def testPdbId(self):
pdbid = "1ddf"
for loc in self.res:
r = Residues("\t 1ddf \t" + loc[0] + "\t\n\n\n")
self.assertEqual(r.pdbid, pdbid)
self.assertEqual(str(r), pdbid + " " + loc[0])
r = Residues(pdbid + " " + loc[0])
self.assertEqual(r.pdbid, pdbid)
self.assertEqual(str(r), pdbid + " " + loc[0])
r = Residues("104l A:112-113")
self.assertEqual(r.pdbid, "104l")
self.assertEqual(r.fragments, (("A", "112", "113"), ))
def getSeqMap(self, residues):
"""Get the sequence map for a collection of residues.
Arguments:
- residues -- A Residues instance, or a string that can be
converted into a Residues instance.
"""
if isinstance(residues, basestring):
residues = Residues(residues)
pdbid = residues.pdbid
frags = residues.fragments
if not frags:
frags = (("_", "", ""),) # All residues of unnamed chain
seqMap = None
for frag in frags:
chainid = frag[0]
if chainid in ["", "-", " ", "_"]:
chainid = "_"
id = pdbid + chainid
sm = self[id]
# Cut out fragment of interest
start = 0
end = len(sm.res)
if frag[1]:
start = int(sm.index(frag[1], chainid))
if frag[2]:
end = int(sm.index(frag[2], chainid)) + 1
sm = sm[start:end]
if seqMap is None:
seqMap = sm
else:
seqMap += sm
return seqMap
def testJustPdbId(self):
r = Residues("1sds")
self.assertEqual(r.pdbid, "1sds")
self.assertFalse(r.fragments)
def testAstralParse(self):
"""Test if we can parse residue subsets enclosed in brackets."""
for loc in self.res:
r = Residues("(" + loc[0] + ")")
self.assertEqual(r.fragments, loc[1])
def testStr(self):
for loc in self.res:
r = Residues(loc[0])
self.assertEqual(str(r), loc[0])
def testParse(self):
for loc in self.res:
r = Residues(loc[0])
self.assertEqual(r.fragments, loc[1])