RDMIF Namespace Reference

Classes
class	Coulomb
	class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric) More...
class	CoulombDielectric
	class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule by taking a distance-dependent dielectric into account: More...
class	HBond
	class for calculation of hydrogen bond potential between probe and molecule More...
class	Hydrophilic
	class for calculation of hydrophilic field of molecule More...
class	MMFFVdWaals
class	UFFVdWaals
class	VdWaals
	Abstract class for calculation of Van der Waals interaction between probe and molecule at gridpoint pt. More...

Functions
RDKIT_MOLINTERACTIONFIELDS_EXPORT std::unique_ptr< RDGeom::UniformRealValueGrid3D >	constructGrid (const RDKit::ROMol &mol, int confId=-1, double margin=5.0, double spacing=0.5)
	constructs a UniformRealValueGrid3D which fits to the molecule mol
template<typename T>
void	calculateDescriptors (RDGeom::UniformRealValueGrid3D &grd, const T &functor, double thres=-1.0)
	calculates a descriptor at every grid point of MIF
RDKIT_MOLINTERACTIONFIELDS_EXPORT void	writeToCubeStream (const RDGeom::UniformRealValueGrid3D &grd, std::ostream &outStrm, const RDKit::ROMol *mol=nullptr, int confid=-1)
	writes the contents of the MIF to a stream
RDKIT_MOLINTERACTIONFIELDS_EXPORT void	writeToCubeFile (const RDGeom::UniformRealValueGrid3D &grd, const std::string &filename, const RDKit::ROMol *mol=nullptr, int confid=-1)
	writes the contents of the MIF to a file
RDKIT_MOLINTERACTIONFIELDS_EXPORT std::unique_ptr< RDKit::RWMol >	readFromCubeStream (RDGeom::UniformRealValueGrid3D &grd, std::istream &inStrm)
	reads the contents of the MIF from a stream in Gaussian cube format
RDKIT_MOLINTERACTIONFIELDS_EXPORT std::unique_ptr< RDKit::RWMol >	readFromCubeFile (RDGeom::UniformRealValueGrid3D &grd, const std::string &filename)
	reads the contents of the MIF from a file in Gaussian cube format

Function Documentation

calculateDescriptors()

template<typename T>

void RDMIF::calculateDescriptors	(	RDGeom::UniformRealValueGrid3D &	grd,
		const T &	functor,
		double	thres = -1.0 )

calculates a descriptor at every grid point of MIF

any unary function/functor can be used taking a grid point of type RDKit::Point3D as parameter

Parameters

grd	a UniformRealValueGrid3D
functor	any unary function/functor which takes four doubles as parameters (3 coordinates, 1 threshold)
thres	cuts off atom contributions if distance of interaction higher than threshold, negative threshold: no threshold, defaults to -1.0

Definition at line 64 of file MIFDescriptors.h.

References RDGeom::UniformRealValueGrid3D::getData(), RDGeom::UniformRealValueGrid3D::getNumX(), RDGeom::UniformRealValueGrid3D::getNumY(), RDGeom::UniformRealValueGrid3D::getNumZ(), RDGeom::UniformRealValueGrid3D::getOffset(), RDGeom::UniformRealValueGrid3D::getSize(), RDGeom::UniformRealValueGrid3D::getSpacing(), RDGeom::Point3D::x, RDGeom::Point3D::y, and RDGeom::Point3D::z.

constructGrid()

RDKIT_MOLINTERACTIONFIELDS_EXPORT std::unique_ptr< RDGeom::UniformRealValueGrid3D > RDMIF::constructGrid	(	const RDKit::ROMol &	mol,
		int	confId = -1,
		double	margin = 5.0,
		double	spacing = 0.5 )

constructs a UniformRealValueGrid3D which fits to the molecule mol

Returns

a pointer to a UniformRealValueGrid which has a spacing of spacing (default: 0.5 Angstrom) and a spatial extent of conformer confId (default: -1) of molecule mol plus a defined margin margin on each side (default: 5.0 Angstrom).

Parameters

mol	Molecule for which the grid is constructed
confId	Id of Conformer which is used
margin	distance from molecule to the grid's wall
spacing	grid's spacing

Returns pointer to a grid

readFromCubeFile()

RDKIT_MOLINTERACTIONFIELDS_EXPORT std::unique_ptr< RDKit::RWMol > RDMIF::readFromCubeFile	(	RDGeom::UniformRealValueGrid3D &	grd,
		const std::string &	filename )

reads the contents of the MIF from a file in Gaussian cube format

The Grid grd is modified according to input values If a molecule was associated to the grid on write, a non-null pointer to a molecule is returned with atoms and a conformer, but NO bond information. If there is no atom information in the cube file, a null pointer is returned.

readFromCubeStream()

RDKIT_MOLINTERACTIONFIELDS_EXPORT std::unique_ptr< RDKit::RWMol > RDMIF::readFromCubeStream	(	RDGeom::UniformRealValueGrid3D &	grd,
		std::istream &	inStrm )

reads the contents of the MIF from a stream in Gaussian cube format

The Grid grd is modified according to input values If a molecule was associated to the grid on write, a non-null pointer to a molecule is returned with atoms and a conformer, but NO bond information. If there is no atom information in the cube file, a null pointer is returned.

References RDKIT_MOLINTERACTIONFIELDS_EXPORT.

writeToCubeFile()

RDKIT_MOLINTERACTIONFIELDS_EXPORT void RDMIF::writeToCubeFile	(	const RDGeom::UniformRealValueGrid3D &	grd,
		const std::string &	filename,
		const RDKit::ROMol *	mol = nullptr,
		int	confid = -1 )

writes the contents of the MIF to a file

The Grid grd is written in Gaussian Cube format A molecule mol and a confId can optionally be provided

References RDKIT_MOLINTERACTIONFIELDS_EXPORT.

writeToCubeStream()

RDKIT_MOLINTERACTIONFIELDS_EXPORT void RDMIF::writeToCubeStream	(	const RDGeom::UniformRealValueGrid3D &	grd,
		std::ostream &	outStrm,
		const RDKit::ROMol *	mol = nullptr,
		int	confid = -1 )

writes the contents of the MIF to a stream

The Grid grd is written in Gaussian Cube format A molecule mol and a confId can optionally be provided

References RDKIT_MOLINTERACTIONFIELDS_EXPORT.