021/ci025599w
21 double NPR1(const ROMol&, int confId = -1, bool useAtomicMasses = true);
22 const std::string NPR1Version = "1.0.0";
23 //! Normalized principal moments ratio 2 (=I2/I3)
24 //! from Sauer and Schwarz JCIM 43:987-1003 (2003)
25 //! https://dx.doi.org/10.1021/ci025599w
26 double NPR2(const ROMol&, int confId = -1, bool useAtomicMasses = true);
27 const std::string NPR2Version = "1.0.0";
28 
29 //! First (smallest) principal moment of inertia
30 double PMI1(const ROMol&, int confId = -1, bool useAtomicMasses = true);
31 const std::string PMI1Version = "1.0.0";
32 //! second principal moment of inertia
33 double PMI2(const ROMol&, int confId = -1, bool useAtomicMasses = true);
34 const std::string PMI2Version = "1.0.0";
35 //! Third (largest) principal moment of inertia
36 double PMI3(const ROMol&, int confId = -1, bool useAtomicMasses = true);
37 const std::string PMI3Version = "1.0.0";
38 
39 /*!
40  Radius of gyration
41  from G. A. Arteca "Molecular Shape Descriptors"
42  Reviews in Computational Chemistry vol 9
43  http://dx.doi.org/10.1002/9780470125861.ch5
44 
45  Definition (eq: A4):
46  sqrt(t_1 + t_2 + t_3) where t_i is the ith moment from the gyration matrix
47 */
48 double radiusOfGyration(const ROMol&, int confId = -1,
49  bool useAtomicMasses = true);
50 const std::string radiusOfGyrationVersion = "1.0.0";
51 /*!
52  Inertial shape factor
53  from Todeschini and Consoni "Descriptors from Molecular Geometry"
54  Handbook of Chemoinformatics
55  http://dx.doi.org/10.1002/9783527618279.ch37
56 
57  Definition:
58  pm2 / (pm1*pm3)
59 */
60 double inertialShapeFactor(const ROMol&, int confId = -1,
61  bool useAtomicMasses = true);
62 const std::string inertialShapeFactorVersion = "1.0.0";
63 /*!
64  Molecular eccentricity
65  from G. A. Arteca "Molecular Shape Descriptors"
66  Reviews in Computational Chemistry vol 9
67  http://dx.doi.org/10.1002/9780470125861.ch5
68 
69  Definition (eq 4):
70  sqrt(pm_3**2 -pm_1**2) / pm_3**2 where pm_i is the ith moment of inertia
71 */
72 double eccentricity(const ROMol&, int confId = -1, bool useAtomicMasses = true);
73 const std::string eccentricityVersion = "1.0.0";
74 /*!
75  molecular asphericity
76  from A. Baumgaertner, "Shapes of flexible vesicles"
77  J. Chem. Phys. 98:7496 (1993)
78  http://dx.doi.org/10.1063/1.464689
79 
80  Definition (eq 11):
81  0.5 * ((t_3-t_2)**2 + (t_3-t_1)**2 + (t_2-t_1)**2)/(t_1+t_2+t_3)**2
82  where t_i is the ith moment from the gyration matrix
83 
84  Some explanation of that definition: the text of the paper mentions axes
85  of inertia, but then the defintion of the radius of gyration in eq.9 clearly
86  uses the moments of the gyration matrix. The text under equation 11 has the
87  appropriate inequalities and limits for the moments of gyration, but the
88  description of the geometry provided corresponds to the moments of inertia.
89  The definition here corresponds to what Dragon generates and seem logical
90 
91 */
92 double asphericity(const ROMol&, int confId = -1, bool useAtomicMasses = true);
93 const std::string asphericityVersion = "1.0.0";
94 /*!
95  Spherocity index
96  from Todeschini and Consoni "Descriptors from Molecular Geometry"
97  Handbook of Chemoinformatics
98  http://dx.doi.org/10.1002/9783527618279.ch37
99 
100  Definition:
101  3 * t_1 / (t_1+t_2+t_3)
102  where the moments of the gyration matrix are calculated without weights
103 */
104 double spherocityIndex(const ROMol&, int confId = -1);
105 const std::string spherocityIndexVersion = "1.0.0";
106 }
107 }
108 #endif
109 #endif
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29