Metadata-Version: 1.1
Name: d3r
Version: 1.7.1
Summary: Drug Design Data Resource CELPP Runner is an application to run the filtering, docking, and evaluation of new sequences from wwpdb
Home-page: https://github.com/drugdata/D3R
Author: Christopher Churas <churas@ncmir.ucsd.edu>,Shaui Liu <shuailiu25@gmail.com>,Jeff Wagner <j5wagner@ucsd.edu>,Rob Swift <rvswift@ucsd.edu>
Author-email: drugdesigndata@gmail.com
License: Other
Description: ======================================
        Drug Design Data Resource CELPP Runner
        ======================================
        
        .. image:: https://img.shields.io/travis/drugdata/D3R.svg
                :target: https://travis-ci.org/drugdata/D3R.svg?branch=master
        
        .. image:: https://img.shields.io/pypi/v/D3R.svg
                :target: https://pypi.python.org/pypi/D3R
                
        .. image:: https://coveralls.io/repos/github/drugdata/D3R/badge.svg?branch=master 
                :target: https://coveralls.io/github/drugdata/D3R?branch=master
        
        
        Drug Design Data Resource is a suite of software to enable 
        filtering, docking, and scoring of new sequences from 
        `wwpdb <http://www.wwpdb.org/>`_.
        
        For more information please visit our wiki page:
        
        https://github.com/drugdata/d3r/wiki
        
        
        Compatibility
        -------------
        
         * Works with Python 2.6, 2.7
        
        
        Dependencies
        ------------
        
         * `argparse <https://pypi.python.org/pypi/argparse>`_
         * `lockfile <https://pypi.python.org/pypi/lockfile>`_
         * `psutil <https://pypi.python.org/pypi/psutil>`_
         * `biopython <https://pypi.python.org/pypi/biopython>`_
         * `xlsxwriter <https://pypi.python.org/pypi/xlsxwriter>`_
         * `ftpretty <https://pypi.python.org/pypi/ftpretty>`_
         * `NCBI Blast <https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>`_ (needed by blastnfilter.py)
         * `rdkit <http://www.rdkit.org/>`_ (needed by blastnfilter.py and proteinligprep.py)
         * `schrodinger <https://www.schrodinger.com/>`_ (needed by proteinligprep.py, glidedocking.py, chimera_proteinligprep.py & vinadocking.py)
         * `babel <http://openbabel.org/wiki/Main_Page>`_ (needed by chimera_proteinligprep.py)
         * `Autodock Vina <http://vina.scripps.edu/>`_ & `MGL Tools <http://mgltools.scripps.edu/downloads>`_ (needed by vinadocking.py)
        
        
        Installation
        ------------
        
        .. code:: bash
        
          pip install d3r
        
        Usage
        -----
        
        Run
        
        .. code:: bash
          
          celpprunner.py --help
        
        
        License
        -------
        
        See LICENSE.txt_
        
        Bugs
        -----
        
        Please report them `here <https://github.com/drugdata/D3R/issues>`_
        
        
        Acknowledgements
        ----------------
        
        * This work is funded in part by NIH grant 1U01GM111528 from the National Institute of General Medical Sciences
        
        * This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _LICENSE.txt: https://github.com/drugdata/D3R/blob/master/LICENSE.txt 
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        
        
        History
        -------
        
        1.7.1 (2017-03-27)
        --------------------
        
        * Bug fix, evaluation task will not fail if call to external
          script fails. `Issue #129 <https://github.com/drugdata/D3R/issues/129>`_
        
        1.7.0 (2017-03-21)
        --------------------
        
        * Added Post Evaluation Stage which summarizes evaluations
          of all docking submissions sending email to addresses set
          by --summaryemail flag
          `Issue #111 <https://github.com/drugdata/D3R/issues/111>`_
          `Issue #110 <https://github.com/drugdata/D3R/issues/110>`_
          `Issue #100 <https://github.com/drugdata/D3R/issues/100>`_
        
        * If any task/stage fails report that via email to addresses
          set by --summaryemail flag
          `Issue #125 <https://github.com/drugdata/D3R/issues/125>`_ 
        
        * Order of evaluation of external dock submissions can now be 
          dictated by a new column in participant_list.csv
          `Issue #124 <https://github.com/drugdata/D3R/issues/124>`_
        
        * A timeout has now been added for blastnfilter stage to prevent
          the task/stage from running too long. Default is 24 hours, but
          can be changed with --blastnfiltertimeout flag.
          `Issue #8 <https://github.com/drugdata/D3R/issues/8>`_
        
        * A timeout has now been added for evaluation stage to prevent
          the task/stage from running too long. Default is 24 hours, but
          can be changed with --evaluationtimeout flag.
          `Issue #123 <https://github.com/drugdata/D3R/issues/123>`_ 
        
        * Fixed bug in blastnfilter to correctly rank the list of 
          hiTanimoto candidates.
        
        1.6.8 (2017-03-07)
        ------------------
        
        * Celpprunner puts lock file within specific week directory. 
          `Issue #122 <https://github.com/drugdata/D3R/issues/122>`_
        
        1.6.7 (2017-02-07)
        ------------------
        
        * Increased retry time for challengedata download to 1 hour
        
        * Updates to evaluation suffix structure (Allows for more complex suffixes after guids)
        
        * Fixed bugs in CELPPade error messages
        
        1.6.6 (2017-01-23)
        ------------------
        
        * Add retry to external submission downloads. 
          `Issue #112 <https://github.com/drugdata/D3R/issues/112>`_
        
        1.6.5 (2017-01-13)
        ------------------
        
        * Fix the bug to skip invalid holo hit instead of terminating the whole blastnfilter process. 
          `Issue #89 <https://github.com/drugdata/D3R/issues/89>`_
        
        * Fix the bug in the set sequence fuction where it original complains about the lower cased chain ID
        
        1.6.4 (2017-01-10)
        ------------------
        
        * Remove intermediate files with pymol prefix from challenge data
          package. `Issue #73 <https://github.com/drugdata/D3R/issues/73>`_
        
        * Place docked files in top-level target directory in submissions.
          `Issue #86 <https://github.com/drugdata/D3R/issues/86>`_
        
        * Fixed sporadically failing unit test. `Issue #104 <https://github.com/drugdata/D3R/issues/104>`_
        
        * Add evaluation chain permuter implementation and tests. `Issue #107 <https://github.com/drugdata/D3R/issues/107>`_
        
        1.6.3 (2016-12-01)
        -------------------
        
        * Modified ParticipantDatabase to optionally strip off _# from guid
          when doing search for Participant. This is to handle case where
          single participant has multiple submissions to CELPP. `Issue #98 <https://github.com/drugdata/D3R/issues/98>`_
        
        * Switched os.getlogin() calls to  pwd.getpwuid(os.getuid())[0] 
          cause os.getlogin() was raising OSError on Travis. `Issue #102 <https://github.com/drugdata/D3R/issues/102>`_
        
        * Fixed bug where evaluation task completed email had log messages
          from other evaluation task emails in them. `Issue #99 <https://github.com/drugdata/D3R/issues/99>`_
        
        * Updated readme.txt file in challenge data package to reflect
          use of new_release_structure_sequence_canonical.tsv instead of
          new_release_structure_sequence.tsv file. `Issue #97 <https://github.com/drugdata/D3R/issues/97>`_
        
        1.6.2 (2016-10-26)
        -------------------
        
        * Fixed bug where large amounts of output to standard out/err caused
          celpprunner.py to exit due to an exception from smtplib due to 
          very large email. `Issue #95 <https://github.com/drugdata/D3R/issues/95>`_
        
        1.6.1 (2016-10-24)
        -------------------
        
        * Added createchallenge stage which is NOT a stage, but a fake stage
          that runs the following stages: makedb,import,blast,challengedata. `Issue #92 <https://github.com/drugdata/D3R/issues/92>`_
        
        * Moved logic to setup logging handlers to start of celpprunner.py to remove
          no handlers found error for d3r.celpp.util. `Issue #91 <https://github.com/drugdata/D3R/issues/91>`_
        
        * Fixed bug where participant_list.csv could not be parsed if file was 
          written with carriage return delimiters instead of newlines. `Issue #93 <https://github.com/drugdata/D3R/issues/93>`_
          
        * Cleaned up CELPPade by updating documentation and simplifying variable names
        
        * Version of d3r is now written to 'start' file in each stage/task. `Issue #94 <https://github.com/drugdata/D3R/issues/94>`_
        
        1.6.0 (2016-10-13)
        -------------------
        
        * Evaluation task now emails results of evaluation to external 
          submitter. Issues `#49 <https://github.com/drugdata/D3R/issues/49>`_ , `#81 <https://github.com/drugdata/D3R/issues/81>`_
        
        * Adjusted files uploaded to ftp server in EvaluationTask to 
          reflect changes in output from genchallengedata.py script.
          Issues `#79 <https://github.com/drugdata/D3R/issues/79>`_ , `#80 <https://github.com/drugdata/D3R/issues/80>`_
        
        * Added WebDavFileTransfer class to enable upload & download
          of files via WebDa for celppade tools. `Issue #76 <https://github.com/drugdata/D3R/issues/76>`_ 
        
        * Added tsv files and Components-inchi.ich files to list of 
          files uploaded to ftp by DataImportTask. `Issue #78 <https://github.com/drugdata/D3R/issues/78>`_
        
        * Updated challenge data package readme.txt to include documentation
          for hiTanimoto. `Issue #75 <https://github.com/drugdata/D3R/issues/75>`_
        
        * Added pdb_seqres.txt.gz to list of files uploaded to ftp by
          MakeBlastDBTask. `Issue #77 <https://github.com/drugdata/D3R/issues/77>`_
        
        * Download canonical tsv file in data import stage. `Issue #84 <https://github.com/drugdata/D3R/issues/84>`_
        
        * Added --rdkitpython flag to celpprunner.py and modified
          code to pass it to chimera_proteinligprep.py. `Issue #88 <https://github.com/drugdata/D3R/issues/88>`_
        
        * Fixed bug where celpprunner would fail if evaluation 
          stage is rerun with completed evaluation tasks. `Issue #87 <https://github.com/drugdata/D3R/issues/87>`_
        
        * Improved documentation in RMSD.txt. Issues `#82 <https://github.com/drugdata/D3R/issues/82>`_ , `#83 <https://github.com/drugdata/D3R/issues/83>`_
        
        1.5.0 (2016-09-11)
        --------------------
        
        * Modified blastnfilter candidate txt file by adding hiTanimoto and 
          adding more information to hiResHolo and SMCSS.
        
        * Genchallengedata.py modified to keep single chains for all holo
          proteins (LMCSS, SMCSS, hiResHolo, hiTanimoto)
        
        * In blastnfilter, hiResHolo now only has top structure 
          reported and only one chain. Where top structure is 
          highest resolution hit.
        
        1.4.0 (2016-08-11)
        --------------------
        
        * Fixed issue #66 Change candidate category names. Largest is now LMCSS,
          Smallest is now SMCSS, Apo is now HiResApo, Holo is now HiResHolo
        
        1.3.4
        --------------------
        
        * Fixed issue #58 in chimera_proteinligprep.py code now uses rdkit 
          for 3d conf gen instead of babel
        
        1.3.3 (2016-07-18)
        --------------------
        
        * Fixed issue #60 where challenge data package was NOT being
          uploaded to remote server
        
        1.3.2 (2016-07-12)
        --------------------
        
        * Removed #8 blastnfilter timeout since it was causing blastnfilter
          script to hang.
        
        * Blastnfilter.py now uses argparse to parse command line arguments
        
        * Added loggging support into blastnfilter.py 
        
        1.3.1 (2016-07-01)
        ---------------------
        
        * In proteinligprep.py ligprep command modified. -s 1 -g flags 
          removed and -ns flag added to preserve stereo information
        
        1.3.0 (2016-06-29)
        ---------------------
        
        * Fixed bug #45 where autodock vina task was being incorrectly
          fed proteinligprep as input. Code now feeds it chimeraprep
        
        * #28 Data import stage waits for TSV files to be updated before
          downloading
        
        * #8 celpprunner will now kill blastnfilter if it runs beyond
          time set via --blastnfiltertimeout flag
        
        * #37 Added external docking submission task which downloads
          external docked results so they can be evaluated the same
          way as the internal docking programs
        
        * #44 Added utility function to call external processes. To
          reduce redundancy in the code base
        
        
        1.2.0 (2016-06-03)
        ---------------------
        
        * proteinligprep.py and chimera_proteinligprep.py
          has been updated to work with genchallenge stage output
        
        * vinadocking.py and glidedocking.py now output receptor as pdb
          and ligand as mol.
        
        * evaluate.py modified to accept new output format as described
          here:  https://github.com/drugdata/D3R/wiki/Proposed-challenge-docked-results-file-structure
        
        * ProteinLigPrepTask #41 modified to use ChallengeDataTask as input
        
        * ChimeraProteinLigPrepTask #30 modified to use ChallengeDataTask as input
        
        1.1.0 (2016-05-24)
        ---------------------
        
        * ChallengeDataTask now uploads challenge data package 
          (celpp_week##_##.tar.gz) to 'challengedata' directory on
          ftp if ftpconfig is set properly.  This is in addition, to
          the default upload directory for that challenge data package
        
        * Added a header line in readme.txt of challenge data package
          to denote start of Blastnfilter summary output.
        
        * Not part of production release, but added prototype vagrant 
          configuration to enable easy creation of a VM that can run
          celpprunner.
        
        1.0.0 (2016-05-12)
        ---------------------
        
        * Added chimeraprep stage to prepare data with Chimera 
          (issue #32)
         
        * Added challengedata stage to generate challenge data package (issue #22)
          and added genchallengedata.py script which does the work (issue #21)
        
        * Added vina stage to run docking with autodock vina (issue #15)
          and added vinadocking.py script to run the docking
        
        * Modified D3rTask to write error message into 'error' file (issue #12)
        
        * Added celppreports.py to provide summary reports (issue #14)
        
        * Modified DataImportTask to compare entries in tsv file with 
          data in pdb_seqres.txt in makeblastdb stage.  As part of this
          fix made dataimport stage dependent on makeblastdb stage so
          the order is now stage.1.makeblastdb => stage.2.dataimport =>
          stage.3.blastnfilter... (issue #16)
        
        0.1.0 (2015-06-30)
        ---------------------
        
        * First release on PyPI
        
        
Keywords: d3r
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: Free for non-commercial use
Classifier: Natural Language :: English
Classifier: Environment :: Console
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Chemistry
