pestifer.scripters.namd_colvar_input module

class pestifer.scripters.namd_colvar_input.NAMDColvarInputScripter(*args, **kwargs)

Bases: GenericScripter

construct_on_pdb(specs: dict = {}, pdb: Path | str = None, **kwargs)

Construct the NAMD colvar input script.

Parameters:

• specs (dict) – A dictionary containing the specifications for the colvar input script.

• **kwargs (Additional keyword arguments to customize the script generation.)

declare_distance_cv(data)

Writes the colvar stanza describing a distance collective variable defined by groups to a colvar input script

Parameters:

data (dict) – dictionary containing colvar specifications

declare_distance_cv_atoms(data)

Writes the colvar stanza describing a distance collective variable defined by two atoms specified by their serial numbers to a colvar input script.

Parameters:

data (dict) – dictionary containing serial numbers of atoms i and j and a colvar name

declare_harmonic_distance_biases(data)

Writes the harmonic distance bias for a colvar defined by two groups of atoms to a colvar input script.

Parameters:

data (dict) – dictionary containing colvar specifications, including the name of the colvar, the groups of atoms involved, the force constant, the distance between the groups, and optional target distance and number of steps.

declare_single_harmonic_distance_bias(data)

Writes the harmonic bias for a colvar defined by a single group of atoms to a colvar input script.

Parameters:

data (dict) – dictionary containing colvar specifications, including the name of the colvar, the force constant, the initial distance, and optional target distance and number of steps.