Issue 257

PANDORA/Database/Database.py

@@ -37,8 +37,8 @@ def set_reverse(self, reverse):
                 self.__reverse()
         self.reverse = reverse
 
-    def download_data(self, data_dir = f'{PANDORA.PANDORA_data}/database', download = True):
-        """download_data(self, data_dir = f'{PANDORA.PANDORA_data}/database', download = True)
+    def download_data(self, data_dir = PANDORA.PANDORA_data + '/database', download = True):
+        """download_data(self, data_dir = PANDORA.PANDORA_data + '/database', download = True)
         Download all MHC structures and get a two lists that contains all MHCI and MHCII IDs respectively"""
 
         if download:

PANDORA/PMHC/Model.py

@@ -1,14 +1,11 @@
 from pyexpat import model
-from Bio.PDB import PDBParser
-from Bio.SeqUtils import seq1
-from Bio import pairwise2
 import os
-from Bio.PDB import PDBIO
-import PANDORA
-import traceback
-from Bio.PDB import *
-import sys
 
+from Bio import pairwise2
+from Bio.SeqUtils import seq1
+from Bio.PDB import PDBParser, PDBIO, Select
+
+import PANDORA
 
 class Model:
 
@@ -117,8 +114,6 @@ def calc_LRMSD(self, reference_pdb, atoms = ['C', 'CA', 'N', 'O'], ligand_zone="
                 self.flanking_lrmsd = sim.compute_lrmsd_pdb2sql(exportpath=None, method='svd', name=atoms)
         except:
             print('An error occurred while calculating the rmsd for target %s, model %s for %s' %(ref_path, decoy_path, ligand_zone))
-            #print('An error occurred while calculating the rmsd for target %s, model %s' %(self.target.id, self.model_path))
-            traceback.print_exc()
             raise Exception('Please check your model and ref info for model %s' %self.model_path)
 
         # remove intermediate files
@@ -519,7 +514,6 @@ def remove_mismatched_atoms_from_pdb(ref, decoy, atoms):
                continue
     return ref, decoy
 
-
 class NotDisordered(Select):  # Inherit methods from Select class
     '''
     Keep one Alternative location for the given atom
@@ -530,6 +524,4 @@ def accept_atom(self, atom):
             atom.set_altloc(" ")  # Eliminate alt location ID before output.
             return True
         else:  # Alt location was not one to be output.
-            return False
-
-
+            return False

PANDORA/PMHC/PMHC.py

@@ -607,6 +607,7 @@ def fill_allele_seq_info(self, use_templ_seq=False):
     def make_output_dir(self):
         ''' Create an output directory and move the template pdb there
             Uses self.output_dir (str): Path to output directory. Defaults to os.getcwd().
+
         Args:
             None
         '''

docs/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
-# DeepRank documentation build configuration file, created by
+# PANDORA documentation build configuration file, created by
 # sphinx-quickstart on Mon Feb 26 14:44:07 2018.
 #
 # This file is execfile()d with the current directory set to its
@@ -23,10 +23,19 @@
 #from unittest import mock
 
 class Mock(MagicMock):
+    # @classmethod
+    # def __getattr__(cls, name):
+    #     return MagicMock()
     @classmethod
     def __getattr__(cls, name):
-        return MagicMock()
-
+        if name == "__file__":
+            return "/dev/null"  # Provide a fake file path if needed
+        elif name == "__path__":
+            return []  # Return an empty list for __path__ (often needed for packages)
+        elif name == "__all__":
+            return []  # Ensure that `import *` works by providing an empty __all__
+        else:
+            return MagicMock()
 
 MOCK_MODULES = [
     'NumPy',
@@ -94,16 +103,16 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = '2.0'
+version = '2.0.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0'
+release = '2.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'English'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.