From 8c19c0fbb067d8ed96625e9f56adacdd58b65c94 Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Wed, 13 Nov 2024 15:13:34 +0100 Subject: [PATCH] additional checks and docs improvements --- prody/proteins/interactions.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/prody/proteins/interactions.py b/prody/proteins/interactions.py index 9cc43962a..629898632 100644 --- a/prody/proteins/interactions.py +++ b/prody/proteins/interactions.py @@ -3374,6 +3374,9 @@ def runFoldseek(pdb_file, chain, **kwargs): https://github.com/steineggerlab/foldseek?tab=readme-ov-file#databasesand This function will not work under Windows. + Example usage: runFoldseek('5kqm.pdb', 'A', database_folder='~/Downloads/foldseek/pdb') + where previous a folder called 'foldseek' were created and PDB database was uploaded using: + >>> foldseek databases PDB pdb tmp (Linux console) :arg pdb_file: A PDB file path :type pdb_file: str @@ -3404,6 +3407,9 @@ def runFoldseek(pdb_file, chain, **kwargs): coverage_threshold = kwargs.pop('coverage_threshold', 0.3) tm_threshold = kwargs.pop('tm_threshold', 0.5) + if not isinstance(pdb_file, str): + raise TypeError('Please provide the name of the PDB file.') + full_path = os.path.expanduser(database_folder) if not os.path.exists(full_path.strip('pdb')): raise ValueError('The required database is not found in {0}. Please download it first.'.format(database_folder.strip('pdb'))) @@ -3682,6 +3688,8 @@ def calcSignatureInteractions(mapping_file, PDB_folder, **kwargs): """Analyzes protein structures to identify various interactions using InSty. Processes data from the MSA file and folder with selected models. + Example usage: calcSignatureInteractions('shortlisted_resind.msa','./struc_homologs') + :arg mapping_file: Aligned residue indices, MSA file type :type mapping_file: str