4.1.5. propka.molecular_container¶
4.1.5.1. 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. |
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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.
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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
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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
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get_pi
(conformation='AVR', grid=[0.0, 14.0, 1], iteration=0)[source]¶ 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
Folded state PI
Unfolded state PI
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