def read_n_files( filenames ) :
"""
`filenames' is a list of file names. Reads the files and deposits them into the `KBASE'. Returns a list of keys.
"""
strucid = []
for fn in filenames :
strucs = read_file( fn )
for e in strucs:
id = KBASE.deposit( e.id(), e )
KBASE.deposit_extra(id, "filename", (fn))
e.set_id( id )
strucid.append( id )
return strucid
def read_n_files( filenames ) :
"""
`filenames' is a list of file names. The format of each file will be determined from the file's extension name. Reads
the files and deposits them into the `KBASE'. Returns a list of keys.
"""
strucid = []
for fn in filenames :
strucs = read_file( fn )
for e in strucs :
id = KBASE.deposit( e.id(), e )
KBASE.deposit_extra(id, "filename", (fn))
e.set_id( id )
strucid.append( id )
return strucid
def deposit_to_kbase(id0, id1, atom_match0, atom_match1):
"""
Deposits a MCS substructure and relevant information into the kbase and returns its ID in the C{KBASE}.
@type id0: C{str}
@param id0: ID of the first (reference) molecule in the C{KBASE}
@type id1: C{str}
@param id1: ID of the second molecule in the C{KBASE}
@type atom_match: C{list} of C{int}
@param atom_match: A list of atom indices of matches atoms in the reference molecule
@type mcs_mol: C{Struc}
@param mcs_mol: C{Struc} object of the MCS substructure
"""
mol0 = KBASE.ask(id0)
mol1 = KBASE.ask(id1)
name0 = mol0.title()
name1 = mol1.title()
mcs_title = "mcs@%s..%s" % (
name0,
name1,
)
mcs_id = hashlib.sha1(mcs_title).hexdigest()
mcs_id = KBASE.deposit(mcs_id, mcs_title)
# Sorts the two lists according to the ascending order of atom indices of the first list.
atom_match0, atom_match1 = zip(*sorted(zip(atom_match0, atom_match1),
cmp=lambda x, y: x[0] - y[0]))
atom_match0, atom_match1 = list(atom_match0), list(atom_match1)
KBASE.deposit_extra(mcs_id, "mcs-parents", (
id0,
id1,
))
KBASE.deposit_extra(mcs_id, "mcs-matches", {
id0: atom_match0,
id1: atom_match1,
})
return mcs_id