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openforcefield / openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
http://openforcefield.org
MIT License
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`Topology.set_positions` chokes when setting positions on `_SimpleMolecule`s which lacked conformers #1867

Closed mattwthompson closed 2 months ago

mattwthompson commented 2 months ago

Describe the bug

To Reproduce

In [1]: import numpy

In [2]: from openff.toolkit import Molecule, Topology, Quantity

In [3]: from openff.toolkit.topology._mm_molecule import _SimpleMolecule

In [4]: simple = _SimpleMolecule.from_molecule(Molecule.from_smiles("CCO"))

In [5]: topology = Topology.from_molecules([simple, simple])

In [6]: topology.set_positions(Quantity(numpy.zeros((topology.n_atoms, 3)), "nanometer"))
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[6], line 1
----> 1 topology.set_positions(Quantity(numpy.zeros((topology.n_atoms, 3)), "nanometer"))

File ~/software/openff-toolkit/openff/toolkit/topology/topology.py:2175, in Topology.set_positions(self, array)
   2173         molecule._conformers = [array[start:stop]]
   2174     else:
-> 2175         molecule.conformers = [array[start:stop]]  # type: ignore[misc]
   2176 else:
   2177     molecule.conformers[0:1] = [array[start:stop]]

AttributeError: property 'conformers' of '_SimpleMolecule' object has no setter

Output

Computing environment (please complete the following information):

``` $ zsh ~/software/status/devtools/support/debug.sh 8:18:34 ☁ 0.16.0 ☂ =====================================HEADER===================================== Run this script with your conda/mamba environment activated Invoke the script like this: source debug.sh | tee -a debug.log Then copy/upload/send us debug.log If pasting to a GitHub issue, it might be useful to put into an expandable block
Debug log (click me!) ``` Copy the debug log here! ```
https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/organizing-information-with-collapsed-sections =====================================SYSTEM===================================== Fri Apr 26 08:18:38 CDT 2024 darwin23.0 arm64 /Users/mattthompson/software/status/devtools/support/debug.sh:31: command not found: nvidia-smi no nvidia-smi, system either does not have an nvidia card or cuda is not properly configured =====================================CONDA====================================== /Users/mattthompson/micromamba/envs/openff-toolkit-test/bin/python /Users/mattthompson/software/status/devtools/support/debug.sh:36: command not found: conda no conda /Users/mattthompson/software/status/devtools/support/debug.sh:37: command not found: mamba no mamba libmamba version : 1.5.8 micromamba version : 1.5.8 curl version : libcurl/8.4.0 (SecureTransport) LibreSSL/3.3.6 zlib/1.2.12 nghttp2/1.58.0 libarchive version : libarchive 3.5.3 zlib/1.2.12 liblzma/5.4.3 bz2lib/1.0.8 envs directories : /Users/mattthompson/micromamba/envs package cache : /Users/mattthompson/micromamba/pkgs /Users/mattthompson/.mamba/pkgs environment : openff-toolkit-test (active) env location : /Users/mattthompson/micromamba/envs/openff-toolkit-test user config files : /Users/mattthompson/.mambarc populated config files : /Users/mattthompson/.mambarc virtual packages : __unix=0=0 __osx=14.4=0 __archspec=1=arm64 channels : base environment : /Users/mattthompson/micromamba platform : osx-arm64 /Users/mattthompson/software/status/devtools/support/debug.sh:40: command not found: conda no conda /Users/mattthompson/software/status/devtools/support/debug.sh:41: command not found: mamba no mamba List of packages in environment: "/Users/mattthompson/micromamba/envs/openff-toolkit-test" Name Version Build Channel ───────────────────────────────────────────────────────────────────────────────────── ambertools 23.3 py311hd5bda53_6 conda-forge appnope 0.1.4 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pyhd8ed1ab_0 conda-forge zlib 1.2.13 h53f4e23_5 conda-forge zlib-ng 2.0.7 h1a8c8d9_0 conda-forge zstandard 0.22.0 py311h67b91a1_0 conda-forge zstd 1.5.5 h4f39d0f_0 conda-forge ====================================TOOLKITS==================================== ("GLOBAL_TOOLKIT_REGISTRY.registered_toolkit_versions={'OpenEye Toolkit': " "'2023.2.3', 'The RDKit': '2023.09.5', 'AmberTools': '22.0', 'Built-in " "Toolkit': None}") 'OpenEyeToolkitWrapper.is_available()=True' ==============================FORCEFIELDS/PLUGINS=============================== 'FORCE FIELD PATHS:' ("_get_installed_offxml_dir_paths()=['/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/smirnoff99frosst/offxml', " "'/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/openff/amber_ff_ports/offxml', " "'/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/openforcefields/offxml']") 'FORCE FIELD FILES IN PATHS:' [['smirnoff99Frosst-1.0.2.offxml', 'smirnoff99Frosst-1.0.0.offxml', 'smirnoff99Frosst-1.1.0.offxml', 'smirnoff99Frosst-1.0.4.offxml', 'smirnoff99Frosst-1.0.8.offxml', 'smirnoff99Frosst-1.0.6.offxml', 'README.md', 'smirnoff99Frosst-1.0.3.offxml', 'smirnoff99Frosst-1.0.1.offxml', 'smirnoff99Frosst-1.0.5.offxml', 'smirnoff99Frosst-1.0.9.offxml', 'smirnoff99Frosst-1.0.7.offxml'], ['ff14sb_off_impropers_0.0.2.offxml', 'ff14sb_0.0.1.offxml', 'ff14sb_off_impropers_0.0.4.offxml', 'ff14sb_0.0.3.offxml', 'ff14sb_off_impropers_0.0.1.offxml', 'ff14sb_off_impropers_0.0.3.offxml', 'ff14sb_0.0.4.offxml', 'ff14sb_0.0.2.offxml'], ['tip3p_fb-1.1.0.offxml', 'tip3p_fb-1.0.0.offxml', 'openff-1.0.1.offxml', 'openff-1.1.1.offxml', 'spce-1.0.0.offxml', 'openff-1.0.0-RC1.offxml', 'opc3.offxml', 'opc3-1.0.0.offxml', 'openff_unconstrained-2.1.1.offxml', 'openff-2.1.0-rc.1.offxml', 'openff-1.2.0.offxml', 'openff-1.3.0.offxml', 'tip3p-1.0.0.offxml', 'openff_unconstrained-2.0.0-rc.1.offxml', 'openff_unconstrained-1.3.1.offxml', 'openff_unconstrained-1.2.1.offxml', 'opc-1.0.2.offxml', 'openff-2.0.0-rc.2.offxml', 'opc-1.0.0.offxml', 'openff_unconstrained-2.2.0-rc1.offxml', 'openff_unconstrained-1.0.0-RC2.offxml', 'openff_unconstrained-1.1.0.offxml', 'openff_unconstrained-1.0.0.offxml', 'openff-2.1.0.offxml', 'openff-2.0.0.offxml', 'tip4p_fb-1.0.1.offxml', 'tip3p.offxml', 'tip4p_ew.offxml', 'opc3-1.0.1.offxml', 'opc.offxml', 'README.md', 'openff_unconstrained-2.1.0.offxml', 'openff_unconstrained-2.0.0.offxml', 'openff_unconstrained-2.0.0-rc.2.offxml', 'tip3p_fb-1.1.1.offxml', 'openff-1.1.0.offxml', 'openff-1.0.0.offxml', 'openff-1.0.0-RC2.offxml', 'openff-2.2.0-rc1.offxml', 'tip3p-1.0.1.offxml', 'openff-1.3.1.offxml', 'openff-1.2.1.offxml', 'tip4p_ew-1.0.0.offxml', 'openff-1.3.1-alpha.1.offxml', 'tip4p_fb.offxml', 'tip3p_fb.offxml', 'openff_unconstrained-1.0.0-RC1.offxml', 'spce.offxml', 'openff_unconstrained-2.1.0-rc.1.offxml', 'tip5p.offxml', 'openff_unconstrained-1.2.0.offxml', 'openff_unconstrained-1.3.0.offxml', 'tip4p_fb-1.0.0.offxml', 'openff-2.1.1.offxml', 'openff-2.0.0-rc.1.offxml', 'openff_unconstrained-1.0.1.offxml', 'openff_unconstrained-1.1.1.offxml', 'openff_unconstrained-1.3.1-alpha.1.offxml', 'tip5p-1.0.0.offxml', 'opc-1.0.1.offxml']] 'HANDLER PLUGINS:' ('load_handler_plugins()=[]") 'COLLECTION PLUGINS:' 'load_smirnoff_plugins()=[]' =====================================OPENMM===================================== test openmm OpenMM Version: 8.1.1 Git Revision: ec797acabe5de4ce9f56c92d349baa889f4b0821 There are 3 Platforms available: 1 Reference - Successfully computed forces 2 CPU - Successfully computed forces 3 OpenCL - Successfully computed forces Median difference in forces between platforms: Reference vs. CPU: 6.30441e-06 Reference vs. OpenCL: 6.7451e-06 CPU vs. OpenCL: 7.36143e-07 All differences are within tolerance. checking plugin load failures () checking which platforms support mixed precision Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'openmmtools' possible openmm errors ```

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