From 7f6e654dedc0d283b63e59ec6d33d2d133e0f9ef Mon Sep 17 00:00:00 2001 From: Jake Anderson Date: Tue, 9 Apr 2024 23:29:22 -0700 Subject: [PATCH 1/2] Specify "standard_names=False" when loading pdb into mdtraj --- openff/evaluator/protocols/paprika/coordinates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openff/evaluator/protocols/paprika/coordinates.py b/openff/evaluator/protocols/paprika/coordinates.py index 0fe4afe2..49ccf439 100644 --- a/openff/evaluator/protocols/paprika/coordinates.py +++ b/openff/evaluator/protocols/paprika/coordinates.py @@ -171,7 +171,7 @@ def _execute(self, directory, available_resources): from openmm import app from paprika.evaluator import Setup - mdtraj_trajectory = mdtraj.load_pdb(self.complex_file_path) + mdtraj_trajectory = mdtraj.load_pdb(self.complex_file_path, standard_names=False) atom_indices_by_role = _atom_indices_by_role( self.substance, self.complex_file_path From 343f3be2c61335851bbd64b7b7b1599604d0e4db Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 10 Apr 2024 06:41:50 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- openff/evaluator/protocols/paprika/coordinates.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/openff/evaluator/protocols/paprika/coordinates.py b/openff/evaluator/protocols/paprika/coordinates.py index 49ccf439..8c18e706 100644 --- a/openff/evaluator/protocols/paprika/coordinates.py +++ b/openff/evaluator/protocols/paprika/coordinates.py @@ -171,7 +171,9 @@ def _execute(self, directory, available_resources): from openmm import app from paprika.evaluator import Setup - mdtraj_trajectory = mdtraj.load_pdb(self.complex_file_path, standard_names=False) + mdtraj_trajectory = mdtraj.load_pdb( + self.complex_file_path, standard_names=False + ) atom_indices_by_role = _atom_indices_by_role( self.substance, self.complex_file_path