global-chem 1.0.2

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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 in 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()

rings_in_drugs = global_chem.get_rings_in_drugs()
kinase_inhitors = global_chem.get_privileged_scaffolds_for_kinase_inhibitors()

Variables List

Chemical List	Languages	Variables	# of Entries	References
Amino Acids	IUPAC/SMILES/SMARTS	get_amino_acids()	20	Common Knowledge
Essential Vitamins	Preferred Name/SMILES/SMARTS	get_essential_vitamins()	13	Common Knowledge
Common Organic Solvents	IUPAC/SMILES/SMARTS	get_common_organic_solvents()	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	get_open_smiles_functional_groups()	94	OpenSMILES Home Page. http://opensmiles.org/.
IUPAC Blue Book (CRC Handbook) 2003	Preferred Name/SMILES/SMARTS	get_iupac_blue_book_common_functional_groups()	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	get_rings_in_drugs()	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	get_common_heterocyclic_rings_phase_2()	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	get_common_privileged_scaffolds()	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	get_common_warhead_covalent_inhibitors()	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	get_common_polymer_repeating_units()	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	get_commonly_used_r_group_replacements()	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	get_common_electrophilic_warheads_for_kinases()	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	get_privileged_scaffolds_for_kinase_inhibitors()	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	get_braf_kinase_inhibitors_for_cancer()	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	get_common_amino_acid_protecting_groups()	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	get_polyfluoroalkyl_substances()	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	get_chemical_adsorption_on_montmorillonite_clays()	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.
Cannabinoids	IUPAC/SMILES/SMARTS	get_cannabinoid_smiles(), get_cannabinoid_smarts()	63	Turner, Carlton E., et al. “Constituents of Cannabis Sativa L. XVII. A Review of the Natural Constituents.” Journal of Natural Products, vol. 43, no. 2, Mar. 1980, pp. 169–234. ACS Publications, https://doi.org/10.1021/np50008a001.
Schedule 1 United States Narcotics	Preferred Name/SMILES/SMARTS	get_schedule_one()	240	ECFR :: 21 CFR Part 1308 - Schedules.
Schedule 2 United States Narcotics	Preferred Name/SMILES/SMARTS	get_schedule_two()	60	ECFR :: 21 CFR Part 1308 - Schedules.
Schedule 3 United States Narcotics	Preferred Name/SMILES/SMARTS	get_schedule_three()	22	ECFR :: 21 CFR Part 1308 - Schedules.
Schedule 4 United States Narcotics	Preferred Name/SMILES/SMARTS	get_schedule_four()	77	ECFR :: 21 CFR Part 1308 - Schedules.
Schedule 5 United States Narcotics	Preferred Name/SMILES/SMARTS	get_schedule_five()	8	ECFR :: 21 CFR Part 1308 - Schedules.
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

It's on it's way