def attempt_symlink_structure_files(pdbid, project_structures_dir, structure_dirs, structure_type='pdb'):
project_structure_filepath = os.path.join(project_structures_dir, structure_type, pdbid + structure_type_file_extension_mapper[structure_type])
for structure_dir in structure_dirs:
structure_filepath = os.path.join(structure_dir, pdbid + structure_type_file_extension_mapper[structure_type])
if os.path.exists(structure_filepath):
if file_exists_and_not_empty(structure_filepath) > 0:
if os.path.exists(project_structure_filepath):
os.remove(project_structure_filepath)
os.symlink(structure_filepath, project_structure_filepath)
break
def get_pdb_and_sifts_files(pdbid, structure_dirs=None):
if type(structure_dirs) != list:
structure_dirs = []
project_structures_dir = 'structures'
for structure_type in ['pdb', 'sifts']:
project_structure_filepath = os.path.join(project_structures_dir, structure_type, pdbid + structure_type_file_extension_mapper[structure_type])
if not file_exists_and_not_empty(project_structure_filepath):
attempt_symlink_structure_files(pdbid, project_structures_dir, structure_dirs, structure_type=structure_type)
if not os.path.exists(project_structure_filepath):
download_structure_file(pdbid, project_structure_filepath, structure_type=structure_type)
def get_structure_files_for_single_pdbchain(pdbid, structure_dirs=None):
if type(structure_dirs) != list:
structure_dirs = []
project_structures_dir = 'structures'
for structure_type in ['pdb', 'sifts']:
project_structure_filepath = os.path.join(
project_structures_dir, structure_type,
pdbid + structure_type_file_extension_mapper[structure_type])
if not file_exists_and_not_empty(project_structure_filepath):
attempt_symlink_structure_files(pdbid,
project_structures_dir,
structure_dirs,
structure_type=structure_type)
if not os.path.exists(project_structure_filepath):
download_structure_file(pdbid,
project_structure_filepath,
structure_type=structure_type)
def attempt_symlink_structure_files(pdbid,
project_structures_dir,
structure_dirs,
structure_type='pdb'):
project_structure_filepath = os.path.join(
project_structures_dir, structure_type,
pdbid + structure_type_file_extension_mapper[structure_type])
for structure_dir in structure_dirs:
structure_filepath = os.path.join(
structure_dir,
pdbid + structure_type_file_extension_mapper[structure_type])
if os.path.exists(structure_filepath):
if file_exists_and_not_empty(structure_filepath) > 0:
if os.path.exists(project_structure_filepath):
os.remove(project_structure_filepath)
os.symlink(structure_filepath, project_structure_filepath)
break
