From 3ba5bb4b8ffc174953d0e06f2f7f31a03b18cb89 Mon Sep 17 00:00:00 2001 From: "James W. Barnett" Date: Tue, 26 May 2015 19:56:04 -0500 Subject: [PATCH 1/6] add setup --- .gitignore | 3 ++ DESCRIPTION.rst | 9 +++++ setup.py | 104 ++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 DESCRIPTION.rst create mode 100644 setup.py diff --git a/.gitignore b/.gitignore index 0d20b64..7db9a19 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,4 @@ +*.egg-info *.pyc +build +dist diff --git a/DESCRIPTION.rst b/DESCRIPTION.rst new file mode 100644 index 0000000..c5cd971 --- /dev/null +++ b/DESCRIPTION.rst @@ -0,0 +1,9 @@ +Alchemical Analysis +======================= + +Analyze alchemical free energy calculations conducted in GROMACS, AMBER or SIRE +using recommended best practices from Klimovich et al., JCAMD 29:397-411 +(2015). This tool handles analysis via a slate of free energy methods, including BAR, +MBAR, TI, and the Zwanzig relationship (exponential averaging) among others, +and provides a good deal of analysis of computed free energies and convergence +in order to help you assess the quality of your results. diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..cb5c36a --- /dev/null +++ b/setup.py @@ -0,0 +1,104 @@ +"""Alchemical Analysis + +See: +https://github.com/MobleyLab/alchemical-analysis +""" + +# Always prefer setuptools over distutils +from setuptools import setup, find_packages +# To use a consistent encoding +from codecs import open +from os import path + +here = path.abspath(path.dirname(__file__)) + +# Get the long description from the relevant file +with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f: + long_description = f.read() + +setup( + name='alchemical_analysis', + + # Versions should comply with PEP440. For a discussion on single-sourcing + # the version across setup.py and the project code, see + # https://packaging.python.org/en/latest/single_source_version.html + version='0.1.0', + + description='Alchemical Analysis', + long_description=long_description, + + # The project's main homepage. + url='https://github.com/MobleyLab/alchemical-analysis', + + # Author details + author='Pavel Klimovich, Michael Shirts, and David Mobley', + author_email='dmobley@mobleylab.org', + + # Choose your license + license='LGPL', + + # See https://pypi.python.org/pypi?%3Aaction=list_classifiers + classifiers=[ + # How mature is this project? Common values are + # 3 - Alpha + # 4 - Beta + # 5 - Production/Stable + 'Development Status :: 5 - Production/Stable', + + # Indicate who your project is intended for + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Chemistry', + 'Topic :: Scientific/Engineering :: Physics', + + # Pick your license as you wish (should match "license" above) + 'License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)', + + # Specify the Python versions you support here. In particular, ensure + # that you indicate whether you support Python 2, Python 3 or both. + 'Programming Language :: Python :: 2.7', + ], + + # What does your project relate to? + keywords='sample setuptools development', + + # You can just specify the packages manually here if your project is + # simple. Or you can use find_packages(). + packages=find_packages(exclude=['contrib', 'docs', 'tests*']), + + # List run-time dependencies here. These will be installed by pip when + # your project is installed. For an analysis of "install_requires" vs pip's + # requirements files see: + # https://packaging.python.org/en/latest/requirements.html + install_requires=['pymbar'], + + # List additional groups of dependencies here (e.g. development + # dependencies). You can install these using the following syntax, + # for example: + # $ pip install -e .[dev,test] + # extras_require={ + # 'dev': ['check-manifest'], + # 'test': ['coverage'], + #}, + + # If there are data files included in your packages that need to be + # installed, specify them here. If using Python 2.6 or less, then these + # have to be included in MANIFEST.in as well. + #package_data={ + # 'sample': ['package_data.dat'], + #}, + + # Although 'package_data' is the preferred approach, in some case you may + # need to place data files outside of your packages. See: + # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa + # In this case, 'data_file' will be installed into '/my_data' + #data_files=[('my_data', ['data/data_file'])], + + # To provide executable scripts, use entry points in preference to the + # "scripts" keyword. Entry points provide cross-platform support and allow + # pip to create the appropriate form of executable for the target platform. + #entry_points={ + # 'console_scripts': [ + # 'sample=sample:main', + # ], + #}, +) From 1d5ed6b2dfc2ac28a1f9f83c766f9fc0f4f4ac7d Mon Sep 17 00:00:00 2001 From: "James W. Barnett" Date: Tue, 26 May 2015 22:35:35 -0500 Subject: [PATCH 2/6] work on file hiearchy for packaging --- .../alchemical_analysis.py | 8 ++++++-- .../parsers/__init__.py | 0 .../parsers}/parser_amber.py | 0 .../parsers}/parser_gromacs.py | 0 .../parsers}/parser_sire.py | 0 .../parsers}/unixlike.py | 0 parsers/__init__.py | 0 setup.py | 16 +++++++++------- 8 files changed, 15 insertions(+), 9 deletions(-) rename alchemical_analysis.py => alchemical_analysis/alchemical_analysis.py (99%) rename __init__.py => alchemical_analysis/parsers/__init__.py (100%) rename {parsers => alchemical_analysis/parsers}/parser_amber.py (100%) rename {parsers => alchemical_analysis/parsers}/parser_gromacs.py (100%) rename {parsers => alchemical_analysis/parsers}/parser_sire.py (100%) rename {parsers => alchemical_analysis/parsers}/unixlike.py (100%) delete mode 100644 parsers/__init__.py diff --git a/alchemical_analysis.py b/alchemical_analysis/alchemical_analysis.py similarity index 99% rename from alchemical_analysis.py rename to alchemical_analysis/alchemical_analysis.py index 4faf0f0..57241d2 100755 --- a/alchemical_analysis.py +++ b/alchemical_analysis/alchemical_analysis.py @@ -1084,13 +1084,13 @@ def stripZeros(a, aa, b, bb): # MAIN #=================================================================================================== -if __name__ == "__main__": - +def main(): # Timing. stime = ttt_time.time() print "Started on %s" % ttt_time.asctime() # Simulation profile P (to be stored in 'results.pickle') will amass information about the simulation. + global P P = parser.parse_args()[0] P.methods = getMethods(P.methods.upper()) @@ -1154,6 +1154,10 @@ def stripZeros(a, aa, b, bb): plotCFM(u_kln, N_k, 50) print "\nTime spent: %s hours, %s minutes, and %s seconds.\nFinished on %s" % timeStatistics(stime) + +if __name__ == "__main__": + main() + #=================================================================================================== # End of the script #=================================================================================================== diff --git a/__init__.py b/alchemical_analysis/parsers/__init__.py similarity index 100% rename from __init__.py rename to alchemical_analysis/parsers/__init__.py diff --git a/parsers/parser_amber.py b/alchemical_analysis/parsers/parser_amber.py similarity index 100% rename from parsers/parser_amber.py rename to alchemical_analysis/parsers/parser_amber.py diff --git a/parsers/parser_gromacs.py b/alchemical_analysis/parsers/parser_gromacs.py similarity index 100% rename from parsers/parser_gromacs.py rename to alchemical_analysis/parsers/parser_gromacs.py diff --git a/parsers/parser_sire.py b/alchemical_analysis/parsers/parser_sire.py similarity index 100% rename from parsers/parser_sire.py rename to alchemical_analysis/parsers/parser_sire.py diff --git a/parsers/unixlike.py b/alchemical_analysis/parsers/unixlike.py similarity index 100% rename from parsers/unixlike.py rename to alchemical_analysis/parsers/unixlike.py diff --git a/parsers/__init__.py b/parsers/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/setup.py b/setup.py index cb5c36a..cfd051b 100644 --- a/setup.py +++ b/setup.py @@ -59,11 +59,12 @@ ], # What does your project relate to? - keywords='sample setuptools development', + keywords='pymbar', # You can just specify the packages manually here if your project is # simple. Or you can use find_packages(). - packages=find_packages(exclude=['contrib', 'docs', 'tests*']), + #packages=find_packages(exclude=['contrib', 'docs', 'tests*']), + packages=['alchemical_analysis','alchemical_analysis.parsers'], # List run-time dependencies here. These will be installed by pip when # your project is installed. For an analysis of "install_requires" vs pip's @@ -96,9 +97,10 @@ # To provide executable scripts, use entry points in preference to the # "scripts" keyword. Entry points provide cross-platform support and allow # pip to create the appropriate form of executable for the target platform. - #entry_points={ - # 'console_scripts': [ - # 'sample=sample:main', - # ], - #}, + #scripts=['alchemical_analysis/alchemical_analysis.py'], + entry_points={ + 'console_scripts': [ + 'alchemical_analysis=alchemical_analysis:main', + ], + }, ) From 0a9d039d1d0884fdabebb2c80943f04c080cc6ae Mon Sep 17 00:00:00 2001 From: "James W. Barnett" Date: Wed, 27 May 2015 08:03:45 -0500 Subject: [PATCH 3/6] create samples directory --- MANIFEST.in | 3 +++ alchemical_analysis/__init__.py | 0 {amber => samples/amber}/README.md | 0 {amber => samples/amber}/data/ti001/ti001.en | 0 {amber => samples/amber}/data/ti001/ti001.out.bz2 | Bin {amber => samples/amber}/data/ti002/ti002.en | 0 {amber => samples/amber}/data/ti002/ti002.out.bz2 | Bin {amber => samples/amber}/data/ti003/ti003.en | 0 {amber => samples/amber}/data/ti003/ti003.out.bz2 | Bin {amber => samples/amber}/data/ti004/ti004.en | 0 {amber => samples/amber}/data/ti004/ti004.out.bz2 | Bin {amber => samples/amber}/data/ti005/ti005.en | 0 {amber => samples/amber}/data/ti005/ti005.out.bz2 | Bin {amber => samples/amber}/results.pickle | 0 {amber => samples/amber}/results.txt | 0 {amber => samples/amber}/screen_printout.txt | 0 {gromacs => samples/gromacs}/README.md | 0 .../3-methylindole-11steps-neighbors/dhdl.0.xvg | 0 .../3-methylindole-11steps-neighbors/dhdl.1.xvg | 0 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rename {sire => samples/sire}/data/actual_grad_07269.dat (100%) rename {sire => samples/sire}/data/actual_grad_07938.dat (100%) rename {sire => samples/sire}/data/actual_grad_09045.dat (100%) rename {sire => samples/sire}/data/actual_grad_09455.dat (100%) rename {sire => samples/sire}/data/actual_grad_09755.dat (100%) rename {sire => samples/sire}/data/actual_grad_09938.dat (100%) rename {sire => samples/sire}/data/actual_grad_1.dat (100%) rename {sire => samples/sire}/dhdl_TI.pdf (100%) rename {sire => samples/sire}/results.pickle (100%) rename {sire => samples/sire}/results.txt (100%) rename {sire => samples/sire}/screen_printout_1.txt (100%) rename {sire => samples/sire}/screen_printout_2.txt (100%) rename {sire => samples/sire}/screen_printout_3.txt (100%) diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..3d3740a --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,3 @@ +include DESCRIPTION.rst +include README.md +recursive-include samples * diff --git 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a/sire/screen_printout_2.txt b/samples/sire/screen_printout_2.txt similarity index 100% rename from sire/screen_printout_2.txt rename to samples/sire/screen_printout_2.txt diff --git a/sire/screen_printout_3.txt b/samples/sire/screen_printout_3.txt similarity index 100% rename from sire/screen_printout_3.txt rename to samples/sire/screen_printout_3.txt diff --git a/setup.py b/setup.py index cfd051b..f7b5994 100644 --- a/setup.py +++ b/setup.py @@ -64,7 +64,7 @@ # You can just specify the packages manually here if your project is # simple. Or you can use find_packages(). #packages=find_packages(exclude=['contrib', 'docs', 'tests*']), - packages=['alchemical_analysis','alchemical_analysis.parsers'], + packages=find_packages(), # List run-time dependencies here. These will be installed by pip when # your project is installed. For an analysis of "install_requires" vs pip's From 4da82a31a055fa4a7387132017710bf952e807c1 Mon Sep 17 00:00:00 2001 From: "James W. Barnett" Date: Wed, 27 May 2015 12:30:19 -0500 Subject: [PATCH 4/6] create scripts, add globals --- alchemical_analysis/alchemical_analysis.py | 43 ++++++++++++++----- .../{parsers => }/parser_amber.py | 0 .../{parsers => }/parser_gromacs.py | 0 .../{parsers => }/parser_sire.py | 0 alchemical_analysis/parsers/__init__.py | 0 alchemical_analysis/{parsers => }/unixlike.py | 0 setup.py | 5 ++- 7 files changed, 35 insertions(+), 13 deletions(-) rename alchemical_analysis/{parsers => }/parser_amber.py (100%) rename alchemical_analysis/{parsers => }/parser_gromacs.py (100%) rename alchemical_analysis/{parsers => }/parser_sire.py (100%) delete mode 100644 alchemical_analysis/parsers/__init__.py rename alchemical_analysis/{parsers => }/unixlike.py (100%) diff --git a/alchemical_analysis/alchemical_analysis.py b/alchemical_analysis/alchemical_analysis.py index 57241d2..d87bf25 100755 --- a/alchemical_analysis/alchemical_analysis.py +++ b/alchemical_analysis/alchemical_analysis.py @@ -116,8 +116,8 @@ def checkUnitsAndMore(units): # If using Gromacs we can read in the temperature directly from dhdl.xvg if P.software.title() == 'Gromacs': - import parsers.parser_gromacs - P.temperature = parsers.parser_gromacs.readTempGromacs(P) + import parser_gromacs + P.temperature = parser_gromacs.readTempGromacs(P) kB = 1.3806488*6.02214129/1000.0 # Boltzmann's constant (kJ/mol/K). beta = 1./(kB*P.temperature) @@ -1085,12 +1085,33 @@ def stripZeros(a, aa, b, bb): #=================================================================================================== def main(): + + global dhdlt + global u_klt + global P + global K + global n_components + global pymbar + global dhdl + global N_k + global lv + global dlam + global ave_dhdl + global std_dhdl + global lchange + global cubspl + global mapl + global u_kln + global Deltaf_ij + global dDeltaf_ij + global df_allk + global ddf_allk + # Timing. stime = ttt_time.time() print "Started on %s" % ttt_time.asctime() # Simulation profile P (to be stored in 'results.pickle') will amass information about the simulation. - global P P = parser.parse_args()[0] P.methods = getMethods(P.methods.upper()) @@ -1105,21 +1126,21 @@ def main(): from matplotlib.font_manager import FontProperties as FP if P.software.title() == 'Gromacs': - import parsers.parser_gromacs - nsnapshots, lv, dhdlt, u_klt = parsers.parser_gromacs.readDataGromacs(P) + import parser_gromacs + nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P) elif P.software.title() == 'Sire': - import parsers.parser_sire - nsnapshots, lv, dhdlt, u_klt = parsers.parser_sire.readDataSire(P) + import parser_sire + nsnapshots, lv, dhdlt, u_klt = parser_sire.readDataSire(P) elif P.software.title() == 'Amber': - import parsers.parser_amber - lv, ave_dhdl, std_dhdl = parsers.parser_amber.readDataAmber(P) + import parser_amber + lv, ave_dhdl, std_dhdl = parser_amber.readDataAmber(P) else: from inspect import currentframe, getframeinfo lineno = getframeinfo(currentframe()).lineno print "\n\n%s\n Looks like there is no yet proper parser to process your files. \n Please modify lines %d and %d of this script.\n%s\n\n" % (78*"*", lineno+3, lineno+4, 78*"*") #### LINES TO BE MODIFIED - import parsers.YOUR_OWN_FILE_PARSER - nsnapshots, lv, dhdlt, u_klt = parsers.YOUR_OWN_FILE_PARSER.yourDataParser(*args, **kwargs) + import YOUR_OWN_FILE_PARSER + nsnapshots, lv, dhdlt, u_klt = YOUR_OWN_FILE_PARSER.yourDataParser(*args, **kwargs) #### All the four are numpy arrays. #### lv is the array of lambda vectors. #### nsnapshots is the number of equilibrated snapshots per each state. diff --git a/alchemical_analysis/parsers/parser_amber.py b/alchemical_analysis/parser_amber.py similarity index 100% rename from alchemical_analysis/parsers/parser_amber.py rename to alchemical_analysis/parser_amber.py diff --git a/alchemical_analysis/parsers/parser_gromacs.py b/alchemical_analysis/parser_gromacs.py similarity index 100% rename from alchemical_analysis/parsers/parser_gromacs.py rename to alchemical_analysis/parser_gromacs.py diff --git a/alchemical_analysis/parsers/parser_sire.py b/alchemical_analysis/parser_sire.py similarity index 100% rename from alchemical_analysis/parsers/parser_sire.py rename to alchemical_analysis/parser_sire.py diff --git a/alchemical_analysis/parsers/__init__.py b/alchemical_analysis/parsers/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/alchemical_analysis/parsers/unixlike.py b/alchemical_analysis/unixlike.py similarity index 100% rename from alchemical_analysis/parsers/unixlike.py rename to alchemical_analysis/unixlike.py diff --git a/setup.py b/setup.py index f7b5994..25885f4 100644 --- a/setup.py +++ b/setup.py @@ -65,12 +65,13 @@ # simple. Or you can use find_packages(). #packages=find_packages(exclude=['contrib', 'docs', 'tests*']), packages=find_packages(), + py_modules=['parser_gromacs','parser_amber','parser_sire','unixlike'], # List run-time dependencies here. These will be installed by pip when # your project is installed. For an analysis of "install_requires" vs pip's # requirements files see: # https://packaging.python.org/en/latest/requirements.html - install_requires=['pymbar'], + install_requires=["pymbar"], # List additional groups of dependencies here (e.g. development # dependencies). You can install these using the following syntax, @@ -97,7 +98,7 @@ # To provide executable scripts, use entry points in preference to the # "scripts" keyword. Entry points provide cross-platform support and allow # pip to create the appropriate form of executable for the target platform. - #scripts=['alchemical_analysis/alchemical_analysis.py'], + scripts={"alchemical_analysis/alchemical_analysis.py","alchemical_analysis/parser_gromacs.py","alchemical_analysis/unixlike.py"}, entry_points={ 'console_scripts': [ 'alchemical_analysis=alchemical_analysis:main', From b8fa951c67bdc14dc87e375ba12df8a823a25470 Mon Sep 17 00:00:00 2001 From: "James W. Barnett" Date: Thu, 28 May 2015 14:21:18 -0500 Subject: [PATCH 5/6] add some more global variables to fix errors --- alchemical_analysis/alchemical_analysis.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/alchemical_analysis/alchemical_analysis.py b/alchemical_analysis/alchemical_analysis.py index d87bf25..77ec430 100755 --- a/alchemical_analysis/alchemical_analysis.py +++ b/alchemical_analysis/alchemical_analysis.py @@ -1106,6 +1106,9 @@ def main(): global dDeltaf_ij global df_allk global ddf_allk + global nsnapshots + global pl + global FP # Timing. stime = ttt_time.time() From 5363e753ceee7336a2b69a278218b4901eb437e8 Mon Sep 17 00:00:00 2001 From: "David L. Mobley" Date: Thu, 28 May 2015 16:50:06 -0700 Subject: [PATCH 6/6] Update alchemical_analysis.py --- alchemical_analysis/alchemical_analysis.py | 1 + 1 file changed, 1 insertion(+) diff --git a/alchemical_analysis/alchemical_analysis.py b/alchemical_analysis/alchemical_analysis.py index 77ec430..da115b0 100755 --- a/alchemical_analysis/alchemical_analysis.py +++ b/alchemical_analysis/alchemical_analysis.py @@ -1109,6 +1109,7 @@ def main(): global nsnapshots global pl global FP + global matplotlib # Timing. stime = ttt_time.time()