From da889c1b9bc95d426d43bee4b74c4d29c539fc09 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Thu, 2 Jan 2025 16:16:42 -0600 Subject: [PATCH 1/3] Remove unused private method --- openff/toolkit/utils/openeye_wrapper.py | 32 ------------------------- 1 file changed, 32 deletions(-) diff --git a/openff/toolkit/utils/openeye_wrapper.py b/openff/toolkit/utils/openeye_wrapper.py index 3e902ec52..fa87a1018 100644 --- a/openff/toolkit/utils/openeye_wrapper.py +++ b/openff/toolkit/utils/openeye_wrapper.py @@ -840,38 +840,6 @@ def _read_oemolistream_molecules( return mols - def _smarts_to_networkx(self, substructure_smarts): - import networkx as nx - from openeye import oechem - - qmol = oechem.OEQMol() - if not oechem.OEParseSmiles(qmol, substructure_smarts): - raise SMILESParseError(f"Error parsing SMARTS '{substructure_smarts}'") - - oechem.OEAssignHybridization(qmol) - - graph: nx.classes.graph.Graph = nx.Graph() - for atom in qmol.GetAtoms(): - atomic_number = atom.GetAtomicNum() - - graph.add_node( - atom.GetIdx(), - atomic_number=atomic_number, - formal_charge=atom.GetFormalCharge(), - map_index=atom.GetMapIdx(), - ) - for bond in qmol.GetBonds(): - bond_order = bond.GetOrder() - if bond_order == 0: - raise SMILESParseError(f"A bond in '{substructure_smarts} has order 0") - - graph.add_edge( - bond.GetBgnIdx(), - bond.GetEndIdx(), - bond_order=bond_order, - ) - return graph - def _assign_aromaticity_and_stereo_from_3d(self, offmol): from openeye import oechem From 85c40d5e741f62978f53ad7130adfee630f879fd Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 3 Jan 2025 09:46:33 -0600 Subject: [PATCH 2/3] Add shims --- devtools/conda-envs/openeye.yaml | 2 ++ devtools/conda-envs/rdkit.yaml | 2 ++ devtools/conda-envs/test_env.yaml | 2 ++ 3 files changed, 6 insertions(+) diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml index 36f06df95..d88eda0f4 100644 --- a/devtools/conda-envs/openeye.yaml +++ b/devtools/conda-envs/openeye.yaml @@ -51,3 +51,5 @@ dependencies: - types-xmltodict - types-cachetools - mongo-types + # shim + - libabseil=20240722.0=*_1 diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml index e48a8dc19..a09c05961 100644 --- a/devtools/conda-envs/rdkit.yaml +++ b/devtools/conda-envs/rdkit.yaml @@ -40,3 +40,5 @@ dependencies: - qcportal >=0.50 - qcengine - nglview + # shim + - libabseil=20240722.0=*_1 diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 3ae44cc0f..1486d70f2 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -60,3 +60,5 @@ dependencies: - types-xmltodict - types-cachetools - mongo-types + # shim + - libabseil=20240722.0=*_1 From 4b786e3901b21d6c9a5fdb7326f7d5ef737b4391 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Mon, 6 Jan 2025 18:08:05 -0800 Subject: [PATCH 3/3] undo shim --- devtools/conda-envs/openeye.yaml | 2 -- devtools/conda-envs/rdkit.yaml | 2 -- devtools/conda-envs/test_env.yaml | 2 -- 3 files changed, 6 deletions(-) diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml index d88eda0f4..36f06df95 100644 --- a/devtools/conda-envs/openeye.yaml +++ b/devtools/conda-envs/openeye.yaml @@ -51,5 +51,3 @@ dependencies: - types-xmltodict - types-cachetools - mongo-types - # shim - - libabseil=20240722.0=*_1 diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml index a09c05961..e48a8dc19 100644 --- a/devtools/conda-envs/rdkit.yaml +++ b/devtools/conda-envs/rdkit.yaml @@ -40,5 +40,3 @@ dependencies: - qcportal >=0.50 - qcengine - nglview - # shim - - libabseil=20240722.0=*_1 diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 1486d70f2..3ae44cc0f 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -60,5 +60,3 @@ dependencies: - types-xmltodict - types-cachetools - mongo-types - # shim - - libabseil=20240722.0=*_1