def test_loop_keyword_case_insensitive(self):
"""Comments may begin outside of column 1."""
test_data = """\
data_verbatim_test
_test_key_value foo # Ignore this comment
loop_
_test_loop
a b c d # Ignore this comment
e f g
"""
mmcif_dict = MMCIF2Dict(io.StringIO(textwrap.dedent(test_data)))
mmcif_dict2 = MMCIF2Dict(
io.StringIO(textwrap.dedent(test_data.replace("loop_", "LOOP_")))
)
self.assertDictEqual(mmcif_dict, mmcif_dict2)
mmcif_dict2 = MMCIF2Dict(
io.StringIO(textwrap.dedent(test_data.replace("loop_", "looP_")))
)
self.assertDictEqual(mmcif_dict, mmcif_dict2)
mmcif_dict2 = MMCIF2Dict(
io.StringIO(textwrap.dedent(test_data.replace("_loop", "_LOOP")))
)
self.assertNotEqual(mmcif_dict, mmcif_dict2)
def loadPDB_CIF_format(pdbId, filePath, pdbl):
pdbFileSavePath = '%s%s.cif' % (filePath, pdbId)
try:
mmcif_dict = MMCIF2Dict(pdbFileSavePath)
except IOError:
# Get the file
pdbl.retrieve_pdb_file(pdbId, file_format='mmCif', pdir=filePath)
mmcif_dict = MMCIF2Dict(pdbFileSavePath)
return mmcif_dict
def test_token_after_multiline(self):
"""Multi-line string followed by token on the same line."""
stream = io.StringIO("data_test _key1\n;foo bar\n; _key2 'value 2'\n")
mmcif_dict = MMCIF2Dict(stream)
self.assertEqual(mmcif_dict, {
"data_": "test",
"_key1": ["foo bar"],
"_key2": ["value 2"]
})
stream = io.StringIO(
"data_test _key1\n;foo bar\n;# missing space here")
with self.assertRaisesRegex(ValueError, "Missing whitespace"):
mmcif_dict = MMCIF2Dict(stream)
def parse_cif(label):
#parse the cif file and return the site information if there is any
mmcif_dict = MMCIF2Dict(label + '.cif')
if "_struct_site.id" in mmcif_dict: #if there is site info documented in cif file, get the info of cat and bind residues.
siteseq = mmcif_dict["_struct_site_gen.auth_comp_id"], mmcif_dict[
"_struct_site_gen.auth_asym_id"], mmcif_dict[
"_struct_site_gen.auth_seq_id"], mmcif_dict[
"_struct_site_gen.site_id"]
siteseq = np.asarray(siteseq)
siteseq.shape = (4, -1)
#extract the id of important sites as "siteinfo"
siteinfo = mmcif_dict["_struct_site.id"], mmcif_dict[
"_struct_site.details"]
siteinfo = np.asarray(siteinfo)
siteinfo.shape = (2, -1)
HasSite = True
else:
siteseq = np.asarray([])
siteinfo = np.asarray([])
HasSite = False
return siteseq, siteinfo, HasSite
def get_info_from_mmcif(self, key):
cifname = 'mmcifs/' + self.code + '.mmcif'
try:
mmcif = MMCIF2Dict(cifname)
return mmcif.get(key)
except:
print 'no %s in %s' % (key, self.code)
def get_structure(self, structure_id, file):
""" Parses file contents and returns Structure object.
Note that parameter order is different to the BioPython's implementation (reversed, as structure_id is optional).
:param structure_id: if None, taken from mmcif (`_entry.id`)
:param file: a file-like object or a file name
:return: Bio.PDB.Structure
"""
with warnings.catch_warnings():
if self.QUIET:
warnings.filterwarnings("ignore",
category=PDBConstructionWarning)
self._mmcif_dict = MMCIF2Dict(file)
# begin change
if structure_id is None:
structure_id = self._mmcif_dict['_entry.id'][0].lower()
# end change
self._build_structure(structure_id)
self._structure_builder.set_header(self._get_header())
return self._structure_builder.get_structure()
def test_get_mmcif_seq(self):
filename = './tests/pdb/4nuv.cif'
mmcif_dict = MMCIF2Dict(filename)
sequence = pdbtools.get_mmcif_canonical_seq(mmcif_dict)
to_match = {
'C':
'GPTGTENSSQLDFEDVWNSSYGVNDSFPDGDYGA',
'D':
'GPTGTENSSQLDFEDVWNSSYGVNDSFPDGDYGA',
'A': ('ASNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDT'
'NFHRDITFRKLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDF'
'GDIIMGTDMEGIGYSKVVENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAM'
'MYSVKKRLKGNFIWICKLNVAVNIEPQIYRWIREWGRDYVSELPTEVQKLK'
'EKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQWDVLSNKFISVKNA'
'EKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCSVEEAKK'
'NTQEVVTNVDN'),
'B': ('ASNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDT'
'NFHRDITFRKLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDF'
'GDIIMGTDMEGIGYSKVVENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAM'
'MYSVKKRLKGNFIWICKLNVAVNIEPQIYRWIREWGRDYVSELPTEVQKLK'
'EKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQWDVLSNKFISVKNA'
'EKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCSVEEAKK'
'NTQEVVTNVDN')
}
self.assertDictEqual(sequence, to_match)
def get_structure(self, structure_id, filename):
with warnings.catch_warnings():
if self.QUIET:
warnings.filterwarnings("ignore", category=PDBConstructionWarning)
self._mmcif_dict = MMCIF2Dict(filename)
self._build_structure(structure_id)
return self._structure_builder.get_structure()
def fasta(t1, pos):
pdb = t1[0:4]
chain = t1[5:len(t1)]
#count = 0
#if count == 0:
try:
fol = pdb[1:3]
pdbfile = "{}/{}/{}.cif.gz".format(pathmmcif, fol, pdb)
tar = gzip.open("{}".format(pdbfile), "rb")
out = open("pdbprocess1.cif", "wb")
out.write(tar.read())
tar.close()
out.close()
mmcif = MMCIF2Dict("pdbprocess1.cif")
idmap1 = seqres_atom_map(mmcif, chain, pos)
k1 = 1
str1 = ""
while k1 <= len(idmap1[0]):
t2 = "{}".format(k1)
key1 = (t2, chain)
res = idmap1[0][key1]
if k1 % 100 == 0:
str1 = str1 + "{}\n".format(res)
else:
str1 = str1 + "{}".format(res)
k1 = k1 + 1
return (str1, idmap1[1])
except:
return ("NA")
def test_quotefix(self):
# Test quote characters parse correctly
filename = "PDB/1MOM_min.cif"
mmcif = MMCIF2Dict(filename)
self.assertEqual(len(mmcif.keys()), 21)
self.assertEqual(
mmcif["_struct_conf.pdbx_PDB_helix_id"],
[
"A",
"A'",
"B",
"C",
"B'",
"D",
"E",
"C'",
"F",
"G",
"H",
"D'",
"E'",
"A'\"",
"BC",
"CD",
"DE",
],
)
def test_splitline(self):
filename = "PDB/4Q9R_min.cif"
mmcif = MMCIF2Dict(filename)
self.assertEqual(list(mmcif._splitline("foo bar")), ["foo", "bar"])
self.assertEqual(list(mmcif._splitline(" foo bar ")), ["foo", "bar"])
self.assertEqual(list(mmcif._splitline("'foo' bar")), ["foo", "bar"])
self.assertEqual(list(mmcif._splitline('foo "bar"')), ["foo", "bar"])
self.assertEqual(list(mmcif._splitline("foo 'bar a' b")),
["foo", "bar a", "b"])
self.assertEqual(list(mmcif._splitline("foo 'bar'a' b")),
["foo", "bar'a", "b"])
self.assertEqual(list(mmcif._splitline('foo "bar\' a" b')),
["foo", "bar' a", "b"])
self.assertEqual(list(mmcif._splitline("foo '' b")), ["foo", "", "b"])
self.assertEqual(list(mmcif._splitline("foo bar' b")),
["foo", "bar'", "b"])
self.assertEqual(list(mmcif._splitline("foo bar b'")),
["foo", "bar", "b'"])
# A hash (#) starts a comment iff it is preceded by whitespace or is at
# the beginning of a line:
# https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#lex
self.assertEqual(list(mmcif._splitline("foo#bar")), ["foo#bar"])
self.assertEqual(list(mmcif._splitline("foo #bar")), ["foo"])
self.assertEqual(list(mmcif._splitline("foo# bar")), ["foo#", "bar"])
self.assertEqual(list(mmcif._splitline("#foo bar")), [])
self.assertRaises(ValueError, list, mmcif._splitline("foo 'bar"))
self.assertRaises(ValueError, list, mmcif._splitline("foo 'ba'r "))
self.assertRaises(ValueError, list, mmcif._splitline("foo \"bar'"))
# quotes are allowed if not followed by whitespace
self.assertEqual(list(mmcif._splitline("foo b'ar'")), ["foo", "b'ar'"])
self.assertEqual(list(mmcif._splitline("foo 'b'ar'")), ["foo", "b'ar"])
def test_MMCIF2dict(self):
filename = "PDB/1A8O.cif"
mmcif = MMCIF2Dict(filename)
self.assertEqual(len(mmcif.keys()), 575)
self.assertEqual(mmcif['_entity_poly_seq.mon_id'], ['MSE', 'ASP', 'ILE', 'ARG', 'GLN', 'GLY', 'PRO', 'LYS', 'GLU', 'PRO', 'PHE', 'ARG', 'ASP', 'TYR', 'VAL', 'ASP', 'ARG', 'PHE', 'TYR', 'LYS', 'THR', 'LEU', 'ARG', 'ALA', 'GLU', 'GLN', 'ALA', 'SER', 'GLN', 'GLU', 'VAL', 'LYS', 'ASN', 'TRP', 'MSE', 'THR', 'GLU', 'THR', 'LEU', 'LEU', 'VAL', 'GLN', 'ASN', 'ALA', 'ASN', 'PRO', 'ASP', 'CYS', 'LYS', 'THR', 'ILE', 'LEU', 'LYS', 'ALA', 'LEU', 'GLY', 'PRO', 'GLY', 'ALA', 'THR', 'LEU', 'GLU', 'GLU', 'MSE', 'MSE', 'THR', 'ALA', 'CYS', 'GLN', 'GLY'])
self.assertEqual(mmcif['_atom_site.Cartn_x'], ['19.594', '20.255', '20.351', '19.362', '19.457', '20.022', '21.718', '21.424', '21.554', '21.835', '21.947', '21.678', '23.126', '23.098', '23.433', '22.749', '22.322', '22.498', '21.220', '20.214', '23.062', '24.282', '23.423', '25.429', '21.280', '20.173', '20.766', '21.804', '19.444', '18.724', '18.011', '17.416', '16.221', '15.459', '15.824', '20.116', '20.613', '20.546', '19.488', '19.837', '20.385', '19.526', '18.365', '20.090', '21.675', '21.698', '20.859', '20.729', '20.260', '19.435', '20.158', '19.512', '18.993', '20.056', '20.300', '21.486', '22.285', '23.286', '24.155', '23.025', '22.117', '21.236', '20.159', '19.231', '23.152', '24.037', '23.563', '22.398', '24.086', '25.003', '24.858', '23.861', '25.748', '24.459', '24.089', '23.580', '24.111', '25.415', '26.116', '25.852', '22.544', '21.960', '22.965', '22.928', '20.793', '19.999', '19.234', '20.019', '18.495', '19.286', '18.523', '23.861', '24.870', '25.788', '26.158', '25.684', '26.777', '26.215', '27.235', '28.136', '28.155', '29.030', '26.137', '26.994', '26.279', '26.880', '27.408', '28.345', '28.814', '28.620', '24.992', '24.151', '24.025', '24.139', '22.787', '21.629', '21.657', '20.489', '20.571', '19.408', '19.450', '18.365', '23.839', '23.720', '24.962', '24.853', '23.502', '23.661', '22.120', '26.137', '27.387', '27.511', '27.925', '28.595', '28.723', '28.016', '29.545', '27.136', '27.202', '26.238', '26.585', '26.850', '27.835', '27.667', '26.352', '25.494', '25.797', '24.325', '25.037', '23.984', '24.456', '24.305', '22.761', '21.538', '21.301', '20.586', '20.130', '19.415', '19.186', '25.033', '25.526', '26.755', '27.015', '25.771', '24.608', '23.508', '24.583', '22.406', '23.490', '22.406', '21.326', '27.508', '28.691', '28.183', '28.705', '29.455', '30.787', '31.428', '32.618', '33.153', '27.116', '26.508', '25.826', '25.827', '25.475', '26.150', '24.741', '25.264', '24.587', '25.587', '25.302', '23.789', '22.707', '21.787', '21.910', '26.767', '27.806', '28.299', '28.656', '29.006', '28.944', '30.295', '30.744', '30.326', '29.441', '30.787', '28.332', '28.789', '27.943', '28.374', '28.803', '26.740', '25.833', '25.775', '24.998', '24.425', '24.354', '24.816', '24.535', '25.454', '26.601', '26.645', '25.240', '24.885', '27.391', '28.884', '29.200', '28.729', '29.998', '24.438', '23.066', '23.001', '23.824', '22.370', '22.035', '21.831', '21.174', '20.852', '20.917', '19.638', '20.949', '20.315', '18.908', '18.539', '20.262', '19.688', '20.414', '21.592', '19.714', '18.136', '16.775', '16.738', '15.875', '16.101', '15.478', '14.341', '13.247', '14.542', '17.668', '17.730', '18.064', '17.491', '18.754', '18.932', '18.279', '18.971', '19.343', '18.126', '17.905', '20.444', '21.777', '22.756', '24.069', '24.913', '17.344', '16.136', '15.146', '14.599', '15.468', '16.242', '17.164', '15.865', '14.932', '14.017', '14.495', '13.700', '13.904', '13.254', '12.332', '13.484', '11.975', '12.666', '14.303', '12.641', '14.280', '13.452', '15.793', '16.368', '16.285', '16.053', '17.815', '17.939', '17.221', '18.427', '16.438', '16.375', '14.950', '14.778', '16.869', '18.228', '16.791', '13.947', '12.529', '12.045', '11.151', '11.625', '11.950', '11.054', '11.086', '10.326', '12.589', '12.177', '13.076', '12.888', '11.978', '13.202', '10.883', '14.054', '14.963', '15.702', '15.846', '15.935', '15.286', '16.327', '14.580', '16.162', '16.876', '15.961', '16.391', '17.402', '18.238', '19.553', '18.506', '14.695', '13.703', '13.270', '13.262', '12.460', '11.372', '12.854', '12.954', '12.503', '13.541', '13.184', '12.008', '10.830', '10.505', '10.626', '10.093', '14.820', '15.887', '16.443', '17.416', '17.014', '16.627', '15.451', '17.619', '15.830', '16.248', '15.758', '14.809', '15.689', '16.404', '16.005', '14.639', '14.122', '17.109', '17.396', '16.559', '18.588', '14.018', '12.706', '12.516', '11.536', '12.617', '13.288', '14.522', '13.454', '13.383', '13.351', '12.406', '14.564', '14.482', '13.353', '15.552', '14.378', '14.488', '13.443', '12.968', '15.902', '16.144', '13.061', '12.087', '10.746', '10.157', '11.879', '11.014', '11.003', '10.171', '10.269', '10.273', '9.002', '9.101', '8.227', '8.612', '8.611', '7.224', '10.191', '10.458', '10.518', '9.916', '11.791', '11.677', '12.184', '12.967', '11.222', '11.377', '10.082', '9.885', '12.416', '13.824', '14.764', '14.287', '9.214', '7.937', '7.048', '6.294', '7.230', '7.828', '7.618', '8.090', '7.916', '7.189', '6.419', '6.871', '6.391', '6.449', '7.815', '8.305', '7.481', '7.371', '9.788', '10.832', '12.217', '10.789', '6.886', '6.080', '6.922', '8.149', '6.294', '7.024', '7.912', '7.680', '5.901', '4.734', '4.839', '8.952', '9.861', '10.886', '11.642', '10.910', '11.884', '13.285', '13.524', '11.599', '14.199', '15.563', '16.391', '16.022', '16.290', '16.498', '15.473', '17.509', '18.426', '18.875', '19.012', '19.645', '20.773', '20.264', '21.920', '19.082', '19.510', '18.471', '18.816', '19.784', '21.035', '20.954', '19.902', '21.955', '17.199', '16.109', '16.001', '15.690', '14.787', '14.776', '13.539', '13.220', '12.888', '16.301', '16.274', '17.413', '17.209', '16.429', '15.284', '15.332', '13.844', '18.606', '19.764', '19.548', '19.922', '21.047', '21.507', '23.105', '22.645', '18.915', '18.636', '17.640', '17.807', '18.050', '18.998', '17.730', '16.631', '15.593', '16.104', '15.685', '14.486', '17.033', '17.572', '18.985', '19.634', '17.525', '15.855', '19.451', '20.802', '21.001', '20.066', '21.152', '20.421', '20.725', '21.768', '19.817', '22.226', '22.536', '23.683', '24.328', '23.949', '15.165', '19.774', '22.152', '12.938', '23.499', '17.568', '13.544', '15.524', '31.249', '11.999', '14.511', '7.439', '19.303', '17.114', '21.867', '17.573', '26.151', '20.974', '20.796', '28.370', '29.565', '21.248', '25.744', '8.691', '30.789', '30.905', '28.623', '24.935', '23.462', '9.924', '28.729', '13.579', '23.652', '25.631', '17.799', '23.547', '16.363', '24.125', '33.063', '29.209', '10.391', '12.221', '18.997', '16.360', '27.915', '28.158', '21.975', '27.069', '30.148', '21.196', '8.864', '13.228', '18.577', '20.526', '25.758', '7.838', '20.569', '13.009', '19.229', '17.655', '30.445', '9.014', '3.398', '31.603', '16.543', '12.037', '7.261', '5.607', '23.532', '30.701', '32.300', '34.351', '9.450', '29.476', '13.681', '26.728', '10.004', '30.553', '23.569', '10.927', '17.983', '8.191', '32.095', '11.520', '13.249', '15.919', '11.187', '16.743'])
self.assertEqual(mmcif['_struct_ref.pdbx_seq_one_letter_code'], 'GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQNKSKKKAQQAAADTGNNSQVSQNYPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQVTNPATIMIQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRPEPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLRSLFGSDPSSQ')
def readPDBFile(filename):
mmcif_dict = MMCIF2Dict(filename)
nbchains, nbres, nbatoms, res = mmcif_dict[
'_struct_sheet.number_strands'], mmcif_dict[
'_struct_site.pdbx_num_residues'], mmcif_dict[
'_refine_hist.number_atoms_total'], mmcif_dict['_exptl.method']
return sum([int(nbchains[i])
for i in range(len(nbchains))]), nbres, nbatoms, res
def test_underscores(self):
# Test values starting with an underscore are not treated as keys
filename = "PDB/4Q9R_min.cif"
mmcif = MMCIF2Dict(filename)
self.assertEqual(len(mmcif.keys()), 5)
self.assertEqual(mmcif['_pdbx_audit_revision_item.item'], [
'_atom_site.B_iso_or_equiv', '_atom_site.Cartn_x',
'_atom_site.Cartn_y', '_atom_site.Cartn_z'
])
def test_quotefix(self):
# Test quote characters parse correctly
filename = "PDB/1MOM_min.cif"
mmcif = MMCIF2Dict(filename)
self.assertEqual(len(mmcif.keys()), 21)
self.assertEqual(mmcif['_struct_conf.pdbx_PDB_helix_id'], [
'A', 'A\'', 'B', 'C', 'B\'', 'D', 'E', 'C\'', 'F', 'G', 'H', 'D\'',
'E\'', 'A\'"', 'BC', 'CD', 'DE'
])
def split_file(filename):
"""
MMCIF2Dict from biopython does not know how to parse this type of file, because it is like multiple
mmcif files in one file. We need to split it
:param filename:
:return: list of mmcifdict ligands
"""
try:
with open(filename, mode='r', encoding='utf-8') as f:
file_string = f.read()
ligands = re.split('([\r\n?|\n]#[\r\n?|\n]data_.*?[\r\n?|\n]#)', file_string)
ligands = [MMCIF2Dict(io.StringIO(x + y)) for x, y in zip(ligands[1:][0::2], ligands[1:][1::2])]
except UnicodeDecodeError:
with open(filename, mode='r', encoding='utf-16') as f:
file_string = f.read()
ligands = re.split('([\r\n?|\n]#[\r\n?|\n]data_.*?[\r\n?|\n]#)', file_string)
ligands = [MMCIF2Dict(io.StringIO(x + y)) for x, y in zip(ligands[1:][0::2], ligands[1:][1::2])]
return ligands
def test_mmcifio_write_dict(self):
"""Write an mmCIF dictionary out, read it in and compare them."""
d1 = MMCIF2Dict(self.mmcif_file)
# Write to temp file
self.io.set_dict(d1)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
d2 = MMCIF2Dict(filename)
k1 = sorted(d1.keys())
k2 = sorted(d2.keys())
self.assertEqual(k1, k2)
for key in k1:
self.assertEqual(d1[key], d2[key])
finally:
os.remove(filename)
def main():
pathmmcif = "/Volumes/BIOINFO/mmCIF"
pathfasta = "/Users/tarunkhanna/Documents/Bioinformatics/file_links/"
f = open("{}/pdb_seqres.txt".format(pathfasta), "r")
ft = f.readlines()
f.close()
g = open("PDB_fasta.txt", "w")
start = sys.argv[1]
end = sys.argv[2]
if end == "END" or end == "end":
end = len(ft)
end = int(end)
start = int(start)
k = start
while k < end:
print(k, len(ft))
ft1 = ft[k].split()
t1 = ft1[0].strip(">")
pdb = t1[0:4]
chain = t1[5:len(t1)]
k = k + 2
#count = 0
#if count == 0:
try:
fol = pdb[1:3]
pdbfile = "{}/{}/{}.cif.gz".format(pathmmcif, fol, pdb)
tar = gzip.open("{}".format(pdbfile), "rb")
out = open("pdbprocess1{}.cif".format(start), "wb")
out.write(tar.read())
tar.close()
out.close()
mmcif = MMCIF2Dict("pdbprocess1{}.cif".format(start))
idmap1 = seqres_atom_map(mmcif, chain)
k1 = 1
str1 = ""
while k1 <= len(idmap1):
t2 = "{}".format(k1)
key1 = (t2, chain)
res = idmap1[key1]
if k % 100 == 0:
str1 = str1 + "{}\n".format(res)
else:
str1 = str1 + "{}".format(res)
k1 = k1 + 1
g.write(">{}\n".format(t1))
g.write("{}\n".format(str1))
except:
print("FILE NOT_FOUND")
def __init__(self, path):
'''
Initialize every PDB_Parser with a path to a structure-file in CIF format.
An example file is included in the repository (7ahl.cif).
Tip: Store the parsed structure in an object variable instead of parsing it
again & again ...
'''
# self.structure = CIF_PARSER.get_structure('name',path) # Parse the structure once and re-use it in the functions below
self.structure = list(MMCIF2Dict(path))
def get_STR(filePath, fileType='pdb'):
if fileType == "pdb":
STR = MMCIFParser(QUIET=True).get_structure("pdb", filePath)
return STR
if fileType == "cif":
DICT = MMCIF2Dict(filePath)
# print(DICT)
return DICT
else:
raise TypeError("%s is not a valid fileType" % fileType)
def assign(filename, dict):
n = 0
#Grab header
mmcif_dict = MMCIF2Dict(filename)
#Grab entity names
details = mmcif_dict['_entity.pdbx_description']
#Grab chain ids
strand_id = mmcif_dict['_entity_poly.pdbx_strand_id']
for x in strand_id:
dict[x] = details[n]
n += 1
return dict
def readLowLevel(self, fileName):
""" Return a dictionary with all mmcif fields. you should parse them
Example: get the list of the y coordinates of all atoms
dict = readLowLevel("kk.pdb")
y_list = dict['_atom_site.Cartn_y']
"""
if fileName.endswith(".pdb"):
print("Low level access to PDB is not implemented")
else:
dict = MMCIF2Dict(fileName)
return dict
def determine_transmembrane_domains(filename):
"""
Compares the helix domains in PDB with the transmembrane domains in
uniprot to determine if it is a transmembrane domain or not.
"""
chain_trans_dom = {}
true_chain_trans_dom = {}
mmcif_dict = MMCIF2Dict(filename)
chains = mmcif_dict['_entity_poly.pdbx_strand_id']
seqs = mmcif_dict['_entity_poly.pdbx_seq_one_letter_code_can']
assembly = mmcif_dict['_pdbx_struct_assembly_gen.asym_id_list']
# Checks if there is present more than one seq for chain.
# If there is only one (it is a string), it is processed below and the domains are added to the dict.
if type(seqs) == list:
i = 0
for seq in seqs:
if seq == None or seq == "\n" or seq == "\t" or seq == "" or seq == "?":
continue
else:
for dom in topconn_run(seq):
list_chains = chains[i].split(",")
for lett in list_chains:
if lett == None or lett == "?":
continue
chain_trans_dom.setdefault(lett, []).append(dom)
i += 1
else:
if seqs == "?":
return
for dom in topconn_run(seqs):
list_chains = chains.split(",")
for lett in list_chains:
if lett == None or lett == "?":
continue
chain_trans_dom.setdefault(lett, []).append(dom)
if type(assembly) == list:
for chain in assembly[0]:
if chain in chain_trans_dom.keys():
true_chain_trans_dom[chain] = chain_trans_dom[chain]
else:
true_chain_trans_dom = chain_trans_dom
print(true_chain_trans_dom)
logging.info('There are {} chains with transmembrane dom: {}'.format(
len(true_chain_trans_dom), true_chain_trans_dom.keys()))
return true_chain_trans_dom
def __init__(self, path):
'''
Initialize every PDB_Parser with a path to a structure-file in CIF format.
An example file is included in the repository (7ahl.cif).
Tip: Store the parsed structure in an object variable instead of parsing it
again & again ...
'''
# get id of the CIF
cif_dict = MMCIF2Dict(path)
identifier = cif_dict['_entry.id']
self.structure = PDB_Parser.CIF_PARSER.get_structure(
identifier, path
) # Parse the structure once and re-use it in the functions below
def mmcif_dict(self):
'''Return the mmcif dictionary.
Only applicable if using an mmCIF file.
Returns:
dict: A dictionary containing mmCIF data.
'''
if self._mmcif and self._mmcif_dict is None:
self._mmcif_dict = MMCIF2Dict(self.pdb_file())
elif not self._mmcif:
raise TypeError("Not an mmCIF file!")
return self._mmcif_dict
def get_structure(self, structure_id, filename):
"""Return the structure.
Arguments:
- structure_id - string, the id that will be used for the structure
- filename - name of the mmCIF file OR an open filehandle
"""
with warnings.catch_warnings():
if self.QUIET:
warnings.filterwarnings("ignore", category=PDBConstructionWarning)
self._mmcif_dict = MMCIF2Dict(filename)
self._build_structure(structure_id)
return self._structure_builder.get_structure()
def test_inline_comments(self):
"""Comments may begin outside of column 1."""
mmcif_dict = MMCIF2Dict(io.StringIO(textwrap.dedent(u"""\
data_verbatim_test
_test_key_value foo # Ignore this comment
loop_
_test_loop
a b c d # Ignore this comment
e f g
""")))
self.assertEqual(mmcif_dict["_test_key_value"], "foo")
self.assertEqual(mmcif_dict["_test_loop"], list("abcdefg"))
def find_ligand_annotations(cif_path, ligands):
"""
Returns a list of ligand annotations in from a PDB structures cif file
if they exist
:Param cif_path: path to PDB structure in mmCIF format
:Param ligans: list of ligands
:return known_interfaces: list of tuples of known interfaces
[(pbid, position, chain, type), ...]
"""
known_interfaces = []
mmcif_dict = MMCIF2Dict(cif_path)
structure_id = cif_path[-8:-4]
ligands = set(ligands)
try:
binding_site_details = mmcif_dict['_struct_site.details']
binding_site_ids = mmcif_dict['_struct_site.id']
except KeyError:
print('No interface annotations found for:\n', cif_path, '\n\n')
return None
# Find binding site ID of first ligand if it exists
site_id = ''
for site, detail in zip(binding_site_ids, binding_site_details):
words = detail.split()
for w in words:
if w in ligands and len(w) > 1:
site_id = site
if site_id == '':
print('No ligand annotations found for: \n', cif_path, '\n\n')
return None
print(site_id)
# Find the residues of the binding site
positions = mmcif_dict['_struct_site_gen.label_seq_id']
chains = mmcif_dict['_struct_site_gen.label_asym_id']
res_ids = mmcif_dict['_struct_site_gen.label_comp_id']
sites = mmcif_dict['_struct_site_gen.site_id']
for position, chain, res_id, site in zip(positions, chains, res_ids,
sites):
if site != site_id: continue
if len(res_id) > 1 and res_id not in 'AUCG': continue
known_interfaces.append((structure_id, position, chain, 'ligand'))
if len(known_interfaces) == 0: return None
return known_interfaces
def all_seqres_pdb_map():
# PATH FOR THE PDB/mmCIF FILES
import gzip
pathmmcif = "/bmm/data/pdbmmcif/data/structures/all/mmCIF"
dis = open("distinct_mutants.txt", "r")
ht = dis.readlines()
dis.close()
h = open("distinct_mutants_pdb.txt", "w")
k = 0
while k < len(ht): # end = len(ht)
mutant = []
mu = ht[k].split(', ')
pdbid = mu[0].strip('[|\,|\'|]')
pdb = pdbid[0:4] # PDB NAME
C = pdbid[5:6] # CHAIN
print("*** {} :: {} of {} ***".format(pdb, k, len(ht)))
# EXCUTE THE CODE TO PICK UP THE DESIRED ZONE AROUD THE RESIDUE
try:
pdbfile = "{}/{}.cif.gz".format(pathmmcif, pdb)
tar = gzip.open("{}".format(pdbfile), "rb")
out = open("pdbprocess.cif", "wb")
out.write(tar.read())
tar.close()
out.close()
mmcif = MMCIF2Dict("pdbprocess.cif")
idmap = seqres_atom_map(mmcif)
reslist = [pdbid]
k1 = 1
while k1 < len(mu):
id1 = int(mu[k1].strip("[|'|]|\n"))
id2 = idmap[id1][0]
reslist.append("{}".format(id2))
k1 = k1 + 1
h.write("{}".format(reslist))
h.write("\n")
except:
print("FILE NOT FOUND")
k = k + 1
def test_inline_comments(self):
"""Comments may begin outside of column 1 if preceded by whitespace."""
mmcif_dict = MMCIF2Dict(
io.StringIO("data_verbatim_test\n"
"_test_key_value_1 foo # Ignore this comment\n"
"_test_key_value_2 foo#NotIgnored\n"
"loop_\n"
"_test_loop\n"
"a b c d # Ignore this comment\n"
"e f g\n"
"\n"))
self.assertEqual(mmcif_dict["_test_key_value_1"], ["foo"])
self.assertEqual(mmcif_dict["_test_key_value_2"], ["foo#NotIgnored"])
self.assertEqual(mmcif_dict["_test_loop"], list("abcdefg"))
