From 074bbd476c8f7dab9f837c1e934d7952b4d5e714 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 22 Dec 2022 08:38:57 +0100
Subject: [PATCH] OMF unit tests
Add unit tests to extract several biounits and compare with PDBize.
Problem here is that PDBize has some non-standard logics implemented.
Maybe needs some thinking on how the biounit business should be solved
in OMF. Or drop it alltogether and make it meta information?
---
modules/io/tests/test_io_omf.py | 69 ++++++++++++++++++++++++++-------
1 file changed, 54 insertions(+), 15 deletions(-)
diff --git a/modules/io/tests/test_io_omf.py b/modules/io/tests/test_io_omf.py
index bbb954a61..840d9f42d 100644
--- a/modules/io/tests/test_io_omf.py
+++ b/modules/io/tests/test_io_omf.py
@@ -20,11 +20,12 @@ def compare_atoms(a1, a2, occupancy_thresh = 0.01, bfactor_thresh = 0.01,
def compare_residues(r1, r2, at_occupancy_thresh = 0.01,
at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
- skip_ss = False):
+ skip_ss = False, skip_rnums=False):
if r1.GetName() != r2.GetName():
return False
- if r1.GetNumber() != r2.GetNumber():
- 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
@@ -51,7 +52,7 @@ def compare_residues(r1, r2, at_occupancy_thresh = 0.01,
def compare_chains(ch1, ch2, at_occupancy_thresh = 0.01,
at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
- skip_ss=False):
+ skip_ss=False, skip_rnums=False):
if len(ch1.residues) != len(ch2.residues):
return False
for r1, r2 in zip(ch1.residues, ch2.residues):
@@ -59,7 +60,7 @@ def compare_chains(ch1, ch2, at_occupancy_thresh = 0.01,
at_occupancy_thresh = at_occupancy_thresh,
at_bfactor_thresh = at_bfactor_thresh,
at_dist_thresh = at_dist_thresh,
- skip_ss = skip_ss):
+ skip_ss = skip_ss, skip_rnums=skip_rnums):
return False
return True
@@ -76,23 +77,27 @@ def compare_bonds(ent1, ent2):
def compare_ent(ent1, ent2, at_occupancy_thresh = 0.01,
at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
- skip_ss=False):
+ skip_ss=False, skip_cnames = False, skip_bonds = False,
+ skip_rnums=False):
chain_names_one = [ch.GetName() for ch in ent1.chains]
chain_names_two = [ch.GetName() for ch in ent2.chains]
- if not sorted(chain_names_one) == sorted(chain_names_two):
- return False
- chain_names = chain_names_one
- for chain_name in chain_names:
- ch1 = ent1.FindChain(chain_name)
- ch2 = ent2.FindChain(chain_name)
+ 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 ch1, ch2 in zip(ent1.chains, ent2.chains):
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_ss=skip_ss, skip_rnums=skip_rnums):
+ return False
+ if not skip_bonds:
+ if not compare_bonds(ent1, ent2):
return False
- if not compare_bonds(ent1, ent2):
- return False
return True
class TestOMF(unittest.TestCase):
@@ -200,6 +205,40 @@ class TestOMF(unittest.TestCase):
self.assertTrue(len(omf_infer_pep_bonds_bytes) < len(omf_bytes))
self.assertTrue(compare_ent(self.ent, loaded_ent))
+ def test_multiple_BU(self):
+ ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3imj.cif.gz",
+ seqres=True,
+ info=True)
+
+ omf = io.OMF.FromMMCIF(ent, info)
+ omf_bytes = omf.ToBytes()
+ omf_loaded = io.OMF.FromBytes(omf_bytes)
+
+ # there are quite some discrepancies between PDBize and OMF
+ # - chain names: PDBize has specific chain names for ligands and
+ # water etc. OMF just iterates A, B, C, D, ...
+ # - skip_bonds: Thats qualified atom name based. PDBize used rnums
+ # and insertion codes for waters...
+ # - skip_rnums: Again, insertion codes for waters...
+ self.assertTrue(compare_ent(omf_loaded.GetBU(0),
+ info.GetBioUnits()[0].PDBize(ent),
+ skip_cnames=True, skip_bonds=True,
+ skip_rnums=True))
+
+ self.assertTrue(compare_ent(omf_loaded.GetBU(1),
+ info.GetBioUnits()[1].PDBize(ent),
+ skip_cnames=True, skip_bonds=True,
+ skip_rnums=True))
+
+ # no check for the full guy... problem: PDBize throws all water
+ # molecules in the same chain, whereas OMF keeps them separate
+ # as in the chains from the assymetric unit... maybe needs some
+ # thinking on how to resolve discrepancies between PDBize and OMF
+ #self.assertTrue(compare_ent(omf_loaded.GetBU(2),
+ # info.GetBioUnits()[2].PDBize(ent),
+ # skip_cnames=True, skip_bonds=True,
+ # skip_rnums=True))
+
if __name__== '__main__':
from ost import testutils
if testutils.SetDefaultCompoundLib():
--
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