GlobalChem: A content variable store for Chemistry!
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).
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.
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
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
|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 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|
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.
If you find my personal dictionary is useful please feel free to cite me under:
Sul, Elena Y. Chow: "Sul's Dictionary"