def test_pdbml_speed():
test_cases = [
'1WSY',
'1YGV',
'487D',
'1HIO',
'1H38',
'3ZKB',
]
for test_case in test_cases:
print("\n")
colortext.message("Creating PDBML object for %s" % test_case)
#PDBML.retrieve(test_case, cache_dir = cache_dir)
print("")
colortext.printf("Using the old minidom class", color = 'cyan')
t1 = time.clock()
p_minidom = PDBML_slow.retrieve(test_case, cache_dir = cache_dir)
t2 = time.clock()
colortext.message("Done in %0.2fs!" % (t2 - t1))
print("")
colortext.printf("Using the new sax class", color = 'cyan')
t1 = time.clock()
p_sax = PDBML.retrieve(test_case, cache_dir = cache_dir)
t2 = time.clock()
colortext.message("Done in %0.2fs!" % (t2 - t1))
colortext.write("\nEquality test: ", color = 'cyan')
try:
assert(p_minidom.atom_to_seqres_sequence_maps.keys() == p_sax.atom_to_seqres_sequence_maps.keys())
for c, s_1 in p_minidom.atom_to_seqres_sequence_maps.iteritems():
s_2 = p_sax.atom_to_seqres_sequence_maps[c]
assert(str(s_1) == str(s_2))
colortext.message("passed\n")
except:
colortext.error("failed\n")
colortext.warning("Trying to match chain %c against UniParc IDs %s" % (c, uniparc_sequences.keys()))
align_three_simple_sequences(fasta_sequence, uniparc_sequences['UPI00001403C6'], uniparc_sequences['UPI0000000356'], sequence1name = '%s:%s|PDBID|CHAIN|SEQUENCE' % (pdb_id, c), sequence2name = 'UPI00001403C6', sequence3name = 'UPI0000000356')
#for uniparc_id, uniparc_sequence in uniparc_sequences.iteritems():
# colortext.warning("Trying to match chain %c against UniParc ID %s" % (c, uniparc_id))
# align_two_simple_sequences(fasta_sequence, uniparc_sequence, sequence1name = '%s:%s|PDBID|CHAIN|SEQUENCE' % (pdb_id, c), sequence2name = uniparc_id)
# sanity check - see if uniprotAC in pdb is in the list of the matched uniprot id
print(chains)
sys.exit(0)
px = PDBML.retrieve('1A2C', cache_dir='/home/oconchus/temp')
for k, v in sorted(px.atom_to_seqres_sequence_maps.iteritems(), key=lambda x:(x[0], x[1])):
print(k,v)
p = PDB.from_filepath('../.testdata/1H38.pdb') # has protein, DNA, RNA
p = PDB.from_filepath('../.testdata/1ZC8.pdb')
p = PDB.from_filepath('../.testdata/4IHY.pdb')
#p = PDB('../.testdata/2GRB.pdb')
p = PDB.from_filepath('../.testdata/1J1M.pdb')
p = PDB.from_filepath('../.testdata/1H38.pdb')
p = PDB.from_filepath('../.testdata/1A2C.pdb')
#print(p.structure_lines)
colortext.message("Resolution")