[PLUG] Linux chemistry software

Tue Aug 11 22:56:18 UTC 2020

On Tue, 11 Aug 2020, Tom wrote:

> I wanted to ask if anybody knew of some Linux software like Kalzium,

Hi Tom,

I know nothing about Kalzium but a quick web search confirmed my belief that
you can find (or create) everything you want using python (with, perhaps
pandas and matplotlib). Here are the first few hits from the search term,
"chemical reaction research with python":

GitHub - bjodah/chempy: ⚗ A package useful for chemistry ...
[Search domain github.com/bjodah/chempy] https://github.com/bjodah/chempy
Balancing stoichiometry of a chemical reaction ... chemistry
physical-chemistry chemical-kinetics chemical-formulas
chemical-reaction-model python speciation Resources. Readme License.
BSD-2-Clause License Releases 50. chempy-0.7.12 Latest Jul 5, 2020 + 49
releases Used ...

CGRtools: Python Library for Molecule, Reaction, and ...
[Search domain pubs.acs.org/doi/10.1021/acs.jcim.9b00102] https://pubs.acs.org/doi/10.1021/acs.jcim.9b00102
CGRtools is an open-source Python library aimed to handle molecular and
reaction information. It is the sole library developed so far which can
process condensed graph of reaction (CGR) handling. CGR provides the
possibility for advanced operations with reaction information and could be
used for reaction descriptor calculation, structure-reactivity modeling,
atom-to-atom mapping comparison ...

functional programming - How to make a python organic ...
[Search domain stackoverflow.com/questions/26428639/how-to-make-a-python-organic-chemistry-retro-synthesis-generator] https://stackoverflow.com/questions/26428639/how-to-make-a-python-organic-chemistry-retro-synthesis-generator
Sometimes you are only given the final product and asked to list the
reactions necessary to synthesize given some parameters (start only with a
compound that has 5 carbons or less, only use alcohol, etc.) So far, I've
done some research, and I think RDkit w/Python is a good place to start.

ChemPy: A package useful for chemistry written in Python
[Search domain www.theoj.org/joss-papers/joss.00565/10.21105.joss.00565.pdf] https://www.theoj.org/joss-papers/joss.00565/10.21105.joss.00565.pdf
ChemPy is a Python library that provides functions and classes for solving
chemistry related problems. It includes classes for representing substances,
reactions, and systems of reactions. It also includes well established
formulae from physical chemistry, as well as analytic solutions to some
differential equations commonly encountered in chemical

Chemical Reaction Engineering Module Updates - COMSOL® 5.5 ...
[Search domain www.comsol.com/release/5.5/chemical-reaction-engineering-module] https://www.comsol.com/release/5.5/chemical-reaction-engineering-module
Chemical Reaction Engineering Module Updates. For users of the Chemical
Reaction Engineering Module, COMSOL Multiphysics ® version 5.5 includes the
ability to generate materials from a thermodynamic system, diffusivity
models for gases and liquids, and water and steam properties. Learn more
about these chemical reaction engineering features below.

CRNT4SBML: a Python package for the detection of ...
[Search domain academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa241/5820009] https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa241/5820009
This interface is achieved through systems biology markup language (SBML), a
community standard format for describing signaling pathways. CRNT4SBML is
developed using Python, which makes it easy to extend and couple with other
numerous Python-based computational biology tools. 2 Features 2.1 Importing
reaction networks

GitHub - lmmentel/awesome-python-chemistry: A curated list ...
[Search domain github.com/lmmentel/awesome-python-chemistry] https://github.com/lmmentel/awesome-python-chemistry
GPAW - Is a density-functional theory (DFT) Python code based on the
projector-augmented wave (PAW) method and the atomic simulation environment
(ASE). horton - Helpful Open-source Research TOol for N-fermion system, a
quantum-chemistry program that can perform computations involving model
Hamiltonians.

Catalysis-Hub.org, an open electronic structure database ...
[Search domain www.nature.com/articles/s41597-019-0081-y] https://www.nature.com/articles/s41597-019-0081-y
We present a new open repository for chemical reactions on catalytic
surfaces, available at https://www.catalysis-hub.org . The featured database
for surface reactions contains more than 100,000 ... Python as alternative
to Matlab for engineering calculations

[Search domain kitchingroup.cheme.cmu.edu/blog/2013/12/30/Python-as-alternative-to-Matlab-for-engineering-calculations/] kitchingroup.cheme.cmu.edu/blog/2013/12/30/Python-as-alternative-to-Matlab-for-engineering-calculations/
It is certainly doable to use Python for many scientific and engineering
calculations. This past Fall I took the plunge, and taught a whole core
course in chemical reaction engineering using Python! It was a Master's
level course with 59 graduate students in it. I have also taught a graduate
elective course in Molecular Simulation using Python. Reactants, products,
and transition states of elementary ... [Search domain
www.nature.com/articles/s41597-020-0460-4]
https://www.nature.com/articles/s41597-020-0460-4 We report quantum chemical
data on more than 16,000 reactions in the form of reactants, products, and
TSs at the B97-D3/def2-mSVP level of theory and 12,000 reactions at the
ωB97X-D3/def2-TZVP ...

Python can do so-o-o much in science.

Wear gloves and eye protection. :-)

Stay well,

Rich