global-chem 0.8.3

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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).

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 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.
Phase 2 Hetereocyclic Rings	IUPAC/SMILES/SMARTS	phase_2_hetereocyclic_rings_smiles, phase_2_hetereocyclic_rings_smarts	Broughton, Howard B., and Ian A. Watson. “Selection of Heterocycles for Drug Design.” Journal of Molecular Graphics & Modelling, vol. 23, no. 1, Sept. 2004, pp. 51–58. PubMed, https://doi.org/10.1016/j.jmgm.2004.03.016.
Privileged Scaffolds	IUPAC/SMILES/SMARTS	privileged_scaffolds_smiles, privileged_scaffolds_smarts	Welsch, Matthew E., et al. “Privileged Scaffolds for Library Design and Drug Discovery.” Current Opinion in Chemical Biology , vol. 14, no. 3, June 2010, pp. 347–61.PubMed, https://doi.org/10.1016/j.cbpa.2010.02.018.
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.

• Lead Developer Suliman sharif
• Artwork Elena Chow

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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