From 2425b4cf7c08047dc27b559b0e5729215f05f002 Mon Sep 17 00:00:00 2001 From: richard gowers Date: Wed, 17 Apr 2024 17:02:16 +0100 Subject: [PATCH] protein loading: review comments --- gufe/components/proteincomponent.py | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/gufe/components/proteincomponent.py b/gufe/components/proteincomponent.py index 32a29608..fce2f65c 100644 --- a/gufe/components/proteincomponent.py +++ b/gufe/components/proteincomponent.py @@ -223,15 +223,11 @@ def _from_openmmPDBFile(cls, openmm_PDBFile: Union[PDBFile, PDBxFile], default_valence = periodicTable.GetDefaultValence(atomic_num) if connectivity == 0: # ions: - if atom_name.upper() in positive_ions: - fc = default_valence # e.g. Sodium ions - elif atom_name.upper() in negative_ions: - fc = - default_valence # e.g. Chlorine ions - elif atom_name.strip(string.digits).upper() in positive_ions: - # catches cases like 'CL1' as name - fc = default_valence + # strip catches cases like 'CL1' as name + if atom_name.strip(string.digits).upper() in positive_ions: + fc = default_valence # e.g. Sodium ions elif atom_name.strip(string.digits).upper() in negative_ions: - fc = - default_valence + fc = - default_valence # e.g. Chlorine ions else: # -no-cov- resn = a.GetMonomerInfo().GetResidueName() resind = int(a.GetMonomerInfo().GetResidueNumber())