Metadata-Version: 1.1
Name: d3r
Version: 1.9.0
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>,Shuai 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
        
        .. image:: https://zenodo.org/badge/32555382.svg
           :target: https://zenodo.org/badge/latestdoi/32555382
        
        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)
         * `OpenEye Python with License <https://docs.eyesopen.com/toolkits/python/index.html>`_ (needed by blastnfilter.py symmetry filter and by evaluate.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
        -------
        
        1.9.0 (2017-06-23)
        --------------------
        
        * EvaluationTask now records evaluate.py task exit code in a file
          `Issue #134 <https://github.com/drugdata/D3R/issues/134>`_
        
        * Symmetry filter added to blastnfilter.py
          `Issue #145 <https://github.com/drugdata/D3R/issues/145>`_
        
        * In RMSD.txt,RMSD.csv renamed Medium to Median and swapped values
          for Maximum and Minimum
          `Issue #144 <https://github.com/drugdata/D3R/issues/144>`_
        
        * Added note about new values in parenthesis in individual results
          email
          `Issue #142 <https://github.com/drugdata/D3R/issues/142>`_
        
        1.8.0 (2017-05-18)
        --------------------
        
        * EvaluationTask modified to pass path to blastnfilter task to evaluate.py
          `Issue #139 <https://github.com/drugdata/D3R/issues/139>`_
        
        * Median RMSD added to post_evaluation.py outputs
          `Issue #136 <https://github.com/drugdata/D3R/issues/136>`_
        
        * Added histogram of RMSD scores to post_evaluation.py outputs
          `Issue #137 <https://github.com/drugdata/D3R/issues/137>`_
        
        * Continuously output the analysis result into the pickle csv and txt files
          `Issue #133 <https://github.com/drugdata/D3R/issues/133>`_
        
        * Align the docked complex using the binding site alignment for each of the crystal template and calculate the RMSD, if the binding site alignment failed, then the whole protein alignment will be applied
        
        * Improve the extraction step in the evaluate.py to ensure the RMSD calculating was only applied to the docked ligand but not all others ligand like solvents or co-factors
        
        * Add the ligand center calculation step in the evaluate.py to output the distance of the docked ligand with the crystal ligand. Also calculate the distance between the original LMCSS ligand center with the crystal ligand center
        
        * Update the genchallengedata.py to extract Apo chain which is closed to the LMCSS ligand `Issue #135 <https://github.com/drugdata/D3R/issues/135>`_
        
        
        1.7.3 (2017-04-11)
        --------------------
        
        * requirements.txt and setup.py modified to require biopython 
          v1.6.8, which is the last version compatible with python2.6
        
        
        1.7.2 (2017-04-11)
        --------------------
        
        * Bug fix, evaluation of a submission will not fail if one
          candidate in that submission fails.
        
        
        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
