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GlobalChem: A content variable store for Chemistry!

License: MPL 2.0 Python Documentation Status Repo Size PyPI version DOI PRs Welcome PEP8

Global Chem is a variable store for common and rare chemical lists using IUPAC as input and SMILES/SMARTS as output. As mostly needed by myself as I search through chemical infinity.

I have found these lists written history to be useful, they come from a variety of different fields but are aggregated into the most common format of organic chemists (IUPAC) and the common language of the cheminformatician (SMILES) and for pattern matching (SMARTS).

Using GlobalChem

GlobalChem, initially, is one class object that have a fixed set of variables. Eventually and hopefully as the package grows it will be abstracted out by field i.e protein chemistry, analytical, and so on.

Installation

GlobalChem is going to be distribute via PyPi and as the content store grows we can expand it to other pieces of software making it accessible to all regardless of what you use. Alternatively, you could have a glance at the source code and copy/paste it yourself.


pip install global-chem

Quick Start

Just with no dependencies, intialize the class and there you go! All the common and rare groups of the world at your disposal


from global_chem import GlobalChem

global_chem = GlobalChem()

compounds = global_chem.rings_in_drugs_smiles

Variables List

Chemical List Languages Variables References
Amino Acids IUPAC/SMILES/SMARTS amino_acid_side_smiles, amino_acid_side_smarts Common Knowledge
Essential Vitamins Preferred Name/SMILES/SMARTS vitamins_smiles, vitamins_smarts Common Knowledge
Common R Group Replacement Preferred Name/SMILES/SMARTS r_groups_replacements_smiles, r_groups_replacements_smarts Takeuchi, Kosuke, et al. “R-Group Replacement Database for Medicinal Chemistry.” Future Science OA, vol. 7, no. 8, Sept. 2021, p. FSO742. future-science.com (Atypon), https://doi.org/10.2144/fsoa-2021-0062.
Common Organic Solvents IUPAC/SMILES/SMARTS common_organic_solvents_smiles, common_organic_solvents_smarts Fulmer, Gregory R., et al. “NMR Chemical Shifts of Trace Impurities: Common Laboratory Solvents, Organics, and Gases in Deuterated Solvents Relevant to the Organometallic Chemist.”Organometallics , vol. 29, no. 9, May 2010, pp. 2176–79.
Open Smiles IUPAC/SMILES/SMARTS open_smiles_functional_groups_smiles, open_smiles_functional_groups_smarts OpenSMILES Home Page. http://opensmiles.org/.
IUPAC Blue Book (CRC Handbook) 2003 Preferred Name/SMILES/SMARTS iupac_blue_book_radical_smiles, iupac_blue_book_radical_smarts, iupac_blue_book_rings_smiles, iupac_blue_book_rings_smarts Chemical Rubber Company. CRC Handbook of Chemistry and Physics: A Ready-Reference Book of Chemical and Physical Data . Edited by David R. Lide, 85. ed, CRC Press, 2004.
Rings in Drugs IUPAC/SMILES/SMARTS rings_in_drugs_smiles, rings_in_drugs_smarts Taylor, Richard D., et al. “Rings in Drugs.” Journal of Medicinal Chemistry, vol. 57, no. 14, July 2014, pp. 5845–59. ACS Publications, https://doi.org/10.1021/jm4017625.
Common Regex Patterns Mol2 common_regex_patterns

Genesis

GlobalChem was created because I noticed I was using the same variable across multiple scripts and figure it would be useful for folk to have.


Citation

If you find my personal dictionary is useful please feel free to cite me under:


Sul, Elena Y. Chow: "Sul's Dictionary" 

External links

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