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 #include <RDGeneral/export.h>
12 #ifndef PMI_H_SEPT2016
13 #define PMI_H_SEPT2016
14 
15 #ifdef RDK_BUILD_DESCRIPTORS3D
16 namespace RDKit {
17 class ROMol;
18 namespace Descriptors {
19 //! Normalized principal moments ratio 1 (=I1/I3)
20 //! from Sauer and Schwarz JCIM 43:987-1003 (2003)
21 //! https://doi.org/10.1021/ci025599w
22 RDKIT_DESCRIPTORS_EXPORT double NPR1(const ROMol&, int confId = -1,
23  bool useAtomicMasses = true,
24  bool force = false);
25 const std::string NPR1Version = "1.0.0";
26 //! Normalized principal moments ratio 2 (=I2/I3)
27 //! from Sauer and Schwarz JCIM 43:987-1003 (2003)
28 //! https://doi.org/10.1021/ci025599w
29 RDKIT_DESCRIPTORS_EXPORT double NPR2(const ROMol&, int confId = -1,
30  bool useAtomicMasses = true,
31  bool force = false);
32 const std::string NPR2Version = "1.0.0";
33 
34 //! First (smallest) principal moment of inertia
35 RDKIT_DESCRIPTORS_EXPORT double PMI1(const ROMol&, int confId = -1,
36  bool useAtomicMasses = true,
37  bool force = false);
38 const std::string PMI1Version = "1.0.0";
39 //! second principal moment of inertia
41  const ROMol&, int confId = -1, bool useAtomicMasses = true,
42  bool force = false);
43 const std::string PMI2Version = "1.0.0";
44 //! Third (largest) principal moment of inertia
45 RDKIT_DESCRIPTORS_EXPORT double PMI3(const ROMol&, int confId = -1,
46  bool useAtomicMasses = true,
47  bool force = false);
48 const std::string PMI3Version = "1.0.0";
49 
50 /*!
51  Radius of gyration
52  from G. A. Arteca "Molecular Shape Descriptors"
53  Reviews in Computational Chemistry vol 9
54  https://doi.org/10.1002/9780470125861.ch5
55 
56  Definition (eq: A4):
57  sqrt(t_1 + t_2 + t_3) where t_i is the ith moment from the gyration matrix
58 */
59 RDKIT_DESCRIPTORS_EXPORT double radiusOfGyration(const ROMol&, int confId = -1,
60  bool useAtomicMasses = true,
61  bool force = false);
62 const std::string radiusOfGyrationVersion = "1.0.0";
63 /*!
64  Inertial shape factor
65  from Todeschini and Consoni "Descriptors from Molecular Geometry"
66  Handbook of Chemoinformatics
67  https://doi.org/10.1002/9783527618279.ch37
68 
69  Definition:
70  pm2 / (pm1*pm3)
71 */
72 RDKIT_DESCRIPTORS_EXPORT double inertialShapeFactor(const ROMol&,
73  int confId = -1,
74  bool useAtomicMasses = true,
75  bool force = false);
76 const std::string inertialShapeFactorVersion = "1.0.0";
77 /*!
78  Molecular eccentricity
79  from G. A. Arteca "Molecular Shape Descriptors"
80  Reviews in Computational Chemistry vol 9
81  https://doi.org/10.1002/9780470125861.ch5
82 
83  Definition (eq 4):
84  sqrt(pm_3**2 -pm_1**2) / pm_3**2 where pm_i is the ith moment of inertia
85 */
86 RDKIT_DESCRIPTORS_EXPORT double eccentricity(const ROMol&, int confId = -1,
87  bool useAtomicMasses = true,
88  bool force = false);
89 const std::string eccentricityVersion = "1.0.0";
90 /*!
91  molecular asphericity
92  from A. Baumgaertner, "Shapes of flexible vesicles"
93  J. Chem. Phys. 98:7496 (1993)
94  https://doi.org/10.1063/1.464689
95 
96  Definition (eq 11):
97  0.5 * ((t_3-t_2)**2 + (t_3-t_1)**2 + (t_2-t_1)**2)/(t_1+t_2+t_3)**2
98  where t_i is the ith moment from the gyration matrix
99 
100  Some explanation of that definition: the text of the paper mentions axes
101  of inertia, but then the defintion of the radius of gyration in eq.9 clearly
102  uses the moments of the gyration matrix. The text under equation 11 has the
103  appropriate inequalities and limits for the moments of gyration, but the
104  description of the geometry provided corresponds to the moments of inertia.
105  The definition here corresponds to what Dragon generates and seem logical
106 
107 */
108 RDKIT_DESCRIPTORS_EXPORT double asphericity(const ROMol&, int confId = -1,
109  bool useAtomicMasses = true,
110  bool force = false);
111 const std::string asphericityVersion = "1.0.0";
112 /*!
113  Spherocity index
114  from Todeschini and Consoni "Descriptors from Molecular Geometry"
115  Handbook of Chemoinformatics
116  https://doi.org/10.1002/9783527618279.ch37
117 
118  Definition:
119  3 * t_1 / (t_1+t_2+t_3)
120  where the moments of the gyration matrix are calculated without weights
121 */
122 RDKIT_DESCRIPTORS_EXPORT double spherocityIndex(const ROMol&, int confId = -1,
123  bool force = false);
124 const std::string spherocityIndexVersion = "1.0.0";
125 } // namespace Descriptors
126 } // namespace RDKit
127 #endif
128 #endif
RDKIT_DESCRIPTORS_EXPORT
#define RDKIT_DESCRIPTORS_EXPORT
Definition: export.h:138
RDKit
Std stuff.
Definition: Atom.h:30
export.h