diff --git a/CMakeLists.txt b/CMakeLists.txt index 3a566df25067c9bb4c29189f432be9f5a380a111..4032c98398459f76e46ca43a81562b531adaa856 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -15,7 +15,7 @@ include(PROMOD3) set(PROMOD3_VERSION_MAJOR 1) set(PROMOD3_VERSION_MINOR 0) -set(PROMOD3_VERSION_PATCH 0) +set(PROMOD3_VERSION_PATCH 1) set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}) set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH}) diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py index 9fe9f49bbda5c4083226401b894c2fddf3bb2f00..53d6bfd33a5e9b1ddcee2ef3be709f6acf6b0ccf 100644 --- a/modelling/pymod/_pipeline.py +++ b/modelling/pymod/_pipeline.py @@ -13,7 +13,7 @@ from _ring_punches import * import ost from ost import mol from ost.mol import mm -import os +import os, math def BuildSidechains(mhandle, merge_distance=4, scorer=None, fragment_db=None, structure_db=None, torsion_sampler=None): @@ -140,6 +140,11 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20, settings.platform = mm.Platform.Reference sim = mm.Simulation(mhandle.model, settings) ost.LogWarning("Switched to slower reference platform of OpenMM!") + # check for certain failure -> we get NaN if atoms are on top each other + if math.isnan(sim.GetEnergy()): + ost.LogError("OpenMM could not minimize energy as atoms are on top of " + "each other!") + return # settings to check for stereochemical problems clashing_distances = mol.alg.DefaultClashingDistances() bond_stereo_chemical_param = mol.alg.DefaultBondStereoChemicalParams()