af_analysis.format package
af_analysis.format.af3_webserver module
af_analysis.format.afpulldown module
- af_analysis.format.afpulldown.read_dir(directory, query=None)[source]
Extract pdb list from a directory.
- Parameters:
- directorystr
Path to the directory containing the pdb files.
- querystr
Name of the query, default is None.
- Returns:
- log_pdpandas.DataFrame
Dataframe containing the information extracted from the directory.
af_analysis.format.colabfold_1_5 module
- af_analysis.format.colabfold_1_5.add_fasta(log_pd, csv)[source]
Add the raw sequence from csv file in the dataframe.
- Parameters:
- log_pdpandas.DataFrame
Dataframe containing the information extracted from the log.txt file.
- csvstr
Path to the csv file containing the raw sequence.
- Returns:
- None
The log_pd dataframe is modified in place.
- af_analysis.format.colabfold_1_5.add_json(log_pd, directory, verbose=True)[source]
Find json files in the directory.
- Parameters:
- log_pdpandas.DataFrame
Dataframe containing the information extracted from the log.txt file.
- directorystr
Path to the directory containing the json files.
- verbosebool
If True, show a progress bar. If False, no progress bar is shown.
- Returns:
- None
The log_pd dataframe is modified in place.
- af_analysis.format.colabfold_1_5.add_pdb(log_pd, directory, verbose=True)[source]
Find pdb files in the directory.
- Parameters:
- log_pdpandas.DataFrame
Dataframe containing the information extracted from the log.txt file.
- directorystr
Path to the directory containing the pdb files.
- Returns:
- None
The log_pd dataframe is modified in place.
- af_analysis.format.colabfold_1_5.read_log(directory, keep_recycles=False)[source]
Read colabfold log.txt file. Extract information about the model and the query.
Return a pandas dataframe.
- Parameters:
- directorystr
Path to the directory containing the log.txt file.
- keep_recyclesbool
If True, keep all the recycles. If False, keep only the last recycle.
- Returns:
- dfpandas.DataFrame
Dataframe containing the information extracted from the log.txt file.
af_analysis.format.default module
- af_analysis.format.default.add_json(log_pd, directory, verbose=True)[source]
Find json files in the directory.
- Parameters:
- log_pdpandas.DataFrame
Dataframe containing the information extracted from the log.txt file.
- directorystr
Path to the directory containing the json files.
- verbosebool
If True, show a progress bar. If False, no progress bar is shown.
- Returns:
- None
The log_pd dataframe is modified in place.