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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Unit test for Raf"""
import unittest
from Bio.SCOP import Raf
from Bio._py3k import StringIO
class RafTests(unittest.TestCase):
rafLine = "101m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 vv 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 vv 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg"
rafLine2 = "101mA 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6Aee 7Aww 8Aqq"
rafLine3 = "101mB 0.01 38 010301 111011 0 153 90 mm 91 vv 92 ll 939ss 94 ee 95 gg"
def testParse(self):
"""Can we 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 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 testSeqMapSlice(self):
r = Raf.SeqMap(self.rafLine)
r = r[r.index("124"): r.index("135") + 1]
self.assertEqual(len(r.res), 12)
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)
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)