Saravanan666/pypi-org huggingface dataset:
Package: pdbg-bcit
pdbg.pyTable of Contentspdbg.pyTable of ContentsIntroductionInstallationUsageExampleOptionsIntroductionpdbgis a debugging tool for python. It is designed to be a simple and lightweight tool for troubleshooting errors in Python code.When run, this tool will run the specified script, while outputting all the variable definitions during the run. This is useful for when you want to watch the changes made to variables during the execution of your code and you don't have an IDE with a debugger. This is also useful even when youdohave a debugger, as many debuggers don't allow you to go back to previous steps in your code, making it easy to forget what the previous values were. This tool will show you all the changes at once in the command line output or in a file, meaning that forgetting what happened will never be an issue.All of the functionality of this module is provided through a single function. The options for this function are detailed in theOptionssection of this documentInstallationYou can installpdbgwithpippip install pdbg-bcitUsageUsing this tool is very simple. In Windows, open CMD in the folder that you would normally run your python script. Then, enter the below command, with$filepathas the absolute path of the python script you want to debug.python -c "import pdbg; pdbg.pdbg(r'$filepath')"This method will run the script and output all the variable definitions and changes in the targeted file. More options for this method are detailed inoptions.ExampleLets say we have a file with the following code.deffoo():bar=0foriinrange(3):bar+=1print(bar)foo()If we wanted to watch the variables changed infoo(), all we would have to do is open command line and run this command, with$filepathas the path of the python file.python -c "import pdbg; pdbg.pdbg(r'$filepath', ['foo'])"And this would be our output:[Function] Entering function foo
[Debug]     bar = 0                                                  bar { None => 0 }
[Debug]     for i in range(3):                                       i { None => 0 }
[Debug]         bar += 1                                             bar { 0 => 1 }
[Debug]     for i in range(3):                                       i { 0 => 1 }
[Debug]         bar += 1                                             bar { 1 => 2 }
[Debug]     for i in range(3):                                       i { 1 => 2 }
[Debug]         bar += 1                                             bar { 2 => 3 }
3Optionspdbg.pdbg(file,func_filter=[],var_filter=[],output_file=None,seperator=", ",output_format="{var_name} {{ {pre_value} => {new_value} }}")[Required]filePath to your Python script.func_filterFilter the output by function name.var_filterFilter the output by variables name.output_fileDefaults to None. Redirect the output of pdbg to a file if specified. Will output by printing in console otherwiseseparatorSeparator used when multiple variables are changed in one line.output_formatA string that formats the output{var_name}will be the name of the variable,{pre-value}will be the initial variable{new_value}will be the variable after changes.Readthe Python docfor more about formatting.
Package: pdbinf
PDBInf allows you to read PDB files using RDKit and assign bond orders from .cif (PDBx) template files.# provide a PDBx defining the TPO nonstandard residuenonstandard_residues=gemmi.cif.read('./tpo.cif')# load a PDB file using the built-in standard amino acid doc and providing information on the nonstandard residuespdbinf.load_pdb_file('./tpo.pdb',templates=[pdbinf.STANDARD_AA_DOC,nonstandard_residues])
Package: pdbinject
InstallYou’ll need GDB compiled with python support, and thepdbinjectpackage:easy_install pdbinjectOS X NotesThe default GDB does not come compiled with Python support.Homebrew fixes that:brew install gdbNoteThere’s more steps, I gave up on figuring out how to make it work.Usage$ python example/loop.py &
Process running with PID 6319

$ sudo pdbinject 6319
Remote PDB has been configured on port 4444

        nc 127.0.0.1 4444

$ nc 127.0.0.1 4444
--Return--
> /home/ubuntu/pdbinject/pdbinject/debugger.py(16)run()->None
-> debugger.set_trace()Now have some fun:from guppy import hpy
hp = hpy()
heap = hp.heap()
heap.get_rp()To print the stacktrace across all the threads:import sys, traceback
for thread_id, stack in sys._current_frames().iteritems(): print 'Thread id: %s\n%s' % (thread_id, ''.join(traceback.format_stack(stack)))
Package: pdbio
pdbioPandas-based Data Handler for VCF, BED, and SAM FilesInstallation$pipinstall-UpdbioPython APIExample of API callfrompprintimportpprintfrompdbio.vcfdataframeimportVcfDataFramevcf_path='test/example.vcf'vcfdf=VcfDataFrame(path=vcf_path)pprint(vcfdf.header)# list of headerpprint(vcfdf.samples)# list of samplesprint(vcfdf.df)# VCF dataframevcfdf.sort()# sort by CHROM, POS, and the otherprint(vcfdf.df)# sorted dataframeCommand-line interfaceExample of commands# Convert VCF data into sorted TSV data$pdbiovcf2csv--sort--tsvtest/example.vcf# Convert VCF data into expanded CSV data$pdbiovcf2csv--expand-info--expand-samplestest/example.vcf# Sort VCF data by CHROM, POS, and the other$pdbiovcfsorttest/example.vcfRunpdbio --helpfor more information.
Package: pdblp
[![PyPI version](https://badge.fury.io/py/pdblp.svg)](https://badge.fury.io/py/pdblp)This is a simple interface to integrate pandas and the Bloomberg Open API.
The standard Bloomberg API provides an extensive set of features for building
applications on top of however does not provide easy and interactive access to
data. This package provides several functions for accessing historical market
data and reference data. A simple set of examples is available
[here](https://matthewgilbert.github.io/pdblp/tutorial.html).The library borrows heavily from a similar package available
[here](https://github.com/kyuni22/pybbg)## Requirespython 3.x[Bloomberg Open API](http://www.bloomberglabs.com/api/)[pandas](http://pandas.pydata.org/)and forpdblp.parser[pyparsing](https://pythonhosted.org/pyparsing/) >= 2.2.0## Installation
You can install from PyPi using` pip install pdblp `or you can clone this repository and pip install the package, i.e.` git clonehttps://github.com/matthewgilbert/pdblp.gitpip install-epdblp `blpapican be installed directly from the above link or you can install from
theconda-forgechannel on Anaconda, e.g.` conda install-nblp_env-cconda-forgeblpapi `If going this route make sure there is a build available for your version of
pythonhttps://anaconda.org/conda-forge/blpapi/filesIf you are getting‘GLIBCXX_3.4.21’ not founderror when attempting to importblpapi, the following appears to resolve this issue.` conda install libgcc `## DocumentationThe documentation can be viewed athttps://matthewgilbert.github.io/pdblp/### Bloomberg DocumentationFor general documentation on the Bloomberg API check out the Developer’s Guide.
For documentation on relevant Bloomberg fields for accessing data, check out
the Reference Guide: Services and Schemas. To access these, from a
Bloomberg Terminal goWAPI <GO>->API Developer’s Guide.### Building the documentationThe documentation relies on [Sphinx](http://www.sphinx-doc.org/en/master/).
Building the documentation can be done by setting up a conda environment usingconda create –name pdblp_doc –file doc-environment.yml, sourcing this
environment and then installing the relevant version ofpdblp. Documentation
can then be built using` cd doc make html `and viewed in ./doc/_build. Before building this ensure that you are
logged into a Bloomberg terminal as this is required for building many of the
examples.
Package: pdb-manip-py
Pdb_Manip_pyPdb_Manip_py is a python library allowing simple operations on pdb coor files.Online Documentation:https://pdb-manip-py.readthedocs.ioSource code repository:https://github.com/samuelmurail/pdb_manip_pyMain features:Basic pdb operationspdb wrapperselection toolsrotationtranslationalignementRMSD calculationinsertion of molecules in solvant…InstallationUsing Pypipip3installpdb_manip_pyUsing Condacondainstallpdb_manip_py-cconda-forgeFrom source codeGet the os_command_py library fromgithub.gitclonehttps://github.com/samuelmurail/pdb_manip_py.git./setup.pyinstall--userAuthorSamuel Murail, Associate Professor -Université Paris Diderot,CMPLI.See also the list ofcontributorswho participated in this project.LicenseThis project is licensed under the GNU General Public License v2.0 - see theLICENSEfile for details.
Package: pdb-numpy
.. image::https://readthedocs.org/projects/pdb-numpy/badge/?version=latest:target:https://pdb-numpy.readthedocs.io/en/latest/?badge=latest:alt: Documentation Status.. image::https://dev.azure.com/samuelmurailRPBS/pdb_numpy/_apis/build/status/samuelmurail.pdb_numpy?branchName=main:target:https://dev.azure.com/samuelmurailRPBS/pdb_numpy/_build/latest?definitionId=1&branchName=main:alt: Build Status.. image::https://codecov.io/gh/samuelmurail/pdb_numpy/branch/main/graph/badge.svg?token=MCVDZ7GD0V:target:https://codecov.io/gh/samuelmurail/pdb_numpy:alt: Code coverageAbout PDB-numpypdb_numpyis a python library designed to facilitate working with PDB files
in the context of structural bioinformatics. The library builds upon the
powerfulnumpylibrary to provide efficient and easy-to-use tools for
reading, manipulating, and analyzing PDB files.The library includes a number of functions for working with PDB files,
including functions for parsing PDB files and extracting relevant information,
such as atomic coordinates, residue identities, and structural information.
Additionally,pdb_numpyprovides a range of functions for performing common
manipulations on PDB structures, such as aligning structures, superimposing
structures, and calculating RMSD values.Source code repository:https://github.com/samuelmurail/pdb_numpyMain features:Reading and writing PDB/MMCIF filesSelecting atomsSuperimposing structures using sequences alignmentRMSD calculationDockQ calculationSecondary Structure calculation (pseudo DSSP)For more examples and documentation, see thepdb_numpydocumentation athttps://pdb-numpy.readthedocs.io/en/latest/readme.html.Installationpdb_numpyis available on PyPI and can be installed usingpip:.. code-block:: bashpip install pdb_numpyAlternatively, you can installpdb_numpyfrom source:.. code-block:: bashgit clone https://github.com/samuelmurail/pdb_numpy
cd pdb_numpy
python setup.py installDependenciespdb_numpyrequires the following dependencies:numpyscipyContributingpdb_numpyis an open-source project and contributions are welcome. If
you find a bug or have a feature request, please open an issue on the GitHub
repository athttps://github.com/samuelmurail/pdb_numpy. If you would like
to contribute code, please fork the repository and submit a pull request.AuthorSamuel Murail <https://samuelmurail.github.io/PersonalPage/>, Associate Professor -Université Paris Cité <https://u-paris.fr>,CMPLI <http://bfa.univ-paris-diderot.fr/equipe-8/>_.See also the list ofcontributors <https://github.com/samuelmurail/pdb_numpy/contributors>_ who participated in this project.LicenseThis project is licensed under the GNU General Public License v2.0 - see theLICENSEfile for details.
Package: pdb-objects
PDB ObjectsSet of classes for object-oriented processing of records from PDB files© 2019  George D. Watson, University of York
(https://georgewatson.me)Available under an MIT license. See the LICENSE file.This package is described ina post on my blog.Supports the following record types:ATOMHETATMTERHELIXSHEETNo other record types are currently implemented, but can be implemented upon
request.Exposes the following classes:PDBRecord(should not normally be used directly, except to implement
another record type)ResidueCoordsAtom(for ATOM and HETATM records)HelixSheetTerExposes the following public functions:read_atomread_helixread_sheetread_terread_recordread_pdbSee class, function, and method docstrings for more information.InstallationAvailableon PyPI.
Usepip3 install pdb-objectsto install,
then putimport pdb_objectsat the top of your script.Alternatively, clonethis repository.
Package: pdbp
pdbp (Pdb+)pdbp (Pdb+)is an advanced console debugger for Python. It can be used as a drop-in replacement forpdbandpdbpp.pdbp (Pdb+)makes Python debugging a lot easier (and more fun!)Installation:pipinstallpdbpThen addimport pdbpto an__init__.pyof your project, which will automatically makePdb+the default debugger at breakpoints:importpdbp(If usingflake8for code-linting, you may want to add# noqato that line):importpdbp# noqaYou can also makepdbpthe default debugger by setting an environmental variable:PYTHONBREAKPOINT=pdbp.set_traceUsage:To trigger a breakpoint in your code withpytest, add--trace(to start tests with a breakpoint) or--pdb(to trigger a breakpoint if a test fails).To trigger a breakpoint from a purepythonrun, use:python-mpdbp<script.py>BasicPdb+console commands:n,c,s,u,d=>next,continue,step,up,down(To learn morePdb+console commands, typehelpin thePdb+console and pressEnter/Return.)pdbp(Pdb+)makes improvements topdbppso that it works in all environments. It also includes other bug-fixes. "Sticky" mode is the default option, which shows multiple lines of code while letting you see where you're going (while typingn+Enter).If you somehow resetpdbto Python's built-in version, you can always replacepdbwithpdbpagain as the default debugger by running this:importpdbimportpdbpforkeyinpdbp.__dict__.keys():pdb.__dict__[key]=pdbp.__dict__[key]Here's how to customizepdbp/pdboptions if you don't like the default settings: (Shown below are the default settings.)importpdbifhasattr(pdb,"DefaultConfig"):pdb.DefaultConfig.filename_color=pdb.Color.fuchsiapdb.DefaultConfig.line_number_color=pdb.Color.turquoisepdb.DefaultConfig.truncate_long_lines=Falsepdb.DefaultConfig.sticky_by_default=TrueYou can also triggerPdb+activation like this:importpdbppdbp.set_trace()pdbp (Pdb+) commands:Post Mortem Debug Mode:Thewhere/wcommand, which displays the current stack:Sticky Mode vs Non-Sticky Mode:The default mode (sticky) lets you see a lot more lines of code from the debugger when active. In Non-Sticky mode, only one line of code is shown at a time. You can switch between the two modes by typingstickyin thePdb+console prompt and pressingEnter/Return.Sticky Mode:Non-Sticky Mode:Tab completion:Multi-layer highlighting in the same stack:More examples:Pdb+is used by packages such asseleniumbase:https://pypi.org/project/seleniumbase/https://github.com/seleniumbase/SeleniumBase(Pdb+is maintained by theSeleniumBase Dev Team)
Package: pdbparse
pdbparseAutomatically exported from code.google.com/p/pdbparsePDBparse is a GPL-licensed library for parsing Microsoft PDB files. Support for these is already available within Windows through the Debug Interface Access API, however, this interface is not usable on other operating systems.PDB files are arranged into streams, each of which contains a specific bit of debug information; for example, stream 1 contains general information on the PDB file, and stream 2 contains information on data structures.Currently, there is support for Microsoft PDB version 7 files (Vista and most Windows XP symbols) as well as version 2 (Windows 2000 and some XP symbols). The following streams are currently supported (seeStreamDescriptionsfor more information on these):Root StreamInfo StreamType StreamDebug Info StreamGlobal Symbol StreamOMAP StreamsSection Header StreamsFPOv1 StreamFPOv2 StreamThe open-source libraryConstructis used to perform the low-level parsing, and is required to run the code.
Package: pdbparser
It’s a Protein Data Bank (.pdb) files manipulation package that is mainly developed to parse and load, duplicate, manipulate and create pdb files.
A full description of a pdb file can be found here:http://deposit.rcsb.org/adit/docs/pdb_atom_format.htmlpdbparser atoms configuration can be visualized by vmd software (http://www.ks.uiuc.edu/Research/vmd/) by simply pointing ‘VMD_PATH’ global variable to the exact path of vmd executable, and using ‘visualize’ method.
At any time and stage of data manipulation, a pdb file of all atoms or a subset of atoms can be exported to a pdb file.
Package: pdbplus
is a proxy for installing(Pdb+).pdbp (Pdb+)pdbp (Pdb+)is an advanced console debugger for Python. It can be used as a drop-in replacement forpdbandpdbpp.pdbp (Pdb+)makes Python debugging a lot easier (and more fun!)Installation:pipinstallpdbpThen addimport pdbpto an__init__.pyof your project, which will automatically makePdb+the default debugger at breakpoints:importpdbp(If usingflake8for code-linting, you may want to add# noqato that line):importpdbp# noqaYou can also makepdbpthe default debugger by setting an environmental variable:PYTHONBREAKPOINT=pdbp.set_traceUsage:To trigger a breakpoint in your code withpytest, add--trace(to start tests with a breakpoint) or--pdb(to trigger a breakpoint if a test fails).To trigger a breakpoint from a purepythonrun, use:python-mpdbp<script.py>BasicPdb+console commands:n,c,s,u,d=>next,continue,step,up,down(To learn morePdb+console commands, typehelpin thePdb+console and pressEnter/Return.)pdbp(Pdb+)makes improvements topdbppso that it works in all environments. It also includes other bug-fixes. "Sticky" mode is the default option, which shows multiple lines of code while letting you see where you're going (while typingn+Enter).If you somehow resetpdbto Python's built-in version, you can always replacepdbwithpdbpagain as the default debugger by running this:importpdbimportpdbpforkeyinpdbp.__dict__.keys():pdb.__dict__[key]=pdbp.__dict__[key]Here's how to customizepdbp/pdboptions if you don't like the default settings: (Shown below are the default settings.)importpdbifhasattr(pdb,"DefaultConfig"):pdb.DefaultConfig.filename_color=pdb.Color.fuchsiapdb.DefaultConfig.line_number_color=pdb.Color.turquoisepdb.DefaultConfig.truncate_long_lines=Falsepdb.DefaultConfig.sticky_by_default=TrueYou can also triggerPdb+activation like this:importpdbppdbp.set_trace()pdbp (Pdb+) commands:Post Mortem Debug Mode:Thewhere/wcommand, which displays the current stack:Sticky Mode vs Non-Sticky Mode:The default mode (sticky) lets you see a lot more lines of code from the debugger when active. In Non-Sticky mode, only one line of code is shown at a time. You can switch between the two modes by typingstickyin thePdb+console prompt and pressingEnter/Return.Sticky Mode:Non-Sticky Mode:Tab completion:Multi-layer highlighting in the same stack:More examples:Pdb+is used by packages such asseleniumbase:https://pypi.org/project/seleniumbase/https://github.com/seleniumbase/SeleniumBase(Pdb+is maintained by theSeleniumBase Dev Team)
Package: pdb-profiling
pdb-profilingProfiling Protein Structures from Protein Data Bank and integrate various resources.FeaturesCollection: Implement various API to collect the well-organized metadata of PDB in real time.Integration: Provide a unified call for API-interface and return-data-form as well as subsequent data processing.Detection: Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB.Interaction: Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level.Selection: Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states.Mapping: Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping.InstallNotice: require Python Environment >= 3.7, Platform IndependentInstall bypipcommand.*Before your InstallationMake sure that your 64-bit machine is installed with 64-bit Python.To avoid some unexpected issues, you should upgrade yourpipbeforehand:python-mpipinstall--upgradepipOfficial Installationpython-mpipinstallpdb-profilingIf you have already installed an older version ofpdb-profiling, use the following command to install the latest version:python-mpipinstall--upgradepdb-profilingBuild From Source (optional, for non-windows environment)python-mpipinstallcython
python-mpipinstallnumpy
gitclonehttps://github.com/NatureGeorge/pdb-profiling.git
pythonsetup.pybuild_ext--inplace# Need GCC or Other Compiler For Cpythonsetup.pyinstall# or "sudo python setup.py install" or "python setup.py install --user"Documentationhttps://pdb-profiling.netlify.app/ExamplesBasic UsageCommand Line ExampleRetrieve Bound Molecule Data From PDBe...Large-Scale-ExampleExACResourcesPDBe Entry-Based APIPDBe Aggregated API (PDBe Graph API)PDBe ModelServer APISWISS-MODEL Repository APIUniProt APIEBI Proteins APIRCSB Data APIRCSB Search APIEutils API (minimum usage)...clickherefor more detailsRelated ResourcesUsing similar data resources but meant to achieve different goals.Click to viewRCSB:Build Customize Tabular Reports of PDB DataMolArtCopyright NoticeThis project is developed byZefeng Zhuand hold byMinghui Group.LicenseThepdb_profiling.cython.py_qcprotmodule is derived from thecython wrapper contributed by Bernhard Thieland is distributed under the terms of a BSD-3-Clause License. And it also contains the dependent C-code fromhttp://theobald.brandeis.edu/QCP/written by Pu Liu and Douglas Theobald (with slight modification by Bernhard Thiel) and is licensed under a BSD-3-Clause License.Thepdb_profilingis distributed under the terms of the MIT License.
Package: pdbreader
PDB readerpdbreaderis a simple python library for parsing PDB (Protein Data Bank) files. It uses pandas DataFrames as its main data structure.Installationpip install pdbreaderUsageimportpdbreaderpdb=pdbreader.read_pdb(pdb_path)The resultingpdbdictionary contains an entry for each record type (ATOM,CONECT, etc) in the form of pandas DataFrames.
Package: pdbreak
A quick break to your python script.Usage#!/usr/bin/env python# encoding: utf-8print1importpdbreak# import pdb;pdb.set_trace()print2Run your script$pythontest.py1--Return--(Pdb)n>/home/lyc/github/pdbreak/test.py(6)<module>()->print2(Pdb)l1#!/usr/bin/env python2# encoding: utf-834print15importpdbreak6->print2[EOF]
Package: pdbstore
pdbstoreis a Python package providing command-line utility to manage PDB symbol store.InstallationAs of first version,pdbstoreis compatible with Python 3.8+.Usepipto install the latest stable version ofpdbstore:$pipinstall--upgradepdbstoreThe current development version is available on bothGitHub.comand can be
installed directly from the git repository:$pipinstallgit+https://github.com/crabisoft/pdbstore.gitBug reportsPlease report bugs and feature requests athttps://github.com/crabisoft/pdbstore/issues.DocumentationThe full documentation for CLI and API is available onreadthedocs.Build the docsWe usetoxto manage our environment and build the documentation:pip install tox
tox -e docsContributingFor guidelines for contributing topdbstore, refer toCONTRIBUTING.rst.
Package: pdbtest
pdbtestUsagepython -m pdbtest [module](after the pattern of python -m unittest [module])Descriptionpdbtestshims the unittest test runner machinery to, when a test fails due to
an exception, print some information about theTestCaseandtest_method, and
then launch the PDB interactive debugger, affording you the opportunity to
easily examine the failure.The library also provides aPDBRunnerMixinclass that you can mix in to your
test runner to achieve the same effect, and a modifiedTestProgramthat will
automatically shim the runner you provide and can be used in the same way asunittest.TestProgram.