global-chem 1.6.0.8

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Global-Chem: A Chemical Knowledge Graph of common small molecules and their IUPAC/SMILES/SMARTS for selection of compounds relevant to diverse chemical communities

Global Chem is an open-source graph database and api 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).

Overview

GlobalChem

Usage	Build	Release	SMILES Validation	Licensing	Stats

GlobalChemExtensions

Release	Licensing	Stats

Different extensions demos can be found below, or download them all. Note the PDF extension is the most dependency heavy.

Extension	Demo
extensions
bioinformatics
cheminformatics
quantum_chemistry
develoment_operations

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.

pip install global-chem

If you want to install the extensions package for extra functionality:

pip install global-chem[extensions]

If you want the full suite of features:

pip install global-chem[all]

QuickStart

GlobalChem

from global_chem import GlobalChem

gc = GlobalChem()

gc.build_global_chem_network(print_output=False, debugger=False)
smiles_list = list(gc.get_node_smiles('pihkal').values())

print (smiles_list)

GlobalChemExtensions

from global_chem_extensions import GlobalChemExtensions

gce = GlobalChemExtensions()

global_chem_molecule = gce.initialize_globalchem_molecule(
    smiles_list[0],
    # stream_file='cgenff.str',
    # frcmod_file='gaff2.frcmod',
)

global_chem_molecule.determine_name()

name = global_chem_molecule.name
attributes = global_chem_molecule.get_attributes()

gce.node_pca_analysis(smiles_list, save_file=False)

GlobalChem

Rules

The Graph Network (GN)s comes with a couple of rules that for now make the software engineering easier on the developer.

• There must be a root node.
• When Adding a Node every node must be connected.
• To remove a node it must not have any children.

The Deep Graph Network (DGN)s comes also with a couple of rules to make the implementation easier:

• There must be a root node of 1 which marks as your "input" node.
• When adding a layer all nodes will be added to all the previous layers as children. (Folk can use the remove node feature to perform dropouts)

Knowledge Graph

Just with no dependencies, intialize the class and there you go! All the common and rare groups of the world at your disposal

gc = GlobalChem()
gc.print_globalchem_network()

                                ┌solvents─common_organic_solvents
             ┌organic_synthesis─└protecting_groups─amino_acid_protecting_groups
             │          ┌polymers─common_monomer_repeating_units
             ├materials─└clay─montmorillonite_adsorption
             │                            ┌privileged_kinase_inhibtors
             │                            ├privileged_scaffolds
             ├proteins─kinases─┌scaffolds─├iupac_blue_book_substituents
             │                 │          └common_r_group_replacements
             │                 └braf─inhibitors
             │              ┌vitamins
             │              ├open_smiles
             ├miscellaneous─├amino_acids
             │              └regex_patterns
global_chem──├environment─emerging_perfluoroalkyls
             │          ┌schedule_one
             │          ├schedule_four
             │          ├schedule_five
             ├narcotics─├pihkal
             │          ├schedule_two
             │          └schedule_three
             ├interstellar_space
             │                    ┌cannabinoids
             │                    │         ┌electrophillic_warheads_for_kinases
             │                    ├warheads─└common_warheads_covalent_inhibitors
             └medicinal_chemistry─│      ┌phase_2_hetereocyclic_rings
                                  └rings─├iupac_blue_book_rings
                                         └rings_in_drugs
                                         

Sul's Selected List

This will be my own personal list of unique and interesting compounds chosen for forcefield parametirization and my chosen highlighted reasons for doing so for and understanding how to use the network for casual inference.

Nodes Contributors

Please follow the node contribution guidelines if you would like to elect your own or someone elses.

    __NODES__ = {
        'global_chem': Node,
        '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 Zhao & 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
        '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
    }

Nodes List

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.
Cannabinoids	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	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.
Common Regex Patterns	1

Adding Your Own Chemical List

If you would like to add your paper or a list you constructed to the chemical knowledge graph then please "File an Issue" with your chemical list and perhaps a suggestion of where to add it or you can leave for up to us to decide. The format of the chemical list can be something like this, and we the community will elect it into the graph and add a couple of representative compounds to the forcefield:

smiles = {
   '3,5-dimethoxyphenylisoproxycarbonyl': 'COC1=CC(C(C)(OC=O)C)=CC(OC)=C1',
   '2-(4-biphenyl)isopropoxycarbonyl': 'CC(C)(OC=O)C(C=C1)=CC=C1C2=CC=CC=C2',
   '2-nitrophenylsulfenyl': 'SC1=CC=CC=C1[N+]([O-])=O',
   'boc': 'O=COC(C)(C)C',
}  

GlobalChemExtensions

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:

Extension List

Extension	Description	Feature Import
GlobalChem Chemical Entities	GlobalChem has internal Molecule objects with all common attributes associated and conversion to SMILES	extensions
GlobalChem Biological Entities	GlobalChem has internal DNA/RNA/Protein/Molecule objects with all common attributes associated and conversion to SMILES	bioinformatics
ForceField Molecules	GlobalChem can parse, manipulate, and write CGenFF and GaFF2 files as objects	extensions
PDF Generation and Parsing	GlobalChem can generate SMILES to PDF and convert the PDF to SMILES	pdf
SMILES Validation	GlobalChem has connection to PySMILES, DeepSMILES, PartialSmiles, SELFIES, MolVS for validation of SMILES sets	validation
SMILES Protonation States	GlobalChem can take a set of compounds and predict the protonation states of a SMILES string over a range of pH	extensions
Open Source Database Monitoring	GlobalChem uses Uptime-Cheminformatics to Keep Track of Open Source Chemical Data	extensions
Networkx Software Adapter	GlobalChem Network can be converted into NetworkX Graph Objects	extensions
SMARTS Pattern Validation	GlobalChem uses the MiniFrag Database to test SMARTS strings accuracy for functional group selection	extensions
Principal Component Analysis	GlobalChem can readily interpret SMILES, fingerprint, cluster and apply PCA analysis user can tweak parameters	machine_learning
Drug Design Filters	GlobalChem can filter compounds based on Common Drug Design Filtering Rules	extensions
Deep Layer Scatter Analysis	To visualize relations between sets of molecules, GlobalChem offers a parallel coordinate diagram generation	machine_learning
Sunbursting Radial Analysis	GlobalChem offers a sunbursting mechanism to allow uses to observe how sets of compounds relate to the common set	machine_learning
Graphing Templates	GlobalChem offers graphing templates to aid in faster data analysis, currently the only offer is Plotly	machine_learning
CGenFF Dissimilarity Score	GlobalChem can offer the difference between two molecules based on their Atom Types	extensions
OneHot Encoding	GlobalChem has it's own one hot encoder and decoder based on the common lists for Machine Learning	extensions
SMARTS Pattern Identifier	GlobalChem connects to the SMARTS Plus and can offer visualization into different SMARTS components	extensions

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)

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

Licensing