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openforcefield / openff-evaluator

A physical property evaluation toolkit from the Open Forcefield Consortium.
https://docs.openforcefield.org/projects/evaluator
MIT License
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AttributeError: Neither Quantity object nor its magnitude has attribute 'unit'. Did you mean: 'units'? in BuildCoordinatesPackmol("") #567

Open MiloszGrabski opened 3 weeks ago

MiloszGrabski commented 3 weeks ago

Hi, I am trying to repeat this tutorial: https://github.com/MobleyLab/drug-computing/blob/f38a4148e9e70238c88fc8110d95b34688f02838/uci-pharmsci/lectures/SMIRNOFF_simulations/mixture_simulations.ipynb

from openff.evaluator.protocols.coordinates import BuildCoordinatesPackmol
from openff.evaluator.substances import Substance, Component, MoleFraction, ExactAmount
from rdkit import Chem
import shutil, os
from openff.toolkit import Molecule
import openmmforcefields

#Number of solute/solvent molecules
Nsolu = 3
Nsolv = 100

#solute names
solute_smiles = ['c1ccccc1', 'c1ccccc1', 'C', 'CCO']
#Solvent names
solvent_smiles = ['C1CCCCC1', 'CCCCO']

# Storage for the mixtures we've built
mixtures = []
outdir = 'coordinate_files'
if not os.path.isdir(outdir): os.mkdir(outdir)

# Loop and build mixtures
for idx in range( len( solute_smiles) ):
    # Define new mixture
    mixture_build = BuildCoordinatesPackmol("")
    substance = Substance()
    # Add solute and solvent
    substance.add_component(Component(solute_smiles[idx], role=Component.Role.Solute), ExactAmount(Nsolu))
    substance.add_component(Component(solvent_smiles[idx], role=Component.Role.Solvent), ExactAmount(Nsolv))
    #substance.add_component(Component("Cc1ccccc1", role=Component.Role.Solvent), MoleFraction(0.1))
    #substance.add_component(Component("C1CCCCC1", role=Component.Role.Solvent), MoleFraction(0.9))
    # Note you can optionally specify mole fraction instead, or a mix of numbers/mole fractions, etc.

    #substance.max_molecules = 150
    mixture_build.substance = substance

    #build
    mixture_build.execute()

    # Do file bookkeeping so the output files don't overwrite one another
    outfile = os.path.join(outdir, f'coordinate_file{idx}.pdb')
    shutil.copy( mixture_build.coordinate_file_path, outfile )
    mixture_build.coordinate_file_path = outfile

    #Store details
    mixtures.append(mixture_build)

    print(f"finished build {idx}")

print("Finished building")

But I am getting a following error:

Traceback (most recent call last): File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/pint/facets/numpy/quantity.py", line 228, in getattr return getattr(self._magnitude, item) AttributeError: 'float' object has no attribute 'unit'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/mnt/c/Users/xxx/_work/testing/from openmmforcefields.py", line 38, in mixture_build.execute() File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/workflow/protocols.py", line 704, in execute self._execute(directory, available_resources) File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/protocols/coordinates.py", line 267, in _execute trajectory, residue_names = packmol.pack_box( File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/utils/packmol.py", line 667, in pack_box box_size = _approximate_box_size_by_density( File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/utils/packmol.py", line 151, in _approximate_box_size_by_density molecule_mass = from_openmm(molecule_mass) / unit.avogadro_constant File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/utilities/utilities.py", line 80, in wrapper return function(*args, **kwargs) File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/units/openmm.py", line 170, in from_openmm openmmunit = openmm_quantity.unit File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/pint/facets/numpy/quantity.py", line 230, in getattr raise AttributeError( AttributeError: Neither Quantity object nor its magnitude (78.112362) has attribute 'unit'. Did you mean: 'units'? (etest) (MD) xxx@xxx-W11X:/mnt/c/Users/xxx/_work/testing$ /home/xxx/conda/envs/etest/bin/python "/mnt/c/Users/xxx/_work/testing/from openmmforcefields.py" Traceback (most recent call last): File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/pint/facets/numpy/quantity.py", line 228, in getattr return getattr(self._magnitude, item) AttributeError: 'float' object has no attribute 'unit'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/mnt/c/Users/xxx/_work/testing/from openmmforcefields.py", line 40, in mixture_build.execute() File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/workflow/protocols.py", line 704, in execute self._execute(directory, available_resources) File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/protocols/coordinates.py", line 267, in _execute trajectory, residue_names = packmol.pack_box( File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/utils/packmol.py", line 667, in pack_box box_size = _approximate_box_size_by_density( File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/evaluator/utils/packmol.py", line 151, in _approximate_box_size_by_density molecule_mass = from_openmm(molecule_mass) / unit.avogadro_constant File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/utilities/utilities.py", line 80, in wrapper return function(*args, **kwargs) File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/openff/units/openmm.py", line 170, in from_openmm openmmunit = openmm_quantity.unit File "/home/xxx/conda/envs/etest/lib/python3.10/site-packages/pint/facets/numpy/quantity.py", line 230, in getattr raise AttributeError( AttributeError: Neither Quantity object nor its magnitude (78.112362) has attribute 'unit'. Did you mean: 'units'?

j-wags commented 3 weeks ago

It's likely there's a mismatch in the versions of packages you have installed and the versions that the notebook expects. Could you post the output of running 'mamba list' (or 'conda list' if you're not using mamba yet)?

MiloszGrabski commented 3 weeks ago

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alabaster 1.0.0 pyhd8ed1ab_0 conda-forge amberlite 22.0 pypi_0 pypi ambertools 22.5 py310hd182041_0 conda-forge amberutils 21.0 pypi_0 pypi annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge anyio 4.3.0 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge arpack 3.7.0 hdefa2d7_2 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge aws-c-auth 0.7.22 hf36ad8f_6 conda-forge aws-c-cal 0.6.15 h816f305_1 conda-forge aws-c-common 0.9.23 h4ab18f5_0 conda-forge aws-c-compression 0.2.18 he027950_7 conda-forge aws-c-event-stream 0.4.2 hb72ac1a_14 conda-forge aws-c-http 0.8.2 h75ac8c9_3 conda-forge aws-c-io 0.14.9 hd3d3696_3 conda-forge aws-c-mqtt 0.10.4 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conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.0 py310hc51659f_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge fsspec 2024.6.1 pyhff2d567_0 conda-forge future 1.0.0 pyhd8ed1ab_0 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge glog 0.7.1 hbabe93e_0 conda-forge greenlet 3.0.3 py310hc6cd4ac_0 conda-forge griddataformats 1.0.2 pyhd8ed1ab_0 conda-forge gsd 3.3.0 py310h261611a_0 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge h5py 3.11.0 nompi_py310hf054cd7_102 conda-forge hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge httpcore 1.0.5 pyhd8ed1ab_0 conda-forge httpx 0.27.0 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge imagesize 1.4.1 pyhd8ed1ab_0 conda-forge 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conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 hd590300_1001 conda-forge markupsafe 2.1.5 py310h2372a71_0 conda-forge matplotlib-base 3.8.4 py310hef631a5_2 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mda-xdrlib 0.2.0 pyhd8ed1ab_0 conda-forge mdanalysis 2.7.0 py310hcc13569_1 conda-forge mdapackmol 0.1.0 pypi_0 pypi mdtraj 1.10.0 py310he673748_0 conda-forge mistune 3.0.2 pyhd8ed1ab_0 conda-forge ml_dtypes 0.4.0 py310hf9f9076_1 conda-forge mmpbsa-py 16.0 pypi_0 pypi mmtf-python 1.1.3 pyhd8ed1ab_0 conda-forge mordred 1.2.0 pyhe5148d4_0 mordred-descriptor mpi 1.0 mpich conda-forge mpich 4.2.2 h4a7f18d_101 conda-forge mpiplus v0.0.2 pyhd8ed1ab_0 conda-forge mrcfile 1.5.0 pyhd8ed1ab_0 conda-forge msgpack-python 1.0.8 py310h25c7140_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge nb_conda_kernels 2.5.1 pyh707e725_2 conda-forge nbclient 0.10.0 pyhd8ed1ab_0 conda-forge nbconvert 7.16.4 hd8ed1ab_0 conda-forge nbconvert-core 7.16.4 pyhd8ed1ab_0 conda-forge 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openff-interchange-base 0.3.29 pyhd8ed1ab_0 conda-forge openff-models 0.1.2 pyhca7485f_0 conda-forge openff-toolkit 0.16.3 pyhd8ed1ab_0 conda-forge openff-toolkit-base 0.16.3 pyhd8ed1ab_0 conda-forge openff-units 0.2.2 pyhca7485f_0 conda-forge openff-utilities 0.1.12 pyhd8ed1ab_0 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openmm 8.1.1 py310h43b6314_1 conda-forge openmmforcefields 0.12.0 pyhd8ed1ab_0 conda-forge openmmtools 0.23.1 pyhd8ed1ab_0 conda-forge openmoltools 0.8.8 pyhd8ed1ab_1 conda-forge openssl 3.3.1 h4bc722e_2 conda-forge opt-einsum 3.3.0 hd8ed1ab_2 conda-forge opt_einsum 3.3.0 pyhc1e730c_2 conda-forge orc 2.0.1 h17fec99_1 conda-forge overrides 7.7.0 pyhd8ed1ab_0 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge packmol 20.14.4 ha36c22a_0 conda-forge packmol-memgen 1.2.3rc0 pypi_0 pypi pandas 2.0.0 py310h9b08913_0 conda-forge pandoc 3.3 ha770c72_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge panedr 0.8.0 pyhd8ed1ab_0 conda-forge parmed 4.2.2 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xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xyzservices 2024.6.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yank 0.25.2 pyhd8ed1ab_0 conda-forge zeromq 4.3.5 h75354e8_4 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.3.1 h4ab18f5_1 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge

j-wags commented 3 weeks ago

I think the issue is arising from using an older version of evaluator - You'll want to use openff-evaluator 0.4

mamba install -c conda-forge openff-evaluator=0.4
j-wags commented 2 weeks ago

Ah, and it turns out there had been a build issue with openff-evaluator 0.4.9, which was intended to improve some environment resolution issues. We caught that today and just got the new package out. So that may solve some of your packaging headaches/reduce the factors that lead to weird environment resolution.