nrgten.anm

class nrgten.anm.ANM(pdb_file, cut=inf, power_dependence=0, kr=1, solve=True, use_pickle=False, added_atypes=None, added_massdef=None, ignore_hetatms=False, atypes_list=None, massdef_list=None, solve_mol=True, one_mass=False)

Class implementing the ANM (Anisotropic Network Model).

Has 3 parameters: cutoff, power dependence and spring constant. Spring constant just rescales fluctuations but doesn’t change their relative values. Cutoff can be infinity (fully connected model). The original ANM paper is: doi.org/10.1016/S0006-3495(01)76033-X and the paper on varying the power dependence is: doi.org/10.1073/pnas.0902159106

Note

ANM extends the ENM class, to see inherited attributes look at the documentation for ENM.

cut

the distance cutoff for interaction between 2 masses.

Type:

float

pd

the power dependence of the interaction.

Type:

float

kr

the interaction constant (does not change the solution but scales the values).

Type:

float

__init__(pdb_file, cut=inf, power_dependence=0, kr=1, solve=True, use_pickle=False, added_atypes=None, added_massdef=None, ignore_hetatms=False, atypes_list=None, massdef_list=None, solve_mol=True, one_mass=False)

Constructor for the ANM class.

Parameters:

  • pdb_file (str) – The PDB file from which to build the model.

  • cut (float, optional) – The interaction cutoff.

  • power_dependence (float, optional) – The power dependence. For consistency with published papers, a power dependence of 0 means that the distance will be squared in the Hessian.

  • solve (bool, optional) – If True, the Hessian matrix will be built and solved.

  • use_pickle (bool, optional) – If True, the ENM object will be solved only once and subsequently built from its pickled representation. Uses a lot of disk space for large systems.

  • ignore_hetatms (bool, optional) – Flag to ignore HETATM records in the PDB file.

  • atypes_list (list, optional) – If supplied, the default .atypes configuration files are ignored and these are the only ones read.

  • massdef_list (list, optional) – If supplied, the default .masses configuration files are ignored and these are the only ones read.

  • solve_mol (bool, optional) – If True, the underlying Macromol object will be solved, i.e. the connectivity of the residues will be inferred.

  • one_mass (bool, optional) – If True, nucleic acids will be built using only one mass per nucleotide instead of 3.

build_from_pickle()

Builds an ANM object from its pickled state.

Returns:

True if successful, False otherwise.

build_hessian()

Builds the Hessian matrix.

Returns:

The Hessian matrix.

pickle()

Builds a pickled state from the ANM object.