propka.molecular_container

PDB molecular container

Molecular container for storing all contents of PDB files.

Classes

MolecularContainer(parameters, options)

Container for storing molecular contents of PDB files.
class propka.molecular_container.MolecularContainer(parameters: Parameters, options: Options)[source]

Container for storing molecular contents of PDB files.

TODO - this class name does not conform to PEP8 but has external use. We should deprecate and change eventually.

Changed in version 3.4.0: Removed write_propka() and additional_setup_when_reading_input_file() as reading and writing PROPKA input files is no longer supported.

average_of_conformations() → None[source]

Generate an average of conformations.

calculate_pka() → None[source]

Calculate pKa values.

extract_groups() → None[source]

Identify the groups needed for pKa calculation.

find_covalently_coupled_groups() → None[source]

Find covalently coupled groups.

find_non_covalently_coupled_groups() → None[source]

Find non-covalently coupled groups.

get_charge_profile(conformation: str = 'AVR', grid=(0.0, 14.0, 0.1))[source]

Get charge profile for conformation as function of pH.

Parameters:

  • conformation – conformation to test

  • grid – grid of pH values [min, max, step]

Returns:

list of charge state values

get_folding_profile(conformation='AVR', reference='neutral', grid: Tuple[float, float, float] = (0.0, 14.0, 0.1))[source]

Get a folding profile.

Parameters:

  • conformation – conformation to select

  • reference – reference state

  • direction – folding direction (folding)

  • grid – the grid of pH values [min, max, step_size]

  • options – options object

Returns:

TODO - figure out what these are 1. profile 2. opt 3. range_80pct 4. stability_range

get_pi(conformation: str = 'AVR', grid=(0.0, 14.0), *, precision: float = 0.0001) → Tuple[float, float][source]

Get the isoelectric points for folded and unfolded states.

Parameters:

  • conformation – conformation to test

  • grid – pH window [min, max]

  • precision – Compute pI up to this precision

Returns:

  1. Folded state PI

  2. Unfolded state PI

top_up_conformations() → None[source]

Makes sure that all atoms are present in all conformations.

write_pka(filename=None, reference='neutral', direction='folding', options=None) → None[source]

Write pKa information to a file.

Parameters:

  • filename – file to write to

  • reference – reference state

  • direction – folding vs. unfolding

  • options – options object