propka.molecular_container¶
PDB molecular container¶
Molecular container for storing all contents of PDB files.
Classes
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Container for storing molecular contents of PDB files. |
- class propka.molecular_container.MolecularContainer(parameters, options=None)[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()
andadditional_setup_when_reading_input_file()
as reading and writing PROPKA input files is no longer supported.- get_charge_profile(conformation='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=[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='AVR', grid=[0.0, 14.0, 1], *, precision: float = 0.0001)[source]¶
Get the isoelectric points for folded and unfolded states.
- Parameters
conformation – conformation to test
grid – grid of pH values [min, max, step]
precision – Compute pI up to this precision
- Returns
Folded state PI
Unfolded state PI