RDKit
Open-source cheminformatics and machine learning.
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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::UniformRealValueGrid3DconstructGrid (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::RWMolreadFromCubeStream (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::RWMolreadFromCubeFile (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
grda UniformRealValueGrid3D
functorany unary function/functor which takes four doubles as parameters (3 coordinates, 1 threshold)
threscuts 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
molMolecule for which the grid is constructed
confIdId of Conformer which is used
margindistance from molecule to the grid's wall
spacinggrid'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.

◆ 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

◆ 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