Saravanan666/pypi-org huggingface dataset:
Package: chemscad
ChemSCADScreenshots:Main interface:Choice dialog box:Reactor dialog box:Canula dialog box:OpenSCAD installation:ChemSCAD requires Python3.6or above. Tested and working with latest Python release (3.8).ChemSCAD was tested with OpenSCAD 2019-05 (most up-to-date version as of March 2020)Install OpenSCAD for your operating system as follows:For Windows:All OpenSCAD dependencies including the binaries are included in the setup.py for ChemSCAD, so will be installed automatically when installing the requirements.txt file.Therefore, please proceed to the ChemSCAD installations instructions below.For Mac:OpenSCAD can be installed using the .dmg installable from the following link:https://files.openscad.org/OpenSCAD-2019.05.dmgInstall this .dmg file, making sure to accept all permissions in Security & Privacy from within System Preferences.For Ubuntu:sudo add-apt-repository ppa:openscad/releases
sudo apt-get update
sudo apt-get install openscad
sudo apt-get install python-dev graphviz libgraphviz-dev pkg-config mesa-common-dev libglu1-mesa-dev -yChemSCAD installation:Prior to installing ChemSCAD it is recommended to make a virtual environment (venv) in order to not have any conflicts with existing installed pip packages.PyQt5mayhave to be installed manually, dependent on your installation. Install with:pip install PyQt5Installation is simple, simply pip-install thechemscadpackage:pip install chemscadChemSCAD can now be run from a command line using the command:chemscadChemSCAD updates:When bug fixes and new features are released for ChemSCAD, you may wish to update to the latest version. Simply install via Pip again for the latest version:pip install chemscadFor developers ONLYIf you wish to work on fixing a bug or implementing a new feature in ChemSCAD you may do so by creating aFeaturebranch from thedevbranch as follows:N.B: the following instructions assume you are currently on themasterbranch and have performed git add and git commit to clean the working tree prior to moving branches.git checkout -b dev # moves current branch from master to dev
git checkout -b [new-branch] # switches from new branch from dev & creates new branch from dev for new feature/bug fix
git push -u origin [new-branch] # sets new branch to track local changes on the remote origin hostOnce a new feature/bug fix is added and tested as working, create amerge requestto mergenew-branchintodevand eventually mergedevintomasterto release the new stable build of ChemSCAD with new features and bug fixes implemented.DevelopmentChemSCAD uses theBlackcode formatter. A
pre-commit hook is included in the repo. Install the dependencies of this
repo (requirements.txt), and before you submit any commit, just run:pre-commit installAny commit you run after that will first trigger Black and will format your
code properly. Run the following command at any point if you're not sure
your code is not formatted properly (recursive command).black .
Package: chemsolve
ChemsolveChemsolve is a library for solving and practicing chemistry problems.
It's made to have easy usability while still retaining a powerful engine
with functionality allowing it to tackle more complicated problems. It was
designed as a tool for lower-level chemistry and problem solving as opposed
to a materials science or higher-level chemistry library.InstallationChemsolve currently runs on Python 3.6 or higher. You can install it from PyPi via pip:pipinstallchemsolveif you want to install it directly from this repository:gitclonehttps://github.com/amogh7joshi/chemsolve.gitcdchemsolve
pythonsetup.pyinstallThen execute:# Install system requirements.python3-mpipinstall-rrequirements.txt# Try it outcdtests
python3elementtest.pyChemsolve makes use of thechempylibrary for backend stoichiometry calculations.Using ChemsolveChemsolve relies heavily on an object-based framework with classes representing important objects in chemistry: elements, compounds, reactions.
The structure of Chemsolve is similar to the following:In addition, Chemsolve includes numerous features to ease chemistry calculations, available in the associated modules within
Chemsolve, such as molarity and molality calculations inchemsolve.solutionsand the ideal gas formula withinchemsolve.gases.ExamplesExamples for all of the primary implemented structures can be found in/examples:TheElement Classand usage.TheCompound Classand usage.TheReaction Classand usage.In this example, we will use the Reaction class.Import the required module(s):fromchemsolveimportCompound,ReactionCreate the Necessary Object and its Object parameters:# Compounds which will be reacted.r1=Compound("NH3",grams=5.00)r2=Compound("O2",grams=3.46)p1=Compound("NO2")p2=Compound("H2O")reaction=Reaction(r1,r2,"-->",p1,p2)From here, you can access the object's attributes.print(reaction.balanced_reaction)print(reaction.limiting_reactant)For further reference, please visit/examples.LicenseAll code in this library is available under theMIT License. You are welcome
to download the repository on your own and work with it, however.IssuesIf you notice an issues or bugs with the library, please feel free to create an issue.
Make sure to follow the issue guidelines.ContributionsContributions are always welcome, and feel free to contribute to the library.
Please make sure to follow the pull request guidelines.
Package: chemspectranslator
chemspectranslatorchemspectranslatoris a universal translator for chemical mechanism speciesBased on the master spreadsheet originally conceived by Bill Carter (UC Riverside),
and adapted by Christoph Knote (Uni Augsburg) / Louisa Emmons (NCAR).Documentationmaintained athttps://mbees.med.uni-augsburg.deChangelog1.1.0 (2021-03-14)Update build system, remove Google online version1.0.0 (2017-12-19)Peer-reviewed version to be published in Knote et al., GMD0.1.0 (2017-08-12)Initial release
Package: chemstruct
ChemStruct: Chemical Structure Analysis PackageAboutChemStruct is a Python package for structural analysis of atomic files (like.xyzfiles) and assistance with molecular dynamics simulations on LAMMPS. ChemStruct computes bonds based on the distance between atoms, as well as angles and dihedrals, hybridization, cycles, etc. It also writes LAMMPS Data Files withatom_style fullfor a given.xyzfile, using CGenFF (CHARMM General Force Field) atomic classification and original parameters.Ready-to-run examples can be found in theexamplesdirectory.UsageInstall ChemStruct using pip:pip3installchemstructThen run Python, import the package and use thewrite_lmpdat()function to convert your xyz file into a LAMMPS Data File:fromchemstruct.quickimportwrite_lmpdat
write_lmpdat("yourdir/yourfile.xyz","outdir/outfile.lmp")Note that:(1) Thewrite_lmpdat()function will take a break while the user is checking the parameters in the.parfile (written in the same directory as the input.xyzfile, with the same name plus_(computed_parameters).par). This is needed because not all bonds/angles/dihedrals found in the input file will always have parameters, so a few manual additions may be necessary. Another necessity is the choice of atomic charges, since CHARMM doesn't have a one-for-one class-charge correspondence. ChemStruct makes suggestions for charges. If your system if simple enough, no manual editing will be necessary.(2) Thewrite_lmpdat()function requires a defined Lattice in the input.xyzfile, e.g. as generated by Ovito (open-source visualization software). The Lattice is needed when the system is periodic -- if that is not the case, writingLattice="10.0 0.0 0.0 0.0 10 0.0 0.0 0.0 10.0"in the second line of your.xyzfile will make it work.ContactSend any bugs or suggestions topdemingos@gmail.com.
Package: chemsys
Chemical System GeneratorGenerator for symbolic functions for both full and simple systemsSymbolic GeneratorSymbol Generatorchemsys.pyis a Gui based chemical reaction system generator that generates the right hand side (RHS) of a chemical system to be used with thesolve_ivpandodeintmethod, thejacobian, and the overall equations for each reactions and each individual chemical species. It will generateLatexformatted equations for the individual chemical reactions, overall mass balances for each species, and both symbolic and numerical text files for theRHSandjacobian.Installationpip install chemsysconda install -c tjczec01 chemsys1. Chemical reactionsThis program will generate theLatexforms of each individual reaction and then save them as both apdfandsvg. The string forms of the equations will be saved in atext(txt) file. An example of some inital reactions are given below.Symbolic Generator2. Overall reactions for each chemical speciesThis program will generate theLatexforms of each individual reaction and then save them as both apdfandsvg. The string forms of the equations will be saved in atext(txt) file. An example of some inital reactions are given below.Symbolic Generator3. Right Hand SideThe right hand side (RHS) of the system of equations will be generated both symbolically and with initial values substituted into their respective places. This is the required system for scipy'ssolve_ivpandodeintmethod. This function requires a callable in the form offun(t, y):Symbolic Generator4. JacobianTheJacobian matrixis symbolically generated in order to improve the accuracy and speed of the solvers used in the aforementioned method.Symbolic Generator5. Use5.1 Generate all necessary lists and values as follows.from chemsys.cs import gui, symbolgen
chemical_names, number_of_reactions, Initial_reactions, Equation_list, indvdf, filepath, kvalues, ea_values, r_gas, pdf_path = gui.fullgui()5.2 Calculate the jacobian and all other desired functions as follows.C_Symbols, K_Vals, EA_Vals, reactants, products, equations, slat, dlat, chem, chemD, chemw, right_hand_side, right_hand_sidef, Jac, Jac_numpy, Jac_math, Jac_Simple, lm, latex_matrix, Jac_symbol, Jac_numpy_symbol, Jac_math_symbol, Jac_simple_symbol, lm_symbol, latex_matrix_symbol, DLatb = symbolgen.fullgen(chemical_names, number_of_reactions, Initial_reactions, Equation_list, indvdf, filepath, kvalues, ea_values, r_gas, chemical_names, pdf_path)6.1 ReferencesCzechorski, Travis J, "A kinetic and thermodynamic model of ethylene dichloride pyrolysis." (2019). Electronic Theses and Dissertations. Paper 3359.
Retrieved fromhttps://ir.library.louisville.edu/etd/3359By Travis Czechorski under the supervision of Dr. Vance Jaeger.
Package: chem-templates
chem_templateschem_templatesprovides an expressive and flexible way of defining
desired chemical spacesSee thedocumentationfor documentation and tutorialsInstallpipinstallchem_templatesBasic UsageFor more detail on the API, see thebasic
tutorialfromrdkit.ChemimportrdMolDescriptors,Descriptorsfromchem_templates.filterimportRangeFunctionFilter,Templatefromchem_templates.chemimportMoleculedefhbd(molecule):returnrdMolDescriptors.CalcNumHBD(molecule.mol)defhba(molecule):returnrdMolDescriptors.CalcNumHBA(molecule.mol)defmolwt(molecule):returnrdMolDescriptors.CalcExactMolWt(molecule.mol)deflogp(molecule):returnDescriptors.MolLogP(molecule.mol)hbd_filter=RangeFunctionFilter(hbd,'hydrogen_bond_donor',None,5)hba_filter=RangeFunctionFilter(hba,'hydrogen_bond_acceptor',None,10)molwt_filter=RangeFunctionFilter(molwt,'mol_weight',None,500)logp_filter=RangeFunctionFilter(logp,'logp',None,5)filters=[hbd_filter,hba_filter,molwt_filter,logp_filter]ro5_template=Template(filters)smiles=['C=CCNC(=O)N1CCN(C(=O)[C@H]2C[C@@H]2c2cccc(F)c2F)CC1','C[C@@H]1CCCC[C@@H]1OCC(=O)OCc1nnc(-c2cccc(Br)c2)o1','CCC[C@@H](OC)C(=O)N[C@@H](CNc1cnc(F)cn1)C(C)C','CC(C)/C=C\\C(=O)N1CCC[C@@](CO)(NC(=O)OC(C)(C)C)C1','C(c1ccccc1)CCC[C@@H](C)c1nnc(N2CCN(C(=O)OC(C)(C)C)[C@@H](C)C2)n1Cc1csc(C(C)(C)C)n1','O=C(c1cccc(F)c1)N1CC[C@]2(CN(CC3=CCCCC3)CCO2)C1']molecules=[Molecule(i)foriinsmiles]results=[ro5_template(i).resultforiinmolecules]>[True,True,True,True,False,True]
Package: chemtools
chemtools: Python toolbox for Computational ChemistryChemtools is a set of modules that is intended to help with more
advanced computations using common electronic structure programs.The main to goal was to enable convenientbasis setmanipulations, including designing and optimizing exponents of basis sets. To achieve that there are several modules abstracting various functionalities.Currently there is support optimizing basis set (or doing general computations) with:DaltonGamess-USMolProPSI4Table of ContentsGetting StartedInstallationDocumentationContributingContactCitingFundingLicenseGetting StartedThe best way to get started is to go over thetutorialsillustrating the functionalities and giving examples of basis set optimization tasks.InstallationMost convenient way to install the package is withpippipinstallchemtoolsDocumentationThe documentation in hosted atRead The Docs.ContributingSourceReport a bugRequest a featureSubmit a pull requestContactŁukasz Mentelgithub:lmmentelemail: lmmentel <at> gmail.comCitingIf you usechemtoolsin a scientific publication, please consider citing the software asŁukasz Mentel,chemtools– A Python toolbox for computational chemistry, 2014– . Available at:https://github.com/lmmentel/chemtools.Here’s the reference in theBibLaTeXformat@software{chemtools2014,
    author ={Mentel, Łukasz},
    title ={{chemtools}-- A Python toolbox for computational chemistry},
    url ={https://github.com/lmmentel/chemtools},
    version ={0.9.2},
    date ={2014--},}or the olderBibTeXformat@misc{chemtools2014,
   auhor ={Mentel, Łukasz},
   title ={{chemtools}-- A Python toolbox for computational chemistry, ver. 0.9.2},
   howpublished ={\url{https://github.com/lmmentel/chemtools}},
   year  ={2014--},}FundingThis project was realized through the support from the National Science Center
(Poland) grant number UMO-2012/07/B/ST4/01347.LicenseThe project is distributed under the MIT License. SeeLICENSEfor more information.
Package: chemtrain
Training Molecular Dynamics Potentials in JAXchemtrainis a library for training MD potentials and integrates withJAX, M.D.as its differentiable MD engine.
Note that this is the first alpha release ofchemtrain, expect breaking changes.
Over the course of the next weeks, several updates will extend its
functionalities and documentation.FeaturesDifferentiable Trajectory Reweighting(DiffTRe)
to train on experimental dataForce Matching and Relative Entropy Minimizationfor coarse-grained systemsIncoming features:Uncertainty Quantification viaDeep Ensembles and Stochastic gradient MCMCActive LearningHybrid Trainers to combine different training methodsMolecular Property PredictionGetting startedTo get started with training MD potentials, using existing trainers that
implement standard training schemes is the most straightforward apprach.
Please refer to the providedexamplesas a refernece on how to set
up the corresponding training environment and dataset.trainer=trainers.Difftre(init_params,optimizer)trainer.add_statepoint(energy_fn_template,simulator_template,neighbor_fn,timings,kbt,compute_fns,reference_state,targets)trainer.train(num_updates)More advanced users may want to extend existing trainers or combine different
trainers to implement custom training pipelines.Installationchemtraincan be installed via pip:pip install jax-dimenetRequirementsThe repository uses the following packages:'jax',
    'jax-md',
    'jax-sgmc',
    'optax',
    'dm-haiku',
    'sympy',
    'tree_math',
    'cloudpickle',
    'chex',The code runs with Python >=3.8.ContributionContributions are always welcome! Please open a pull request to discuss the code
additions.Since this is a very early alpha release, do not hesitate to reach out if some
feature or example is failing. If the specific feature is a priority for you,
its support can be accelerated.ContactFor questions, please contactstephan.thaler@tum.deor open an Issue on GitHub.
Package: chemviewer
ChemviewerChemviewer is a web based application to view 2D chemical structures or reactions in a table.
The local version supports both text input and file selection (from local directory).How to use locallyStart the applicationType inchemviewerin the work directory or typechemviewer table.txtto browse thetable.txt. The input file should have title line and
there should be one column of which the title is "smi", "smiles", or
"cannonical_smiles" (case insensitive).How to installpip install chemviewerIf you do not have a Python environment including RDKit and Flask,
you can downloadanacondaand install them as the following:wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.shThen install the dependencies:conda create -n chemviewer -c conda-forge rdkit
conda activate chemviewer
conda install flaskDependencyRDKitFlask
Package: chencode
Ch encodeAuthor: JeefyEmail:jeefyol@outlook.com/jeeefy163@163.comThe encode rule for encoding a chinese letter.According to the pinyin of a letterRULEChinese WordsUsepypinyinto convert each letter into a pinyin.Notice that, there's no Chinese TONE here.So you just can guess what you have written by yourself.English Words_
It's all can decode back to origin.PunctuationsNotice that the Chinese punctuations would change to English punctuations.SpecialsThe specials letters will convert into unicode number, and then save as the code starts with '6'.The followed codes are the number based on base 8 (0 -> 8).NoticeIt's not wise to encode a numeric str!
It will be 4 times longer!GUIThe gui can be opened withpython -m chencodeRemember you should call it under the readme file folder.The template for the text editor will fork into another package.Waiting for the docs then...
Package: chenosis
MTN Chenosis APINB: Not affiliated with MTN's official Chenosis Platform (05 Jan 2023)A python client for MTN's Chenosis platform:https://chenosis.io.Installationpip install chenosisUsagefromchenosis.clientimportChenosisClientchenosis_client=ChenosisClient(host="https://sandbox.api.chenosis.io",# Use live API when going to productionclient_id="xxxxxx",client_secret="yyyyyy")# GET user's get_mobile_carrier_detailsphone_number="27123456789"response=chenosis_client.get_mobile_carrier_details(phone_number=phone_number)print(response)# TODO: Put correct informationReporting Issues:You can open issues on the GitHub repository for library-level issues and contact Chenosis support for any issues with the API itself.TODO ListUpdate tests and readme examples with more response data once the chenosis sandbox/production is up and running (11 Feb 2023).Use pydantic for response models.Add more endpoints once POC is acceptable.Add more client methods.Add an async client.
Package: chenpz
BriefA simple xml parse and build library.Installationpipinstalldb0905Examplesxml to python object>>>importdb0905
>>>xml='<demo><foo>foo</foo><bar>bar</bar></demo>'>>>db0905.loads(xml){'bar':'bar','foo':'foo'}>>>db0905.loads(xml,strip_root=False){'demo':{'bar':'bar','foo':'foo'}}>>>xml='<demo><foo>foo</foo><bar>1</bar><bar>2</bar></demo>'>>>db0905.loads(xml){'bar':['1','2'],'foo':'foo'}python object to xml>>>data={'demo':{'bar':['1','2'],'foo':'<foo>'}}>>>db0905.dumps(data)'<?xml version="1.0" encoding="utf-8"?><demo><foo><![CDATA[<foo>]]></foo><bar><![CDATA[1]]></bar><bar><![CDATA[2]]></bar></demo>'>>>db0905.dumps(data,cdata=False)'<?xml version="1.0" encoding="utf-8"?><demo><foo>&lt;foo&gt;</foo><bar>1</bar><bar>2</bar></demo>'>>>printdb0905.dumps(data,indent=' '*4)<?xmlversion="1.0"encoding="utf-8"?>
<demo><foo><![CDATA[<foo>]]></foo><bar><![CDATA[1]]></bar><bar><![CDATA[2]]></bar>
</demo>DocumentationSeedocs in readthedocsChangelogSeechangelog
Package: chenv
_
  ___| |__   ___ _ ____   __
 / __| '_ \ / _ | '_ \ \ / /
| (__| | | |  __| | | \ V /
 \___|_| |_|\___|_| |_|\_/ . modern local environment managementThis command-line interface creates and manages local.envfiles from various sources.Coupled withpython-dotenvfor python,
ordotenvfor node.js development,
it provides better, more consistent environment variable management and developement.InstallationTo installchenv,
run this command in your terminal:$pipinstall--userchenvAlso make sure that your$PATHincludes$HOME/.local/bin.
If not, add this line to your.bashrc/.zshrc:exportPATH=$HOME/.local/bin:$PATH;Usagechenv’s usage looks like:$chenvCOMMAND[ARGS]Commands currently include:blankChoose to set.envas a new, blank,.env.blankfile.herokuChoose to set.envfrom a remote heroku app config-vars, as.env.[app-name].-t<team>,--team<team>Pre-fill team name-a<app>,--app<app>Pre-fill app namelocalChoose to set.envfrom a local, pre-exsiting.env.*file.filenamePre-fill file-suffix nameProject Configurationschenvalso provides two file types that manipulate the output of new.env.*files being set..envignoreSpecifies intentionally unwanted environment-variables.
Each line in a envignore file specifies a pattern.When deciding whether to ignore an environment variable,chenvchecks it’s key against the list of patterns described in this file.Pattern:.envignoreuses the unix filename pattern matching, similar to.gitignore’s, and as specified athttps://docs.python.org/3/library/fnmatch.html.envmergeSepecifies environment variables to merge / override after any input is chosen. This provides consistency to preffered settings such as thelogging-level, orNODE_ENVfor local development usage in node.js.
Package: chenzgi1
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Package: cheomseongdae
첨성대 (cheomseongdae)Let's express the operating principles of Apache Spark interestingly and visually. I hope the process is more fun than the result.User Guidehttps://cheomseongdae.github.iohttps://pypi.org/project/cheomseongdaepip install cheomseongdae>>> cheomseongdae-ping
pong

>>> cheomseongdae-ping 10
ppppppppppongDeveloper Guidedockstringhttps://cheomseongdae.github.io/docs.htmlbuildpython3 -m buildinstalllocalpip install cheomseongdae -I --no-index --find-links ./dist/gitpip install git+https://github.com/cheomseongdae/cheomseongdae.github.io.gitdeploy -> pypipython3 -m twine upload --repository pypi dist/*deploy -> docsmkodcs gh-deploy
Package: chephren
Description:An extension to Sphinx for managing blogs and static websites.Status:Alpha - incomplete, not well tested, breaking changes likelyPython Support:2.7, further compatibility to come in betaChephren is an extension forSphinxthat adds features for managing static
websites that are not software documentation. Sphinx is a great tool for
documenting software projects, but it is missing some common features that
would make it just as good for managing static websites. Features provided by
Chephren include:Marking a distinction between “posts” and utility pages like the search or about pageAllow posts to bypass the “not found in any toctree” warningRSS feed for your postsDate-based archive page for your postsCategory-based archive page for your postsWhat’s MissingLots of planned features don’t yet exist, even features you might expect.
Here’s a list of things you cannot do (yet).Rename the archive pages (you’re stuck with blog-bydate and blog-bycategory
for now)Create a separate page for each categoryPaginate the feedProduce a feed in any format except Atom (but Atom is widely supported)Create a traditional-looking blog home page (without custom coding anyway)Apply a custom template to a postCopyright and LicenseCopyright 2015 Vincent Veselosky and contributors.Unless otherwise noted, files in this distribution are licensed under the
Apache License, Version 2.0 (the “License”); you may not use these files
except in compliance with the License.You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.Documentation and non-software assets included in this distribution are
licensed underCreative Commons Attribution 4.0 International License.