schrodinger.application.bioluminate.pose_filtering.hdx_calc module¶

Provides a function for computing the residue-resolved deuteration uptake from a HDX CSV file.

Based in part on the methods described here:

T. R. Keppel and D. D. Weis. "Mapping Residual Structure in Intrinsically
    Disordered Proteins at Residue Resolution using Millisecond
    Hydrogen/Deuterium Exchange and Residue Averaging". _J. Am. Soc. Mass
    Spectrom._ (2015). 26:547--554. DOI: 10.1007/s13361-014-1033-6

exception schrodinger.application.bioluminate.pose_filtering.hdx_calc.MissingColumnsError(missing_columns=None)¶

Bases: ValueError

__init__(missing_columns=None)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.bioluminate.pose_filtering.hdx_calc.calc_residue_uptake(filename)¶

Compute the deuteration uptake from an HDX CSV file.

This function expects a CSV file in the following format:

+----------------+----------------------+
| Column Name    | Column Description   |
+================|======================+
| Chain          | Chain                |
+----------------+----------------------+
| Sequence       | Sequence             |
+----------------+----------------------+
| Start          | Start Residue Number |
+----------------+----------------------+
| End            | End Residue Number   |
+----------------+----------------------+
| MaxUptake      | Maximum Uptake       |
+----------------+----------------------+
| Uptake         | Observed Uptake      |
+----------------+----------------------+

All columns must exist and column headers must be present. Header names must conform to the naming convention in ‘Column Name’.

Parameters: filename – A string or path-like object pointing to the data file.
Returns: A series containing the weighted percent uptake per residue.
Return type: pd.Series
Raises: MissingColumnsError – If all columns are not present in file provided.

schrodinger.application.bioluminate.pose_filtering.hdx_calc.calc_delta_residue_uptake(filename_bound: str, filename_unbound: str) → Optional[Dict[str, float]]¶