Mark J. Williamson

IndexOutOfBoundsException via org.wikidata.wdtk.storage.datastructures.BitVectorImpl.assertRange(BitVectorImpl.java:169)

2

Dear Devs, I'm making use of the wikidata-toolkit in a little project at https://bitbucket.org/mjw99/wikidatachemscraper/overview . Essentially, I'm trying to harvest all chemical structure diagrams that are in the SVG format...

Unable to find package after %maven magic

2

First, thank you for a wonderful tool. I can checkout your code and reproduce your xchart example. However if I try the following: ``` %maven com.google.guava:guava:27.1-jre import com.google.common.collect.Multimap; ``` I...

Difference in InChIKey values, from SMILES, when comparing to RDKit

5

If I run the following with RDKit (2021.09.2): ``` from rdkit import Chem m1 = Chem.MolFromSmiles("N1C[C@@]2(CC[C@H](C)CC2)CC1") print(Chem.MolToInchiKey(m1)) m2 = Chem.MolFromSmiles("N1C[C@]2(CC[C@H](C)CC2)CC1") print(Chem.MolToInchiKey(m2)) ``` I obtain: ``` SGJOFPWLAFWQEP-AOOOYVTPSA-N SGJOFPWLAFWQEP-MGCOHNPYSA-N ``` If I...

Using openmmtools 0.20.3 pyhd8ed1ab_0 conda-forge and running the following test: ``` cd /home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/openmmtools/tests nosetests --verbosity=2 test_alchemy.py:TestAbsoluteAlchemicalFactorySlow ``` I am seeing: ``` ====================================================================== ERROR: test suite for ---------------------------------------------------------------------- Traceback (most recent...

Possible synonym issue with 4-phenylazophenol

3

With the current https://opsin.ch.cam.ac.uk/ instance, for 4-phenylazophenol , it is returning: ``C1(=CC=CC=C1)C1=CC(=C(C=C1)O)N=NC1=C(C=CC=C1)O`` Sigma have 4-phenylazophenol as the [following](https://www.sigmaaldrich.com/catalog/product/sial/131083?lang=en&region=GB) and note the structures are different. OPSIN does correctly return with the...

Optimisation failure with flat potential energy surface near minimum

11

The following example, with PySCF 1.5.3 and Pyberny 0.4.0: ``` # c1(F)c(F)c(F)c(F)c(F)c1C#CCN(C)(C(=O)c1ccccc1) # ZCUWMRDRNFJWEK-UHFFFAOYSA from pyscf import gto, dft from pyscf.geomopt import berny_solver atomic_coords = ''' C 7.403569010821 -0.674065308632 1.565827066815...

openbabel==3.1.1 from conda-forge has incorrectly versioned BABEL_LIBDIR

1

## Environment Information Open Babel version: 3.1.1 (conda-forge) Operating system and version: Ubuntu 22.04.4 LTS, conda 4.12.0 ``` conda create -n foo python=3.11 -y conda activate foo conda install -c...

The use of CustomCentroidBondForce as a BiasVariable in a metadynamics simulation of a protein-protein dissociation

5

I have been looking at the new metadynamics functionality in OpenMM 8.1.1 and I am trying to reproduce a protocol in the following [paper](https://www.nature.com/articles/s41598-022-05875-8#Sec11): _....a complex is dissociated by performing...