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GlobalChem: A content variable store for Chemistry!

License: MPL 2.0 Python Build Status Coverage 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 # 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.


Citation

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


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

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