4.1.5. propka.molecular_container

4.1.5.1. 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, options=None)

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.

additional_setup_when_reading_input_file()

Additional setup.

average_of_conformations()

Generate an average of conformations.

calculate_pka()

Calculate pKa values.

extract_groups()

Identify the groups needed for pKa calculation.

find_covalently_coupled_groups()

Find covalently coupled groups.

find_non_covalently_coupled_groups()

Find non-covalently coupled groups.

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

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=[0.0, 14.0, 0.1])

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='AVR', grid=[0.0, 14.0, 1], iteration=0)

Get the isoelectric points for folded and unfolded states.

Parameters

• conformation – conformation to test

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

• iteration – iteration number of process

Returns

1. Folded state PI

2. Unfolded state PI

top_up_conformations()

Makes sure that all atoms are present in all conformations.

write_pka(filename=None, reference='neutral', direction='folding', options=None)

Write pKa information to a file.

Parameters

• filename – file to write to

• reference – reference state

• direction – folding vs. unfolding

• options – options object

write_propka(filename=None)

Write PROPKA input file.

Parameters

filename – file to write to