From fa1f00e34d776403a08acf30a84ffbe0fce74372 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 11 Jul 2019 20:40:25 +0200
Subject: [PATCH] SCHWED-4333: remove early inf-catch as OpenMM may recover
from it.
Instead, we catch the exception thrown when energy minimization fails. OpenMM
can recover from inf-energy which appears due to clashing hydrogens.
---
modelling/pymod/_pipeline.py | 23 +++++++++++++----------
modelling/tests/test_pipeline.py | 8 ++++----
2 files changed, 17 insertions(+), 14 deletions(-)
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index d8202b42..b8aef45f 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -315,7 +315,7 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
# setup mm simulation
sim = _SetupMmSimulation(mhandle.model, force_fields)
- # check for certain failure -> we get NaN/Inf if atoms are on top each other
+ # check for certain failure -> we get NaN if atoms are on top each other
cur_energy = sim.GetEnergy()
if math.isnan(cur_energy):
msg = "OpenMM could not minimize energy as atoms are on top of "\
@@ -323,12 +323,6 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
ost.LogError(msg)
AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MAJOR)
return
- if math.isinf(cur_energy):
- 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
clashing_distances = mol.alg.DefaultClashingDistances()
@@ -339,9 +333,18 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
# update atoms
ost.LogInfo("Perform energy minimization "
"(iteration %d, energy: %g)" % (i+1, cur_energy))
- sim.ApplySD(tolerance = 1.0, max_iterations = max_iter_sd)
- sim.ApplyLBFGS(tolerance = 1.0, max_iterations = max_iter_lbfgs)
- sim.UpdatePositions()
+ try:
+ sim.ApplySD(tolerance = 1.0, max_iterations = max_iter_sd)
+ sim.ApplyLBFGS(tolerance = 1.0, max_iterations = max_iter_lbfgs)
+ sim.UpdatePositions()
+ except Exception as ex:
+ # ABORT ON FAIL
+ msg = "OpenMM could not minimize energy! Usually this is caused "\
+ "by atoms which are almost on top of each other. Exception: "\
+ "%s('%s')!" % (type(ex).__name__, ex)
+ ost.LogError(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MAJOR)
+ return
# check for stereochemical problems
if ignore_stereo_log:
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index ac4e4bac..61c8f44d 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -342,11 +342,11 @@ class PipelineTests(unittest.TestCase):
modelling.MinimizeModelEnergy(mhandle)
self.assertEqual(len(log.messages['ERROR']), 1)
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)
+ exp_msg = "OpenMM could not minimize energy! Usually this is caused "\
+ "by atoms which are almost on top of each other."
+ self.assertTrue(log.messages['ERROR'][0].startswith(exp_msg))
issue = mhandle.modelling_issues[0]
- self.assertEqual(issue.text, exp_msg)
+ self.assertTrue(issue.text.startswith(exp_msg))
self.assertTrue(issue.is_major())
self.assertEqual(len(issue.residue_list), 0)
--
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