Macs in Chemistry

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ChemDoodle v10.2 Released

 

The latest update of the popular chemical ChemDoodle 2D drawing package has been released.

This is a significant feature update to ChemDoodle 2D v10. This update is recommended for all ChemDoodle 2D users. Major changes include an updated shape system allowing you to edit shapes while you draw them, greatly speeding up figure drawing. A significant amount of work has culminated in a brand new and powerful table tool for creating rich data graphics. ChemDoodle 2D can also now balance any drawn reactions or typed chemical equations.

10_2_release_social_post

Full release notes are available here

In particular note

Quicklook plugin works again and has been rebuilt with the latest version of Xcode on Catalina.


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Vega Hub

 

Vega Hub a variety of models for predicting properties.

Compared with many existing QSAR models, we have put greater emphasis on ensuring that the models generate transparent, understandable, reproducible and verifiable results. To achieve this, a series of tools has been optimised, which can relate the results obtained for the target chemical to the results obtained for similar (structurally related) compounds.

Models can be downloaded here

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PLUMED PLUgin for MolEcular Dynamics

 

PLUMED is a community-developed PLUgin for MolEcular Dynamics. PLUMED works together with some of the most popular MD engines, such as ACEMD, Amber, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum Espresso. In addition, PLUMED can be used to augment the capabilities of analysis tools such as VMD, HTMD, OpenPathSampling, and as a standalone utility to analyze pre-calculated MD trajectories.

Installation

  • MacPorts, ports plumed and py-plumed, both as a pre-compiled binary (with basic capabilities) and source code (with more MPI and compiler options and including optional modules). Port plumed-devel provides a snapshot of the current development version.
  • Conda-forge, recipes plumed and py-plumed, as pre-compiled binaries with basic capabilities. Other conda binaries containing development versions or nightly builds are available on the plumed channel.

The API is accessible from multiple languages (C, C++, FORTRAN, and Python).

The PLUMED consortium. Promoting transparency and reproducibility in enhanced molecular simulations, Nat. Methods 16, 670 (2019) DOI

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Interactive plots in Jupyter Notebooks updated

 

I've been using Jupyter notebooks for a while for a wide variety of projects.

I've been looking at ways to produce interactive plots within a Jupyter notebook and after trying a couple of options to produce interactive data frames, in addition to 2D and 3D scatterplots including structures on tooltips.

Full review and the Jupyter notebook are here.

plotjupyter

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Interactive plots in Jupyter notebooks

 

I've been looking at ways to produce interactive plots within a Jupyter notebook and after trying a couple of options I used Plotly. This seems fairly straight-forward to use and I can produce interactive data frames, in addition to 2D and 3D scatterplots.

More details are shown here together with the jupyter notebook. It is very much a work in progress and suggestions are welcome. In particular, whilst I can get text to appear when hovering over a data point I'd be interested in ideas of how to get the structure displayed when you mouse over a point.

3DplotinJupyter


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