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# Copyright 2020 by Rob Miller. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Unit tests for PARTS of the parse_pdb_header module of Bio.PDB."""
import unittest
import re
import warnings
try:
import numpy # noqa F401
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError("Install NumPy if you want to use Bio.PDB.")
from Bio.PDB.ic_rebuild import structure_rebuild_test, write_PDB
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.MMCIFParser import MMCIFParser
from io import StringIO
from Bio.PDB.SCADIO import write_SCAD
from Bio.PDB.PICIO import write_PIC
from Bio.File import as_handle
from Bio.PDB.Model import Model
from Bio.PDB.Residue import Residue
from Bio.PDB.internal_coords import IC_Residue
from Bio.PDB.PDBExceptions import PDBConstructionWarning
class Rebuild(unittest.TestCase):
"""Read PDB and mmCIF structures, convert to/from internal coordinates."""
PDB_parser = PDBParser(PERMISSIVE=True, QUIET=True)
CIF_parser = MMCIFParser(QUIET=True)
pdb_1LCD = PDB_parser.get_structure("1LCD", "PDB/1LCD.pdb")
pdb_2XHE = PDB_parser.get_structure("2XHE", "PDB/2XHE.pdb")
cif_3JQH = CIF_parser.get_structure("3JQH", "PDB/3JQH.cif")
cif_4CUP = CIF_parser.get_structure("4CUP", "PDB/4CUP.cif")
def test_rebuild_multichain_missing(self):
"""Convert multichain missing atom protein to internal coordinates and back."""
# 2XHE has regions of missing chain, last residue has only N
r = structure_rebuild_test(self.pdb_2XHE, False)
self.assertEqual(r["residues"], 787)
self.assertEqual(r["rCount"], 835)
self.assertEqual(r["rMatchCount"], 835)
self.assertEqual(r["aCount"], 6267)
self.assertEqual(r["disAtmCount"], 0)
self.assertEqual(r["aCoordMatchCount"], 6267)
self.assertEqual(len(r["chains"]), 2)
self.assertTrue(r["pass"])
def test_rebuild_disordered_atoms_residues(self):
"""Convert disordered protein to internal coordinates and back."""
# 3jqh has both disordered residues
# and disordered atoms in ordered residues
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", PDBConstructionWarning)
r = structure_rebuild_test(self.cif_3JQH, False)
# print(r)
self.assertEqual(r["residues"], 26)
self.assertEqual(r["rCount"], 47)
self.assertEqual(r["rMatchCount"], 47)
self.assertEqual(r["aCount"], 217)
self.assertEqual(r["disAtmCount"], 50)
self.assertEqual(r["aCoordMatchCount"], 217)
self.assertEqual(len(r["chains"]), 1)
self.assertTrue(r["pass"])
def test_model_change_internal_coords(self):
"""Get model internal coords, modify psi and chi1 values and check."""
for mdl in self.pdb_1LCD:
if mdl.serial_num == 2:
break
mdl.atom_to_internal_coordinates()
# other tests show can build with arbitrary internal coords
# build here so changes below trigger more comlicated
# xAtoms_needs_update mask arrays
mdl.internal_to_atom_coordinates()
nvt = {}
nvc1 = {}
nvpsi = {}
tcount = 0
c1count = 0
psicount = 0
for r in mdl.get_residues():
ric = r.internal_coord
if ric:
# hedra change
tau = ric.get_angle("tau")
if ric.rprev != [] and tau is not None:
tcount += 1
nv = tau + 0.5
ric.set_angle("tau", nv)
nvt[str(r)] = nv
# sidechain dihedron change
chi1 = ric.get_angle("chi1")
if chi1 is not None:
c1count += 1
nv = chi1 + 90
if nv > 180.0:
nv -= 360.0
ric.set_angle("chi1", nv)
nvc1[str(r)] = nv
# backbone dihedron change
psi = ric.get_angle("psi")
if psi is not None:
psicount += 1
nv = psi - 90
if nv < -180.0:
nv += 360.0
ric.set_angle("psi", nv)
nvpsi[str(r)] = nv
mdl.internal_to_atom_coordinates()
sf = StringIO()
write_PDB(self.pdb_1LCD, sf)
sf.seek(0)
new_1LCD = self.PDB_parser.get_structure("1LCD", sf)
for mdl in new_1LCD:
if mdl.serial_num == 2:
break
mdl.atom_to_internal_coordinates()
ttcount = 0
c1tcount = 0
psitcount = 0
for r in mdl.get_residues():
ric = r.internal_coord
if ric:
tau = ric.get_angle("tau")
if ric.rprev != [] and tau is not None:
ttcount += 1
self.assertAlmostEqual(tau, nvt[str(r)], places=1)
chi1 = ric.get_angle("chi1")
if chi1 is not None:
c1tcount += 1
self.assertAlmostEqual(chi1, nvc1[str(r)], places=1)
psi = ric.get_angle("psi")
if psi is not None:
psitcount += 1
self.assertAlmostEqual(psi, nvpsi[str(r)], places=1)
self.assertEqual(tcount, ttcount)
self.assertEqual(c1count, c1tcount)
self.assertEqual(psicount, psitcount)
self.assertTrue(ttcount > 0)
self.assertTrue(c1count > 0)
self.assertTrue(psicount > 0)
def test_write_SCAD(self):
"""Check SCAD output plus MaxPeptideBond and Gly CB.
SCAD tests: scaling, transform mtx, extra bond created (allBonds)
"""
sf = StringIO()
write_SCAD(
self.cif_4CUP, sf, 10.0, pdbid="4cup", backboneOnly=True, includeCode=False
)
sf.seek(0)
next_one = False
with as_handle(sf, mode="r") as handle:
for aline in handle.readlines():
if "// (1856_S_CB, 1856_S_CA, 1856_S_C)" in aline:
m = re.search(r"\[\s+(\d+\.\d+)\,", aline)
if m:
# test correctly scaled atom bond length
self.assertAlmostEqual(float(m.group(1)), 15.30582, places=3)
else:
self.fail("scaled atom bond length not found")
elif '[ 1, "1857M",' in aline:
next_one = True
elif next_one:
next_one = False
# test last residue transform looks roughly correct
# some differences due to sorting issues on different python
# versions
target = [-12.413, -3.303, 35.771, 1.0]
ms = re.findall( # last column of each row
r"\s+(-?\d+\.\d+)\s+\]", aline
)
if ms:
for i in range(0, 3):
self.assertAlmostEqual(float(ms[i]), target[i], places=0)
else:
self.fail("transform not found")
sf.seek(0)
IC_Residue.gly_Cbeta = True
write_SCAD(
self.pdb_2XHE[0]["A"],
sf,
10.0,
pdbid="2xhe",
maxPeptideBond=100.0,
includeCode=False,
)
sf.seek(0)
allBondsPass = False
maxPeptideBondPass = False
glyCbetaFound = False
with as_handle(sf, mode="r") as handle:
for aline in handle.readlines():
# test extra bond created in TRP (allBonds is True)
if '"Cres", 0, 0, 1, 0, StdBond, "W", 24, "CD2CE3CZ3"' in aline:
allBondsPass = True
# test 509_K-561_E long bond created
if "509_K" in aline and "561_E" in aline:
maxPeptideBondPass = True
if "(21_G_CB, 21_G_CA, 21_G_C)" in aline:
glyCbetaFound = True
target = [15.33630, 110.17513, 15.13861]
ms = re.findall(r"\s+(-?\d+\.\d+)", aline)
if ms:
for i in range(0, 3):
self.assertAlmostEqual(float(ms[i]), target[i], places=0)
else:
self.fail("Cbeta internal coords not found")
self.assertTrue(allBondsPass)
self.assertTrue(glyCbetaFound)
self.assertTrue(maxPeptideBondPass)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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