From 5493557d6955b9db4190d5fbcb8c5c4e2f93e592 Mon Sep 17 00:00:00 2001 From: Lily Wang <31115101+lilyminium@users.noreply.github.com> Date: Tue, 11 Jan 2022 10:00:51 +1100 Subject: [PATCH] index conformers not... ids (#1091) Co-authored-by: Jeff Wagner --- openff/toolkit/utils/rdkit_wrapper.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/openff/toolkit/utils/rdkit_wrapper.py b/openff/toolkit/utils/rdkit_wrapper.py index 683720ba9..452da4222 100644 --- a/openff/toolkit/utils/rdkit_wrapper.py +++ b/openff/toolkit/utils/rdkit_wrapper.py @@ -1175,13 +1175,14 @@ def _elf_compute_rms_matrix(cls, molecule: "Molecule") -> np.ndarray: n_conformers = len(molecule.conformers) + # rdkit does not have conformer indices but conformer "ids" conformer_ids = [conf.GetId() for conf in rdkit_molecule.GetConformers()] # Compute the RMS matrix making sure to take into account any automorhism (e.g # a phenyl or nitro substituent flipped 180 degrees. rms_matrix = np.zeros((n_conformers, n_conformers)) - for i, j in itertools.combinations(conformer_ids, 2): + for i, j in itertools.combinations(np.arange(n_conformers), 2): rms_matrix[i, j] = AllChem.GetBestRMS( rdkit_molecule,