Various fixes

- Fixed paths
- Uniclust 2020 is the default sequence database
- Few fixes to allow parallel processing of DSSP/MSAs.

preprocessing/PDB_processing.py

@@ -11,7 +11,7 @@ from utilities.paths import structures_folder,path_to_dssp,path_to_msms
 from preprocessing.protein_chemistry import list_atoms,list_atoms_types,VanDerWaalsRadii,atom_mass,atom_type_to_index,atom_to_index,index_to_type,atom_type_mass
 from preprocessing.protein_chemistry import residue_dictionary,hetresidue_field
 from preprocessing import PDBio
-
+from datetime import datetime
 #%% Functions for parsing PDB files.
 
 def is_residue(residue):
@@ -268,9 +268,9 @@ def apply_DSSP(chain_obj, pdbparser=None, io=None, path_to_dssp=path_to_dssp):
         for atom in residue:
             atom.disordered_flag = 0
 
+    hash = str(datetime.now())[-6:]
     name = 'tmp_' + pdb_id + \
-        '_model_%s_chain_%s' % (model, chain) + '.pdb'
-
+        '_model_%s_chain_%s' % (model, chain) + '_'+hash + '.pdb'
 
 
     io.save(name)

preprocessing/PDBio.py

@@ -331,7 +331,7 @@ def load_chains(pdb_id=None,
     if (file is None) & (pdb_id is not None):
         file = getPDB(pdb_id, biounit=biounit, structures_folder=structures_folder)[0]
     else:
-        pdb_id = 'abcd'
+        pdb_id = file.split('/')[-1].split('.')[0][-4:]
 
     if file[-4:] == '.cif':
         parser = mmcifparser