motif_conformations.motif_to_coordinates

motif_conformations.motif_to_coordinates(motif: str, query_list: str, pdb_directory: str, pdb_format: str, gzipped: bool, output_file: str) → None

Read the protein structure files in the specified directory, search for the motif sequence in each structure and output the internal coordinates of the motifs as a csv file

Parameters:

• motif (str) – an amino acid sequence to find in the protein structures

• query_list (str) – a csv file specifying protein file paths and polymer instances

• pdb_directory (str) – a directory containing protein structure files

• pdb_format (str) – the format of the protein structure files. Either “pdb” or “cif”

• gzipped (bool) – true if the protein structure files are compressed with gzip, false if uncompressed

• output_file (str) – name of the file to which the internal coordinates are written