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import unittest
import math
from ost import geom
from ost import io
from ost import mol
def compare_atoms(a1, a2, occupancy_thresh = 0.01, bfactor_thresh = 0.01,
dist_thresh = 0.001):
if abs(a1.occupancy - a2.occupancy) > occupancy_thresh:
return False
if abs(a1.b_factor - a2.b_factor) > bfactor_thresh:
return False
if geom.Distance(a1.GetPos(), a2.GetPos()) > dist_thresh:
return False
if a1.is_hetatom != a2.is_hetatom:
return False
if a1.element != a2.element:
return False
return True
def compare_residues(r1, r2, at_occupancy_thresh = 0.01,
at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
skip_ss = False, skip_rnums=False):
if r1.GetName() != r2.GetName():
return False
if skip_rnums is False:
if r1.GetNumber() != r2.GetNumber():
return False
if skip_ss is False:
if str(r1.GetSecStructure()) != str(r2.GetSecStructure()):
return False
if r1.one_letter_code != r2.one_letter_code:
return False
if r1.chem_type != r2.chem_type:
return False
if r1.chem_class != r2.chem_class:
return False
anames1 = [a.GetName() for a in r1.atoms]
anames2 = [a.GetName() for a in r2.atoms]
if sorted(anames1) != sorted(anames2):
return False
anames = anames1
for aname in anames:
a1 = r1.FindAtom(aname)
a2 = r2.FindAtom(aname)
if not compare_atoms(a1, a2,
occupancy_thresh = at_occupancy_thresh,
bfactor_thresh = at_bfactor_thresh,
dist_thresh = at_dist_thresh):
return False
return True
def compare_chains(ch1, ch2, at_occupancy_thresh = 0.01,
at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
skip_ss=False, skip_rnums=False):
if len(ch1.residues) != len(ch2.residues):
return False
for r1, r2 in zip(ch1.residues, ch2.residues):
if not compare_residues(r1, r2,
at_occupancy_thresh = at_occupancy_thresh,
at_bfactor_thresh = at_bfactor_thresh,
at_dist_thresh = at_dist_thresh,
skip_ss = skip_ss, skip_rnums=skip_rnums):
return False
return True
def compare_bonds(ent1, ent2):
bonds1 = list()
for b in ent1.bonds:
bond_partners = [str(b.first), str(b.second)]
bonds1.append([min(bond_partners), max(bond_partners), b.bond_order])
bonds2 = list()
for b in ent2.bonds:
bond_partners = [str(b.first), str(b.second)]
bonds2.append([min(bond_partners), max(bond_partners), b.bond_order])
return sorted(bonds1) == sorted(bonds2)
def compare_ent(ent1, ent2, at_occupancy_thresh = 0.01,
at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
skip_ss=False, skip_cnames = False, skip_bonds = False,
skip_rnums=False, bu_idx = None, ignore_chain_order=False):
if bu_idx is not None:
if ent1.GetName() + ' ' + str(bu_idx) != ent2.GetName():
return False
else:
if ent1.GetName() != ent2.GetName():
return False
chain_names_one = [ch.GetName() for ch in ent1.chains]
chain_names_two = [ch.GetName() for ch in ent2.chains]
if ignore_chain_order:
chain_names_one = sorted(chain_names_one)
chain_names_two = sorted(chain_names_two)
if skip_cnames:
# only check whether we have the same number of chains
if len(chain_names_one) != len(chain_names_two):
return False
else:
if chain_names_one != chain_names_two:
return False
for cname1, cname2 in zip(chain_names_one, chain_names_two):
ch1 = ent1.FindChain(cname1)
ch2 = ent2.FindChain(cname2)
if not compare_chains(ch1, ch2,
at_occupancy_thresh = at_occupancy_thresh,
at_bfactor_thresh = at_bfactor_thresh,
at_dist_thresh = at_dist_thresh,
skip_ss=skip_ss, skip_rnums=skip_rnums):
return False
if not skip_bonds:
if not compare_bonds(ent1, ent2):
return False
return True
class TestOMF(unittest.TestCase):
def setUp(self):
ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3T6C.cif.gz",
seqres=True,
info=True)
self.ent = ent
self.seqres = seqres
self.info = info
self.ent.SetName("This is a name 123")
def test_AU(self):
omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
loaded_omf = io.OMF.FromBytes(omf_bytes)
loaded_ent = loaded_omf.GetAU()
self.assertTrue(compare_ent(self.ent, loaded_ent))
def test_default_peplib(self):
omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
omf_def_pep = io.OMF.FromEntity(self.ent, options = io.OMFOption.DEFAULT_PEPLIB)
omf_def_pep_bytes = omf_def_pep.ToBytes()
loaded_omf_def_pep = io.OMF.FromBytes(omf_def_pep_bytes)
loaded_ent = loaded_omf_def_pep.GetAU()
self.assertTrue(len(omf_def_pep_bytes) < len(omf_bytes))
self.assertTrue(compare_ent(self.ent, loaded_ent))
def test_avg_bfactors(self):
omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
omf_avg_bfac = io.OMF.FromEntity(self.ent, options = io.OMFOption.AVG_BFACTORS)
omf_avg_bfac_bytes = omf_avg_bfac.ToBytes()
loaded_omf_avg_bfac = io.OMF.FromBytes(omf_avg_bfac_bytes)
loaded_ent = loaded_omf_avg_bfac.GetAU()
self.assertTrue(len(omf_avg_bfac_bytes) < len(omf_bytes))
self.assertFalse(compare_ent(self.ent, loaded_ent))
# just give a huge slack for bfactors and check averaging manually
self.assertTrue(compare_ent(self.ent, loaded_ent,
at_bfactor_thresh=1000))
self.assertEqual(len(self.ent.residues), len(loaded_ent.residues))
for r_ref, r in zip(self.ent.residues, loaded_ent.residues):
exp_bfac = sum([a.b_factor for a in r_ref.atoms])
exp_bfac /= r_ref.atom_count
for a in r.atoms:
self.assertTrue(abs(a.b_factor - exp_bfac) < 0.008)
def test_round_bfactors(self):
omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
omf_round_bfac = io.OMF.FromEntity(self.ent, options = io.OMFOption.ROUND_BFACTORS)
omf_round_bfac_bytes = omf_round_bfac.ToBytes()
loaded_omf_round_bfac = io.OMF.FromBytes(omf_round_bfac_bytes)
loaded_ent = loaded_omf_round_bfac.GetAU()
self.assertTrue(len(omf_round_bfac_bytes) < len(omf_bytes))
self.assertFalse(compare_ent(self.ent, loaded_ent))
self.assertTrue(compare_ent(self.ent, loaded_ent,
at_bfactor_thresh=0.5))
def test_skip_ss(self):
omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
omf_skip_ss = io.OMF.FromEntity(self.ent, options = io.OMFOption.SKIP_SS)
omf_skip_ss_bytes = omf_skip_ss.ToBytes()
loaded_omf_skip_ss = io.OMF.FromBytes(omf_skip_ss_bytes)
loaded_ent = loaded_omf_skip_ss.GetAU()
self.assertTrue(len(omf_skip_ss_bytes) < len(omf_bytes))
self.assertFalse(compare_ent(self.ent, loaded_ent))
self.assertTrue(compare_ent(self.ent, loaded_ent, skip_ss=True))
def test_infer_pep_bonds(self):
omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
omf_infer_pep_bonds = io.OMF.FromEntity(self.ent,
options = io.OMFOption.INFER_PEP_BONDS)
omf_infer_pep_bonds_bytes = omf_infer_pep_bonds.ToBytes()
loaded_omf_infer_pep_bonds = io.OMF.FromBytes(omf_infer_pep_bonds_bytes)
loaded_ent = loaded_omf_infer_pep_bonds.GetAU()
self.assertTrue(len(omf_infer_pep_bonds_bytes) < len(omf_bytes))
self.assertTrue(compare_ent(self.ent, loaded_ent))
def test_lower_precition(self):
omf = io.OMF.FromEntity(self.ent, max_error=0.5)
omf_bytes = omf.ToBytes()
loaded_omf = io.OMF.FromBytes(omf_bytes)
loaded_ent = loaded_omf.GetAU()
self.assertFalse(compare_ent(self.ent, loaded_ent))
self.assertTrue(compare_ent(self.ent, loaded_ent, at_dist_thresh=0.5))
def test_assembly_construction(self):
omf = io.OMF.FromEntity(self.ent)
bu_infos = [mol.alg.BUInfo(bu) for bu in self.info.GetBioUnits()]
self.assertEqual(len(bu_infos), 1)
bu_info = bu_infos[0]
omf_assembly = omf.ToAssembly(bu_info)
ent_assembly = mol.alg.CreateBU(self.ent, bu_info)
self.assertTrue(compare_ent(omf_assembly.GetEntity(), ent_assembly,
ignore_chain_order=True))
def test_trace(self):
omf = io.OMF.FromEntity(self.ent)
rnums, pos = omf.Trace("B", "CA")
ent_rnums = list()
ent_pos = geom.Vec3List()
for r in self.ent.FindChain("B").residues:
ca = r.FindAtom("CA")
if ca.IsValid():
ent_rnums.append(r.GetNumber().GetNum())
ent_pos.append(ca.GetPos())
self.assertEqual(rnums, ent_rnums)
for a,b in zip(pos, ent_pos):
d = geom.Distance(a,b)
self.assertTrue(d < 0.001)
if __name__== '__main__':
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound library available. Ignoring test_stereochemistry.py tests.')
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