<h1 align="center">Organizing The Chemical Universe</h1>
Global Chem is a public dictionary of common chemical lists using the Common Chemical Name as input and SMILES/SMARTS as output organized by their respective community in a knowledge graph.
Global-Chem serves as an open source platform where writing the molecules directly allows for the name to not be ambiguous to what a chemical is is anymore and allows for full transparency.
Our hope is this repository serves as a base for the population to govern how the chemicals we use in things like Food, Clothing, Environment, Materials, Drugs, War and a lot more are beneficial for all of us.
#### Links
- Demo https://colab.research.google.com/drive/1HaDvAYpaX0_2Eqx1NSl5uJTRkE_0na-L?usp=sharing
- Documentation: https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/
- Join Our Community: https://discord.gg/global-chem
<p align="center">
<img width="800" alt="Screen Shot 2022-07-16 at 5 29 41 PM" src="https://user-images.githubusercontent.com/11812946/179372564-c286b115-af14-4ad8-a37f-0a216297b6c1.png">
</p>
Just with no dependencies, intialize the class and there you go! All the common and rare groups of the world
at your disposal.
Overview
========
## GlobalChem
#### - Validation
|[](https://www.rdkit.org/)| [](https://github.com/baoilleach/partialsmiles) | [](https://github.com/baoilleach/deepsmiles) | [](https://github.com/aspuru-guzik-group/selfies) | [](https://github.com/mcs07/MolVS) | [](https://github.com/pckroon/pysmiles) |
|-|-|-|-|-|-|
#### - Statistics
| [](https://pepy.tech/project/global-chem) | | [](https://jessemillar.com/r/man-hours) | |
|-|-|-|-|
#### - Github Actions
|[](https://github.com/Sulstice/global-chem/actions/workflows/continous_integration.yml) | [](https://results.pre-commit.ci/latest/github/Sulstice/global-chem/master) | [](https://github.com/Sulstice/global-chem/actions/workflows/publish_package.yml) | [](https://github.com/Sulstice/global-chem/actions/workflows/translate_readme.yml) | [](https://github.com/Sulstice/global-chem/actions/workflows/speed-test-website.yml) |
|-|-|-|-|-|
#### - Public Notifications
| [](https://github.com/Sulstice/global-chem/actions/workflows/essential_medicines_bot.yml) | [](https://github.com/Sulstice/global-chem/actions/workflows/public_notifications.yml) |
|-|-|
#### - Build Information
| [](https://badge.fury.io/py/global-chem) | [](https://coveralls.io/github/Sulstice/global-chem?branch=master) | | [](https://zenodo.org/badge/latestdoi/259046250) | [](https://app.fossa.com/projects/git%2Bgithub.com%2FSulstice%2Fglobal-chem?ref=badge_shield) | [](https://www.python.org/dev/peps/pep-0008/) | [](https://github.com/tophat/getting-started/blob/master/scorecard.md) | [](https://www.repostatus.org) | [](https://opensource.org/licenses/MPL-2.0)|
|-|-|-|-|-|-|-|-|-|
#### Regulatory Compliance
| [](https://bestpractices.coreinfrastructure.org/projects/6399) | [](https://fair-software.eu) |
|-|-|
#### - GlobalChemExtensions
| [](https://badge.fury.io/py/global-chem-extensions) | [](https://opensource.org/licenses/MPL-2.0) | [](https://pepy.tech/project/global-chem-extensions) |
|-|-|-|
### Extension Demo Reel
| Application | Introduction | Advanced Usage | |
| ---------------------- | ---- | ---------------------- |-|
| forcefields | [](https://colab.research.google.com/drive/1hW0K6V5zPDFdZvFkYarbOr9wRoof2n4s?usp=sharing) | CGenFF Molecule Loader and Atom Type Similarity | [](https://colab.research.google.com/drive/1OEm1dACd_wkw_JQITemy18pgfKdE4XlX?usp=sharing) |
| bioinformatics | [](https://colab.research.google.com/drive/1sCNw9FIcFfTEgmrdokADXgJGnsPEOGbX?usp=sharing) | Use the Bostrom Algorithm to Filter Ligands By PDB | [](https://colab.research.google.com/drive/1a3Ys1rpqFzxBz95DQwJVHfunBxpywP7f?usp=sharing) |
| cheminformatics | [](https://colab.research.google.com/drive/1z0ilrakoRJ8maapMNHwtPf83pKK1THST?usp=sharing) | Principal Component Analysis of Common Universe & Visualizing Common Molecule Scaffold Graphs & WordClouds of Tainted Products | [](https://colab.research.google.com/drive/1E6roBxG4XeSHW_50jYy25A08aJKkBdPu?usp=sharing) |
| quantum_chemistry | [](https://colab.research.google.com/drive/1BGLQphP1IMLndeyavHM_6_qXQJI_7gFU?usp=sharing) | Plot Quantum Theory and Basis Set versuses the Hamiltonian of small molecules | [](https://colab.research.google.com/drive/11JGsen912TmyR5Dds-Opon5cRkrtVoT7?usp=sharing) |
| development_operations | [](https://colab.research.google.com/drive/1v_yXPXPilbWUZGkel_yekBr3EFnIUNUL?usp=sharing) |
Installation
============
GlobalChem is going to be distribute via PyPi and as the tree and it's extensions 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.
```bash
pip install global-chem
```
QuickStart
==========
Here we load the `global-chem[cheminformatics]` extensions package and the `GlobalChem` tree. We extract SMILES from the popular book, Pihkal, and perform cheminformatic principal component analysis on the chemical list.
```python
from global_chem import GlobalChem
gc = GlobalChem()
gc.build_global_chem_network()
smiles_list = list(gc.get_node_smiles('pihkal').values())
print (f"SMILES: {smiles_list[0]}")
```
GlobalChem
==========
### Nodes Contributors
Please follow the node contribution guidelines if you would like to elect your own or someone elses.
```
'global_chem': Node, # Suliman Sharif
'emerging_perfluoroalkyls': EmergingPerFluoroAlkyls, # Asuka Orr & Suliman Sharif
'montmorillonite_adsorption': MontmorilloniteAdsorption, # Asuka Orr & Suliman Sharif
'common_monomer_repeating_units': CommonMonomerRepeatingUnits, # Suliman Sharif
'electrophilic_warheads_for_kinases': ElectrophilicWarheadsForKinases, # Ruibin Liu & Suliman Sharif
'common_warheads_covalent_inhibitors': CommonWarheadsCovalentInhibitors, # Shaoqi Zhan & Suliman Sharif
'rings_in_drugs': RingsInDrugs, # Alexander Mackerell & Suliman Sharif
'iupac_blue_book_rings': IUPACBlueBookRings, # Suliman Sharif
'phase_2_hetereocyclic_rings': Phase2HetereoCyclicRings, # Suliman Sharif
'privileged_scaffolds': PrivilegedScaffolds, # Suliman Sharif
'iupac_blue_book': IUPACBlueBook, # Suliman Sharif
'common_r_group_replacements': CommonRGroupReplacements, # Sunhwan Jo & Suliman Sharif
'braf_inhibitors': BRAFInhibitors, # Aarion Romany & Suliman Sharif
'privileged_kinase_inhibitors': PrivilegedKinaseInhibitors, # Suliman Sharif
'common_organic_solvents': CommonOrganicSolvents, # Suliman Sharif
'amino_acid_protecting_groups': AminoAcidProtectingGroups, # Aziza Frank & Suliman Sharif
'schedule_one': ScheduleOne, # Suliman Sharif
'schedule_two': ScheduleTwo, # Suliman Sharif
'schedule_three': ScheduleThree, # Suliman Sharif
'schedule_four': ScheduleFour, # Suliman Sharif
'schedule_five': ScheduleFive, # Suliman Sharif
'interstellar_space': InterstellarSpace, # Suliman Sharif
'vitamins': Vitamins, # Suliman Sharif
'open_smiles': OpenSmiles, # Suliman Sharif
'amino_acids': AminoAcids, # Suliman Sharif
'pihkal': Pihkal, # Suliman Sharif
'nickel_ligands': NickelBidendatePhosphineLigands, # Suliman Sharif
'cimetidine_and_acyclovir': CimetidineAndAcyclovir, # Suliman Sharif
'common_regex_patterns': CommonRegexPatterns, # Chris Burke & Suliman Sharif
'how_to_live_longer': HowToLiveLonger, # Suliman Sharif
'monoclonal_antibodies': MonoclonalAntibodies, # Asuka Orr & Suliman Sharif
'lube': Lube, # Daniel Khavrutskii & Suliman Sharif
'tainted_sexual_enhancements': TaintedSexualEnhancements, # Suliman Sharif
'exsens_products': ExsensProducts, # Rebecca Pinette-Dorin & Suliman Sharif
'fda_list_one': FDAListOne, # Mike Wostner & Suliman Sharif
'fda_list_two': FDAListTwo, # Mike Wostner & Suliman Sharif
'fda_list_three': FDAListThree, # Mike Wostner & Suliman Sharif
'fda_list_four': FDAListFour, # Mike Wostner & Suliman Sharif
'fda_list_five': FDAListFive, # Mike Wostner & Suliman Sharif
'fda_list_six': FDAListSix, # Mike Wostner & Suliman Sharif
'fda_list_seven': FDAListSeven, # Mike Wostner & Suliman Sharif
'constituents_of_cannabis_sativa': ConstituentsOfCannabisSativa, # Ian Jones & Bettina Lier & Suliman Sharif
'phytocannabinoids': PhytoCannabinoids, # Ian Jones & Bettina Lier & Suliman Sharif
'organophosphorous_nerve_agents': OrganoPhosphorousNerveAgents, # Suliman Sharif
'organic_and_inorganic_bronsted_acids': OrganicAndInorganicBronstedAcids, # Nathaniel McClean & Suliman Sharif
'chemicals_from_biomass': ChemicalsFromBioMass, # Anthony Maiorana & Suliman Sharif
'salt': Salt, # Suliman Sharif
'drugs_from_snake_venom': DrugsFromSnakeVenom, # Suliman Sharif
'oral_contraceptives': OralContraceptives, # Suliman Sharif
'surfactants': Surfactants, # Yiling Nan & Suliman Sharif
'lanthipeptides: LanthiPeptides # Prabin Baral & Suliman Sharif
'alternative_jet_fuels': AlternativeJetFuels # Suliman Sharif
'mango_amino_acids': MangoPhytocompounds, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif
'mango_amino_acids': MangoAminoAcids, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif
'mango_phenolic_acids': MangoPhenolicAcids, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif
'mango_fatty_acids': MangoFattyAcids, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif
'mango_vitamins': MangoVitamins, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif
'mango_flavonoids': MangoFlavonoids # Damilola Bodun & Sevien Schulhofff & Suliman Sharif
'thai_ginger_cyclic_dipeptides': ThaiGingerCyclicDipeptides, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif
'thai_ginger_diaryl_heptanoids': ThaiGingerDiarylHeptanoids, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif
'thai_ginger_fatty_acids_and_esters': ThaiGingerFattyAcidsAndEsters, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif
'thai_ginger_flavonoids': ThaiGingerFlavonoids, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif
'thai_ginger_phenolics': ThaiGingerPhenolics, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif
'thai_ginger_polysaccharides': ThaiGingerPolysaccharides, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif
'thai_ginger_terpenoids': ThaiGingerTerpenoids # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif
```
| Chemical List | # of Entries | References |
|-------------------------------------|--------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Amino Acids | 20 | Common Knowledge |
| Essential Vitamins | 13 | Common Knowledge |
| 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 | 94 | OpenSMILES Home Page. http://opensmiles.org/. |
| IUPAC Blue Book (CRC Handbook) 2003 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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. |
| Schedule 1 United States Narcotics | 240 | ECFR :: 21 CFR Part 1308 - Schedules. |
| Schedule 2 United States Narcotics | 60 | ECFR :: 21 CFR Part 1308 - Schedules. |
| Schedule 3 United States Narcotics | 22 | ECFR :: 21 CFR Part 1308 - Schedules. |
| Schedule 4 United States Narcotics | 77 | ECFR :: 21 CFR Part 1308 - Schedules. |
| Schedule 5 United States Narcotics | 8 | ECFR :: 21 CFR Part 1308 - Schedules. |
| Pihkal | 179 | Shulgin, Alexander T., and Ann Shulgin. Pihkal: A Chemical Love Story. 1. ed., 8. print, Transform, 2010. |
| Excipients Cimetidine & Acyclovir | 14 | Vaithianathan, Soundarya, et al. “Effect of Common Excipients on the Oral Drug Absorption of Biopharmaceutics Classification System Class 3 Drugs Cimetidine and Acyclovir.” Journal of Pharmaceutical Sciences, vol. 105, no. 2, Feb. 2016, pp. 996–1005. PubMed, https://doi.org/10.1002/jps.24643. |
| Nickel Bidendate Phosphine Ligands | N/A | Clevenger, Andrew L., et al. “Trends in the Usage of Bidentate Phosphines as Ligands in Nickel Catalysis.” Chemical Reviews, vol. 120, no. 13, July 2020, pp. 6124–96. DOI.org (Crossref), https://doi.org/10.1021/acs.chemrev.9b00682. |
| HowToLiveLonger | 4 | https://github.com/geekan/HowToLiveLonger |
| Monoclonal Antibodies | 19 | https://labels.fda.gov/ |
| Common Lubricants for Sex | 38 | https://exsens-usa.com/blogs/your-body-your-pleasure/lube-lessons-glossary-of-common-sex-lube-ingredients |
| Tainted Sexual Enhancements | 4 | FDA Tainted Sexual Enhancements |
| Salt | 14 | OpenFoodFacts https://github.com/openfoodfacts |
| Exsens Sexual Wellness | 59 | https://exsens-usa.com/ |
| FDA Color Additive List 1 | 12 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |
| FDA Color Additive List 2 | 15 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |
| FDA Color Additive List 3 | 16 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |
| FDA Color Additive List 4 | 39 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |
| FDA Color Additive List 5 | 27 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |
| FDA Color Additive List 6 | 29 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |
| FDA Color Additive List 7 | 37 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |
| Constituents of Cannabis Sativa | 394 | Turner, C. E., et al. “Constituents of Cannabis Sativa L. XVII. A Review of the Natural Constituents.” Journal of Natural Products, vol. 43, no. 2, Apr. 1980, pp. 169–234. PubMed |
| Phytocannabinoids | 111 | Hanuš, Lumír Ondřej, et al. “Phytocannabinoids: A Unified Critical Inventory.” Natural Product Reports, vol. 33, no. 12, Nov. 2016, pp. 1357–92. PubMed, |
| OrganoPhosphorous Nerve Agents | 14 | Mukherjee, Sudisha, and Rinkoo Devi Gupta. “Organophosphorus Nerve Agents: Types, Toxicity, and Treatments.” Journal of Toxicology, vol. 2020, Sept. 2020, p. 3007984. |
| Cengage Bronsted Acids | 42 | https://cxp.cengage.com/contentservice/assets/owms01h/references/chemtables/org_chem/pKaTable.html |
| Chemicals From Biomass | 17 | Wittcoff, Harold A., et al. Industrial Organic Chemicals: Wittcoff/Organic Chemicals. John Wiley & Sons, Inc., 2004 |
| Drugs From Snake Venom | 7 | Oliveira, Ana L., et al. “The Chemistry of Snake Venom and Its Medicinal Potential.” Nature Reviews Chemistry, vol. 6, no. 7, July 2022, pp. 451–69 |
| Oral Contraceptives | 17 | Coleman, William F. “The Molecules of Oral Contraceptives.” Journal of Chemical Education, vol. 87, no. 7, July 2010, pp. 760–61. |
| Surfactants for Skin | 36 | Date, Abhijit A., and Vandana B. Patravale. “Microemulsions: Applications in Transdermal and Dermal Delivery.” Critical Reviews™ in Therapeutic Drug Carrier Systems, vol. 24, no. 6, 2007. |
| LanthiPeptides | 2 | Pokhrel, Rudramani, et al. “Molecular Mechanisms of Pore Formation and Membrane Disruption by the Antimicrobial Lantibiotic Peptide Mutacin 1140.” Physical Chemistry Chemical Physics, vol. 21, no. 23, June 2019, pp. 12530–39. |
| Alternative Jet Fuels | 59 | Chemical Composition and Fuel Properties of Alternative Jet Fuels :: BioResources. https://bioresources.cnr.ncsu.edu/. |
| Mango Phytocompounds | 87 | Maldonado-Celis, Maria Elena, et al. “Chemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.” Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |
| Mango Amino Acids | 19 | Maldonado-Celis, Maria Elena, et al. “Chemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.” Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |
| Mango Phenoloic Acids | 10 | Maldonado-Celis, Maria Elena, et al. “Chemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.” Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |
| Mango Fatty Acids | 24 | Maldonado-Celis, Maria Elena, et al. “Chemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.” Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |
| Mango Vitamins | 10 | Maldonado-Celis, Maria Elena, et al. “Chemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.” Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |
| Mango Flavonoids | 11 | Maldonado-Celis, Maria Elena, et al. “Chemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.” Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |
| Thai Ginger Cyclic Dipeptides | 6 | Wang, Si-Yu, et al. “Kaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.” Frontiers in Pharmacology, vol. 12, 2021. |
| Thai Ginger Diaryl Heptanoids | 6 | Wang, Si-Yu, et al. “Kaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.” Frontiers in Pharmacology, vol. 12, 2021. |
| Thai Ginger Fatty Acids/Esters | 16 | Wang, Si-Yu, et al. “Kaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.” Frontiers in Pharmacology, vol. 12, 2021. |
| Thai Ginger Flavonoids | 6 | Wang, Si-Yu, et al. “Kaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.” Frontiers in Pharmacology, vol. 12, 2021. |
| Thai Ginger Phenolics | 14 | Wang, Si-Yu, et al. “Kaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.” Frontiers in Pharmacology, vol. 12, 2021. |
| Thai Ginger Polysaccharides | 9 | Wang, Si-Yu, et al. “Kaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.” Frontiers in Pharmacology, vol. 12, 2021. |
| Thai Ginger Terpenoids | 26 | Wang, Si-Yu, et al. “Kaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.” Frontiers in Pharmacology, vol. 12, 2021. |
GlobalChemExtensions
====================
Installation
============
GlobalChemExtensions is going to be distribute via PyPi as saperate modules and as the tree and it's extensions 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.
```python
pip install 'global-chem[graphing]'
pip install 'global-chem[forcefields]'
pip install 'global-chem[bioinformatics]'
pip install 'global-chem[cheminformatics]'
pip install 'global-chem[quantum_chemistry]'
pip install 'global-chem[development_operations]'
pip install 'global-chem[all]'
```
Quickstart
==========
To conduct PCA Analysis on a list of SMILES in the network:
```python
from global_chem import GlobalChem
from global_chem_extensions import GlobalChemExtensions
gc = GlobalChem()
gc_cheminfo = GlobalChemExtensions().cheminformatics()
gc.build_global_chem_network()
smiles_list = list(gc.get_node_smiles('pihkal').values())
print (f"SMILES: {smiles_list[0]}")
gc_cheminfo.node_pca_analysis(smiles_list)
```
A Variety of Tools are available for you to browse and analyze data and with the full list of different applications can be found in the google colab demo or the Gitbook documentation. A demonstration of the data visualization extensions designed with plotly and bokeh are displayed below:
<p align="center">
<img width="800" height="600" src="https://raw.githubusercontent.com/Sulstice/global-chem/master/images/figures/figure_10.png">
</p>
<details><summary><h3>Extension List</h1><br/></summary>
| Extension | Description | Appplication |
|---------------------------------|-------------------------------------------------------------------------------------------------------------------------|------------------|
| GlobalChem Chemical Entities | GlobalChem has internal Molecule objects with all common attributes associated and conversion to SMILES | forcefields |
| GlobalChem Biological Entities | GlobalChem has internal DNA/RNA/Protein/Molecule objects with all common attributes associated and conversion to SMILES | bioinformatics |
| Visualize DNA/RNA Strands | Visualize DNA and RNA Strands and add labels to them | bioinformatics |
| ForceField Molecules | GlobalChem can parse, manipulate, and write CGenFF and GaFF2 files as objects | forcefields |
| PDF Generation and Parsing | GlobalChem can generate SMILES to PDF and convert the PDF to SMILES | cheminformatics |
| SMILES Validation | GlobalChem has connection to PySMILES, DeepSMILES, PartialSmiles, SELFIES, MolVS for validation of SMILES sets | cheminformatics |
| SMILES Protonation States | GlobalChem can take a set of compounds and predict the protonation states of a SMILES string over a range of pH | chemfinformatics |
| Open Source Database Monitoring | GlobalChem uses Uptime-Cheminformatics to Keep Track of Open Source Chemical Data | development_operations |
| Networkx Software Adapter | GlobalChem Network can be converted into NetworkX Graph Objects | cheminformatics |
| SMARTS Pattern Validation | GlobalChem uses the MiniFrag Database to test SMARTS strings accuracy for functional group selection | cheminformatics |
| Principal Component Analysis | GlobalChem can readily interpret SMILES, fingerprint, cluster and apply PCA analysis user can tweak parameters | cheminformatics |
| Drug Design Filters | GlobalChem can filter compounds based on Common Drug Design Filtering Rules | cheminformatics |
| Deep Layer Scatter Analysis | To visualize relations between sets of molecules, GlobalChem offers a parallel coordinate diagram generation | cheminformatics |
| Sunbursting Radial Analysis | GlobalChem offers a sunbursting mechanism to allow uses to observe how sets of compounds relate to the common set | cheminformatics |
| Graphing Templates | GlobalChem offers graphing templates to aid in faster data analysis, currently the only offer is Plotly | cheminformatics |
| CGenFF Dissimilarity Score | GlobalChem can offer the difference between two molecules based on their Atom Types | forcefields |
| OneHot Encoding | GlobalChem has it's own one hot encoder and decoder based on the common lists for Machine Learning | cheminformatics |
| SMARTS Pattern Identifier | GlobalChem connects to the SMARTS Plus and can offer visualization into different SMARTS components | cheminformatics |
| Psi4 Parser | Offer parsing of Psi4 Output Files and extracting values | quantum_chemistry |
| Coordinate Store | A warehouse for coodinates of small molecules for distribution in xyz and zm-matrix | quantum_chemistry |
| Visualize Molecular Orbitals | Visualize the Cube Files from Psi4 Output cubeprop | quantum_chemistry |
</details>
Open Source Software Compliance
===============================
`GlobalChem` follows the same principles outlined in part 11 of Title 21 of the Code of Federal Regulations; Electronic Records,
Electronic Signatures (21 CFR Part 11) guidance documentation. Since there are no formal guidelines for how open source software should be handled, we
attempt at completing requirements. The FDA considers part 11 to be applicable to the following criteria of electronic records and how
`GlobalChem` accomplishes each component:
- **Plausabilitiy:** `GlobalChem` was built on data that was abstracted from books and papers using reading and redrawing. It adds a component of
IUPAC/SMILES/SMARTS strings to store it electronically which give it's data it's unique component. The records are open sourced
and appropiately version controlled by maintainers of the repository and open source community feedback.
`GlobalChem`'s purposes are still unknown as it enters open source deployment. We have built extended functions that live in
a seperate package `GlobalChemExtensions` that do depend on `GlobalChem`. Since each version is packaged appropiately, if
reliance on a version is a need then it's software is available on `Github` and `PyPi`. A Standard Operating Procedure (SOP)
can be filed submitted from the extensions utility documentation maintained on `Gitbook`.
- **Validation:** `GlobalChem` follows Good Automated Manufacturing Practice (GAMP) Category 3 which is "software that is used as installed"
and potentially "configurable". `GlobalChem` testing comes from within, the documentation serves as the ultimate test
for functionality because that is what the users will test the most since we rely on open source. A continous integration (CI)
system is also built concomitantly to serve as basic functionality testing of the `GlobalChem` graph network. The Data stored
is maintained by experts in the field but subject to change based on community feedback if an error is found.
- **Audit Trail:** `GlobalChem` is version controlled with `Git` and hosted on Microsoft's platform `Github`. `GlobalChem` follows a semantic
versioning control of the schema `X1.X2.X3`: `X1` marks formal stable releases with tests and docuementation and mean
big refactoring to the software or in functionality, `X2` means a new feature is added with or without tests and documentation but
iterates as so. `X3` means a "hot" fix (something that is a an easy bug), small feature or additional parameter to add to a function
, or iteration to the data.
- **Legacy Systems:** `GlobalChem` has been operational for nearly 2 years since it's first release with version `0.3.0` in May 2020. `GlobalChem`
was built with a full trail in the open source community with each version catalogued and visibility to all. This satisfies
the rules outlines for determining a legacy system. We use community feedback provided from social media platforms (Twitter, Github, LinkedIn)
as documented evidence and justification that `GlobalChem` is fit for it's intended use of cheminformatics.
- **Copies of Records:** `GlobalChem` has records stored on `Github` for the software that can be exported to a variety of formats as provided by
Microsoft. For documentation, it is hosted on `Gitbook` and versioning controlled in accordance to the software. Each "book"
can be exported into Portable Data Format (PDF) appropiate for FDA submission.
- **Record Retention:** `GlobalChem` has a record of the documentation versioned controlled to a unique id (UUID) that serves as it's identifier
for each iteration stored on `Gitbook`. Each version is stored as markdown files and be converted to PDF, if needed.
`GlobalChem` has a Mozilla Public License version 2.0. `GlobalChem` allows you to use the software in your larger work and
extend it with modifications if you wish. The contingency is that if you install `GlobalChem` and release new software
then you must follow the same principles installed in our license for the open source community.
Data Collection
===============
References and associatied compound lists are selected based on the interests of the scientific contributors. This should include consideration of relevance to the scientific community.
The SMILES strings may be abstracted in a variety of methods:
- For simple molecules one representation of the SMILES can be directly translated using visual
inspection. This is typically appropriate for compounds at the beginning of a reported list that contain the most common denominator rings.
- For complex molecules the image can be redrawn in the free version of ChemDraw and then translated into SMILES.
- For sources where the SMILES are written and the IUPAC is not known the SMILES are translated into ChemDraw and the name retrieved.
Note that some of the names may be modified based on human inspection in favor of preferred names.
- For polymer papers, the site points were omitted from the name and some of the nomenclature adjusted for preferred names
over traditional. For example: 'yl' to mark site points for polymer connections was removed in favor of reduced english complexity.
- In the case of radicals, some SMILES were adjusted to remove the radical chemical feature as they serve as connection points. However in some cases the radical component was maintained, especially in the case of IUPAC blue book common substituents.
- SMARTS strings were adapted from the SMILES using RDKit (4).
* * * * *
Licensing
=========
[](https://app.fossa.com/projects/git%2Bgithub.com%2FSulstice%2Fglobal-chem?ref=badge_large)
Raw data
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"home_page": "https://www.github.com/Sulstice/global-chem",
"name": "global-chem",
"maintainer": null,
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"maintainer_email": null,
"keywords": "smiles molecules chemistry organic iupac",
"author": "Suliman Sharif",
"author_email": "sharifsuliman1@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/f1/2c/2e8056ffd451a6b6b1e946447889aaffee24bbc99745062620a8b24ee215/global_chem-1.10.0.tar.gz",
"platform": null,
"description": "<h1 align=\"center\">Organizing The Chemical Universe</h1>\n\nGlobal Chem is a public dictionary of common chemical lists using the Common Chemical Name as input and SMILES/SMARTS as output organized by their respective community in a knowledge graph.\n\nGlobal-Chem serves as an open source platform where writing the molecules directly allows for the name to not be ambiguous to what a chemical is is anymore and allows for full transparency.\n\nOur hope is this repository serves as a base for the population to govern how the chemicals we use in things like Food, Clothing, Environment, Materials, Drugs, War and a lot more are beneficial for all of us.\n\n#### Links\n\n- Demo https://colab.research.google.com/drive/1HaDvAYpaX0_2Eqx1NSl5uJTRkE_0na-L?usp=sharing\n\n- Documentation: https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/\n\n- Join Our Community: https://discord.gg/global-chem\n\n\n<p align=\"center\">\n<img width=\"800\" alt=\"Screen Shot 2022-07-16 at 5 29 41 PM\" src=\"https://user-images.githubusercontent.com/11812946/179372564-c286b115-af14-4ad8-a37f-0a216297b6c1.png\">\n</p>\n\nJust with no dependencies, intialize the class and there you go! All the common and rare groups of the world\nat your disposal.\n\nOverview\n========\n\n## GlobalChem\n\n#### - Validation\n\n|[](https://www.rdkit.org/)| [](https://github.com/baoilleach/partialsmiles) | [](https://github.com/baoilleach/deepsmiles) | [](https://github.com/aspuru-guzik-group/selfies) | [](https://github.com/mcs07/MolVS) | [](https://github.com/pckroon/pysmiles) |\n|-|-|-|-|-|-|\n\n#### - Statistics\n\n| [](https://pepy.tech/project/global-chem) | | [](https://jessemillar.com/r/man-hours) | |\n|-|-|-|-|\n\n#### - Github Actions\n\n|[](https://github.com/Sulstice/global-chem/actions/workflows/continous_integration.yml) | [](https://results.pre-commit.ci/latest/github/Sulstice/global-chem/master) | [](https://github.com/Sulstice/global-chem/actions/workflows/publish_package.yml) | [](https://github.com/Sulstice/global-chem/actions/workflows/translate_readme.yml) | [](https://github.com/Sulstice/global-chem/actions/workflows/speed-test-website.yml) |\n|-|-|-|-|-|\n\n#### - Public Notifications\n\n| [](https://github.com/Sulstice/global-chem/actions/workflows/essential_medicines_bot.yml) | [](https://github.com/Sulstice/global-chem/actions/workflows/public_notifications.yml) |\n|-|-|\n\n#### - Build Information\n\n| [](https://badge.fury.io/py/global-chem) | [](https://coveralls.io/github/Sulstice/global-chem?branch=master) | | [](https://zenodo.org/badge/latestdoi/259046250) | [](https://app.fossa.com/projects/git%2Bgithub.com%2FSulstice%2Fglobal-chem?ref=badge_shield) | [](https://www.python.org/dev/peps/pep-0008/) | [](https://github.com/tophat/getting-started/blob/master/scorecard.md) | [](https://www.repostatus.org) | [](https://opensource.org/licenses/MPL-2.0)|\n|-|-|-|-|-|-|-|-|-|\n\n#### Regulatory Compliance\n\n| [](https://bestpractices.coreinfrastructure.org/projects/6399) | [](https://fair-software.eu) |\n|-|-|\n\n#### - GlobalChemExtensions\n\n| [](https://badge.fury.io/py/global-chem-extensions) | [](https://opensource.org/licenses/MPL-2.0) | [](https://pepy.tech/project/global-chem-extensions) |\n|-|-|-|\n\n### Extension Demo Reel\n\n| Application | Introduction | Advanced Usage | |\n| ---------------------- | ---- | ---------------------- |-|\n| forcefields | [](https://colab.research.google.com/drive/1hW0K6V5zPDFdZvFkYarbOr9wRoof2n4s?usp=sharing) | CGenFF Molecule Loader and Atom Type Similarity | [](https://colab.research.google.com/drive/1OEm1dACd_wkw_JQITemy18pgfKdE4XlX?usp=sharing) |\n| bioinformatics | [](https://colab.research.google.com/drive/1sCNw9FIcFfTEgmrdokADXgJGnsPEOGbX?usp=sharing) | Use the Bostrom Algorithm to Filter Ligands By PDB | [](https://colab.research.google.com/drive/1a3Ys1rpqFzxBz95DQwJVHfunBxpywP7f?usp=sharing) |\n| cheminformatics | [](https://colab.research.google.com/drive/1z0ilrakoRJ8maapMNHwtPf83pKK1THST?usp=sharing) | Principal Component Analysis of Common Universe & Visualizing Common Molecule Scaffold Graphs & WordClouds of Tainted Products | [](https://colab.research.google.com/drive/1E6roBxG4XeSHW_50jYy25A08aJKkBdPu?usp=sharing) |\n| quantum_chemistry | [](https://colab.research.google.com/drive/1BGLQphP1IMLndeyavHM_6_qXQJI_7gFU?usp=sharing) | Plot Quantum Theory and Basis Set versuses the Hamiltonian of small molecules | [](https://colab.research.google.com/drive/11JGsen912TmyR5Dds-Opon5cRkrtVoT7?usp=sharing) |\n| development_operations | [](https://colab.research.google.com/drive/1v_yXPXPilbWUZGkel_yekBr3EFnIUNUL?usp=sharing) |\n\nInstallation\n============\n\nGlobalChem is going to be distribute via PyPi and as the tree and it's extensions grows we can expand it to other pieces of software\nmaking it accessible to all regardless of what you use. Alternatively, you could have a glance at the source code and copy/paste\nit yourself.\n\n```bash\n\npip install global-chem\n\n```\n\n\nQuickStart\n==========\n\nHere we load the `global-chem[cheminformatics]` extensions package and the `GlobalChem` tree. We extract SMILES from the popular book, Pihkal, and perform cheminformatic principal component analysis on the chemical list.\n\n```python\n\nfrom global_chem import GlobalChem\n\ngc = GlobalChem()\n\ngc.build_global_chem_network()\nsmiles_list = list(gc.get_node_smiles('pihkal').values())\n\nprint (f\"SMILES: {smiles_list[0]}\")\n\n```\n\nGlobalChem\n==========\n\n### Nodes Contributors\n\n\nPlease follow the node contribution guidelines if you would like to elect your own or someone elses.\n\n```\n'global_chem': Node, # Suliman Sharif\n'emerging_perfluoroalkyls': EmergingPerFluoroAlkyls, # Asuka Orr & Suliman Sharif\n'montmorillonite_adsorption': MontmorilloniteAdsorption, # Asuka Orr & Suliman Sharif\n'common_monomer_repeating_units': CommonMonomerRepeatingUnits, # Suliman Sharif\n'electrophilic_warheads_for_kinases': ElectrophilicWarheadsForKinases, # Ruibin Liu & Suliman Sharif\n'common_warheads_covalent_inhibitors': CommonWarheadsCovalentInhibitors, # Shaoqi Zhan & Suliman Sharif\n'rings_in_drugs': RingsInDrugs, # Alexander Mackerell & Suliman Sharif\n'iupac_blue_book_rings': IUPACBlueBookRings, # Suliman Sharif\n'phase_2_hetereocyclic_rings': Phase2HetereoCyclicRings, # Suliman Sharif\n'privileged_scaffolds': PrivilegedScaffolds, # Suliman Sharif\n'iupac_blue_book': IUPACBlueBook, # Suliman Sharif\n'common_r_group_replacements': CommonRGroupReplacements, # Sunhwan Jo & Suliman Sharif\n'braf_inhibitors': BRAFInhibitors, # Aarion Romany & Suliman Sharif\n'privileged_kinase_inhibitors': PrivilegedKinaseInhibitors, # Suliman Sharif\n'common_organic_solvents': CommonOrganicSolvents, # Suliman Sharif\n'amino_acid_protecting_groups': AminoAcidProtectingGroups, # Aziza Frank & Suliman Sharif\n'schedule_one': ScheduleOne, # Suliman Sharif\n'schedule_two': ScheduleTwo, # Suliman Sharif\n'schedule_three': ScheduleThree, # Suliman Sharif\n'schedule_four': ScheduleFour, # Suliman Sharif\n'schedule_five': ScheduleFive, # Suliman Sharif\n'interstellar_space': InterstellarSpace, # Suliman Sharif\n'vitamins': Vitamins, # Suliman Sharif\n'open_smiles': OpenSmiles, # Suliman Sharif\n'amino_acids': AminoAcids, # Suliman Sharif\n'pihkal': Pihkal, # Suliman Sharif\n'nickel_ligands': NickelBidendatePhosphineLigands, # Suliman Sharif\n'cimetidine_and_acyclovir': CimetidineAndAcyclovir, # Suliman Sharif\n'common_regex_patterns': CommonRegexPatterns, # Chris Burke & Suliman Sharif\n'how_to_live_longer': HowToLiveLonger, # Suliman Sharif\n'monoclonal_antibodies': MonoclonalAntibodies, # Asuka Orr & Suliman Sharif\n'lube': Lube, # Daniel Khavrutskii & Suliman Sharif\n'tainted_sexual_enhancements': TaintedSexualEnhancements, # Suliman Sharif\n'exsens_products': ExsensProducts, # Rebecca Pinette-Dorin & Suliman Sharif\n'fda_list_one': FDAListOne, # Mike Wostner & Suliman Sharif\n'fda_list_two': FDAListTwo, # Mike Wostner & Suliman Sharif\n'fda_list_three': FDAListThree, # Mike Wostner & Suliman Sharif\n'fda_list_four': FDAListFour, # Mike Wostner & Suliman Sharif\n'fda_list_five': FDAListFive, # Mike Wostner & Suliman Sharif\n'fda_list_six': FDAListSix, # Mike Wostner & Suliman Sharif\n'fda_list_seven': FDAListSeven, # Mike Wostner & Suliman Sharif\n'constituents_of_cannabis_sativa': ConstituentsOfCannabisSativa, # Ian Jones & Bettina Lier & Suliman Sharif\n'phytocannabinoids': PhytoCannabinoids, # Ian Jones & Bettina Lier & Suliman Sharif\n'organophosphorous_nerve_agents': OrganoPhosphorousNerveAgents, # Suliman Sharif\n'organic_and_inorganic_bronsted_acids': OrganicAndInorganicBronstedAcids, # Nathaniel McClean & Suliman Sharif\n'chemicals_from_biomass': ChemicalsFromBioMass, # Anthony Maiorana & Suliman Sharif\n'salt': Salt, # Suliman Sharif\n'drugs_from_snake_venom': DrugsFromSnakeVenom, # Suliman Sharif\n'oral_contraceptives': OralContraceptives, # Suliman Sharif\n'surfactants': Surfactants, # Yiling Nan & Suliman Sharif\n'lanthipeptides: LanthiPeptides # Prabin Baral & Suliman Sharif\n'alternative_jet_fuels': AlternativeJetFuels # Suliman Sharif\n'mango_amino_acids': MangoPhytocompounds, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif\n'mango_amino_acids': MangoAminoAcids, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif\n'mango_phenolic_acids': MangoPhenolicAcids, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif\n'mango_fatty_acids': MangoFattyAcids, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif\n'mango_vitamins': MangoVitamins, # Damilola Bodun & Sevien Schulhofff & Suliman Sharif\n'mango_flavonoids': MangoFlavonoids # Damilola Bodun & Sevien Schulhofff & Suliman Sharif\n'thai_ginger_cyclic_dipeptides': ThaiGingerCyclicDipeptides, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif\n'thai_ginger_diaryl_heptanoids': ThaiGingerDiarylHeptanoids, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif\n'thai_ginger_fatty_acids_and_esters': ThaiGingerFattyAcidsAndEsters, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif\n'thai_ginger_flavonoids': ThaiGingerFlavonoids, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif\n'thai_ginger_phenolics': ThaiGingerPhenolics, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif\n'thai_ginger_polysaccharides': ThaiGingerPolysaccharides, # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif\n'thai_ginger_terpenoids': ThaiGingerTerpenoids # Katukoliya Gamage Anuththara Samadhi & Suliman Sharif\n```\n\n| Chemical List | # of Entries | References |\n|-------------------------------------|--------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| Amino Acids | 20 | Common Knowledge |\n| Essential Vitamins | 13 | Common Knowledge |\n| Common Organic Solvents | 42 | Fulmer, Gregory R., et al. \u201cNMR Chemical Shifts of Trace Impurities: Common Laboratory Solvents, Organics, and Gases in Deuterated Solvents Relevant to the Organometallic Chemist.\u201dOrganometallics, vol. 29, no. 9, May 2010, pp. 2176\u201379. |\n| Open Smiles | 94 | OpenSMILES Home Page. http://opensmiles.org/. |\n| IUPAC Blue Book (CRC Handbook) 2003 | 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. |\n| Rings in Drugs | 92 | Taylor, Richard D., et al. \u201cRings in Drugs.\u201d Journal of Medicinal Chemistry, vol. 57, no. 14, July 2014, pp. 5845\u201359. ACS Publications, https://doi.org/10.1021/jm4017625. |\n| Phase 2 Hetereocyclic Rings | 19 | Broughton, Howard B., and Ian A. Watson. \u201cSelection of Heterocycles for Drug Design.\u201d Journal of Molecular Graphics & Modelling, vol. 23, no. 1, Sept. 2004, pp. 51\u201358. PubMed, https://doi.org/10.1016/j.jmgm.2004.03.016. |\n| Privileged Scaffolds | 47 | Welsch, Matthew E., et al. \u201cPrivileged Scaffolds for Library Design and Drug Discovery.\u201d Current Opinion in Chemical Biology , vol. 14, no. 3, June 2010, pp. 347\u201361.PubMed, https://doi.org/10.1016/j.cbpa.2010.02.018. |\n| Common Warheads | 29 | Gehringer, Matthias, and Stefan A. Laufer. \u201cEmerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology.\u201dJournal of Medicinal Chemistry , vol. 62, no. 12, June 2019, pp. 5673\u2013724. ACS Publications, https://doi.org/10.1021/acs.jmedchem.8b01153. |\n| Common Polymer Repeating Units | 78 | Hiorns, R. C., et al. \u201cA brief guide to polymer nomenclature (IUPAC Technical Report).\u201dPure and Applied Chemistry , vol. 84, no. 10, Oct. 2012, pp. 2167\u201369., https://doi.org/10.1351/PAC-REP-12-03-05. |\n| Common R Group Replacements | 499 | Takeuchi, Kosuke, et al. \u201cR-Group Replacement Database for Medicinal Chemistry.\u201d Future Science OA , vol. 7, no. 8, Sept. 2021, p. FSO742. future-science.com (Atypon) , https://doi.org/10.2144/fsoa-2021-0062. |\n| Electrophillic Warheads for Kinases | 24 | Petri, L\u00e1szl\u00f3, et al. \u201cAn Electrophilic Warhead Library for Mapping the Reactivity and Accessibility of Tractable Cysteines in Protein Kinases.\u201d European Journal of Medicinal Chemistry, vol. 207, Dec. 2020, p. 112836. PubMed, https://doi.org/10.1016/j.ejmech.2020.112836. |\n| Privileged Scaffolds for Kinases | 29 | Hu, Huabin, et al. \u201cSystematic Comparison of Competitive and Allosteric Kinase Inhibitors Reveals Common Structural Characteristics.\u201d European Journal of Medicinal Chemistry, vol. 214, Mar. 2021, p. 113206. ScienceDirect, https://doi.org/10.1016/j.ejmech.2021.113206. |\n| BRaf Inhibitors | 54 | Agianian, Bogos, and Evripidis Gavathiotis. \u201cCurrent Insights of BRAF Inhibitors in Cancer.\u201d Journal of Medicinal Chemistry, vol. 61, no. 14, July 2018, pp. 5775\u201393. ACS Publications, https://doi.org/10.1021/acs.jmedchem.7b01306. |\n| Common Amino Acid Protecting Groups | 346 | Isidro-Llobet, Albert, et al. \u201cAmino Acid-Protecting Groups.\u201d Chemical Reviews, vol. 109, no. 6, June 2009, pp. 2455\u2013504. DOI.org (Crossref), https://doi.org/10.1021/cr800323s. |\n| Emerging Perfluoroalkyls | 27 | Pelch, Katherine E., et al. \u201cPFAS Health Effects Database: Protocol for a Systematic Evidence Map.\u201d Environment International, vol. 130, Sept. 2019, p. 104851. ScienceDirect, https://doi.org/10.1016/j.envint.2019.05.045. |\n| Chemicals For Clay Adsorption | 33 | Orr, Asuka A., et al. \u201cCombining Experimental Isotherms, Minimalistic Simulations, and a Model to Understand and Predict Chemical Adsorption onto Montmorillonite Clays.\u201d ACS Omega, vol. 6, no. 22, June 2021, pp. 14090\u2013103. PubMed, https://doi.org/10.1021/acsomega.1c00481. |\n| Schedule 1 United States Narcotics | 240 | ECFR\u202f:: 21 CFR Part 1308 - Schedules. |\n| Schedule 2 United States Narcotics | 60 | ECFR\u202f:: 21 CFR Part 1308 - Schedules. |\n| Schedule 3 United States Narcotics | 22 | ECFR\u202f:: 21 CFR Part 1308 - Schedules. |\n| Schedule 4 United States Narcotics | 77 | ECFR\u202f:: 21 CFR Part 1308 - Schedules. |\n| Schedule 5 United States Narcotics | 8 | ECFR\u202f:: 21 CFR Part 1308 - Schedules. |\n| Pihkal | 179 | Shulgin, Alexander T., and Ann Shulgin. Pihkal: A Chemical Love Story. 1. ed., 8. print, Transform, 2010. |\n| Excipients Cimetidine & Acyclovir | 14 | Vaithianathan, Soundarya, et al. \u201cEffect of Common Excipients on the Oral Drug Absorption of Biopharmaceutics Classification System Class 3 Drugs Cimetidine and Acyclovir.\u201d Journal of Pharmaceutical Sciences, vol. 105, no. 2, Feb. 2016, pp. 996\u20131005. PubMed, https://doi.org/10.1002/jps.24643. |\n| Nickel Bidendate Phosphine Ligands | N/A | Clevenger, Andrew L., et al. \u201cTrends in the Usage of Bidentate Phosphines as Ligands in Nickel Catalysis.\u201d Chemical Reviews, vol. 120, no. 13, July 2020, pp. 6124\u201396. DOI.org (Crossref), https://doi.org/10.1021/acs.chemrev.9b00682. |\n| HowToLiveLonger | 4 | https://github.com/geekan/HowToLiveLonger |\n| Monoclonal Antibodies | 19 | https://labels.fda.gov/ |\n| Common Lubricants for Sex | 38 | https://exsens-usa.com/blogs/your-body-your-pleasure/lube-lessons-glossary-of-common-sex-lube-ingredients |\n| Tainted Sexual Enhancements | 4 | FDA Tainted Sexual Enhancements |\n| Salt | 14 | OpenFoodFacts https://github.com/openfoodfacts |\n| Exsens Sexual Wellness | 59 | https://exsens-usa.com/ |\n| FDA Color Additive List 1 | 12 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |\n| FDA Color Additive List 2 | 15 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |\n| FDA Color Additive List 3 | 16 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |\n| FDA Color Additive List 4 | 39 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |\n| FDA Color Additive List 5 | 27 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |\n| FDA Color Additive List 6 | 29 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |\n| FDA Color Additive List 7 | 37 | https://www.fda.gov/industry/color-additive-inventories/color-additive-status-list |\n| Constituents of Cannabis Sativa | 394 | Turner, C. E., et al. \u201cConstituents of Cannabis Sativa L. XVII. A Review of the Natural Constituents.\u201d Journal of Natural Products, vol. 43, no. 2, Apr. 1980, pp. 169\u2013234. PubMed |\n| Phytocannabinoids | 111 | Hanu\u0161, Lum\u00edr Ond\u0159ej, et al. \u201cPhytocannabinoids: A Unified Critical Inventory.\u201d Natural Product Reports, vol. 33, no. 12, Nov. 2016, pp. 1357\u201392. PubMed, |\n| OrganoPhosphorous Nerve Agents | 14 | Mukherjee, Sudisha, and Rinkoo Devi Gupta. \u201cOrganophosphorus Nerve Agents: Types, Toxicity, and Treatments.\u201d Journal of Toxicology, vol. 2020, Sept. 2020, p. 3007984. |\n| Cengage Bronsted Acids | 42 | https://cxp.cengage.com/contentservice/assets/owms01h/references/chemtables/org_chem/pKaTable.html |\n| Chemicals From Biomass | 17 | Wittcoff, Harold A., et al. Industrial Organic Chemicals: Wittcoff/Organic Chemicals. John Wiley & Sons, Inc., 2004 |\n| Drugs From Snake Venom | 7 | Oliveira, Ana L., et al. \u201cThe Chemistry of Snake Venom and Its Medicinal Potential.\u201d Nature Reviews Chemistry, vol. 6, no. 7, July 2022, pp. 451\u201369 |\n| Oral Contraceptives | 17 | Coleman, William F. \u201cThe Molecules of Oral Contraceptives.\u201d Journal of Chemical Education, vol. 87, no. 7, July 2010, pp. 760\u201361. |\n| Surfactants for Skin | 36 | Date, Abhijit A., and Vandana B. Patravale. \u201cMicroemulsions: Applications in Transdermal and Dermal Delivery.\u201d Critical Reviews™ in Therapeutic Drug Carrier Systems, vol. 24, no. 6, 2007. |\n| LanthiPeptides | 2 | Pokhrel, Rudramani, et al. \u201cMolecular Mechanisms of Pore Formation and Membrane Disruption by the Antimicrobial Lantibiotic Peptide Mutacin 1140.\u201d Physical Chemistry Chemical Physics, vol. 21, no. 23, June 2019, pp. 12530\u201339. |\n| Alternative Jet Fuels | 59 | Chemical Composition and Fuel Properties of Alternative Jet Fuels\u202f:: BioResources. https://bioresources.cnr.ncsu.edu/. |\n| Mango Phytocompounds | 87 | Maldonado-Celis, Maria Elena, et al. \u201cChemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.\u201d Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |\n| Mango Amino Acids | 19 | Maldonado-Celis, Maria Elena, et al. \u201cChemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.\u201d Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |\n| Mango Phenoloic Acids | 10 | Maldonado-Celis, Maria Elena, et al. \u201cChemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.\u201d Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |\n| Mango Fatty Acids | 24 | Maldonado-Celis, Maria Elena, et al. \u201cChemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.\u201d Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |\n| Mango Vitamins | 10 | Maldonado-Celis, Maria Elena, et al. \u201cChemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.\u201d Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |\n| Mango Flavonoids | 11 | Maldonado-Celis, Maria Elena, et al. \u201cChemical Composition of Mango (Mangifera Indica L.) Fruit: Nutritional and Phytochemical Compounds.\u201d Frontiers in Plant Science, vol. 10, Oct. 2019, p. 1073. |\n| Thai Ginger Cyclic Dipeptides | 6 | Wang, Si-Yu, et al. \u201cKaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.\u201d Frontiers in Pharmacology, vol. 12, 2021. |\n| Thai Ginger Diaryl Heptanoids | 6 | Wang, Si-Yu, et al. \u201cKaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.\u201d Frontiers in Pharmacology, vol. 12, 2021. |\n| Thai Ginger Fatty Acids/Esters | 16 | Wang, Si-Yu, et al. \u201cKaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.\u201d Frontiers in Pharmacology, vol. 12, 2021. |\n| Thai Ginger Flavonoids | 6 | Wang, Si-Yu, et al. \u201cKaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.\u201d Frontiers in Pharmacology, vol. 12, 2021. |\n| Thai Ginger Phenolics | 14 | Wang, Si-Yu, et al. \u201cKaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.\u201d Frontiers in Pharmacology, vol. 12, 2021. |\n| Thai Ginger Polysaccharides | 9 | Wang, Si-Yu, et al. \u201cKaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.\u201d Frontiers in Pharmacology, vol. 12, 2021. |\n| Thai Ginger Terpenoids | 26 | Wang, Si-Yu, et al. \u201cKaempferia Galanga L.: Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses.\u201d Frontiers in Pharmacology, vol. 12, 2021. |\n\n\n\nGlobalChemExtensions\n====================\n\nInstallation\n============\n\nGlobalChemExtensions is going to be distribute via PyPi as saperate modules and as the tree and it's extensions grows we can expand it to other pieces of software\nmaking it accessible to all regardless of what you use. Alternatively, you could have a glance at the source code and copy/paste\nit yourself.\n\n\n```python\n\npip install 'global-chem[graphing]'\npip install 'global-chem[forcefields]'\npip install 'global-chem[bioinformatics]'\npip install 'global-chem[cheminformatics]'\npip install 'global-chem[quantum_chemistry]'\npip install 'global-chem[development_operations]'\npip install 'global-chem[all]'\n\n```\n\nQuickstart\n==========\n\nTo conduct PCA Analysis on a list of SMILES in the network:\n\n```python\n\nfrom global_chem import GlobalChem\nfrom global_chem_extensions import GlobalChemExtensions\n\ngc = GlobalChem()\ngc_cheminfo = GlobalChemExtensions().cheminformatics()\n\ngc.build_global_chem_network()\nsmiles_list = list(gc.get_node_smiles('pihkal').values())\n\nprint (f\"SMILES: {smiles_list[0]}\")\n\ngc_cheminfo.node_pca_analysis(smiles_list)\n\n```\n\nA Variety of Tools are available for you to browse and analyze data and with the full list of different applications can be found in the google colab demo or the Gitbook documentation. A demonstration of the data visualization extensions designed with plotly and bokeh are displayed below:\n\n<p align=\"center\">\n <img width=\"800\" height=\"600\" src=\"https://raw.githubusercontent.com/Sulstice/global-chem/master/images/figures/figure_10.png\">\n</p>\n\n<details><summary><h3>Extension List</h1><br/></summary>\n\n| Extension | Description | Appplication |\n|---------------------------------|-------------------------------------------------------------------------------------------------------------------------|------------------|\n| GlobalChem Chemical Entities | GlobalChem has internal Molecule objects with all common attributes associated and conversion to SMILES | forcefields |\n| GlobalChem Biological Entities | GlobalChem has internal DNA/RNA/Protein/Molecule objects with all common attributes associated and conversion to SMILES | bioinformatics |\n| Visualize DNA/RNA Strands | Visualize DNA and RNA Strands and add labels to them | bioinformatics |\n| ForceField Molecules | GlobalChem can parse, manipulate, and write CGenFF and GaFF2 files as objects | forcefields |\n| PDF Generation and Parsing | GlobalChem can generate SMILES to PDF and convert the PDF to SMILES | cheminformatics |\n| SMILES Validation | GlobalChem has connection to PySMILES, DeepSMILES, PartialSmiles, SELFIES, MolVS for validation of SMILES sets | cheminformatics |\n| SMILES Protonation States | GlobalChem can take a set of compounds and predict the protonation states of a SMILES string over a range of pH | chemfinformatics |\n| Open Source Database Monitoring | GlobalChem uses Uptime-Cheminformatics to Keep Track of Open Source Chemical Data | development_operations |\n| Networkx Software Adapter | GlobalChem Network can be converted into NetworkX Graph Objects | cheminformatics |\n| SMARTS Pattern Validation | GlobalChem uses the MiniFrag Database to test SMARTS strings accuracy for functional group selection | cheminformatics |\n| Principal Component Analysis | GlobalChem can readily interpret SMILES, fingerprint, cluster and apply PCA analysis user can tweak parameters | cheminformatics |\n| Drug Design Filters | GlobalChem can filter compounds based on Common Drug Design Filtering Rules | cheminformatics |\n| Deep Layer Scatter Analysis | To visualize relations between sets of molecules, GlobalChem offers a parallel coordinate diagram generation | cheminformatics |\n| Sunbursting Radial Analysis | GlobalChem offers a sunbursting mechanism to allow uses to observe how sets of compounds relate to the common set | cheminformatics |\n| Graphing Templates | GlobalChem offers graphing templates to aid in faster data analysis, currently the only offer is Plotly | cheminformatics |\n| CGenFF Dissimilarity Score | GlobalChem can offer the difference between two molecules based on their Atom Types | forcefields |\n| OneHot Encoding | GlobalChem has it's own one hot encoder and decoder based on the common lists for Machine Learning | cheminformatics |\n| SMARTS Pattern Identifier | GlobalChem connects to the SMARTS Plus and can offer visualization into different SMARTS components | cheminformatics |\n| Psi4 Parser | Offer parsing of Psi4 Output Files and extracting values | quantum_chemistry |\n| Coordinate Store | A warehouse for coodinates of small molecules for distribution in xyz and zm-matrix | quantum_chemistry |\n| Visualize Molecular Orbitals | Visualize the Cube Files from Psi4 Output cubeprop | quantum_chemistry |\n\n</details>\n\nOpen Source Software Compliance\n===============================\n\n`GlobalChem` follows the same principles outlined in part 11 of Title 21 of the Code of Federal Regulations; Electronic Records,\nElectronic Signatures (21 CFR Part 11) guidance documentation. Since there are no formal guidelines for how open source software should be handled, we\nattempt at completing requirements. The FDA considers part 11 to be applicable to the following criteria of electronic records and how\n`GlobalChem` accomplishes each component:\n\n- **Plausabilitiy:** `GlobalChem` was built on data that was abstracted from books and papers using reading and redrawing. It adds a component of\nIUPAC/SMILES/SMARTS strings to store it electronically which give it's data it's unique component. The records are open sourced\nand appropiately version controlled by maintainers of the repository and open source community feedback.\n`GlobalChem`'s purposes are still unknown as it enters open source deployment. We have built extended functions that live in\na seperate package `GlobalChemExtensions` that do depend on `GlobalChem`. Since each version is packaged appropiately, if\nreliance on a version is a need then it's software is available on `Github` and `PyPi`. A Standard Operating Procedure (SOP)\ncan be filed submitted from the extensions utility documentation maintained on `Gitbook`.\n\n- **Validation:** `GlobalChem` follows Good Automated Manufacturing Practice (GAMP) Category 3 which is \"software that is used as installed\"\nand potentially \"configurable\". `GlobalChem` testing comes from within, the documentation serves as the ultimate test\nfor functionality because that is what the users will test the most since we rely on open source. A continous integration (CI)\nsystem is also built concomitantly to serve as basic functionality testing of the `GlobalChem` graph network. The Data stored\nis maintained by experts in the field but subject to change based on community feedback if an error is found.\n\n- **Audit Trail:** `GlobalChem` is version controlled with `Git` and hosted on Microsoft's platform `Github`. `GlobalChem` follows a semantic\nversioning control of the schema `X1.X2.X3`: `X1` marks formal stable releases with tests and docuementation and mean\nbig refactoring to the software or in functionality, `X2` means a new feature is added with or without tests and documentation but\niterates as so. `X3` means a \"hot\" fix (something that is a an easy bug), small feature or additional parameter to add to a function\n, or iteration to the data.\n\n- **Legacy Systems:** `GlobalChem` has been operational for nearly 2 years since it's first release with version `0.3.0` in May 2020. `GlobalChem`\nwas built with a full trail in the open source community with each version catalogued and visibility to all. This satisfies\nthe rules outlines for determining a legacy system. We use community feedback provided from social media platforms (Twitter, Github, LinkedIn)\nas documented evidence and justification that `GlobalChem` is fit for it's intended use of cheminformatics.\n\n- **Copies of Records:** `GlobalChem` has records stored on `Github` for the software that can be exported to a variety of formats as provided by\nMicrosoft. For documentation, it is hosted on `Gitbook` and versioning controlled in accordance to the software. Each \"book\"\ncan be exported into Portable Data Format (PDF) appropiate for FDA submission.\n\n- **Record Retention:** `GlobalChem` has a record of the documentation versioned controlled to a unique id (UUID) that serves as it's identifier\nfor each iteration stored on `Gitbook`. Each version is stored as markdown files and be converted to PDF, if needed.\n\n`GlobalChem` has a Mozilla Public License version 2.0. `GlobalChem` allows you to use the software in your larger work and\nextend it with modifications if you wish. The contingency is that if you install `GlobalChem` and release new software\nthen you must follow the same principles installed in our license for the open source community.\n\nData Collection\n===============\n\nReferences and associatied compound lists are selected based on the interests of the scientific contributors. This should include consideration of relevance to the scientific community.\nThe SMILES strings may be abstracted in a variety of methods:\n\n- For simple molecules one representation of the SMILES can be directly translated using visual\ninspection. This is typically appropriate for compounds at the beginning of a reported list that contain the most common denominator rings.\n\n- For complex molecules the image can be redrawn in the free version of ChemDraw and then translated into SMILES.\n\n- For sources where the SMILES are written and the IUPAC is not known the SMILES are translated into ChemDraw and the name retrieved.\nNote that some of the names may be modified based on human inspection in favor of preferred names.\n\n- For polymer papers, the site points were omitted from the name and some of the nomenclature adjusted for preferred names\nover traditional. For example: 'yl' to mark site points for polymer connections was removed in favor of reduced english complexity.\n\n- In the case of radicals, some SMILES were adjusted to remove the radical chemical feature as they serve as connection points. However in some cases the radical component was maintained, especially in the case of IUPAC blue book common substituents.\n\n- SMARTS strings were adapted from the SMILES using RDKit (4).\n\n* * * * *\n\nLicensing\n=========\n\n[](https://app.fossa.com/projects/git%2Bgithub.com%2FSulstice%2Fglobal-chem?ref=badge_large)\n\n\n",
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