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theresearchsoftwarecompany / pdb_prep python
Repository URL to install this package:
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Version:
0.0.8.9 ▾
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import unittest
from Chemistry.PDB.pdb_chain import *
class Test_pdb_chain(unittest.TestCase):
def setUp(self):
self.pdb_lines = [
'ATOM 1 N GLY 1 -1.105 -0.267 -0.062 1.00 0.00 N1+',
'ATOM 2 CA GLY 1 0.112 0.550 0.170 1.00 0.00 C',
'ATOM 3 C GLY 1 1.240 -0.152 -0.119 1.00 0.00 C',
'ATOM 4 O GLY 1 1.176 -1.323 -0.522 1.00 0.00 O',
'ATOM 5 H1 GLY 1 -0.933 -1.171 0.368 1.00 0.00 H',
'ATOM 6 H2 GLY 1 -1.222 -0.423 -1.054 1.00 0.00 H',
'ATOM 7 H3 GLY 1 -1.924 0.172 0.330 1.00 0.00 H',
'ATOM 8 HA2 GLY 1 0.107 1.445 -0.451 1.00 0.00 H',
'ATOM 9 HA3 GLY 1 0.177 0.840 1.228 1.00 0.00 H',
'ATOM 10 N GLY 2 2.371 0.492 0.057 1.00 0.00 N',
'ATOM 11 CA GLY 2 3.674 -0.160 -0.222 1.00 0.00 C',
'ATOM 12 C GLY 2 4.711 0.684 0.027 1.00 0.00 C',
'ATOM 13 O GLY 2 4.510 1.838 0.434 1.00 0.00 O',
'ATOM 14 H GLY 2 2.354 1.437 0.384 1.00 0.00 H',
'ATOM 15 HA2 GLY 2 3.809 -1.056 0.397 1.00 0.00 H',
'ATOM 16 HA3 GLY 2 3.738 -0.441 -1.272 1.00 0.00 H',
'ATOM 17 N GLY 3 5.910 0.193 -0.192 1.00 0.00 N',
'ATOM 18 CA GLY 3 7.126 1.010 0.050 1.00 0.00 C',
'ATOM 19 C GLY 3 8.254 0.308 -0.249 1.00 0.00 C',
'ATOM 20 O GLY 3 8.691 0.305 -1.375 1.00 0.00 O',
'ATOM 21 OXT GLY 3 8.839 -0.334 0.651 1.00 0.00 O1-',
'ATOM 22 H GLY 3 6.005 -0.747 -0.522 1.00 0.00 H',
'ATOM 23 HA2 GLY 3 7.122 1.905 -0.581 1.00 0.00 H',
'ATOM 24 HA3 GLY 3 7.191 1.300 1.088 1.00 0.00 H',
]
self.ter_line = 'TER 25 GLY 3 '
# ATOM 24 HA3 GLY 3 7.191 1.300 1.088 1.00 0.00 H
# TER 25 GLY 3
# TER 25 GLY
def test_pdb_chain(self):
chain = pdb_chain.from_pdb_atoms_lines(self.pdb_lines, self.ter_line)
self.assertTrue(chain[0].pdb_line == self.pdb_lines[0])
self.assertTrue(len(chain) == len(self.pdb_lines))
def test_pdb_create_ter_line(self):
ter_line = pdb_chain.create_ter_line(self.pdb_lines[-1])
self.assertEqual(ter_line, self.ter_line)
class Test_pdb_chain_utils(unittest.TestCase):
def setUp(self):
self.pdb_lines = [
'ATOM 1 N GLY 1 -1.105 -0.267 -0.062 1.00 0.00 N1+',
'ATOM 2 CA GLY 1 0.112 0.550 0.170 1.00 0.00 C',
'ATOM 3 C GLY 1 1.240 -0.152 -0.119 1.00 0.00 C',
'ATOM 4 O GLY 1 1.176 -1.323 -0.522 1.00 0.00 O',
'ATOM 5 H1 GLY 1 -0.933 -1.171 0.368 1.00 0.00 H',
'ATOM 6 H2 GLY 1 -1.222 -0.423 -1.054 1.00 0.00 H',
'ATOM 7 H3 GLY 1 -1.924 0.172 0.330 1.00 0.00 H',
'ATOM 8 HA2 GLY 1 0.107 1.445 -0.451 1.00 0.00 H',
'ATOM 9 HA3 GLY 1 0.177 0.840 1.228 1.00 0.00 H',
'ATOM 10 N GLY 2 2.371 0.492 0.057 1.00 0.00 N',
'ATOM 11 CA GLY 2 3.674 -0.160 -0.222 1.00 0.00 C',
'ATOM 12 C GLY 2 4.711 0.684 0.027 1.00 0.00 C',
'ATOM 13 O GLY 2 4.510 1.838 0.434 1.00 0.00 O',
'ATOM 14 H GLY 2 2.354 1.437 0.384 1.00 0.00 H',
'ATOM 15 HA2 GLY 2 3.809 -1.056 0.397 1.00 0.00 H',
'ATOM 16 HA3 GLY 2 3.738 -0.441 -1.272 1.00 0.00 H',
'ATOM 17 N GLY 3 5.910 0.193 -0.192 1.00 0.00 N',
'ATOM 18 CA GLY 3 7.126 1.010 0.050 1.00 0.00 C',
'ATOM 19 C GLY 3 8.254 0.308 -0.249 1.00 0.00 C',
'ATOM 20 O GLY 3 8.691 0.305 -1.375 1.00 0.00 O',
'ATOM 21 OXT GLY 3 8.839 -0.334 0.651 1.00 0.00 O1-',
'ATOM 22 H GLY 3 6.005 -0.747 -0.522 1.00 0.00 H',
'ATOM 23 HA2 GLY 3 7.122 1.905 -0.581 1.00 0.00 H',
'ATOM 24 HA3 GLY 3 7.191 1.300 1.088 1.00 0.00 H',
]
self.ter_line = 'TER 25 GLY 3 '
chain = pdb_chain.from_pdb_atoms_lines(self.pdb_lines, self.ter_line)
def test_chain2residues_list(self):
chain = pdb_chain.from_pdb_atoms_lines(self.pdb_lines, self.ter_line)
chain_util = chain_utils(chain)
residues = chain_util.chain2residues_list()
self.assertEqual(len(residues), 3)
res_names = list(map(lambda r: r.resname, residues))
self.assertEqual(res_names, ['GLY', 'GLY', 'GLY'])
res_seqs = list(map(lambda r: r.resseq, residues))
self.assertEqual(res_seqs, [1, 2, 3])
def test_remove_residues(self):
chain = pdb_chain.from_pdb_atoms_lines(self.pdb_lines, self.ter_line)
chain_util = chain_utils(chain)
new_chain = chain_util.remove_residues_by_resseqs([2])
residues = chain_utils(new_chain).chain2residues_list()
self.assertEqual(len(residues), 2)
res_names = list(map(lambda r: r.resname, residues))
self.assertEqual(res_names, ['GLY', 'GLY'])
res_seqs = list(map(lambda r: r.resseq, residues))
self.assertEqual(res_seqs, [1, 3])