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/*=================================================================*/
/* Copyright (C) 2024 Greg Landrum and other RDKit contributors */
/* Contributed by NextMove Software, Cambridge, UK. */
/* */
/* */
/* @@ All Rights Reserved @@ */
/* The contents are covered by the terms of the */
/* BSD license, which is included in the file */
/* license.txt. */
/*=================================================================*/
#ifndef RDKIT_DCLV_H
#define RDKIT_DCLV_H
#include <iostream>
#include <string>
#include <list>
#include <cmath>
#include <GraphMol/GraphMol.h>
#include <GraphMol/MolOps.h>
#include <Geometry/point.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/export.h>
namespace RDKit {
namespace Descriptors {
class RDKIT_DESCRIPTORS_EXPORT DoubleCubicLatticeVolume {
public:
/*!
\param mol: input molecule or protein
\param isProtein: flag to calculate burried surface area of a protein ligand
complex [default=false, free ligand]
\param includeLigand: flag to trigger
inclusion of bound ligand in surface area and volume calculations where
molecule is a protein [default=true]
\param probeRadius: radius of the
sphere representing the probe solvent atom
\param depth: controls the number
of dots per atom
\param dotDensity: controls density of dots per atom
*/
DoubleCubicLatticeVolume(const ROMol &mol, bool isProtein = false,
bool includeLigand = true, double probeRadius = 1.2,
int depth = 4, int dotDensity = 0);
//! Class for calculation of the Shrake and Rupley surface area and volume
//! using the Double Cubic Lattice Method.
//!
//! Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander and
//! Michael Scharf, "The Double Cubic Lattice Method: Efficient Approaches
//! to Numerical Integration of Surface Area and Volume and to Dot Surface
//! Contouring of Molecular Assemblies", Journal of Computational Chemistry,
//! Vol. 16, No. 3, pp. 273-284, 1995.
// value returns
double getSurfaceArea() {
/*! \return Solvent Accessible Surface Area */
return surfaceArea;
}
double getVolume() {
/*! \return Volume bound by probe sphere */
return totalVolume;
}
double getVDWVolume() { /*! \return van der Waals Volume */
return vdwVolume;
}
double getCompactness() {
/*! \return Compactness of the protein */
return compactness;
}
double getPackingDensity() {
/*! \return Packing Density of the protein */
return packingDensity;
}
private:
// outputs
double surfaceArea;
double totalVolume;
double vdwVolume;
double compactness;
double packingDensity;
};
} // namespace Descriptors
} // namespace RDKit
#endif
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