Merge pull request #184 from mrshirts/master

Removal of alchemical-analysis.py and linking to the new version

README.md

@@ -43,7 +43,7 @@ or compute expectations of given observables A(x) for all states:
 >>> (A_k_estimated, dA_k_estimated) = mbar.computeExpectations(x_k)
 ```
 See the help for these individual methods for more information on exact usage; in Python or IPython, you can view the docstrings with `help()`.  
-Additional examples can be found in [pymbar-examples](http://github.com/choderalab/pymbar-examples/).
+Additional examples can be found in [pymbar-examples](http://github.com/choderalab/pymbar-examples/).  Note that the example for free energy calculations found in pymbar-examples/alchemical-free-energy has moved to https://github.com/MobleyLab/alchemical-analysis
 
 
 Prerequisites

examples/README.md

@@ -6,7 +6,7 @@ Examples illustrating the use of [MBAR](http://github.com/choderalab/pymbar) for
 Contents
 --------
 
-* `alchemical-free-energy/` - example illustrating calculation of free energy difference from simulations of alchemical intermediates
+* `alchemical-free-energy/` - example illustrating the calculation of free energy differences from simulations with alchemical intermediates between two end states with a number of methods.  Note that this example has moved to https://github.com/MobleyLab/alchemical-analysis
 * `constant-force-optical-trap/` - calculation of PMF of dsDNA extension from constant-force optical trap experiments
 * `harmonic-oscillators/` - examples all of the functionality of pymbar, including validation of the distribution of error estimates. 
 * `heat-capacity/` - calculation of heat capacities using the fluctuation theorem, including Cv at interpolated temperatures.

examples/alchemical-free-energy/README.md

@@ -1,82 +1,11 @@
-Script: `alchemical_analysis.py`
+The alchemical_analysis.y script has been moved to
 
-An illustration of MBAR applied to alchemical free energy
-calculations, and comparison of MBAR to a number of other free energy
-methods described in Paliwal and Shirts, J. Chem. Theory Comp, v. 7,
-4115-4134 (2011).
+https://github.com/MobleyLab/alchemical-analysis
 
-See description in `gromacs/README.md`, `sire/README.md`, and `amber/README.md`.
+It contains an implementation of the recommended practices for
+analyzing alchemical free energy calculations, as described in
+Klimovich et al., JCAMD 29:397-411 (2015). This is based on earlier
+work illustrating how to apply MBAR to alchemical free energy
+calculations (and a comparison with other methods) as in Paliwal and
+Shirts, J. Chem. Theory Comp, v. 7, 4115-4134 (2011).
 
-
-Help for `alchemical_analysis.py` (obtained with `python alchemical_analysis.py -h`) is:
-
-```Options:
-  -h, --help            show this help message and exit
-  -a SOFTWARE, --software=SOFTWARE
-                        Package's name the data files come from: Gromacs,
-                        Sire, or AMBER. Default: Gromacs.
-  -c, --cfm             The Curve-Fitting-Method-based consistency inspector.
-                        Default: False.
-  -d DATAFILE_DIRECTORY, --dir=DATAFILE_DIRECTORY
-                        Directory in which data files are stored. Default:
-                        Current directory.
-  -f BFORWREV, --forwrev=BFORWREV
-                        Plotting the free energy change as a function of time
-                        in both directions. The number of time points (an
-                        integer) is to be followed the flag. Default: 0
-  -g, --breakdown       Plotting the free energy differences evaluated for
-                        each pair of adjacent states for all methods. Default:
-                        False.
-  -i UNCORR_THRESHOLD, --threshold=UNCORR_THRESHOLD
-                        Perform the analysis with rather all the data if the
-                        number of uncorrelated samples is found to be less
-                        than this number. If 0 is given, the time series
-                        analysis will not be performed at all. Default: 50.
-  -k BSKIPLAMBDAINDEX, --koff=BSKIPLAMBDAINDEX
-                        Give a string of lambda indices separated by '-' and
-                        they will be removed from the analysis. (Another
-                        approach is to have only the files of interest present
-                        in the directory). Default: None.
-  -m METHODS, --methods=METHODS
-                        A list of the methods to esitimate the free energy
-                        with. Default: [TI, TI-CUBIC, DEXP, IEXP, BAR, MBAR].
-                        To add/remove methods to the above list provide a
-                        string formed of the method strings preceded with +/-.
-                        For example, '-ti_cubic+gdel' will turn methods into
-                        [TI, DEXP, IEXP, BAR, MBAR, GDEL]. 'ti_cubic+gdel', on
-                        the other hand, will call [TI-CUBIC, GDEL]. 'all'
-                        calls the full list of supported methods [TI, TI-
-                        CUBIC, DEXP, IEXP, GINS, GDEL, BAR, UBAR, RBAR, MBAR].
-  -o OUTPUT_DIRECTORY, --out=OUTPUT_DIRECTORY
-                        Directory in which the output files produced by this
-                        script will be stored. Default: Same as
-                        datafile_directory.
-  -p PREFIX, --prefix=PREFIX
-                        Prefix for datafile sets, i.e.'dhdl' (default).
-  -q SUFFIX, --suffix=SUFFIX
-                        Suffix for datafile sets, i.e. 'xvg' (default).
-  -r DECIMAL, --decimal=DECIMAL
-                        The number of decimal places the free energies are to
-                        be reported with. No worries, this is for the text
-                        output only; the full-precision data will be stored in
-                        'results.pickle'. Default: 3.
-  -s EQUILTIME, --skiptime=EQUILTIME
-                        Discard data prior to this specified time as
-                        'equilibration' data. Units picoseconds. Default: 0
-                        ps.
-  -t TEMPERATURE, --temperature=TEMPERATURE
-                        Temperature in K. Default: 298 K.
-  -u UNITS, --units=UNITS
-                        Units to report energies: 'kJ', 'kcal', and 'kBT'.
-                        Default: 'kJ'
-  -v, --verbose         Verbose option. Default: False.
-  -w, --overlap         Print out and plot the overlap matrix. Default: False.
-  -x, --ignoreWL        Do not check whether the WL weights are equilibrated.
-                        No log file needed as an accompanying input.
-  -y RELATIVE_TOLERANCE, --tolerance=RELATIVE_TOLERANCE
-                        Convergence criterion for the energy estimates with
-                        BAR and MBAR. Default: 1e-10.
-  -z INIT_WITH, --initialize=INIT_WITH
-                        The initial MBAR free energy guess; either 'BAR' or
-                        'zeroes'. Default: 'BAR'.
-```