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 _______________________________________________ PLUG: https://pdxlinux.org PLUG mailing list PLUG@pdxlinux.org http://lists.pdxlinux.org/mailman/listinfo/plug
