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improved automation #6

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improved automation #6

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743f9f2
Added header to modules with information regarding authorship and lic…
Aug 23, 2013
8209def
Added header to modules with authorship and licensing information
Aug 23, 2013
a130d29
Added header to scripts and modules with authorship and licensing inf…
Aug 23, 2013
575d10e
Added copyright to modules
Aug 25, 2013
1b25999
Added copyright info to scripts
Aug 25, 2013
ef01f4b
Added copyright to ez_setup.py
Aug 25, 2013
7f4ef9d
Implemented numpy within apbs-mem-properties.py
Aug 25, 2013
5f823b0
Updated author information with recent copyrights and Added Lennard v…
Aug 26, 2013
d8d1650
Altered mem-properties.py to include a try statement which returns an…
Sep 1, 2013
49998f6
Added default title to pdb2dat and improved writing method.
Sep 1, 2013
f4eb0f6
Improved straightpath writing methodology and added title option. Als…
Sep 1, 2013
16d5d03
Fixed typo in mem-potential comment
Sep 3, 2013
11cd1da
Added option to input local PDB to mem-properties. Allows for finding…
Sep 14, 2013
2cd04e1
Clarified mem-properties output.
Sep 14, 2013
93e958b
added no-membrane potential argument handling to io.py
Sep 16, 2013
4ddba52
added non-membrane methods to membrane.py for use in potential calcul…
Sep 16, 2013
2013dc2
Got output from bornprofile-potential.py, a clone of mem-potential wi…
Sep 17, 2013
1e5b22b
changed output format from .dat to .pdb
Sep 17, 2013
a4136c4
fixed pdb format in straightpath script
Sep 17, 2013
9d8888a
Renamed membrane file "electrostatics.py" to account for the addition…
Sep 18, 2013
800bcce
email update
Sep 18, 2013
b56a006
Logging, text file output, and input allowances added to mem-properti…
Sep 18, 2013
4596747
improved wording, flow of mem-properties.
Sep 19, 2013
39a947a
Improved error message organization
Sep 20, 2013
37edd33
In mem-properties, relocated all sys.exit to main function body.
Sep 22, 2013
21d649f
fixed numbering in output of straightpath.
Sep 23, 2013
61e7a19
Put logger after options in analyze3D.py to allow for easier help access
Oct 1, 2013
dc6505c
Added graphing, pdb download, and NEBpath scripts. Included these in …
Jan 21, 2014
102a504
fixed issues regarding installation of NEBpath.py and treatment of ca…
Jan 21, 2014
d1e0589
fixed typo in 1Dgraph.py
Jan 21, 2014
c3a7fb3
fixed logging in protein_pdb
Jan 25, 2014
345ab2c
Improved logging messages in protein_pdb for use in automation of 1D …
Jan 25, 2014
e7f7013
Updated mem-properties.py to improve logging placement and return val…
Jan 28, 2014
c289f16
added graphing section to config file defaults.
Jan 28, 2014
eba2659
cleaned up leftover files and added new function library for function…
Feb 7, 2014
4dd788d
cleaned up leftover perl files and moved functions in scripts relatin…
Feb 7, 2014
3372b69
actually cleaned up perl files.
Feb 7, 2014
419d969
fixed __init__ function for basemem class
Feb 8, 2014
2f85dee
introduced plotting library to hold function definitions for 1dgraph …
Feb 24, 2014
13059b2
Moved plotting functions to library in bornprofiler and changed atomn…
Feb 24, 2014
67cd9c2
First working build of BPauto.py completed.
Feb 25, 2014
bcbdaa2
Updated BPauto.py to edit glen and dime to avoid failed calculations
Feb 27, 2014
4e190d9
Added logging statements to BPauto.py
Mar 13, 2014
4bc4297
added scripts to setup.py
Mar 13, 2014
2b073e6
added autoanalyze script
Mar 13, 2014
e1fc25c
Added submit command to BPauto
Mar 15, 2014
73ee71f
Added checking of glen values against points for calculation for plac…
Mar 19, 2014
a3bf344
Improved grid checking algorithm and logging messages in core.py
Mar 20, 2014
3297b6c
Removed attempted glen automation from Placeion class in core.py
Mar 31, 2014
eb4eb05
Merged placeion and mplaceion functionalities into new placeion script
Mar 31, 2014
a823907
Removed reference to mplaceion from setup.py
Mar 31, 2014
5cf3001
cleanup of placeion classes and improvement of grid checking algorithm.
Apr 3, 2014
febc89e
Removed template option from placeion.
Apr 3, 2014
b8c07ad
Cleanup and renaming of io.py to bpio.py and changing references from…
Apr 5, 2014
56e5db3
1Dgraph changed to enable submission of cfg file. BPauto minor cleanup.
Apr 5, 2014
7598eec
Add cfg_template script which produces a default cfg file under some …
Apr 8, 2014
b211a35
Made changes to allow for template cfg creation to omit certain secti…
Apr 8, 2014
744b917
corrected 'graphing' section of BPauto script to 'plotting'
Apr 15, 2014
0853644
Corrected naming of graphing functions in 1Dgraph.py
Apr 15, 2014
ebdb688
Added protein and membrane plotting, fixed minor typos
Apr 15, 2014
567e982
imrpoved logging in plotting functions regarding cfg reading.
Apr 16, 2014
1b08b05
Added documentation,comments, and licensing to 1Dgraph and autoanalyze
Apr 16, 2014
2c9f653
Changed legend to loc='best'on all functions in plotting.py
Apr 16, 2014
50191b1
added pdf format saving to plotting.py
Apr 20, 2014
c759082
Added fancier formatting to 1Dgraph.py
Apr 24, 2014
1953d17
Corrected small formatting mistake in 1Dgraph.py
Apr 25, 2014
abc3127
Fixed more graphing/plotting naming errors, adapted Run_Parameters' _…
May 19, 2014
742d7cd
updated anaylsis to update import io statement to import bpio and Run…
May 24, 2014
31eaa94
Changed from pyplot to matplotlib in analysis.py plotting and altered…
Jun 3, 2014
41e50cd
Added pH option to BPauto script, and changed submission from default…
Jun 16, 2014
1be1e1c
Adapted 1dgraph.py to submit to a single function in bornprofiler/plo…
Jul 28, 2014
c8b194d
Updated placeion.py help info
Jul 28, 2014
0c5fd59
Added warning message to bpio.RunParameters to alert user if H ion is…
Jul 28, 2014
d29ca2a
fixed bpio.RunParameters hydrogen warning
Jul 28, 2014
321be5d
Finally staged changes that had gone unadded due to negligence. Recen…
Sep 2, 2014
e5ecc34
Comments to explain BPauto process for ensuring coarse grids complete…
Sep 2, 2014
c17cad3
Added datalgebra with capacity to take difference between two 1d BP d…
Oct 22, 2014
68f7ce6
Refactored datalgebra functions into array_alg and bpio. Added averag…
Oct 25, 2014
c2fe842
Added ability to choose axis for operations in array_alg and error me…
Oct 26, 2014
95e2108
tweaked NEB cutoff to better value(spacing/10.0 instead of spacing/10…
Dec 12, 2014
f7374e1
"Prepping for merge with master"
May 11, 2015
93b404d
More merge prep
May 11, 2015

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