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improved automation #6

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improved automation #6

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Commits on Aug 23, 2013

  1. Added header to modules with information regarding authorship and lic… 

    …ensing
    Lennard van der Feltz committed Aug 23, 2013
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  2. Added header to modules with authorship and licensing information

    Lennard van der Feltz committed Aug 23, 2013
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  3. Added header to scripts and modules with authorship and licensing inf… 

    …ormation
    Lennard van der Feltz committed Aug 23, 2013
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Commits on Aug 25, 2013

  1. Added copyright to modules

    Lennard van der Feltz committed Aug 25, 2013
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  2. Added copyright info to scripts

    Lennard van der Feltz committed Aug 25, 2013
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  3. Added copyright to ez_setup.py

    Lennard van der Feltz committed Aug 25, 2013
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  4. Implemented numpy within apbs-mem-properties.py

    Lennard van der Feltz committed Aug 25, 2013
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Commits on Aug 26, 2013

  1. Updated author information with recent copyrights and Added Lennard v… 

    …an der Feltz's copyright.
    Lennard van der Feltz committed Aug 26, 2013
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Commits on Sep 1, 2013

  1. Altered mem-properties.py to include a try statement which returns an… 

    … ImportError if MDAnalysis is not present. Also added comments.
    Lennard van der Feltz committed Sep 1, 2013
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  2. Added default title to pdb2dat and improved writing method.

    Lennard van der Feltz committed Sep 1, 2013
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  3. Improved straightpath writing methodology and added title option. Als… 

    …o changed pdb2dat to make use of default from argparse.
    Lennard van der Feltz committed Sep 1, 2013
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Commits on Sep 3, 2013

  1. Fixed typo in mem-potential comment

    Lennard van der Feltz committed Sep 3, 2013
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Commits on Sep 14, 2013

  1. Added option to input local PDB to mem-properties. Allows for finding… 

    … radii of selections of protein.
    Lennard van der Feltz committed Sep 14, 2013
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  2. Clarified mem-properties output.

    Lennard van der Feltz committed Sep 14, 2013
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Commits on Sep 16, 2013

  1. added no-membrane potential argument handling to io.py

    Lennard van der Feltz committed Sep 16, 2013
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  2. added non-membrane methods to membrane.py for use in potential calcul… 

    …ations.
    Lennard van der Feltz committed Sep 16, 2013
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Commits on Sep 17, 2013

  1. Got output from bornprofile-potential.py, a clone of mem-potential wi… 

    …th membrane references removed. As a result alterations were made to membrane.py and io.py and a new template was introduced. setup.py altered to include new script. Still need to check output, update documentation, and possibly refactor code.
    Lennard van der Feltz committed Sep 17, 2013
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  2. changed output format from .dat to .pdb

    Lennard van der Feltz committed Sep 17, 2013
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  3. fixed pdb format in straightpath script

    Lennard van der Feltz committed Sep 17, 2013
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Commits on Sep 18, 2013

  1. Renamed membrane file "electrostatics.py" to account for the addition… 

    … of a membrane-free class. Updated email in init.py
    Lennard van der Feltz committed Sep 18, 2013
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  2. email update

    Lennard van der Feltz committed Sep 18, 2013
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  3. Logging, text file output, and input allowances added to mem-properti… 

    …es.py. Corrected logger name for electrostatics.py(formerly membrane.py)
    Lennard van der Feltz committed Sep 18, 2013
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Commits on Sep 19, 2013

  1. improved wording, flow of mem-properties.

    Lennard van der Feltz committed Sep 19, 2013
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Commits on Sep 20, 2013

  1. Improved error message organization

    Lennard van der Feltz committed Sep 20, 2013
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Commits on Sep 22, 2013

  1. In mem-properties, relocated all sys.exit to main function body.

    Lennard van der Feltz committed Sep 22, 2013
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Commits on Sep 23, 2013

  1. fixed numbering in output of straightpath.

    Lennard van der Feltz committed Sep 23, 2013
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Commits on Oct 1, 2013

  1. Put logger after options in analyze3D.py to allow for easier help access

    Lennard van der Feltz committed Oct 1, 2013
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Commits on Jan 21, 2014

  1. Added graphing, pdb download, and NEBpath scripts. Included these in … 

    …setup.py.
    Lennard van der Feltz committed Jan 21, 2014
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  2. fixed issues regarding installation of NEBpath.py and treatment of ca… 

    …ses where no options are submitted to 1dgraph.py
    Lennard van der Feltz committed Jan 21, 2014
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  3. fixed typo in 1Dgraph.py

    Lennard van der Feltz committed Jan 21, 2014
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Commits on Jan 25, 2014

  1. fixed logging in protein_pdb

    Lennard van der Feltz committed Jan 25, 2014
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  2. Improved logging messages in protein_pdb for use in automation of 1D … 

    …profiles
    Lennard van der Feltz committed Jan 25, 2014
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Commits on Jan 28, 2014

  1. Updated mem-properties.py to improve logging placement and return val… 

    …ues for use in automation.
    Lennard van der Feltz committed Jan 28, 2014
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  2. added graphing section to config file defaults.

    Lennard van der Feltz committed Jan 28, 2014
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Commits on Feb 7, 2014

  1. cleaned up leftover files and added new function library for function… 

    …s relating to run preparation.
    Lennard van der Feltz committed Feb 7, 2014
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  2. cleaned up leftover perl files and moved functions in scripts relatin… 

    …g to run preparation to library in bornprofiler.
    Lennard van der Feltz committed Feb 7, 2014
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  3. actually cleaned up perl files.

    Lennard van der Feltz committed Feb 7, 2014
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Commits on Feb 8, 2014

  1. fixed __init__ function for basemem class

    Lennard van der Feltz committed Feb 8, 2014
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Commits on Feb 24, 2014

  1. introduced plotting library to hold function definitions for 1dgraph … 

    …script
    Lennard van der Feltz committed Feb 24, 2014
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  2. Moved plotting functions to library in bornprofiler and changed atomn… 

    …um in NEB.dat to int.
    Lennard van der Feltz committed Feb 24, 2014
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Commits on Feb 25, 2014

  1. First working build of BPauto.py completed.

    Lennard van der Feltz committed Feb 25, 2014
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Commits on Feb 27, 2014

  1. Updated BPauto.py to edit glen and dime to avoid failed calculations

    Lennard van der Feltz committed Feb 27, 2014
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Commits on Mar 13, 2014

  1. Added logging statements to BPauto.py

    Lennard van der Feltz committed Mar 13, 2014
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  2. added scripts to setup.py

    Lennard van der Feltz committed Mar 13, 2014
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  3. added autoanalyze script

    Lennard van der Feltz committed Mar 13, 2014
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Commits on Mar 15, 2014

  1. Added submit command to BPauto

    Lennard van der Feltz committed Mar 15, 2014
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Commits on Mar 19, 2014

  1. Added checking of glen values against points for calculation for plac… 

    …eion and mplaceion in core.py.
    Lennard van der Feltz committed Mar 19, 2014
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Commits on Mar 20, 2014

  1. Improved grid checking algorithm and logging messages in core.py

    Lennard van der Feltz committed Mar 20, 2014
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Commits on Mar 31, 2014

  1. Removed attempted glen automation from Placeion class in core.py

    Lennard van der Feltz committed Mar 31, 2014
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  2. Merged placeion and mplaceion functionalities into new placeion script

    Lennard van der Feltz committed Mar 31, 2014
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  3. Removed reference to mplaceion from setup.py

    Lennard van der Feltz committed Mar 31, 2014
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Commits on Apr 3, 2014

  1. cleanup of placeion classes and improvement of grid checking algorithm.

    Lennard van der Feltz committed Apr 3, 2014
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  2. Removed template option from placeion.

    Lennard van der Feltz committed Apr 3, 2014
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Commits on Apr 5, 2014

  1. Cleanup and renaming of io.py to bpio.py and changing references from… 

    … io.py to bpio.py in relevant files.
    Lennard van der Feltz committed Apr 5, 2014
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  2. 1Dgraph changed to enable submission of cfg file. BPauto minor cleanup.

    Lennard van der Feltz committed Apr 5, 2014
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Commits on Apr 8, 2014

  1. Add cfg_template script which produces a default cfg file under some … 

    …specifications. Also leaned up some io references(corrected to bpio)
    Lennard van der Feltz committed Apr 8, 2014
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  2. Made changes to allow for template cfg creation to omit certain secti… 

    …ons.
    Lennard van der Feltz committed Apr 8, 2014
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Commits on Apr 15, 2014

  1. corrected 'graphing' section of BPauto script to 'plotting'

    Lennard van der Feltz committed Apr 15, 2014
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  2. Corrected naming of graphing functions in 1Dgraph.py

    Lennard van der Feltz committed Apr 15, 2014
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  3. Added protein and membrane plotting, fixed minor typos

    Lennard van der Feltz committed Apr 15, 2014
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Commits on Apr 16, 2014

  1. imrpoved logging in plotting functions regarding cfg reading.

    Lennard van der Feltz committed Apr 16, 2014
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  2. Added documentation,comments, and licensing to 1Dgraph and autoanalyze

    Lennard van der Feltz committed Apr 16, 2014
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  3. Changed legend to loc='best'on all functions in plotting.py

    Lennard van der Feltz committed Apr 16, 2014
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Commits on Apr 20, 2014

  1. added pdf format saving to plotting.py

    Lennard van der Feltz committed Apr 20, 2014
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Commits on Apr 24, 2014

  1. Added fancier formatting to 1Dgraph.py

    Lennard van der Feltz committed Apr 24, 2014
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Commits on Apr 25, 2014

  1. Corrected small formatting mistake in 1Dgraph.py

    Lennard van der Feltz committed Apr 25, 2014
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Commits on May 19, 2014

  1. Fixed more graphing/plotting naming errors, adapted Run_Parameters' _… 

    …populate_default to work with both placeion and cfg_template scripts.
    Lennard van der Feltz committed May 19, 2014
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Commits on May 24, 2014

  1. updated anaylsis to update import io statement to import bpio and Run… 

    …Parameters call to include additional options for compatibility with new populate defaults function.
    Lennard van der Feltz committed May 24, 2014
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Commits on Jun 3, 2014

  1. Changed from pyplot to matplotlib in analysis.py plotting and altered… 

    … backend to AGG to allow for remote use.
    Lennard van der Feltz committed Jun 3, 2014
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Commits on Jun 16, 2014

  1. Added pH option to BPauto script, and changed submission from default… 

    … to optional.
    Lennard van der Feltz committed Jun 16, 2014
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Commits on Jul 28, 2014

  1. Adapted 1dgraph.py to submit to a single function in bornprofiler/plo… 

    …tting.py with the option to use seaborn to improve plot quality.
    Lennard van der Feltz committed Jul 28, 2014
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  2. Updated placeion.py help info

    Lennard van der Feltz committed Jul 28, 2014
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  3. Added warning message to bpio.RunParameters to alert user if H ion is… 

    … selected and suggest use of H30 instead
    Lennard van der Feltz committed Jul 28, 2014
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  4. fixed bpio.RunParameters hydrogen warning

    Lennard van der Feltz committed Jul 28, 2014
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Commits on Sep 2, 2014

  1. Finally staged changes that had gone unadded due to negligence. Recen… 

    …t fixes include membraneless bp runs and the addition of support for runs larger than 10k points.
    Lennard van der Feltz committed Sep 2, 2014
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  2. Comments to explain BPauto process for ensuring coarse grids complete… 

    …ly enclose all fine grids.
    Lennard van der Feltz committed Sep 2, 2014
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Commits on Oct 22, 2014

  1. Added datalgebra with capacity to take difference between two 1d BP d… 

    …at files using z interpolation of energies
    Lennard van der Feltz committed Oct 22, 2014
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Commits on Oct 25, 2014

  1. Refactored datalgebra functions into array_alg and bpio. Added averag… 

    …e to datalgebra and added object algebra to datarray objects.
    Lennard van der Feltz committed Oct 25, 2014
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Commits on Oct 26, 2014

  1. Added ability to choose axis for operations in array_alg and error me… 

    …ssages for when attempting unreasonable manipulations.
    Lennard van der Feltz committed Oct 26, 2014
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Commits on Dec 12, 2014

  1. tweaked NEB cutoff to better value(spacing/10.0 instead of spacing/10… 

    …0.0)
    Lennard van der Feltz committed Dec 12, 2014
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Commits on May 11, 2015

  1. "Prepping for merge with master"

    Lennard van der Feltz committed May 11, 2015
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  2. More merge prep

    Lennard van der Feltz committed May 11, 2015
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