Saravanan666/pypi-org huggingface dataset:
Package: chembox
chemboxIntroductionchemboxis a package for molecular information calculator based on empirical formulas of chemicals in raw text. It is designed to intelligently process text input containing the chemical formula and provide associated information on the inquired molecule. It is able to provide the molar mass, check a formula's validity, and provide a balanced combustion equation if the input is combustible. This tool can be utilized for various educational and research purposes for simple and fast information retrieval.We are using a dataset that contains established element data properties fromthis site.Installationchemboxis developed and tested on Python 3.10. You can install it from PyPi via pip:$pipinstallchemboxUsageThe package includes 4 functions for solving chemistry problems:get_elementsa parser that takes a chemical formula in string format and returns a dictionary that contains the elements and their respective count.is_valid: a checker that returns a boolean indicating whether a given input is chemically reasonable.get_molec_props: a method that takes a chemical formula in string format and returns a dataframe with various useful properties of each element in the formula.get_combustion_equation: a method that takes a text chemical formula that only contains carbon (C) and hydrogen (H) and outputs a balanced equation resulting from combustion.A detailed example of usage can be foundhere.DatasetIn order to be able to perform some of the functions above, a dataset will need to be used that contains various atomic properties of the elements in the periodic table. The data can be found in the Chembox repoherewhich was sourced fromhere. Please note that we do not take credit for the dataset, it is merely for use with our functions.Fitting into the Python ecosystemA similar packagechemsolveis available online that employs a similar string-parsing design and molar mass calculation.What we do differently:We include a dataframe of the molecule properties to give the user enhanced functionality and insights.chemsolveaccepts user-defined reactions. In our package, we include methods for automated combustion equation generation and balancing.ContributingInterested in contributing? Check out the contributing guidelines. Please note that this project is released with aCode of Conduct. By contributing to this project, you agree to abide by its terms.Licensechemboxis licensed under the terms of the MIT license.ContributorsThe contributors of this project are
Wilfred Hass, Vikram Grewal, Luke Yang, and Nate Puangpanbut.Creditschemboxwas created withcookiecutterand thepy-pkgs-cookiecuttertemplate.
Package: chem-calc
chem_calcThe module chem_calc calculates chemical and physical properties based on the stoichometry of a chemical compound.The 20+ available properties (or features) used in this package are elemental properties from the CRC Handbook of Chemistry and Physics as well as the NIST X-ray Mass Attenuation Coefficients Database.Available propertiesCRC Handbook of Chemistry and PhysicsProperty / FeatureTagNumber of 4f electrons'4f'Number of 5d electrons'5d'Combined number of 4f and 5d electrons'add4f5d'Absolute value of the difference of number of 4f and 5d electrons'sub4f5dabs'Number of electrons'allelectrons'Number of valence outer shell electrons'val_e'Atomic number'atomicnumber'Atomic weight'atomicweight'First ionization energy'ionenergy'Pauling electronegativity of most common oxidation state'el_neg_chi'van der Waals radius'R_vdw_element'Covalent radius'R_cov_element'Atomic number to mass number ratio'zaratio'Excitation energy'ex_energy'Period'period'Elemental density'density'NIST X-ray Mass Attenuation Coefficients Database for features at 662 keV and include the following:Property / FeatureTagCoherent scattering coefficient'co_scatt'Incoherent scattering coefficient'inco_scatt'Photoelectric absorption'pe_abs'Coherent attenutation coefficient'atten_co'Incoherent attenutation coefficient'atten_inco'Methodshow_many -- Returns the number of atoms in a given chemical formula.>>> import chem_calc
>>> chem_calc.chem_calc('H2O').howmany
3.0total --  Returns the feature total for a given chemical formula.>>> import chem_calc
>>> chem_calc.chem_calc('H2O',feature='atomicweight').total
18.014710000000001avg_feature -- Returns the average value of a property for a given chemical formula.>>> import chem_calc
>>> chem_calc.chem_calc('H2O',feature='atomicweight').avg_feature
6.0049033333333339InstallationUse 'pip' to install from pypi:pip install chem_calcor 'pip' to install from github:pip install git+https://github.com/garne041/chem_calc.gitor clone the package using git:git clone https://github.com/garne041/chem_calc.gitRequirementsRequires numpy, pickle, and pandasLicenseThe original code that this project is based onhttps://repl.it/@Supakri2680/Molecular-Mass-Calculator2. In keeping with this mentality, all code is released under the MIT.
Package: chemcalculator
chemcalculatorOverviewchemcalculator is a python package useful for chemistry for the purpose of calculating chemical formula mass in g/mol. The mole allows scientists to calculate the number of elementary entities (usually atoms or molecules) in a certain mass of a given substance. The mass of one mole of a substance is equal to that substance’s molecular weight; as for instance, the mean molecular weight of water is 18.015 atomic mass units (amu), and so one mole of water weighs 18.015 grams. This property simplifies many chemical computations. This python package will be helpful to easily calculate the chemical formula mass, convert moles to grams and vice versa, and lastly calculate the percentage mass for the atomic nature of the elements in chemistry.This package of basic chemistry calculations is meant to supplement an existing package,ChemPy, which already handles complex calculations for primarily physical/inorganic/analytical chemistry consisting of, but not limited to, the following:Solver for equilibria (including multiphase systems)Numerical integration routines for chemical kinetics (ODE solver front-end)Integrated rate expressions (and convenience fitting routines)Relations in Physical chemistryDebye-Hückel expressionsArrhenius equationEinstein-Smoluchowski equationProperties, such as : water density as function of temperature, water permittivity as function of temperature and pressure, and water diffusivity as function of temperatureFunctionsThis package contains three functions. Each function will have it's own required and optional arguments.compute_mass: Calculate the mass of the atoms or chemical formula for the input chemical formula.moles_grams_converter: Convert moles to grams and convert grams to moles.percent_mass: Calculate percentage mass for the desired atom or molecule.Installation$pipinstallchemcalculatorUsagechemcalculatorcan be used as follows:fromchemcalculator.chemcalculatorimportcompute_mass
compute_mass("H2O")fromchemcalculator.chemcalculatorimportmoles_grams_converter
moles_grams_converter("H2O",0.05555,"moles")fromchemcalculator.chemcalculatorimportpercent_mass
percent_mass("H2O","O")ContributorsDevelopment LeadContributor NameGitHub UsernameKingslin LvKingslin0810Joyce Wangjo4356Allyson StolldatallurgyWe welcome and recognize all contributions. Please find the guide for contribution inContributing Document.Licensechemcalculatorwas created by Joyce Wang, Kingslin Lv, Allyson Stoll. It is licensed under the terms of the MIT license.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: chemcat
chemcatChemistry Calculator for AtmospheresInstall as:pip install chemcator:conda install -c conda-forge chemcatDocs at:https://chemcat.readthedocs.io/en/latest/Cite as:@ARTICLE{CubillosBlecicEtal2024journalRadiativeChemicalEquilibrium,author={{Cubillos}, Patricio and {Blecic}, Jasmina and {Fossati}, Luca},title="{Radiative and Chemical Equilibrium Calculations with Application to Exoplanets}",journal={journal},year=2024,adsurl={https://ui.adsabs.harvard.edu/abs/2024journ.000....0C},adsnote={Provided by the SAO/NASA Astrophysics Data System}}
Package: chemcomp
chemcompModeling the chemical composition of gas giants by accretion of pebbles, planetesimals and gas.docs:WIKIinstall:clone project:git clone https://github.com/AaronDavidSchneider/chemcomp.gitmove into directory:cd chemcompInstall conda environment:conda create -n chemcomp numpy "astropy>=4.0" scipy matplotlib pyyaml jupyter parse h5py pip pytablesInstall a development versionchemcomp:pip install -e .or install from pypipip install chemcompAdjust paths inchemcomp/helper/main_helperif you need different directories for output and config.PublicationsOriginal PublicationsSchneider & Bitsch (2021a)How drifting and evaporating pebbles shape giant planets. I. Heavy element content and atmospheric C/OSchneider & Bitsch (2021b)How drifting and evaporating pebbles shape giant planets. II. Volatiles and refractories in atmospheresBitsch, Schneider & Kreidberg (2022)How drifting and evaporating pebbles shape giant planets. III. The formation of WASP-77A b and $\tau$ Boötis bPlease citeSchneider & Bitsch(2021a), if you usechemcompin your work.Publications usingchemcompBitsch et al. (2021)Dry or water world? How the water contents of inner sub-Neptunes constrain giant planet formation and the location of the water ice lineHühn & Bitsch (2023)How accretion of planet-forming disks influences stellar abundancesBitsch & Mah (2023)Enriching inner discs and giant planets with heavy elementsMah & Bitsch (2023a)Forming super-Mercuries: Role of stellar abundancesMah & Bitsch (2023b)Close-in ice lines and the super-stellar C/O ratio in discs around very low-mass starsSavvidou & Bitsch (2023)How to make giant planets via pebble accretionDanti, Bitsch & Mah (2023)Composition of giant planets: the roles of pebbles and planetesimalsAnd several more in preperation (last updated: 22.11.2023)Thanks:I would like to thank Bertram Bitsch for his enormous support during the development of this code and for continuing to use the code together with his students.I would like to thank Cornelis Dullemond for providing the solver which (in adapted version) is used to solve the gas viscous disk equation and dust transport equation.I would like to thank everyone, who has already used chemcomp in their work and has contributed in fixing small bugs.
Package: chemcoord
Latest ReleasePackage StatusDocumentationLicenseBuild StatusCoverageWebsiteThe project’s website with documentation is:http://chemcoord.readthedocs.org/FeaturesMolecules are reliably transformed between cartesian space and non
redundant internal coordinates (Zmatrices). Dummy atoms are inserted
and removed automatically on the fly if necessary.The created Zmatrix is not only a structure expressed in internal
coordinates, it is a “chemical” Zmatrix. “Chemical” Zmatrix means,
that e.g. distances are along bonds or dihedrals are defined as they
are drawn in chemical textbooks (Newman projections).Analytical gradients for the transformations between the different
coordinate systems are implemented.Performance intensive functions/methods are implemented with
Fortran/C like speed usingnumba.Geometries may be defined with symbolic expressions usingsympy.Built on top ofpandaswith very
similar syntax. This allows for example distinct label or row based
indexing.It derived from my own work and I heavily use it during the day. So
all functions are tested and tailored around the work flow in
theoretical chemistry.It as a python module ;)Installation guideA working python 3 installation is required (>=3.7 are possible).It is highly recommended to use this module in combination withIpythonandjupyter.
They come shipped by default with theanaconda3
installerUnixFor the packaged version, the following commands have to be executed in
the terminal:pip install chemcoordFor the up to date development version (experimental):git clone https://github.com/mcocdawc/chemcoord.git
cd chemcoord
pip install .WindowsNeither installation nor running the module are tested on windows. To
the best of my knowledge it should work there as well. Just use the same
steps as for UNIX.Citation and mathematical backgroundThe theory behind chemcoord is described inthis paper.
If this package is used in a project that leads to a scientific
publication, please acknowledge it by citing.@article{https://doi.org/10.1002/jcc.27029,
    author = {Weser, Oskar and Hein-Janke, Björn and Mata, Ricardo A.},
    title = {Automated handling of complex chemical structures in Z-matrix coordinates—The chemcoord library},
    journal = {Journal of Computational Chemistry},
    volume = {44},
    number = {5},
    pages = {710-726},
    keywords = {analytical gradients, geometry optimization, non-linear constraints, transition state search, Z-matrix},
    doi = {10.1002/jcc.27029},
    year = {2023}
}My (Oskar Weser) master thesis including a more detailed derivation of implemented equations and
the mathematical background can be foundhere.AcknowledgementZulip is an open-source modern team chat app designed to keep both live and asynchronous conversations organized,
that supports the development of chemcoord with a free plan.
Package: chemcrow
ChemCrow is an open source package for the accurate solution of reasoning-intensive chemical tasks.Built with Langchain, it uses a collection of chemical tools including RDKit, paper-qa, as well as some relevant databases in chemistry, like Pubchem and chem-space.🤗 Try it out inHuggingFace!⚠️ NoteThis package does not contain all the tools described in theChemCrow paperbecause
of API usage restrictions. This repo will not give the same results as that paper.All the experiments have been released underChemCrow runs.👩‍💻 Installationpip install chemcrow🔥 UsageFirst set up your API keys in your environment.export OPENAI_API_KEY=your-openai-api-keyYou can optionally use Serp API:export SERP_API_KEY=your-serpapi-api-keyIn a Python session:fromchemcrow.agentsimportChemCrowchem_model=ChemCrow(model="gpt-4-0613",temp=0.1,verbose=True)chem_model.run("What is the molecular weight of tylenol?")✅ CitationBran, Andres M., et al. "ChemCrow: Augmenting large-language models with chemistry tools." arXiv preprint arXiv:2304.05376 (2023).@article{bran2023chemcrow,title={ChemCrow: Augmenting large-language models with chemistry tools},author={Andres M Bran and Sam Cox and Oliver Schilter and Carlo Baldassari and Andrew D White and Philippe Schwaller},year={2023},eprint={2304.05376},archivePrefix={arXiv},primaryClass={physics.chem-ph},publisher={arXiv}}
Package: chemdataextractor2
ChemDataExtractorChemDataExtractor v2 is a toolkit for extracting chemical information from the scientific literature. Python 3.5 to Python 3.8 supported.Installationpip install chemdataextractor2FeaturesHTML, XML and PDF document readersChemistry-aware natural language processing pipelineChemical named entity recognitionRule-based parsing grammars for property and spectra extractionTable parser for extracting tabulated dataDocument processing to resolve data interdependenciesDocumentation & DevelopmentPlease read the documentation for instructions on contributing to the project.https://cambridgemolecularengineering-chemdataextractor-development.readthedocs-hosted.com/en/latest/LicenseChemDataExtractor v2 is licensed under theMIT license_, a permissive, business-friendly license for open source
software.MIT license:https://github.com/CambridgeMolecularEngineering/ChemDataExtractor/blob/master/LICENSE
Package: chemdb
Chemdb is a chemical inventory system written inPythonusing theDjangoframework.  It makes it easy for us to keep track of what we
have in the lab.  It also generates the required safety information
automatically (door warnings and inventories).InstallationPackagesGentooI’ve packaged chemdb forGentoo.  You needlaymanand mywtk
overlay.  Install with:# emerge -av app-portage/layman
# layman --add wtk
# emerge -av dev-python/chemdbDependenciesIf you’re installing by hand or packaging calibcant for another
distribution, you’ll need the following dependencies:PackageDebianGentooDjangopython-djangodev-python/djangoGrappellidev-python/django-grappelli[1][1]In thewtk overlay.Installing by handChemdb is available as aGitrepository:$ git clone git://tremily.us/chemdb.gitSee thehomepagefor details.  To install the checkout, run the
standard:$ python setup.py installUsageSetupIf you don’t have a Django project and you just want to run chemdb as
a stand-alone service, you can use the example project written up inexample.  Set up the project (once):$ python example/manage.py syncdbSee theDjango documentationfor more details.You may also want to load some example data, to make your initial
browsing more interesting:$ python example/manage.py loaddata example_dataRunningRun the app on your local host (as many times as you like):$ python example/manage.py runserverYou may need to add the current directory toPYTHONPATHsopythoncan find thechemdbpackage.  If you’re runningbash, that will look like:$ PYTHONPATH=".:$PYTHONPATH" python example/manage.py runserverHackingThis project was largely build following theDjango tutorial.
That’s a good place to start if you’re new to Django.Other resourcesYou cansearch CAS Registry numbersat NIST.  This is useful for
decoding MSDS information.NFPA fire diamondThese are the meanings of the various NFPA warnings:Blue: Health HazardHazard no greater than ordinary materialMay cause irritation; minimal residual injuryIntense or prolonged exposure may cause incapacitation;
Residual injury may occur if not treatedExposure could cause serious injury even if treatedExposure may cause deathRed: Fire HazardWill not burnMust be preheated for ignition; flashpoint above 200°F (93°C)Must be moderately heated for ignition, flashpoint above 100°F (38°C)Ignition may occur under most ambient conditions,
Flashpoint below 100°F (38°C)Extremely flammable and will readily disperse through air under
standard conditions, flashpoint below 73°F (23°C)Reactivity hazards:StableMay become unstable at elevated temperatures and pressures.
May be mildly water reactiveUnstable; may undergo violent decomposition, but will not detonate.
May form explosive mixtures with waterDetonates with strong ignition sourceReadily detonatesSpecial Hazards have the following codes:OX   strong oxidizerW̶    water reactiveSA   simple asphyxiants (The only gases for which this symbol is
permitted are nitrogen, helium, neon, argon, krypton, and xenon.)LicenceThis project is distributed under theGNU General Public License
Version 3or greater.AuthorW. Trevor Kingwking@drexel.edu
Package: chemeco
# ChemEco…….::::::: A General-Purpose Framework for Data Mining Without Coding :::::::…….ChemEco is a flexible and versatile framework to compile a diverse collection of data mining and machine learning techniques from different sources.
It allows the user to build and run an arbitrary graph of operations via configuration files and graphical user interface (GUI).Many customizable templates are provided in the GUI to share best practices in the data mining projects. Furthermore, these templates can be used for the
educational purposes, since they clearly show different elements and flow of data in a machine learning task.## History
ChemEco was initially implemented to interface with Python libraries that are being developed in Hachmann group, i.e, ChemML and ChemLG.
The main focus of those packages is on the molecular and materials data-driven research.
That’s why the name of all these packages express the word chem (chemistry).
However, we later used the code structure to interface with even more Python libraries or commercial software.
Thus, ChemEco now is able to carry out data mining and machine learning tasks on a broader range of domain applications.
Package: chemex
ChemEx: NMR Chemical Exchange Analysis ToolTable of ContentsAbout ChemExQuick OverviewPrerequisitesInstallationPerformance OptimizationContributingSupport and DocumentationLicenseAbout ChemExChemEx is an advanced, open-source software specifically designed for analyzing NMR experimental data to characterize chemical exchange processes. Ideal for researchers and scientists in the field of biochemistry and molecular biology, ChemEx aids in the analysis of NMR experiments like Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion and Chemical Exchange Saturation Transfer (CEST).PrerequisitesBefore installing ChemEx, ensure you have Python installed on your system. For beginners and for a seamless setup, we recommend using theAnaconda Distribution, which includes Python, Numpy, and other essential scientific computing tools.InstallationChemEx offers several installation methods to suit your specific setup:Using condacondacreate-nchemex
condaactivatechemex
condainstallpython=3.11
condaconfig--env--addchannelsconda-forge
condainstallchemexUsing pippipinstallchemexFrom sourcepipinstallgit+https://github.com/gbouvignies/ChemEx.gitPerformance OptimizationFor the best performance, installNumPyandSciPywith Intel® Math Kernel Library (Intel® MKL), available viaAnacondaor theIntel® Distribution for Python.ContributingWe encourage contributions from the community. Please see ourCONTRIBUTING.mdfor guidelines on how to make ChemEx better. For any issues or suggestions, please open an issue or a discussion on ourGitHub repository.Support and DocumentationFor additional support, tutorials, and detailed documentation, visit theChemEx Documentation.LicenseChemEx is licensed under theGPL-3.0. See theLICENSEfile for more details.Developed with ❤️ by theChemEx Contributors
Package: chemexp
ChemexpA Chemprop explainer based onLIMEandPathExplain.InstallationMake sure your Python version is >=3.8condais required for ChemProp. If it is not installed on your machine, you can take a look atminicondaInstallChempropThen simply runpip install chemexpYou're good to go!ExplanationUsing Pythonimportchemexpfromchemprop.utilsimportload_checkpointmodel=chemexp.ExplanationModel(load_checkpoint("models/fusion_db_1.pt"))exp=model.explain_molecule("COC(=N)Cc1ccccc1")chemexp.exp_to_png(exp,"mol.png")A little more detail is available intest/test.py.Web interfaceAlthough you can use this Python module in your scripts, you can also experiment a user-friendly interface.⚠️Warning:this only works on Linux for the moment(this is due to thelinux-specific pathsused to save some files, but it can be adapted for Windows or Mac).Use the following command to run the web server:python-mchemexp<path>wherepathis a folder containing chemprop models / checkpoints (.pt files)AuthorsBELLANGER ClémentBERNIER FabienMAIGRET BernardNAPOLI AmedeoTo cite our work:@mastersthesis{bernier:hal-03371070,
  TITLE = {{A Study about Explainability and Fairness in Machine Learning and Knowledge Discovery}},
  AUTHOR = {Bernier, Fabien},
  URL = {https://hal.inria.fr/hal-03371070},
  PAGES = {58},
  SCHOOL = {{TELECOM Nancy}},
  YEAR = {2021},
  MONTH = Sep,
  KEYWORDS = {machine learning ; explainability ; fairness ; antibiotic classification ; machine learning ; explicabilit{\'e} ; fairness ; classification antibiotique},
  PDF = {https://hal.inria.fr/hal-03371070/file/M_moire_ing_nieur_Fabien.pdf#chapter.5},
  HAL_ID = {hal-03371070},
  HAL_VERSION = {v1},
}
Package: chemfileconverter
A python converter for Chemical Table Files.Free software: BSD 2-Clause LicenseInstallationpip install chemfileconverterYou can also install the in-development version with:pip install https://github.com/CollinStark/chemfileconverter/archive/master.zipDocumentationhttps://chemfileconverter.readthedocs.io/DevelopmentTo run all the tests run:toxNote, to combine the coverage data from all the tox environments run:Windowsset PYTEST_ADDOPTS=--cov-append
toxOtherPYTEST_ADDOPTS=--cov-append toxChangelog0.0.0 (2022-07-02)First release on PyPI.