def test_SeqMap_getAtoms_err(self):
r = Raf.SeqMap(self.rafLine)
# There is no overlap with this PDB file...
with open("PDB/1A8O.pdb") as pdb_handle:
out_handle = StringIO()
self.assertRaises(RuntimeError, r.getAtoms,
*(pdb_handle, out_handle))
def testSeqMapIndex(self):
filename = "./SCOP/raftest.txt"
index = Raf.SeqMapIndex(filename)
r = index.getSeqMap("103m")
self.assertEqual(r.pdbid, "103m")
self.assertEqual(len(r.res), 154)
self.assertEqual(r.pdb_datestamp, "010301")
self.assertEqual(r.flags, "111011")
r = index.getSeqMap("103m 1-10")
self.assertEqual(r.pdbid, "103m")
self.assertEqual(len(r.res), 10)
self.assertEqual(r.pdb_datestamp, "010301")
self.assertEqual(r.flags, "111011")
r = index.getSeqMap("104l A:")
self.assertEqual(r.pdbid, "104l")
r = index.getSeqMap("104l A:112-113")
self.assertEqual(r.pdbid, "104l")
self.assertEqual(len(r.res), 2)
r = index.getSeqMap("104l A:112-113,B:146-148")
self.assertEqual(r.pdbid, "104l")
self.assertEqual(len(r.res), 5)
def testSeqMapAdd(self):
r2 = Raf.SeqMap(self.rafLine2)
r3 = Raf.SeqMap(self.rafLine3)
length = len(r2.res) + len(r3.res)
r2 += r3
self.assertEqual(len(r2.res), length)
r2.extend(r2)
self.assertEqual(len(r2.res), length * 2)
r4 = r2 + r2
self.assertEqual(len(r4.res), length * 4)
r4.append(Raf.Res())
self.assertEqual(len(r4.res), (length * 4) + 1)
def testSeqMapIndex(self):
filename = ("./SCOP/raftest.txt")
index = Raf.SeqMapIndex(filename)
r = index.getSeqMap("103m")
assert r.pdbid == "103m", r.pdbid
assert len(r.res) == 154, len(r.res)
assert r.pdb_datestamp == "010301"
assert r.flags == "111011"
r = index.getSeqMap("103m 1-10")
assert r.pdbid == "103m", r.pdbid
assert len(r.res) == 10, len(r.res)
assert r.pdb_datestamp == "010301"
assert r.flags == "111011"
r = index.getSeqMap("104l A:")
assert r.pdbid == "104l", r.pdbid
r = index.getSeqMap("104l A:112-113")
assert r.pdbid == "104l", r.pdbid
assert len(r.res) == 2
r = index.getSeqMap("104l A:112-113,B:146-148")
assert r.pdbid == "104l", r.pdbid
assert len(r.res) == 5
def testSeqMapAdd(self):
r2 = Raf.SeqMap(self.rafLine2)
r3 = Raf.SeqMap(self.rafLine3)
l = len(r2.res) + len(r3.res)
r2 += r3
assert len(r2.res) == l
r2.extend(r2)
assert len(r2.res) == l * 2
r4 = r2 + r2
assert len(r4.res) == l * 4
r4.append(Raf.Res())
assert len(r4.res) == (l * 4) + 1
def testParse(self):
"""Parse a RAF record."""
r = Raf.SeqMap(self.rafLine)
self.assertEqual(r.pdbid, "101m")
self.assertEqual(r.pdb_datestamp, "010301")
self.assertEqual(r.flags, "111011")
i = r.index("143")
res = r.res[i]
self.assertEqual(res.chainid, "_")
self.assertEqual(res.resid, "143")
self.assertEqual(res.seqres, "A")
self.assertEqual(res.atom, "A")
r = Raf.SeqMap(self.rafLine2)
res = r.res[r.index("6A", chainid="A")]
self.assertEqual(res.resid, "6A")
self.assertEqual(res.atom, "E")
def testParse(self):
"""Can we parse a RAF record?"""
r = Raf.SeqMap(self.rafLine)
assert r.pdbid == "101m"
assert r.pdb_datestamp == "010301"
assert r.flags == "111011"
i = r.index("143")
res = r.res[i]
assert res.chainid == "_"
assert res.resid == "143"
assert res.seqres == "A"
assert res.atom == "A"
r = Raf.SeqMap(self.rafLine2)
res = r.res[r.index("6A", chainid="A")]
assert res.resid == "6A"
assert res.atom == "E"
def main():
try:
opts, args = getopt.getopt(
sys.argv[1:], "hp:o:i:",
["help", "usage", "pdb=", "output=", "input="])
except getopt.GetoptError:
# show help information and exit:
usage()
sys.exit(2)
input = None
in_handle = None
output = None
pdb_url = None
cla_url = None
raf_url = None
for o, a in opts:
if o in ("-h", "--help", "--usage"):
usage()
sys.exit()
elif o in ("-o", "--output"):
output = a
elif o in ("-i", "--input"):
input = a
elif o in ("-p", "--pdb"):
pdb_url = a
if len(args) < 2:
sys.stderr.write(
"Not enough arguments. Try --help for more details.\n")
sys.exit(2)
raf_url = args[0]
cla_url = args[1]
(raf_filename, headers) = _urlretrieve(raf_url)
seqMapIndex = Raf.SeqMapIndex(raf_filename)
(cla_filename, headers) = _urlretrieve(cla_url)
claIndex = Cla.Index(cla_filename)
if input is None:
sids = args[2:]
elif input == '-':
sids = sys.stdin
else:
in_handle = open(input)
sids = in_handle
try:
for sid in sids:
if not sid or sid[0:1] == '#':
continue
id = sid[0:7]
pdbid = id[1:5]
s = pdbid[0:1]
if s == '0' or s == 's':
sys.stderr.write("No coordinates for domain %s\n" % id)
continue
if output is None:
filename = id + ".ent"
out_handle = open(filename, "w+")
elif output == '-':
out_handle = sys.stdout
else:
out_handle = open(output, "w+")
try:
try:
claRec = claIndex[id]
residues = claRec.residues
seqMap = seqMapIndex.getSeqMap(residues)
pdbid = residues.pdbid
f = open_pdb(pdbid, pdb_url)
try:
seqMap.getAtoms(f, out_handle)
finally:
f.close()
except (IOError, KeyError, RuntimeError) as e:
sys.stderr.write("I cannot do SCOP domain %s : %s\n" %
(id, e))
finally:
out_handle.close()
finally:
if in_handle is not None:
in_handle.close()
def testSeqMapSlice(self):
r = Raf.SeqMap(self.rafLine)
r = r[r.index("124") : r.index("135") + 1]
self.assertEqual(len(r.res), 12)
def testSeqMapSlice(self):
r = Raf.SeqMap(self.rafLine)
r = r[r.index("124"):r.index("135") + 1]
assert len(r.res) == 12
