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PMI.h
Go to the documentation of this file.
//
// Copyright (C) 2016 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef PMI_H_SEPT2016
#define PMI_H_SEPT2016
#ifdef RDK_BUILD_DESCRIPTORS3D
namespace RDKit {
class ROMol;
namespace Descriptors {
//! Normalized principal moments ratio 1 (=I1/I3)
//! from Sauer and Schwarz JCIM 43:987-1003 (2003)
//! https://doi.org/10.1021/ci025599w
RDKIT_DESCRIPTORS_EXPORT double NPR1(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string NPR1Version = "1.0.0";
//! Normalized principal moments ratio 2 (=I2/I3)
//! from Sauer and Schwarz JCIM 43:987-1003 (2003)
//! https://doi.org/10.1021/ci025599w
RDKIT_DESCRIPTORS_EXPORT double NPR2(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string NPR2Version = "1.0.0";
//! First (smallest) principal moment of inertia
RDKIT_DESCRIPTORS_EXPORT double PMI1(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string PMI1Version = "1.0.0";
//! second principal moment of inertia
RDKIT_DESCRIPTORS_EXPORT double PMI2(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string PMI2Version = "1.0.0";
//! Third (largest) principal moment of inertia
RDKIT_DESCRIPTORS_EXPORT double PMI3(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string PMI3Version = "1.0.0";
/*!
Radius of gyration
from G. A. Arteca "Molecular Shape Descriptors"
Reviews in Computational Chemistry vol 9
https://doi.org/10.1002/9780470125861.ch5
Definition (eq: A4):
sqrt(t_1 + t_2 + t_3) where t_i is the ith moment from the gyration matrix
*/
RDKIT_DESCRIPTORS_EXPORT double radiusOfGyration(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string radiusOfGyrationVersion = "1.0.0";
/*!
Inertial shape factor
from Todeschini and Consoni "Descriptors from Molecular Geometry"
Handbook of Chemoinformatics
https://doi.org/10.1002/9783527618279.ch37
Definition:
pm2 / (pm1*pm3)
*/
RDKIT_DESCRIPTORS_EXPORT double inertialShapeFactor(const ROMol &,
int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string inertialShapeFactorVersion = "1.0.0";
/*!
Molecular eccentricity
from G. A. Arteca "Molecular Shape Descriptors"
Reviews in Computational Chemistry vol 9
https://doi.org/10.1002/9780470125861.ch5
Definition (eq 4):
sqrt(pm_3**2 -pm_1**2) / pm_3**2 where pm_i is the ith moment of inertia
*/
RDKIT_DESCRIPTORS_EXPORT double eccentricity(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string eccentricityVersion = "1.0.0";
/*!
molecular asphericity
from A. Baumgaertner, "Shapes of flexible vesicles"
J. Chem. Phys. 98:7496 (1993)
https://doi.org/10.1063/1.464689
Definition (eq 11):
0.5 * ((t_3-t_2)**2 + (t_3-t_1)**2 + (t_2-t_1)**2)/(t_1+t_2+t_3)**2
where t_i is the ith moment from the gyration matrix
Some explanation of that definition: the text of the paper mentions axes
of inertia, but then the definition of the radius of gyration in eq.9 clearly
uses the moments of the gyration matrix. The text under equation 11 has the
appropriate inequalities and limits for the moments of gyration, but the
description of the geometry provided corresponds to the moments of inertia.
The definition here corresponds to what Dragon generates and seem logical
*/
RDKIT_DESCRIPTORS_EXPORT double asphericity(const ROMol &, int confId = -1,
bool useAtomicMasses = true,
bool force = false);
const std::string asphericityVersion = "1.0.0";
/*!
Spherocity index
from Todeschini and Consoni "Descriptors from Molecular Geometry"
Handbook of Chemoinformatics
https://doi.org/10.1002/9783527618279.ch37
Definition:
3 * t_1 / (t_1+t_2+t_3)
where the moments of the gyration matrix are calculated without weights
*/
RDKIT_DESCRIPTORS_EXPORT double spherocityIndex(const ROMol &, int confId = -1,
bool force = false);
const std::string spherocityIndexVersion = "1.0.0";
} // namespace Descriptors
} // namespace RDKit
#endif
#endif
export.h
RDKIT_DESCRIPTORS_EXPORT
#define RDKIT_DESCRIPTORS_EXPORT
Definition export.h:105
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::rdvalue_is
bool rdvalue_is(const RDValue_cast_t)
Definition RDValue-doublemagic.h:372