schrodinger.application.livedesign.io_utils module¶
LiveDesign protocol io utils
Copyright Schrodinger, LLC. All rights reserved.
- schrodinger.application.livedesign.io_utils.get_structure_ids(infile: str) Set[str]¶
Create a set of titles for all structures found in the input file
- Parameters
infile – Input SD file
- Returns
Set containing all structure titles
- schrodinger.application.livedesign.io_utils.read_csv_columns(csv_file: str, columns: List[str]) Generator[List[str], None, None]¶
Reads specified columns from a CSV file and yields the values as a list for each row.
- Parameters
csv_file – The path to the CSV file.
columns – The list of column names to read from the CSV file.
- Yield
A list of values for each row, corresponding to the specified columns.
- schrodinger.application.livedesign.io_utils.apply_random_color(st: schrodinger.structure._structure.Structure) None¶
Apply a random color scheme to the structure
- Parameters
st – Structure to be colored
- schrodinger.application.livedesign.io_utils.record_failures(results_list: List[Dict[str, Union[str, float, int]]], header: Union[KeysView[str], List[str]], failures: List[Tuple[List[str], str]]) List[Dict[str, Union[str, float, int]]]¶
Create a dictionary with empty values for the corporate ID that failed a stage in a LiveDesign protocol and updated the list that is passed in.
- Parameters
results_list – List of dictionaries where each dictionary contains the required data to write to the CSV file
header – Header in the CSV file
failures – List of list where each nested list contains a list of IDs that failed the task, and the task name
- Returns
Update list of dictionaries where each dictionary contains the required data to write to the output CSV file
- schrodinger.application.livedesign.io_utils.create_csv(results_list: List[Dict[str, Union[str, float, int]]], csv_file: str) None¶
Write a CSV file from a list of dictionaries. The output file name ‘results.csv’, is required by LiveDesign so the module-level constant will always be used
- Parameters
results_list – List of dictionaries where each dictionary contains the required data to write to the CSV file. Column headers will be take from the keys of the first dict
csv_file – CSV filename
- schrodinger.application.livedesign.io_utils.create_postmortem(job_ids: List[str]) List[str]¶
Run postmortem on for the given job_ids
- Parameters
job_ids – List of job_control/jobserver job ids
- Returns
List of postmortem file names
- schrodinger.application.livedesign.io_utils.str_remove_suffix(s: str, suffix: str) str¶
Remove a suffix from a string
- Parameters
s – String to remove the suffix from
suffix – Suffix to remove
- Returns
String with suffix removed
- schrodinger.application.livedesign.io_utils.license_check(required_licenses: List) None¶
Check the existance of all required licenses If any license is missing, process will exit
- Parameters
required_licenses – List of license to check for
- schrodinger.application.livedesign.io_utils.write_unique_ligands(input_file: str, output_file: str)¶
Get the unique ligands from the structure file
- Parameters
input_file – Input structure file
output_file – Output structure file name