biological assembly download option added

packman/molecule/molecule.py

@@ -486,7 +486,7 @@ def load_structure(filename: str, ftype: str= 'cif') -> Protein:
 ##################################################################################################
 '''
 
-def download_structure(pdbid: str, save_name: str=None, ftype: str='cif'):
+def download_structure(pdbid: str, save_name: str=None, ftype: str='cif', biological_assembly: bool = False):
  """This function downloads the 3D protein structure.
 
  Example::
@@ -495,16 +495,23 @@ def download_structure(pdbid: str, save_name: str=None, ftype: str='cif'):
  molecule.download_structure('1prw')
 
  Args:
- pdbid (str) : A Unique 4 Letter PDB ID (eg.. 1PRW) 
- save_name (str) : Save name of the downloaded file (extension will be added automatically depending on the ftype argument).
- ftype (str) : Format name ('.cif' or '.pdb')
+ pdbid (str) : A Unique 4 Letter PDB ID (eg.. 1PRW) 
+ save_name (str) : Save name of the downloaded file (extension will be added automatically depending on the ftype argument).
+ ftype (str) : Format name ('.cif' or '.pdb')
+ biological_assembly (bool) : Download biological assemblies in lieu of PDB entry. (Default: False)
  """
  import urllib.request as ur
 
  if(ftype == 'cif'):
- response=ur.urlopen('https://files.rcsb.org/view/'+pdbid+'.cif')
+ if(biological_assembly):
+ response=ur.urlopen('https://files.rcsb.org/view/'+pdbid+'-assembly1.cif')
+ else:
+ response=ur.urlopen('https://files.rcsb.org/view/'+pdbid+'.cif')
  elif(ftype == 'pdb'):
- response=ur.urlopen('https://files.rcsb.org/view/'+pdbid+'.pdb')
+ if(biological_assembly):
+ response=ur.urlopen('https://files.rcsb.org/view/'+pdbid+'.pdb1')
+ else:
+ response=ur.urlopen('https://files.rcsb.org/view/'+pdbid+'.pdb')
  else:
  logging.warning('Please provide appropriate "ftype" argument. (cif/pdb).')
  return