This module implements deformational energies for use in the analysis of motions and conformational changes in macromolecules. A description of the techniques can be found in [Hinsen1998] and [Hinsen1999].
Constructor: DeformationFunction(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation function should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above.
A DeformationFunction object must be called with a single parameter, which is a ParticleVector object containing the infinitesimal displacements of the atoms for which the deformation is to be evaluated. The return value is a ParticleScalar object containing the deformation value for each atom.
Constructor: NormalizedDeformationFunction(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation function should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above. The normalization is defined by equation 10 of reference 1.
A NormalizedDeformationFunction object must be called with a single parameter, which is a ParticleVector object containing the infinitesimal displacements of the atoms for which the deformation is to be evaluated. The return value is a ParticleScalar object containing the deformation value for each atom.
Constructor: FiniteDeformationFunction(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation function should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above.
A FiniteDeformationFunction object must be called with a single parameter, which is a Configuration or a ParticleVector object containing the alternate configuration of the universe for which the deformation is to be evaluated. The return value is a ParticleScalar object containing the deformation value for each atom.
The deformation energy is the sum of the deformation values over all atoms of a system.
Constructor: DeformationEnergyFunction(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation energy should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation energy calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above.
A DeformationEnergyFunction is called with one or two parameters. The first parameter is a ParticleVector object containing the infinitesimal displacements of the atoms for which the deformation energy is to be evaluated. The optional second argument can be set to a non-zero value to request the gradients of the energy in addition to the energy itself. In that case there are two return values (energy and the gradients in a ParticleVector object), otherwise only the energy is returned.
The normalized deformation energy is the sum of the normalized deformation values over all atoms of a system.
Constructor: NormalizedDeformationEnergyFunction(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation energy should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation energy calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above. The normalization is defined by equation 10 of reference 1.
A NormalizedDeformationEnergyFunction is called with one or two parameters. The first parameter is a ParticleVector object containing the infinitesimal displacements of the atoms for which the deformation energy is to be evaluated. The optional second argument can be set to a non-zero value to request the gradients of the energy in addition to the energy itself. In that case there are two return values (energy and the gradients in a ParticleVector object), otherwise only the energy is returned.
The deformation energy is the sum of the deformation values over all atoms of a system.
Constructor: FiniteDeformationEnergyFunction(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation energy should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation energy calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above.
A FiniteDeformationEnergyFunction is called with one or two parameters. The first parameter is a ParticleVector object containing the alternate configuration of the universe for which the deformation energy is to be evaluated. The optional second argument can be set to a non-zero value to request the gradients of the energy in addition to the energy itself. In that case there are two return values (energy and the gradients in a ParticleVector object), otherwise only the energy is returned.
Constructor: DeformationReducer(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation function should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above.
A DeformationReducer is called with two arguments. The first is a ParticleVector containing the initial infinitesimal displacements for all atoms. The second is an integer indicating the number of iterations. The result is a modification of the displacements by steepest-descent minimization of the deformation energy.
Constructor: FiniteDeformationReducer(universe, range=0.7, cutoff=1.2, factor=46402.)
the universe for which the deformation function should be defined
the range parameter r_0 in the pair interaction term
the cutoff used in the deformation calculation
a global scaling factor
The default values are appropriate for a C_alpha model of a protein with the global scaling described in the reference cited above.
A FiniteDeformationReducer is called with two arguments. The first is a ParticleVector or Configuration containing the alternate configuration for which the deformation energy is evaluated. The second is the RMS distance that defines the termination condition. The return value a configuration that differs from the input configuration by approximately the specified RMS distance, and which is obtained by iterative steepest-descent minimization of the finite-displacement deformation energy.