4.2.2. propka.lib¶
4.2.2.1. Set-up of a PROPKA calculation¶
Implements many of the main functions used to call PROPKA.
Functions
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Build an argument parser for PROPKA. |
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TODO - figure out what this function does. |
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Log a message to debug. |
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Generate combinations of interactions. |
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Extract and sort configurations. |
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Log a message to info. |
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Load the arguments parser with options. |
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Make a specific set of combinations. |
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Make a grid across the specified tange. |
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Make a molecule from atoms. |
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Returns a ‘tidier’ atom label for printing to the new PDB file. |
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Parse a residue string. |
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Check protein for correct number of atoms, etc. |
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Return string with atom residue information. |
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Maps atoms into molecules. |
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Log a message to warning. |
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propka.lib.
build_parser
(parser=None)[source]¶ Build an argument parser for PROPKA.
- Parameters
parser – existing parser. If this is not None, then the PROPKA parser will be created as a subparser to this existing parser. Otherwise, a new parser will be created.
- Returns
ArgumentParser object.
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propka.lib.
debug
(*args)[source]¶ Log a message to debug.
Level defaults to DEBUG unless overridden.
- Parameters
args – argument list
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propka.lib.
generate_combinations
(interactions)[source]¶ Generate combinations of interactions.
- Parameters
interactions – list of interactions
- Returns
list of combinations
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propka.lib.
get_sorted_configurations
(configuration_keys)[source]¶ Extract and sort configurations.
- Parameters
configuration_keys – list of configuration keys
- Returns
list of configurations
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propka.lib.
info
(*args)[source]¶ Log a message to info.
Level defaults to INFO unless overridden.
- Parameters
args – argument list
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propka.lib.
loadOptions
(args=None)[source]¶ Load the arguments parser with options. Note that verbosity is set as soon as this function is invoked.
- Parameters
args – list of arguments
- Returns
argparse namespace
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propka.lib.
make_combination
(combis, interaction)[source]¶ Make a specific set of combinations.
- Parameters
combis – list of combinations
interaction – interaction to add to combinations
- Returns
list of combinations
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propka.lib.
make_grid
(min_, max_, step)[source]¶ Make a grid across the specified tange.
TODO - figure out if this duplicates existing generators like range or numpy function.
- Parameters
min – minimum value of grid
max – maximum value of grid
step – grid step size
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propka.lib.
make_molecule
(atom, atoms)[source]¶ Make a molecule from atoms.
- Parameters
atom – one of the atoms
atoms – a list of the remaining atoms
- Returns
list of atoms
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propka.lib.
make_tidy_atom_label
(name, element)[source]¶ Returns a ‘tidier’ atom label for printing to the new PDB file.
- Parameters
name – atom name
element – atom element
- Returns
string
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propka.lib.
parse_res_string
(res_str)[source]¶ Parse a residue string.
- Parameters
res_string – residue string in format “chain:resnum[inscode]”
- Returns
a tuple of (chain, resnum, inscode).
- Raises
ValueError if the input string is invalid. –
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propka.lib.
protein_precheck
(conformations, names)[source]¶ Check protein for correct number of atoms, etc.
- Parameters
names – conformation names to check
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propka.lib.
resid_from_atom
(atom)[source]¶ Return string with atom residue information.
- Parameters
atom – atom to generate string for
- Returns
string