diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst
index f5fa202666feef0d0c7bc1482cdc15f7238288a6..fb5b239c057bc2f6beda172c78a373f25a93588a 100644
--- a/modelling/doc/pipeline.rst
+++ b/modelling/doc/pipeline.rst
@@ -146,6 +146,23 @@ Build Raw Modelling Handle
:type: :class:`~promod3.modelling.SidechainReconstructor`
+ .. attribute:: fragger_handles
+
+ Optional attribute which is set in :meth:`SetFraggerHandles`. Use
+ :meth:`hasattr` to check if it's available. If it's set, it is used in
+ :meth:`BuildFromRawModel`.
+
+ :type: :class:`list` of :class:`FraggerHandle`
+
+ .. attribute:: modelling_issues
+
+ Optional attribute which is set in :meth:`AddModellingIssue`. Use
+ :meth:`hasattr` to check if it's available. If it's set, it can be used to
+ check issues which occurred in :meth:`BuildFromRawModel` (see
+ :meth:`MinimizeModelEnergy` and :meth:`CheckFinalModel` for details).
+
+ :type: :class:`list` of :class:`ModellingIssue`
+
.. method:: Copy()
Generates a deep copy. Everything will be copied over to the returned
@@ -422,3 +439,7 @@ Modelling Steps
.. autofunction:: CheckFinalModel
+.. autoclass:: ModellingIssue
+ :members:
+
+.. autofunction:: AddModellingIssue
diff --git a/modelling/pymod/_mhandle_helper.py b/modelling/pymod/_mhandle_helper.py
index 0e7fad147f5f749f47abd93e76c981228e228ecc..c7f1048a9b35fe7149b2c5fe54cdcf631857b102 100644
--- a/modelling/pymod/_mhandle_helper.py
+++ b/modelling/pymod/_mhandle_helper.py
@@ -13,9 +13,75 @@
# See the License for the specific language governing permissions and
# limitations under the License.
+class ModellingIssue:
+ """
+
+ :param text: Sets :attr:`text`.
+ :param severity: Sets :attr:`severity`.
+ :param residue_list: Sets :attr:`residue_list`.
+
+ .. attribute:: text
+
+ Description of issue.
+
+ :type: :class:`str`
+
+ .. attribute:: severity
+
+ Severity of issue.
+
+ :type: :class:`Severity`
+
+ .. attribute:: residue_list
+
+ List of residues affected by issue (or empty list if global issue).
+
+ :type: :class:`list` of :class:`~ost.mol.ResidueHandle` /
+ :class:`~ost.mol.ResidueView`
+ """
+
+ class Severity:
+ """Enumerates severities."""
+ #: Minor issues like remaining stereo-chemistry problems after MM.
+ MINOR = 0
+ #: Major issues like MM-failures, incomplete models and ring punches.
+ MAJOR = 10
+
+ def __init__(self, text, severity, residue_list=[]):
+ self.text = text
+ self.severity = severity
+ self.residue_list = residue_list
+
+ def is_major(self):
+ """
+ :return: True if this is a major issue.
+ :rtype: :class:`bool`
+ """
+ return self.severity == ModellingIssue.Severity.MAJOR
+
+def AddModellingIssue(mhandle, text, severity, residue_list=[]):
+ """Adds a new :class:`ModellingIssue` to
+ :attr:`~ModellingHandle.modelling_issues` in *mhandle*.
+
+ If *mhandle* doesn't contain the :attr:`~ModellingHandle.modelling_issues`
+ attribute yet, it is added.
+
+ :param mhandle: Will have the issue added to.
+ :type mhandle: :class:`ModellingHandle`
+ :param text: Sets :attr:`ModellingIssue.text`.
+ :param severity: Sets :attr:`ModellingIssue.severity`.
+ :param residue_list: Sets :attr:`ModellingIssue.residue_list`.
+ """
+ modelling_issue = ModellingIssue(text, severity, residue_list)
+ if hasattr(mhandle, "modelling_issues"):
+ mhandle.modelling_issues.append(modelling_issue)
+ else:
+ mhandle.modelling_issues = [modelling_issue]
+
+
def SetFraggerHandles(mhandle, fragger_handles):
- """ Sets the :attr:`fragger_handles` in **mhandle** while ensuring
- consistency with the :attr:`ModellingHandle.seqres`
+ """Sets :attr:`~ModellingHandle.fragger_handles` in *mhandle* while
+ ensuring consistency with the :attr:`ModellingHandle.seqres`.
:param mhandle: Will have the fragger handles attached afterwards
:param fragger_handles: The fragger handles to attach
@@ -23,8 +89,8 @@ def SetFraggerHandles(mhandle, fragger_handles):
:type mhandle: :class:`ModellingHandle`
:type fragger_handles: :class:`list` of :class:`FraggerHandle`
- :raises: :class:`ValueError` when the given **fragger_handles** are not
- consistent with seqres in **mhandle**
+ :raises: :class:`ValueError` when the given *fragger_handles* are not
+ consistent with seqres in *mhandle*
"""
if len(mhandle.seqres) != len(fragger_handles):
@@ -34,3 +100,6 @@ def SetFraggerHandles(mhandle, fragger_handles):
raise RuntimeError("Sequence in FraggerHandle must match sequence "+
"in SEQRES!")
mhandle.fragger_handles = fragger_handles
+
+# these classes/methods will be exported into module
+__all__ = ('ModellingIssue', 'AddModellingIssue', 'SetFraggerHandles')
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index ec1e88f70ff43aa7ebf9d881ff4359133d0c4f9e..d8202b4266d5ae843331c02cda0070c10117f42f 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -25,6 +25,7 @@ from _modelling import *
from _reconstruct_sidechains import *
from _closegaps import *
from _ring_punches import *
+from _mhandle_helper import *
# external
import ost
from ost import mol, conop
@@ -272,6 +273,11 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
env. variable ``PM3_OPENMM_CPU_THREADS`` to the number of desired threads.
If the variable is not set, 1 thread will be used by default.
+ If the starting model is so bad that the energy is NaN or Inf from the start
+ (happens if atoms are on top of each other or almost), the energy
+ minimization is aborted. This issue is logged and added as a major issue to
+ :attr:`~ModellingHandle.modelling_issues` of *mhandle*.
+
:param mhandle: Modelling handle on which to apply change.
:type mhandle: :class:`ModellingHandle`
@@ -312,12 +318,16 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
# check for certain failure -> we get NaN/Inf if atoms are on top each other
cur_energy = sim.GetEnergy()
if math.isnan(cur_energy):
- ost.LogError("OpenMM could not minimize energy as atoms are on top of "
- "each other!")
+ msg = "OpenMM could not minimize energy as atoms are on top of "\
+ "each other!"
+ ost.LogError(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MAJOR)
return
if math.isinf(cur_energy):
- ost.LogError("OpenMM could not minimize energy as atoms are almost "
- "on top of each other!")
+ msg = "OpenMM could not minimize energy as atoms are almost "\
+ "on top of each other!"
+ ost.LogError(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MAJOR)
return
# settings to check for stereochemical problems
@@ -365,6 +375,21 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
def CheckFinalModel(mhandle):
'''Performs samity checks on final models and reports problems.
+
+ Issues are logged and tracked in :attr:`~ModellingHandle.modelling_issues`
+ of *mhandle*. Major issues:
+
+ - Chains with less than 3 residues (usually due to bad templates).
+ - Incomplete models (i.e. some gaps couldn't be closed). One issue is
+ created per unclosed gap and the stems of the gap are added to the issue.
+ - Complete models with sequence mismatches (should never happen).
+ - Residues with rings which have been punched by another bond.
+
+ Minor issues:
+
+ - Remaining stereo-chemical problems after energy minimization. The affected
+ residues will have the boolean property "stereo_chemical_problem_backbone"
+ set to True, if the problem affects backbone atoms.
:param mhandle: Modelling handle for which to perform checks.
:type mhandle: :class:`ModellingHandle`
@@ -374,14 +399,19 @@ def CheckFinalModel(mhandle):
# report incomplete models
for chain in mhandle.model.chains:
if chain.residue_count < 3:
- ost.LogWarning("Chain %s of returned model contains only %d "\
- "residues! This typically indicates that the "\
- "template is mostly a Calpha trace or contains "\
- "too many D-peptides."\
- % (chain.name, chain.residue_count))
+ msg = "Chain %s of returned model contains only %d residues! "\
+ "This typically indicates that the template is mostly "\
+ "a Calpha trace or contains too many D-peptides."\
+ % (chain.name, chain.residue_count)
+ ost.LogWarning(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MAJOR)
if len(mhandle.gaps) > 0:
ost.LogWarning("Failed to close %d gap(s). Returning incomplete model!"\
% len(mhandle.gaps))
+ for gap in mhandle.gaps:
+ AddModellingIssue(mhandle, "Failed to close gap (%s)." % (str(gap)),
+ ModellingIssue.Severity.MAJOR,
+ [gap.before, gap.after])
else:
# check sequences
for chain, seq in zip(mhandle.model.chains, mhandle.seqres):
@@ -390,15 +420,18 @@ def CheckFinalModel(mhandle):
expected_seq = seq[a-1:b]
actual_seq = ''.join([r.one_letter_code for r in chain.residues])
if expected_seq != actual_seq:
- ost.LogWarning("Sequence mismatch in chain %s!"\
- " Expected '%s'. Got '%s'" \
- % (chain.name, expected_seq, actual_seq))
+ msg = "Sequence mismatch in chain %s! Expected '%s'. Got '%s'" \
+ % (chain.name, expected_seq, actual_seq)
+ ost.LogWarning(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MAJOR)
# report ring punchings
rings = GetRings(mhandle.model)
ring_punches = GetRingPunches(rings, mhandle.model)
for res in ring_punches:
- ost.LogWarning("Ring of " + str(res) + " has been punched!")
+ msg = "Ring of " + str(res) + " has been punched!"
+ ost.LogWarning(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MAJOR, [res])
# report stereo-chemical problems
ost.PushVerbosityLevel(0)
@@ -429,12 +462,14 @@ def CheckFinalModel(mhandle):
for res in model_src.residues:
if res.HasProp("stereo_chemical_problem_backbone") and\
res.GetBoolProp("stereo_chemical_problem_backbone"):
- ost.LogInfo("Stereo-chemical problem in backbone " + \
- "of residue " + str(res))
+ msg = "Stereo-chemical problem in backbone of residue " + str(res)
+ ost.LogInfo(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MINOR, [res])
elif res.HasProp("stereo_chemical_problem") and\
res.GetBoolProp("stereo_chemical_problem"):
- ost.LogInfo("Stereo-chemical problem in sidechain " + \
- "of residue " + str(res))
+ msg = "Stereo-chemical problem in sidechain of residue " + str(res)
+ ost.LogInfo(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MINOR, [res])
def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list(),
model_termini=False):
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index 65a43b325782640bd7720cc197bdb80402c217ea..ac4e4bac43404c911e311fdffdaf554f1870a4a7 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -235,15 +235,27 @@ class PipelineTests(unittest.TestCase):
self.assertEqual(log.messages['WARNING'][-1],
"Failed to close %d gap(s). " \
"Returning incomplete model!" % exp_gaps)
+ self.assertGreaterEqual(len(mhandle.modelling_issues), exp_gaps)
+ for i in range(exp_gaps):
+ issue = mhandle.modelling_issues[i]
+ self.assertTrue(issue.text.startswith("Failed to close"))
+ self.assertTrue(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 2)
# fake remove gaps to get sequence mismatch warnings
mhandle.gaps = modelling.StructuralGapList()
+ mhandle.modelling_issues = list()
log.messages['WARNING'] = list()
modelling.CheckFinalModel(mhandle)
- # 1 warning per chain expected
+ # 1 warning/issue per chain expected
exps = "Sequence mismatch in chain"
self.assertGreaterEqual(len(log.messages['WARNING']), num_chains)
+ self.assertGreaterEqual(len(mhandle.modelling_issues), num_chains)
for i in range(num_chains):
self.assertTrue(log.messages['WARNING'][i].startswith(exps))
+ issue = mhandle.modelling_issues[i]
+ self.assertTrue(issue.text.startswith(exps))
+ self.assertTrue(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 0)
#######################################################################
@@ -305,7 +317,7 @@ class PipelineTests(unittest.TestCase):
modelling.MinimizeModelEnergy(mhandle)
self.compare(mhandle.model, 'data/1crn_final.pdb')
- def testMinimizeModelEnergy(self):
+ def testMinimizeModelEnergyFails(self):
'''Check energy minimization fails.'''
# setup log
log = _FetchLog()
@@ -316,17 +328,27 @@ class PipelineTests(unittest.TestCase):
log.messages['ERROR'] = list()
modelling.MinimizeModelEnergy(mhandle)
self.assertEqual(len(log.messages['ERROR']), 1)
- self.assertEqual(log.messages['ERROR'][0],
- "OpenMM could not minimize energy as atoms are on "
- "top of each other!")
+ self.assertEqual(len(mhandle.modelling_issues), 1)
+ exp_msg = "OpenMM could not minimize energy as atoms are on "\
+ "top of each other!"
+ self.assertEqual(log.messages['ERROR'][0], exp_msg)
+ issue = mhandle.modelling_issues[0]
+ self.assertEqual(issue.text, exp_msg)
+ self.assertTrue(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 0)
# catch atoms almost on top
mhandle = self.getMockModel(io.LoadPDB('data/gly_almost_on_top.pdb'))
log.messages['ERROR'] = list()
modelling.MinimizeModelEnergy(mhandle)
self.assertEqual(len(log.messages['ERROR']), 1)
- self.assertEqual(log.messages['ERROR'][0],
- "OpenMM could not minimize energy as atoms are "
- "almost on top of each other!")
+ self.assertEqual(len(mhandle.modelling_issues), 1)
+ exp_msg = "OpenMM could not minimize energy as atoms are "\
+ "almost on top of each other!"
+ self.assertEqual(log.messages['ERROR'][0], exp_msg)
+ issue = mhandle.modelling_issues[0]
+ self.assertEqual(issue.text, exp_msg)
+ self.assertTrue(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 0)
def testBuildFromRawModel(self):
'''Check that BuildFromRawModel works.'''
@@ -387,8 +409,14 @@ class PipelineTests(unittest.TestCase):
log.messages['WARNING'] = list()
modelling.CheckFinalModel(mhandle)
self.assertEqual(len(log.messages['WARNING']), 1)
- self.assertEqual(log.messages['WARNING'][0],
- "Ring of A.TYR321 has been punched!")
+ self.assertGreaterEqual(len(mhandle.modelling_issues), 1)
+ exp_msg = "Ring of A.TYR321 has been punched!"
+ self.assertEqual(log.messages['WARNING'][0], exp_msg)
+ issue = mhandle.modelling_issues[0]
+ self.assertEqual(issue.text, exp_msg)
+ self.assertTrue(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 1)
+ self.assertEqual(str(issue.residue_list[0]), "A.TYR321")
def testCheckFinalModelClash(self):
'''Check that we report models with stereo-chemical problems.'''
@@ -402,12 +430,21 @@ class PipelineTests(unittest.TestCase):
log.messages['INFO'] = list()
modelling.CheckFinalModel(mhandle)
self.assertEqual(len(log.messages['INFO']), 2)
- self.assertEqual(log.messages['INFO'][0],
- "Stereo-chemical problem in backbone of residue "\
- "A.GLY79")
- self.assertEqual(log.messages['INFO'][1],
- "Stereo-chemical problem in sidechain of residue "\
- "A.HIS98")
+ self.assertEqual(len(mhandle.modelling_issues), 2)
+ exp_msg = "Stereo-chemical problem in backbone of residue A.GLY79"
+ self.assertEqual(log.messages['INFO'][0], exp_msg)
+ issue = mhandle.modelling_issues[0]
+ self.assertEqual(issue.text, exp_msg)
+ self.assertFalse(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 1)
+ self.assertEqual(str(issue.residue_list[0]), "A.GLY79")
+ exp_msg = "Stereo-chemical problem in sidechain of residue A.HIS98"
+ self.assertEqual(log.messages['INFO'][1], exp_msg)
+ issue = mhandle.modelling_issues[1]
+ self.assertEqual(issue.text, exp_msg)
+ self.assertFalse(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 1)
+ self.assertEqual(str(issue.residue_list[0]), "A.HIS98")
def testMolProbity(self):
'''Check if binding to molprobity works.'''
@@ -503,11 +540,15 @@ class PipelineTests(unittest.TestCase):
log.messages['WARNING'] = list()
modelling.CheckFinalModel(mhandle)
self.assertEqual(len(log.messages['WARNING']), 1)
- self.assertEqual(log.messages['WARNING'][-1],
- "Chain A of returned model contains only 2 "\
- "residues! This typically indicates that the "\
- "template is mostly a Calpha trace or contains "\
- "too many D-peptides.")
+ self.assertEqual(len(mhandle.modelling_issues), 1)
+ exp_msg = "Chain A of returned model contains only 2 residues! "\
+ "This typically indicates that the template is mostly a "\
+ "Calpha trace or contains too many D-peptides."
+ self.assertEqual(log.messages['WARNING'][-1], exp_msg)
+ issue = mhandle.modelling_issues[0]
+ self.assertEqual(issue.text, exp_msg)
+ self.assertTrue(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 0)
if __name__ == "__main__":
from ost import testutils