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IMP Reference Guide  2.11.0
The Integrative Modeling Platform
estimates.h File Reference

Estimates of various physical quantities. More...

#include <IMP/atom/atom_config.h>
#include "Residue.h"
#include <IMP/base_types.h>
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Namespaces

 IMP
 Base functionality and abstract base classes for representation, scoring and sampling.
 
 IMP::atom
 Functionality for loading, creating, manipulating and scoring atomic structures.
 

Functions

double IMP::atom::get_diffusion_angle (double D, double dtfs)
 
double IMP::atom::get_diffusion_coefficient (const algebra::Vector3Ds &displacements, double dt)
 
double IMP::atom::get_diffusion_coefficient (const algebra::Vector3Ds &displacements, const Floats &dts)
 
double IMP::atom::get_diffusion_length (double D, double t)
 
double IMP::atom::get_diffusion_length (double D, double force, double t, double temp=-1)
 
double IMP::atom::get_einstein_diffusion_coefficient (double r, double temp=-1)
 
double IMP::atom::get_einstein_rotational_diffusion_coefficient (double r, double temp=-1)
 
double IMP::atom::get_kd (double na, double nb, double nab, double volume)
 
double IMP::atom::get_molarity (double n, double volume)
 
double IMP::atom::get_rotational_diffusion_coefficient (const algebra::Rotation3Ds &orientations, double dt)
 

Estimator Functions

These functions allow you to estimate physical quantities relating to biomolecules.

enum  IMP::atom::ProteinDensityReference {
  ALBER, HARPAZ, ANDERSSON, TSAI,
  QUILLIN, SQUIRE
}
 
double IMP::atom::get_protein_density_from_reference (ProteinDensityReference densityReference)
 
double IMP::atom::get_volume_from_mass (double m, ProteinDensityReference ref=ALBER)
 Estimate the volume of a protein from its mass. More...
 
double IMP::atom::get_mass_from_volume (double v, ProteinDensityReference ref=ALBER)
 Estimate the mass of a protein from its volume. More...
 
double IMP::atom::get_mass_from_number_of_residues (unsigned int num_aa)
 Estimate the mass of a protein from the number of amino acids. More...
 
double IMP::atom::get_volume_from_residue_type (ResidueType rt)
 Return an estimate for the volume of a given residue. More...
 

Energy conversions

Convert energy from kcal/mol to femtojoules

double IMP::atom::get_energy_in_femto_joules (double energy_in_kcal_per_mol)
 
double IMP::atom::get_force_in_femto_newtons (double force_in_kcal_per_mol_per_angstrom)
 Convert force from kcal/mol/A to femtonewtons. More...
 
double IMP::atom::get_spring_constant_in_femto_newtons_per_angstrom (double k_in_kcal_per_mol_per_angstrom_square)
 Convert spring constant from kcal/mol/A^2 to femtonewton/A. More...
 

Detailed Description

Estimates of various physical quantities.

Copyright 2007-2019 IMP Inventors. All rights reserved.

Definition in file estimates.h.