global-chem 0.9.9.8

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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	# of Entries	References
Amino Acids	IUPAC/SMILES/SMARTS	amino_acid_side_smiles, amino_acid_side_smarts	20	Common Knowledge
Essential Vitamins	Preferred Name/SMILES/SMARTS	vitamins_smiles, vitamins_smarts	13	Common Knowledge
Common Organic Solvents	IUPAC/SMILES/SMARTS	common_organic_solvents_smiles, common_organic_solvents_smarts	42	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	94	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	333	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	92	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	19	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	47	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 Warheads	IUPAC/SMILES/SMARTS	common_warhead_smiles, common_warhead_smarts	29	Gehringer, Matthias, and Stefan A. Laufer. “Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology.”Journal of Medicinal Chemistry , vol. 62, no. 12, June 2019, pp. 5673–724. ACS Publications, https://doi.org/10.1021/acs.jmedchem.8b01153.
Common Polymer Repeating Units	IUPAC/SMILES/SMARTS	common_polymer_repeating_units_smiles, common_polymer_repeating_units_smarts	78	Hiorns, R. C., et al. “A brief guide to polymer nomenclature (IUPAC Technical Report).”Pure and Applied Chemistry , vol. 84, no. 10, Oct. 2012, pp. 2167–69., https://doi.org/10.1351/PAC-REP-12-03-05.
Common R Group Replacements	IUPAC/SMILES/SMARTS	r_groups_replacements_smiles, r_groups_replacements_smarts	499	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.
Electrophillic Warheads for Kinases	Preferred Name/SMILES/SMARTS	kinase_electrophilic_warheads_smiles, kinase_electrophilic_warheads_smarts	24	Petri, László, et al. “An Electrophilic Warhead Library for Mapping the Reactivity and Accessibility of Tractable Cysteines in Protein Kinases.” European Journal of Medicinal Chemistry, vol. 207, Dec. 2020, p. 112836. PubMed, https://doi.org/10.1016/j.ejmech.2020.112836.
Privileged Scaffolds for Kinases	IUPAC/SMILES/SMARTS	kinase_privileged_scaffolds_smiles, kinase_privileged_scaffolds_smarts	29	Hu, Huabin, et al. “Systematic Comparison of Competitive and Allosteric Kinase Inhibitors Reveals Common Structural Characteristics.” European Journal of Medicinal Chemistry, vol. 214, Mar. 2021, p. 113206. ScienceDirect, https://doi.org/10.1016/j.ejmech.2021.113206.
BRaf Inhibitors	IUPAC/SMILES/SMARTS	ribose_subpocket_smiles, ribose_subpocket_smarts, adenine_subpocket_smiles, adenine_subpocket_smarts (Check File)	54	Agianian, Bogos, and Evripidis Gavathiotis. “Current Insights of BRAF Inhibitors in Cancer.” Journal of Medicinal Chemistry, vol. 61, no. 14, July 2018, pp. 5775–93. ACS Publications, https://doi.org/10.1021/acs.jmedchem.7b01306.
Common Amino Acid Protecting Groups	IUPAC/ACRONYM/SMILES/SMARTS	Check File Here	346	Isidro-Llobet, Albert, et al. “Amino Acid-Protecting Groups.” Chemical Reviews, vol. 109, no. 6, June 2009, pp. 2455–504. DOI.org (Crossref), https://doi.org/10.1021/cr800323s.
Emerging Perfluoroalkyls	IUPAC/SMILES/SMARTS	polyfluoroalkyl_smiles, polyfluoroalkyl_smarts	27	Pelch, Katherine E., et al. “PFAS Health Effects Database: Protocol for a Systematic Evidence Map.” Environment International, vol. 130, Sept. 2019, p. 104851. ScienceDirect, https://doi.org/10.1016/j.envint.2019.05.045.
Chemicals For Clay Adsorption	IUPAC/SMILES/SMARTS	montmorillonite_chemical_adsorption_smiles, montmorillonite_chemical_adsorption_smarts	33	Orr, Asuka A., et al. “Combining Experimental Isotherms, Minimalistic Simulations, and a Model to Understand and Predict Chemical Adsorption onto Montmorillonite Clays.” ACS Omega, vol. 6, no. 22, June 2021, pp. 14090–103. PubMed, https://doi.org/10.1021/acsomega.1c00481.
Common Regex Patterns	Mol2	common_regex_patterns	1

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