def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
root_numbers = count_special_lines("^ROOT", dataset.file_name)
branch_numbers = count_special_lines("^BRANCH", dataset.file_name)
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = f"{root_numbers} roots and {branch_numbers} branches"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
atom_numbers = count_special_lines("^ATOM", dataset.file_name)
hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "%s atoms and %s HET-atoms\nchain_ids: %s" % (atom_numbers, hetatm_numbers, str(chain_ids))
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_meta(self, dataset, **kwd):
"""
Set the number of models in dataset.
"""
dataset.metadata.number_of_models = generic_util.count_special_lines(
'^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', dataset.file_name)
def set_meta(self, dataset, **kwd):
"""
Set the number of models and the version of CM file in dataset.
"""
dataset.metadata.number_of_models = generic_util.count_special_lines('^INFERNAL', dataset.file_name)
with open(dataset.file_name) as f:
first_line = f.readline()
if first_line.startswith("INFERNAL"):
dataset.metadata.cm_version = (first_line.split()[0]).replace('INFERNAL', '')
def set_meta(self, dataset, **kwd):
"""
Set the number of models and the version of CM file in dataset.
"""
dataset.metadata.number_of_models = generic_util.count_special_lines('^INFERNAL', dataset.file_name)
with open(dataset.file_name, 'r') as f:
first_line = f.readline()
if first_line.startswith("INFERNAL"):
dataset.metadata.cm_version = (first_line.split()[0]).replace('INFERNAL', '')
def set_meta( self, dataset, **kwd ):
dataset.metadata.number_of_models = generic_util.count_special_lines('^#Sequence([[:digit:]]+)Entry', dataset.file_name)
def set_meta( self, dataset, **kwd ):
"""
Set the number of models in dataset.
"""
dataset.metadata.number_of_models = generic_util.count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', dataset.file_name)
def sniff( self, filename ):
if generic_util.count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', filename) > 0:
return True
else:
return False
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines(
r'^\s*<molecule', dataset.file_name)
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines(
'\"ligand id\"', dataset.file_name, invert=True)
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines(
"@<TRIPOS>MOLECULE", dataset.file_name)
def set_meta(self, dataset, **kwd):
"""
Set the number of molecules in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines(
r"^\$\$\$\$$", dataset.file_name)
