Saravanan666/pypi-org huggingface dataset:
Package: chemfiles
Python binding for the chemfiles libraryChemfiles is a library for reading and writing molecular trajectory files. These
files are created by your favorite theoretical chemistry program, and contains
information about atomic or residues names and positions. Chemfiles offers
abstraction on top of these formats, and a consistent interface for loading and
saving data to these files.This repository contains the Python binding for the chemfiles library. This
binding is created with the ctypes module, calling directly the C interface of
chemfiles, and thus is compatible with Python 2 and 3, and with all versions of
Numpy.InstallationYou can use your favorite package manager (condaorpip) to install
pre-built versions of Chemfiles, that support Linux/Windows/macOS, and Python
2.7 and 3.# Using pip
pip install chemfiles
# Using conda
conda install -c conda-forge chemfilesSource compilationYou can install this python module from sources if you have all thedependenciesof the C++ chemfiles library installed on your computer.# To get the latest development version:gitclonehttps://github.com/chemfiles/chemfiles.pycdchemfiles.py
gitsubmoduleupdate--init# Install development dependenciespipinstall-rdev-requirements.txt# Install chemfilespipinstall.# Optionally run the test suitetoxUsage exampleHere is a simple usage example for thechemfilesmodule. Please see theexamplesfolder for more examples.fromchemfilesimportTrajectory,Frametrajectory=Trajectory("filename.xyz")frame=trajectory.read()print(f"There are{len(frame.atoms)}atoms in the frame")positions=frame.positions()# Do awesome things with the positions here !Bug reports, feature requestsPlease report any bug you find and any feature you may want as agithub
issue.
Package: chemfp
This version of chemfp includes command-lines tools to generatecheminformatics fingerprints and search those fingerprints byTanimoto similarity, as well as a Python library which you can useto build new tools.It is the no-cost/open source chemfp release track. It only supportsPython 2.7. It is being maintained only to provide a good referencebaseline for benchmarking other similarity search tools.The commercial track, currently chemfp 3.4, includes fasterperformance, many new features, and support for Python 3.Chemfp is designed for the dense, 100-10,000 bit fingerprints whichoccur in small-molecule/pharmaceutical chemisty. The Tanimoto searchalgorithms are implemented in C and assembly for performance, andsupport both threshold and k-nearest searches using the BitBoundalgorithm of Swamidass and Baldi.Fingerprint generation can be done either by extracting existingfingerprint data from an SD file or by using an existing chemistrytoolkit. chemfp supports the Python libraries from Open Babel,OpenEye, and RDKit toolkits. Be aware that those vendors no longersupport Python 2.7.The main web site is https://chemfp.com/ .Extensive documentation is at https://chemfp.readthedocs.io/ .To cite chemfp use:Dalke, Andrew. The chemfp project. J. Cheminformatics 11, 76(2019). https://doi.org/10.1186/s13321-019-0398-8https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0398-8
Package: chemfp-converters
chemfp_converters 0.9.1A Python library and set of command-line tools to convert
cheminformatics fingerprint files from/to the chemfp FPS format.The supported formats are:fs2fps, fps2fs – Open Babel’s “FastSearch” formathttp://openbabel.org/wiki/FastSearchflush2fps, fps2flush – Dave Cosgrove’s “flush” formathttps://github.com/OpenEye-Contrib/Flushfpbin2fps, fps2fpbin – OpenEye’s OEFastFPDatabase “fpbin” formathttps://docs.eyesopen.com/toolkits/cpp/graphsimtk/OEGraphSimClasses/OEFastFPDatabase.htmlThese converters have many features though they are of are beta
quality. They have only been lightly tested and there is still some
code cleanup to do.
Package: chemic
ChemicChemic is a Python library for chemistry students and teachers. It is designed to be easy to use and to provide a simple interface to search for information and to perform calculations.The core of Chemic can be found inmain.pyandutils.py. Themain.pyfile contains the main functions for searching and calculating. Theutils.pyfile contains the functions for parsing the data files and for performing calculations.InstallationChemic is available on PyPI. To install it, run the following command:pipinstallchemicUsageImporting ChemicTo use Chemic, import it into your Python script:importchemicRun the CLITo start the CLI, add/adjust the following to your Python script:fromchemicimportrunrun.cli()Start the GUITo start the GUI, add/adjust the following to your Python script:fromchemicimportrunrun.gui()This will start a local server and open a web browser to the GUI.Source and InstallableYou can run Chemic without installing by grabbing thebuild/main.pyfile on GitHub. Also in thebuildfolder is thechemicinstallable. Run it and ignore any errors in the console.
Package: chemica
ChemicaA simple library that takes chemistry to the next level 👨‍🔬🔬🥽🧪🧬Installation:Download the latest version of the library using pip$pip3installchemica-UUsage examples:Solving equation:fromchemicaimportChemicaprint(Chemica.solve("CuCl2","Zn"))This example will return this equation object:Equation(substances=('CuCl2','Zn'),result='CuCl2(aq) + Zn(s) → Cu(s) + ZnCl2(aq)')Getting info about substance:fromchemicaimportChemicaprint(Chemica.info("Zn"))This example will return this substance object:Substance(substance='Zn',name='Zinc, Zinc powder (pyrophoric), Zn, Element 30, 30Zn, Cinc, Zink, Zn(ii), Zn2+, Zincum, Blue powder',condition='Grey-to-blue powder')LicenseThe library is under the MIT license.Read theLICENSEfor more information.
Package: chemical
ChemicalRust-Style Iterators in Python!Compose iterator sequences like chemical compounds!Quickstart>>>fromchemicalimportit>>>my_iter=it([1,2,3])>>>my_iter.next()1>>>my_iter.next()2>>>my_iter.next()3>>>it('abc').map(lambdax:x.upper()).collect(str)'ABC'>>>it('abc').inspect(print).go()abc>>>fornuminit(range(100)).skip(10).take(10).rev().step_by(4):...print(num)191511>>># Same as above but written as an expression:>>>it(range(100)).skip(10).take(10).rev().step_by(4).for_each(print).go()191511>>># Large Chemical compositions can span multiple lines using parentheses:>>>(it(range(100)....skip(10)....take(10)....rev()....step_by(4)....for_each(print)....go()...)191511AboutChemical takes heavy inspiration from the iterators that can be found in theRust Programming Language. Chemical provides
composable, customizable, and powerful iterators that can be combined, chained,
aggregated, and so much more.Although Python has very powerful iterators already, Chemical provides a way to
programatically compose them to create highly compact but comprehendible
behaviors.You can even add your own "traits" to theitclass at runtime and they will be
available for use anywhere in your program! This allows you to create custom
functionality without having to use your own type derived fromit.Installation$pipinstallchemicalChemical has been tested on:WindowsMacOSLinuxPython 3.6Python 3.7Python 3.8To run the unit tests:$gitclonehttps://github.com/Pebaz/Chemical
$cdChemical
$pipinstall-rrequirements.txt
$pytestDocumentationYou can view the generated documentationhere.You can also look at the source code for more insight on how you can extenditto have more iterators and aggregators specific to your own application.The unit tests also provide an abundant amount of examples as they cover every
iterator/aggregator in Chemical.
Package: chemical-formula
Chemical FormulaA package for handling achemical formula: parsing text formulae, producing standard
text formats, and other useful utilities.Free software: Lesser GPL (LGPL)Documentation:https://chemical-formula.readthedocs.io.FeaturesAccepts with a SMILES string directly or from a variable.The generated structure can optionally be optimized using one of
several forcefields.AcknowledgementsThis package was created withCookiecutterand themolssi-seamm/cookiecutter-seamm-pluginproject template.Developed by the Molecular Sciences Software Institute (MolSSI),
which receives funding from theNational Science Foundationunder
award ACI-1547580History0.1.0 (2017-12-07)First release on PyPI.
Package: chemics
ChemicsChemics is a Python package for chemistry and chemical engineering applications. It is open-source and contributions from the scientific community are encouraged.InstallationIf you don't have Python installed on your computer, theAnacondaorMinicondadistribution of Python is recommended for scientific computing. After setting up Python, the Chemics package can be downloaded and installed using the pip package manager.$pipinstallchemicsUsageThe example below imports the Chemics package and uses theGasclass to calculate the density and viscosity of nitrogen gas at a temperature of 773 K and pressure of 101,325 Pa.importchemicsascmgas=cm.Gas("N2",773)rho=gas.density()mu=gas.viscosity()print("Nitrogen gas properties at 773 K and 101,325 Pa")print(f"density{rho:.4f}kg/m³")print(f"viscosity{mu:.2f}μP")This prints the following:Nitrogen gas properties at 773 K and 101,325 Pa
density    0.4416 kg/m³
viscosity  363.82 μPThis example uses theChemicalEquationclass to get properties of the reactants and products from a given chemical equation.importchemicsascmce=cm.ChemicalEquation("2 HCl + 2 Na -> 2 NaCl + H2")ce.is_balanced()# This returns True for balanced equationce.rct_properties# This returns a dataframe of the reactant properties#                HCl        Na# moles            2         2# species        HCl        Na# molwt       36.458     22.99# mass        72.916     45.98# molfrac        0.5       0.5# massfrac  0.613275  0.386725More examples are available in the documentation.DocumentationDocumentation for the Chemics package is available atchemics.readthedocs.io.ContributingSee theCONTRIBUTING.mddocument for guidelines on contributing to the Chemics package.LicenseChemics is available under the MIT License - see theLICENSEfile for more information.
Package: cheminfopy
cheminfopyPython SDK for interacting with the cheminfo ELN💪 Getting StartedTODO show in a very small amount of space theMOSTuseful thing your package can do.
Make it as short as possible! You have an entire set of docs for later.Command Line InterfaceThe cheminfopy command line tool is automatically installed. It can
be used from the shell with the--helpflag to show all subcommands:$cheminfopy--helpTODO show the most useful thing the CLI does! The CLI will have documentation auto-generated
bysphinx.🚀 InstallationThe most recent code and data can be installed directly from GitHub with:$pipinstallgit+https://github.com/cheminfo-py/cheminfopy.gitTo install in development mode, use the following:$gitclonegit+https://github.com/cheminfo-py/cheminfopy.git
$cdcheminfopy
$pipinstall-e.👐 ContributingContributions, whether filing an issue, making a pull request, or forking, are appreciated. SeeCONTRIBUTING.rstfor more information on getting involved.👋 Attribution⚖️ LicenseThe code in this package is licensed under the MIT License.🍪 CookiecutterThis package was created with@audreyfeldroy'scookiecutterpackage using@cthoyt'scookiecutter-snekpacktemplate.🛠️ For DevelopersSee developer instrutionsThe final section of the README is for if you want to get involved by making a code contribution.❓ TestingAfter cloning the repository and installingtoxwithpip install tox, the unit tests in thetests/folder can be
run reproducibly with:$toxAdditionally, these tests are automatically re-run with each commit in aGitHub Action.📦 Making a ReleaseAfter installing the package in development mode and installingtoxwithpip install tox, the commands for making a new release are contained within thefinishenvironment
intox.ini. Run the following from the shell:$tox-efinishThis script does the following:Uses BumpVersion to switch the version number in thesetup.cfgandsrc/cheminfopy/version.pyto not have the-devsuffixPackages the code in both a tar archive and a wheelUploads to PyPI usingtwine. Be sure to have a.pypircfile configured to avoid the need for manual input at this
stepPush to GitHub. You'll need to make a release going with the commit where the version was bumped.Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
usetox -e bumpversion minorafter.
Package: chemio
Chemio Chemical files Input/OutputChemical file Input/OutputChemio: convert from one to anotherread/writeimportchemiochemio.read(inputobj,index)chemio.write(filename,inputobj,format)chemio.convert(inputobj,input_index,input_format,output_filename,output_index,output_format)chemio.preview(arrays,format)cli# chemio -husage:chemio[-h][--version][-T]{help,info,convert}...

ChemIOcommandlinetool.

optionalarguments:-h,--helpshowthishelpmessageandexit--versionshowprogram'sversionnumberandexit-T,--traceback

Sub-commands:{help,info,convert}helpHelpforsub-command.infoPrintinformationaboutfilesorsystem.convertConvertbetweenfileformats.usage:chemioinfo[-h][-v][-kKEY][filename[filename...]]Printinformationaboutfilesorsystem.

Withfilename(s),thefileformatwillbedeterminedforeachfile.

positionalarguments:filenameNameoffiletodetermineformatfor.

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseShowmoreinformationaboutfiles.-kKEY,--keyKEYkeytoshowusage:chemioconvert[-h][-v][-iFORMAT][-oFORMAT][-f][-nNUMBER][-s]input-file[input-file...]output-file

Convertbetweenfileformats.

Use"-"forstdin/stdout.See"chemio info --formats"forknownformats.

positionalarguments:input-fileoutput-file

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verbosePrintnamesofconvertedfiles-iFORMAT,--input-formatFORMATSpecifyinputFORMAT-oFORMAT,--output-formatFORMATSpecifyoutputFORMAT-f,--forceOverwriteanexistingfile-nNUMBER,--image-numberNUMBERPickimagesfromtrajectory.NUMBERcanbeasinglenumber(useanegativenumbertocountfromtheback)orarange:start:stop:step,wherethe":step"partcanbeleftout-defaultvaluesare0:nimages:1.-s,--split-outputWriteoutputframestoindividualfiles.Outputfilenameshouldbeaformatstringwithasingleintegerfield,e.g.out-{:0>5}.xyz
Package: chemiscope
Python helpers for chemiscopeThis package contains Python code to help generate input files for thechemiscopedefault visualizer, and integrate
chemiscope with jupyter notebooks.InstallationYou should use pip to install this package:pipinstallchemiscopeThis installs both achemiscope-inputcommand line tool, and thechemiscopepackage.UsageTo create a new chemiscope input file:importchemiscopeimportase.io# read frames using aseframes=ase.io.read("structures.xyz",":")# add additional properties to displayproperties={"<property name>":{target:"atom",values:[3,4,2,8,9,10],}}chemiscope.write_input("my-input.json.gz",frames=frames,properties=properties)To display a chemiscope widget inside a jupyter notebook:importchemiscopeimportase.io# read frames using aseframes=ase.io.read("structures.xyz",":")# add additional properties to displayproperties={"<property name>":[3,4,2,8,9,10],}chemiscope.show(frames=frames,properties=properties)
Package: chemispy
Chemistry in pythonInstallationpip install chemispyUsagefromchemispyimport*Atomic Number Queryquery.query_atomic_number(1)Return's the name of the element corresponding to the atomic numberElements Listprint(query.list_types())Returns a list of all elements (Used mostly for debugging)Custom Elementsfromchemispy.utils.atomic_number_queryimportatomic_number_queryatomic_number_query.elements.append("ELEMENT_119")
Package: chemist
A simple, flexible and testable active-record powered by SQLAlchemy.InstallpipinstallchemistDocumentationchemist.readthedocs.ioBasic Usagefromchemistimport(Model,db,DefaultTableset_default_uri,)engine=set_default_uri('sqlite:///example.db')classBlogPost(Model):table=DefaultTable('blog_post'db.Column('id',db.Integer,primary_key=True),db.Column('title',db.Unicode(200),nullable=False),db.Column('content',db.UnicodeText,nullable=False),)post1=BlogPost.create(title='Hello World',content='\n'.join(['Introduction...','Supporting Theory 1...','Supporting Theory 2...','Supporting Theory 3...','Conclusion',]))forpostinBlogPost.all():print(post.title,post.id)Examplesflask app
Package: chemistry-adapters
Chemistry AdaptersA place for quick conversions between languages using SMILES as the base key. A Quick Converter From Amino Acid Sequences to Smiles and Back again.InstallationChemistryAdapters is going to be distribute via PyPi and as the content store grows we can expand it to other pieces of software
making it accessible to all regardless of what you use. Alternatively, you could have a glance at the source code and copy/paste
it yourself.pip install chemistry-adaptersUsing AdaptersCurrently only one adapter is implemented which is the Amino Acids to SMILES and back again.test='RSTEFGHIKLADPQ'adapter=AminoAcidAdapter()smiles=adapter.convert_amino_acid_sequence_to_smiles(test)>>>NC(CCCCNC(N)=N)C(NC(CO)C(NC(C(C)([H])O)C(NC(CCC(O)=O)C(NC(CC1=CC=CC=C1)C(NC([H])C(NC(CC1=CNC=N1)C(NC(C(CC)([H])C)C(NC(CCCCN)C(NC(CC(C)C)C(NC(C)C(NC(CC(O)=O)C(NC(C2CCCN2)C(NC(CCC(N)=O)C(NCC(O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=Osequence=adapter.convert_smiles_to_amino_acid_sequence(smiles)>>>RSTEFGHIKLADPQGenesisI demonstrated I have a need for this so I built a quick one.Lead DeveloperSuliman sharifCitationSul: "ChemistryAdapters"External links
Package: chemistry-ch
Project Portfolio:https://github.com/calebyhan/CalebHanchemistry-chPython library for chemistry equations and formulas.InstallationUse the package managerpipto install chemistry-ch.pipinstallchemistry-chUsageimportchemistry# returns atomic mass of Hydrogenchemistry.mass(1)chemistry.mass("H")# returns a metric conversion from 1 cm to kmchemistry.Conversions.metric(1,"c","k")# returns molarity of a solution with 1 mol in 2 Lchemistry.Formulas(moles=1,volume=1)Documentationhttps://chemistry-ch.readthedocs.io/en/latest/ContributingPull requests are welcome. For major changes, please open an issue firstto discuss what you would like to change.Please make sure to update tests as appropriate.LicenseMIT
Package: chemistry-tools
Python tools for analysis of chemical compounds.DocsTestsPyPIAnacondaActivityQAOtherInstallationchemistry_toolscan be installed from PyPI or Anaconda.To install withpip:$python-mpipinstallchemistry_toolsTo install withconda:First add the required channels$condaconfig--addchannelshttps://conda.anaconda.org/conda-forge$condaconfig--addchannelshttps://conda.anaconda.org/domdfcodingThen install$condainstallchemistry_toolslookup and pubchem adapted from PubChemPyPython interface to the PubChem REST APICopyright 2017 Matt Swain <m.swain@me.com>https://github.com/mcs07/PubChemPyAvailable under the MIT LicenseSpectrumSimilarityPerform mass spectrum similarity calculationsAdapted from SpectrumSimilarity.RPart of OrgMassSpecRCopyright 2011-2017 Nathan Dodder <nathand@sccwrp.org>https://cran.r-project.org/web/packages/OrgMassSpecR/index.htmlAvailable under the BSD 2-Clause Licenseelements and formulaeProvides properties for the elements in the periodic table, and functions
for parsing formulae and calculating isotope distributions.Calculations are based on the isotopic composition of the elements. Mass
deficiency due to chemical bonding is not taken into account.Examples of valid formulae areH2O,[2H]2O,CH3COOH,EtOH,CuSO4.5H2O, and(COOH)2. Formulae are case sensitive.Based on ChemPy (https://github.com/bjodah/chempy)Copyright (c) 2015-2018, Björn DahlgrenAll rights reserved.Also based on molmass (https://github.com/cgohlke/molmass)Copyright (c) 1990-2020, Christoph GohlkeAll rights reserved.Licensed under the BSD 3-Clause LicenseAlso based on Pyteomics (https://github.com/levitsky/pyteomics)Copyright (c) 2011-2015, Anton Goloborodko & Lev LevitskyLicensed under the Apache License
Package: chemivec
ChemivecVectorized Cheminformatics Python library, based on EPAM Indigo toolkit C-API
and using NumPy for input/output.Supported operations:rxn_subsearch(input, query) - reaction substructure match
    input : reaction SMILES array (numpy, pandas and python list supported)
    query : reaction query SMARTS, ex "C=C>>C-C"Example usage:importnumpyasnpimportchemivecarr=np.array(['[C:1]=O>>[C:1]O','C=O>>CO'])query="[C:1]=O>>[C:1]O"res=chemivec.rxn_subsearch(arr,query=query)print(res)# Output: array([ True, False])MultithreadingMultithreading realized by OpenMP library. By default, tries to use maximum available number of cores.
Number of cores can be specified as a global option or passed as a parameter.importchemivecchemivec.rxn_subsearch(arr,query=query)# default max available coreschemivec.set_option("n_jobs",12)# change defaultschemivec.rxn_subsearch(arr,query=query,n_jobs=8)Atom-to-atom matching (AAM)If atom mapping is present in the query, ex[C:1]>>[C:1]chemivec follows the standard DAYLIGHT SMARTS rules
declared herehttps://www.daylight.com/dayhtml/doc/theory/theory.smarts.html(Section 4.6 Reaction Queries)InstallDownload from pippip install chemivecBuild from sourcespython3 -m twine check wheelhouse/*Ubuntusudo apt install build-essential ninja-build mc wget git libcairo2-dev zlib1g-dev -y
git clonehttps://github.com/alkorolyov/chemivecwgethttps://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh;chmod+x Mambaforge-Linux-x86_64.sh;bash Mambaforge-Linux-x86_64.sh;export MAMBA_NO_BANNER=1if conda still not seen then ~/.bashrc is not sourced when you log in using SSH.You need to source it in your ~/.bash_profile like this:echo "if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi" >> ~/.bash_profilerestart shellconda config --set auto_activate_base false
mamba create -n dev
mamba activate dev
mamba install pip pytest -y
pip install .(optional) to build in cibuildwheelpip install cibuildwheel
sudo apt-get install docker.io -y; sudo groupadd docker; sudo usermod -aG docker $USER
sudo reboot now
cd chemivec
cibuildwheel --platform linuxWindowsmingw64 on windows
download stable mingw64 release, extract and add to %Path%https://github.com/brechtsanders/winlibs_mingw/releases/download/11.2.0-10.0.0-msvcrt-r1/winlibs-x86_64-posix-seh-gcc-11.2.0-mingw-w64msvcrt-10.0.0-r1.zipdownload ninja and also add to %Path%https://github.com/ninja-build/ninja/releases/download/v1.11.1/ninja-win.zipcmake -B build -G "Ninja" -D CMAKE_C_COMPILER=gcc.exe -D CMAKE_CXX_COMPILER=g++.exe .cmake --build build --target _chemivecMacOShttps://github.com/DrDonk/unlockerhttps://www.wikigain.com/how-to-install-macos-monterey-on-vmware-on-windows-pc/https://intoguide.com/install-vmware-tools-on-macos-monterey/https://href.li/?https://softwareupdate.vmware.com/cds/vmw-desktop/fusion/11.1.0/13668589/packages/com.vmware.fusion.tools.darwin.zip.tarMiscTo check dependencies of your*.pydlibrary
dumpbin should be run from developer command prompt of VS 2022dumpbin mylib_c_ext.pyd /DEPENDENTS