class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric)
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#include <MIFDescriptors.h>
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| Coulomb ()=default |
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| ~Coulomb ()=default |
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| Coulomb (const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0) |
| constructs Coulomb object from vectors of charges and positions
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| Coulomb (const RDKit::ROMol &mol, int confId=-1, double probeCharge=1.0, bool absVal=false, const std::string &prop="_GasteigerCharge", double alpha=0.0, double cutoff=1.0) |
| constructs Coulomb object from a molecule object
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double | operator() (double x, double y, double z, double thres) const |
| calculated the electrostatic interaction at point pt in the molecules field in [kJ mol^-1]
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class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric)
Definition at line 110 of file MIFDescriptors.h.
◆ Coulomb() [1/3]
RDMIF::Coulomb::Coulomb |
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◆ ~Coulomb()
RDMIF::Coulomb::~Coulomb |
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default |
◆ Coulomb() [2/3]
RDMIF::Coulomb::Coulomb |
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const std::vector< double > & |
charges, |
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const std::vector< RDGeom::Point3D > & |
positions, |
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double |
probeCharge = 1.0 , |
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bool |
absVal = false , |
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double |
alpha = 0.0 , |
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double |
cutoff = 1.0 |
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constructs Coulomb object from vectors of charges and positions
- Parameters
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charges | vector of charges [e] |
pos | vector of postions [A] |
probeCharge | charge of probe [e] (default: 1.0) |
absVal | if true, negative (favored) values of interactions are calculated (default: false) |
alpha | softcore interaction parameter [A^2]; if zero, a minimum cutoff distance is used (default: 0.0) |
cutoff | minimum cutoff distance [A] (default: 1.0) |
◆ Coulomb() [3/3]
RDMIF::Coulomb::Coulomb |
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const RDKit::ROMol & |
mol, |
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int |
confId = -1 , |
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double |
probeCharge = 1.0 , |
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bool |
absVal = false , |
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const std::string & |
prop = "_GasteigerCharge" , |
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double |
alpha = 0.0 , |
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double |
cutoff = 1.0 |
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constructs Coulomb object from a molecule object
The molecule mol
needs to have partial charges set as property of atoms.
- Parameters
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mol | molecule object |
confId | conformation id which is used to get positions of atoms (default=-1) |
absVal | if true, absolute values of interactions are calculated (default: false) |
probeCharge | charge of probe [e] (default: 1.0) |
prop | property key for retrieving partial charges of atoms (default: "_GasteigerCharge") |
alpha | softcore interaction parameter [A^2], if zero, a minimum cutoff distance is used (default: 0.0) |
cutoff | minimum cutoff distance [A] (default: 1.0) |
◆ operator()()
double RDMIF::Coulomb::operator() |
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double |
x, |
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double |
y, |
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double |
z, |
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double |
thres |
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calculated the electrostatic interaction at point pt
in the molecules field in [kJ mol^-1]
- Parameters
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x,y,z | coordinates at which the interaction is calculated |
thres | squared max distance until interactions are calc. |
- Returns
- electrostatic interaction energy in [kJ mol^-1]
The documentation for this class was generated from the following file: