Merge branch 'master' of github.com:danijoo/WHAM

.gitignore

@@ -1,4 +1,5 @@
 target
 reference
 .idea
-*bench.*
+*bench.*
+*.sublime*

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Cargo.toml

@@ -1,20 +1,24 @@
 [package]
 name = "wham"
-version = "0.9.2"
-authors = ["D. Bauer <bauer@bio.tu-darmstadt.de>"]
+version = "0.9.9"
+authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
 description = "An implementation of the weighted histogram analysis method"
 license = "GPL-3.0"
 repository = "https://github.com/danijoo/WHAM"
+readme = "README.md"
+categories = ["science", "command-line-utilities", "molecular-dynamics", "algorithms"]
+keywords = ["math", "statistics", "histogram", "bioinformatics", "molecular-dynamics"]
 
 [dependencies]
 clap = {version="2.32.0", features=['yaml']}
 error-chain = "0.12.0"
-rand = "0.5.5"
-GSL = "1.0.0"
+rand = "0.7.*"
+GSL = "1.1"
 rayon = "1.0.3"
 
-[profile.release]
-opt-level = 2
+[dev-dependencies]
+assert_approx_eq = "1.1.0"
+
+[profile.release]
+opt-level = 3
 
-[features]
-default = ["GSL/v2"]

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.com/danijoo/WHAM.svg?branch=master)](https://travis-ci.com/danijoo/WHAM) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/wham) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1488598.svg)](https://doi.org/10.5281/zenodo.1488598)
+[![Build Status](https://travis-ci.com/danijoo/WHAM.svg?branch=master)](https://travis-ci.com/danijoo/WHAM) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/wham) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1488597.svg)](https://doi.org/10.5281/zenodo.1488597)
 
 
 
@@ -38,6 +38,56 @@ Usage
 wham has a convenient command line interface. You can see all options with
 ```wham -h```:
 
+```
+wham 0.9.9
+D. Bauer <bauer@bio.tu-darmstadt.de>
+wham is a fast implementation of the weighted histogram analysis method (WHAM) written in Rust. It currently supports
+potential of mean force (PMF) calculations in multiple dimensions at constant temperature.
+
+Metadata file format:
+    /path/to/timeseries_file1  x_1  x_2  x_N  fc_1  fc_2  fc_N
+    /path/to/timeseries_file2  x_1  x_2  x_N  fc_1  fc_2  fc_N
+    /path/to/timeseries_file3  x_1  x_2  x_N  fc_1  fc_2  fc_N
+The first column is a path to a timeseries file _relative_ to the metadata file (see below). This is followed by the
+position of the umbrella potential x in N dimensions and the force constant fc in each dimension. Lines starting with a
+# are treated as comments and will not be parsed.
+
+Timeseries file format:
+    time  x_1  x_2  x_N
+    time  x_1  x_2  x_N
+    time  x_1  x_2  x_N
+The first column will be ignored and is followed by N reaction coordinates x.
+
+Shipped under the GPLv3 license.
+
+USAGE:
+    wham [FLAGS] [OPTIONS] --bins <BINS> --max <HIST_MAX> --file <METADATA> --min <HIST_MIN> --temperature <temperature>
+
+FLAGS:
+    -c, --cyclic     For periodic reaction coordinates. If this is set, the first and last coordinate bin in each
+                     dimension are treated as neighbors for the bias calculation.
+    -h, --help       Prints help information
+    -V, --version    Prints version information
+    -v, --verbose    Enables verbose output.
+
+OPTIONS:
+    -b, --bins <BINS>                  Number of histogram bins (comma separated).
+        --bt <bootstrap>               Number of bayesian bootstrapping runs for error analysis by assigning random
+                                       weights (defaults to 0).
+        --seed <bootstrap_seed>        Random seed for bootstrapping runs.
+        --end <end>                    Skip rows in timeseries with an index larger than this value (defaults to 1e+20)
+    -i, --iterations <ITERATIONS>      Stop WHAM after this many iterations without convergence (defaults to 100,000).
+        --max <HIST_MAX>               Histogram maxima (comma separated). Also accepts "pi".
+    -f, --file <METADATA>              Path to the metadata file.
+        --min <HIST_MIN>               Histogram minima (comma separated for multiple dimensions). Also accepts "pi".
+    -o, --output <output>              Free energy output file (defaults to wham.out).
+        --start <start>                Skip rows in timeseries with an index smaller than this value (defaults to 0)
+    -T, --temperature <temperature>    WHAM temperature in Kelvin.
+    -t, --tolerance <TOLERANCE>        Abortion criteria for WHAM calculation. WHAM stops if abs(F_new - F_old) <
+                                       tolerance (defaults to 0.000001).
+
+```
+
 To run the two dimensional example (simulation of dialanine phi and psi angle):
 ```bash
 wham --max 3.14,3.14 --min -3.14,-3.14 -T 300 --bins 100,100 --cyclic -f example/2d/metadata.dat       
@@ -81,15 +131,15 @@ one can estimate the error as standard deviation between the N bootstrapping run
 Autocorrelation Estimates, JCTC, 6(12), 3713-3720*.
 
 To perform bayesian bootstrapping in WHAM, use the ```-bt <RUNS>``` flag to perform <RUNS> individual bootstrapping
-runs. The error estimates of bin probabilities and free energy will be given as separate column (+/-) in the output file.
-If no error analysis is performed, these columns are set to 0.0.
+runs. The error estimates of bin probabilities and free energy will be given as standard error (SE) in a 
+separate column (+/-) in the output file. If no error analysis is performed, these columns are set to 0.0.
 
 Examples
 ---
 The example folder contains input and output files for two simple test systems:
 
-- 1d: Phi torsion angle of dialanine in vaccum
-- 2d: Phi and psi torsion angles of the same system
+- 1d_cyclic: Phi torsion angle of dialanine in vaccum
+- 2d_cyclic: Phi and psi torsion angles of the same system
 
 
 TODO

example/1d/wham.out

@@ -1,101 +0,0 @@
-#coord1    Free Energy    +/-    Probability    +/-
--3.108600    7.118166    0.000000    0.003561    0.000000
--3.045800    5.331290    0.000000    0.007290    0.000000
--2.983000    3.879241    0.000000    0.013048    0.000000
--2.920200    2.968659    0.000000    0.018796    0.000000
--2.857400    1.942494    0.000000    0.028362    0.000000
--2.794600    1.418408    0.000000    0.034994    0.000000
--2.731800    1.169398    0.000000    0.038668    0.000000
--2.669000    0.843024    0.000000    0.044073    0.000000
--2.606200    0.636021    0.000000    0.047887    0.000000
--2.543400    0.720123    0.000000    0.046299    0.000000
--2.480600    1.066434    0.000000    0.040297    0.000000
--2.417800    1.509855    0.000000    0.033734    0.000000
--2.355000    2.015549    0.000000    0.027544    0.000000
--2.292200    2.226942    0.000000    0.025306    0.000000
--2.229400    2.573176    0.000000    0.022026    0.000000
--2.166600    2.591946    0.000000    0.021861    0.000000
--2.103800    2.476835    0.000000    0.022893    0.000000
--2.041000    2.513953    0.000000    0.022555    0.000000
--1.978200    2.470032    0.000000    0.022956    0.000000
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--1.789800    1.778779    0.000000    0.030286    0.000000
--1.727000    1.447127    0.000000    0.034593    0.000000
--1.664200    0.906384    0.000000    0.042968    0.000000
--1.601400    0.304263    0.000000    0.054699    0.000000
--1.538600    0.247397    0.000000    0.055960    0.000000
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--1.413000    0.536142    0.000000    0.049843    0.000000
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--1.161800    5.696583    0.000000    0.006297    0.000000
--1.099000    7.656158    0.000000    0.002870    0.000000
--1.036200    9.955000    0.000000    0.001142    0.000000
--0.973400    12.357407    0.000000    0.000436    0.000000
--0.910600    14.954254    0.000000    0.000154    0.000000
--0.847800    17.745327    0.000000    0.000050    0.000000
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-2.983000    13.069599    0.000000    0.000328    0.000000
-3.045800    11.036085    0.000000    0.000740    0.000000
-3.108600    9.015657    0.000000    0.001664    0.000000

example/1d_cyclic/README.txt

@@ -0,0 +1,9 @@
+Example data: Dialanine torsion angle at 300K
+wham.out was produced with the folling settings:
+
+wham --max pi --min -pi --cyclic\
+    --bins 100 \
+    -T 300 \
+    -f metadata.dat \
+    -o wham.out \
+    --bt 100 --seed 1234

example/1d_cyclic/wham.out

@@ -0,0 +1,101 @@
+#coord1    Free Energy    +/-    Probability    +/-
+-3.110177    7.158102    0.071438    0.003494    0.000068
+-3.047345    5.365727    0.069449    0.007168    0.000135
+-2.984513    3.873190    0.067495    0.013039    0.000232
+-2.921681    2.953162    0.067589    0.018855    0.000343
+-2.858849    1.949554    0.064640    0.028195    0.000480
+-2.796017    1.391747    0.063570    0.035261    0.000584
+-2.733186    1.128270    0.061710    0.039189    0.000620
+-2.670354    0.839970    0.060445    0.043991    0.000667
+-2.607522    0.624769    0.060762    0.047955    0.000739
+-2.544690    0.663757    0.060786    0.047211    0.000731
+-2.481858    1.051932    0.059774    0.040407    0.000617
+-2.419026    1.463048    0.060422    0.034267    0.000527
+-2.356194    1.990616    0.055242    0.027734    0.000360
+-2.293363    2.190692    0.044458    0.025597    0.000210
+-2.230531    2.553036    0.042144    0.022136    0.000159
+-2.167699    2.572522    0.043313    0.021964    0.000165
+-2.104867    2.472360    0.039799    0.022863    0.000157
+-2.042035    2.517562    0.036792    0.022453    0.000203
+-1.979203    2.469778    0.036324    0.022887    0.000237
+-1.916372    2.223125    0.049496    0.025266    0.000565
+-1.853540    2.080157    0.039205    0.026756    0.000453
+-1.790708    1.793841    0.041488    0.030011    0.000558
+-1.727876    1.458784    0.042362    0.034326    0.000565
+-1.665044    0.914441    0.037561    0.042697    0.000682
+-1.602212    0.303813    0.028701    0.054540    0.000761
+-1.539380    0.268335    0.025765    0.055321    0.000771
+-1.476549    0.000000    0.023371    0.061604    0.000866
+-1.413717    0.537061    0.026370    0.049671    0.000715
+-1.350885    1.439940    0.025620    0.034586    0.000547
+-1.288053    2.391838    0.027653    0.023614    0.000393
+-1.225221    3.779470    0.027093    0.013538    0.000229
+-1.162389    5.685555    0.027762    0.006305    0.000111
+-1.099557    7.661896    0.028996    0.002855    0.000051
+-1.036726    9.946594    0.032118    0.001142    0.000021
+-0.973894    12.359408    0.042801    0.000434    0.000009
+-0.911062    14.954655    0.052443    0.000153    0.000004
+-0.848230    17.742242    0.063261    0.000050    0.000002
+-0.785398    20.555785    0.068133    0.000016    0.000001
+-0.722566    22.811160    0.075518    0.000007    0.000000
+-0.659734    25.178094    0.086226    0.000003    0.000000
+-0.596903    26.442288    0.091783    0.000002    0.000000
+-0.534071    27.897565    0.093175    0.000001    0.000000
+-0.471239    29.062473    0.096027    0.000001    0.000000
+-0.408407    30.384521    0.096855    0.000000    0.000000
+-0.345575    31.638454    0.099956    0.000000    0.000000
+-0.282743    32.817727    0.107689    0.000000    0.000000
+-0.219911    33.770369    0.108946    0.000000    0.000000
+-0.157080    34.505503    0.112902    0.000000    0.000000
+-0.094248    35.431659    0.120856    0.000000    0.000000
+-0.031416    35.615810    0.122046    0.000000    0.000000
+0.031416    35.561946    0.118225    0.000000    0.000000
+0.094248    35.382089    0.108652    0.000000    0.000000
+0.157080    34.934827    0.118384    0.000000    0.000000
+0.219911    33.673460    0.119195    0.000000    0.000000
+0.282743    32.731563    0.121592    0.000000    0.000000
+0.345575    31.261855    0.129698    0.000000    0.000000
+0.408407    29.717377    0.139789    0.000000    0.000000
+0.471239    28.076620    0.137289    0.000001    0.000000
+0.534071    26.481097    0.135712    0.000002    0.000000
+0.596903    24.487358    0.135156    0.000003    0.000000
+0.659734    22.344251    0.131027    0.000008    0.000000
+0.722566    20.241543    0.133145    0.000018    0.000001
+0.785398    18.341869    0.131952    0.000039    0.000002
+0.848230    16.261582    0.134676    0.000091    0.000006
+0.911062    14.301801    0.134417    0.000199    0.000013
+0.973894    12.603788    0.131018    0.000394    0.000024
+1.036726    11.249601    0.131276    0.000678    0.000043
+1.099557    10.087886    0.132498    0.001079    0.000070
+1.162389    9.443303    0.132990    0.001398    0.000092
+1.225221    9.152799    0.132250    0.001570    0.000104
+1.288053    9.331937    0.133178    0.001462    0.000099
+1.350885    9.905546    0.133357    0.001161    0.000078
+1.413717    11.042050    0.133807    0.000736    0.000051
+1.476549    12.598167    0.132722    0.000395    0.000027
+1.539380    14.520167    0.131816    0.000183    0.000012
+1.602212    16.569783    0.131773    0.000080    0.000005
+1.665044    18.687390    0.132601    0.000034    0.000002
+1.727876    20.775408    0.133867    0.000015    0.000001
+1.790708    22.905200    0.129265    0.000006    0.000000
+1.853540    24.643852    0.128894    0.000003    0.000000
+1.916372    26.301740    0.130266    0.000002    0.000000
+1.979203    27.372071    0.128620    0.000001    0.000000
+2.042035    28.697726    0.133263    0.000001    0.000000
+2.104867    29.417901    0.133513    0.000000    0.000000
+2.167699    30.008351    0.130925    0.000000    0.000000
+2.230531    30.406016    0.124398    0.000000    0.000000
+2.293363    30.171275    0.122493    0.000000    0.000000
+2.356194    29.884646    0.130278    0.000000    0.000000
+2.419026    29.428153    0.130844    0.000000    0.000000
+2.481858    28.546982    0.148114    0.000001    0.000000
+2.544690    27.757520    0.133045    0.000001    0.000000
+2.607522    26.505787    0.134364    0.000001    0.000000
+2.670354    24.491866    0.115061    0.000003    0.000000
+2.733186    22.320664    0.110036    0.000008    0.000000
+2.796017    20.052723    0.107894    0.000020    0.000001
+2.858849    17.655650    0.105964    0.000052    0.000002
+2.921681    15.471590    0.107005    0.000125    0.000005
+2.984513    13.138167    0.099378    0.000318    0.000012
+3.047345    11.092386    0.087770    0.000722    0.000022
+3.110177    9.065722    0.077092    0.001626    0.000038