added test_data

TamaLab · Aug 28, 2024 · a0468c3 · a0468c3
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diff --git a/.DS_Store b/.DS_Store
diff --git a/docs/760ns_test.py b/docs/760ns_test.py
diff --git a/docs/Installation.md b/docs/Installation.md
@@ -9,12 +9,12 @@
 
 ```
 
-Installation of ResiDEM requires few dependency such as [Computational Crystallography Toolbox (CCTBX)](https://cctbx.github.io/).
+Installation of ResiDEM requires few dependencies such as [Computational Crystallography Toolbox (CCTBX)](https://cctbx.github.io/).
 It also some requires some basic python packages for data processing such as numpy, pandas, scipy etc...
 
 ## Installation
 
-ResiDEM is a python tool written in python 3, and it is recommended that a new environment is created for better package
+ResiDEM is a python tool written in python 3 version, and it is recommended that a new environment is created for better package
 management and to avoid any dependency conflicts.
 
 1. Creating a conda virtual environment and installation :
@@ -51,11 +51,10 @@ pip install dist/residem-0.1.0.tar.gz
 
 The ResiDEM package might also need [CCP4 scaleit](https://www.ccp4.ac.uk/html/scaleit.html). It
 will be used for scaling between reference and triggered state if that particular user option in given.
-It also has inbuilt scaling method, but works well with
-isomorphous data sets.
+It also has inbuilt scaling method, which works well with isomorphous data sets.
 ```
 
-To check if the CCP4 package or scaleit in the path the following command can used.
+To check if the CCP4 package or scaleit in the path, the following command can used.
 
 ```bash
 if command -v ccp4 &> /dev/null
@@ -68,11 +67,11 @@ fi
 
 ## Unit test
 
-Testing the tool with Bacteriorhodopsin data.
+Testing the tool with `Bacteriorhodopsin` data.
 There are two python scripts which can be used to run, reproduce images as in the [published article](https://doi.org/10.1021/acs.jcim.4c00858)
 .
-The name of the scripts are `residem_unit_test.py` and `SVD_unit_test.py` which are available in tests directory.
-The main script `residem_unit_test.py` can be used to test the tool and reproduce the certain figures as in [published article](https://doi.org/10.1021/acs.jcim.4c00858)
+The name of the scripts are `residem_unit_test.py` and `SVD_unit_test.py` which are available in `test_data` directory in tests as zip file.
+The main script `residem_unit_test.py` can be used to test the tool and reproduce certain figures as in [published article](https://doi.org/10.1021/acs.jcim.4c00858)
 .
 This script computes the isomorphous difference density for Bacteriorhodopsin(bR) for 13 time delays as published by [Nango et al.](https://www.science.org/doi/10.1126/science.aah3497)
 
@@ -84,6 +83,8 @@ The testing can be done using the following commands.
 ```bash
 conda activate residem
 cd tests
+unzip test_data.zip
+cd test_data
 python residem_unit_test.py
 # after completeion of the above the follwoing can be submitted.
 python SVD_unit_test.py

diff --git a/docs/Quickstart.md b/docs/Quickstart.md
@@ -11,18 +11,19 @@ Getting started with `ResiDEM`.
 
 The main command line utility of the ResiDEM is ``residem``. 
 This utility generates isomorphous difference density map and identifies the residues associated with difference density. 
-The basic command line argument to run the calculation to generate isomorphous difference density (DED) map  and identification is as follows:
+The basic command line argument to run the calculation, generate isomorphous difference density (DED) map  and residue identification is as follows:
 
 ~~~bash 
-residem -r 5b6v.pdb -m 5b6v.mtz -t 5b6x.mtz
-residem -r 5b6v.pdb -m 5b6v.mtz -t 5b6x.mtz --scale aniso/iso/no -w ursby/ren/hekstra/default -sm cctbx/ccp4 
+# given the working directory is test_data
+residem -r dark/5b6v.pdb -m dark/5b6v.mtz -t 05_760ns/5b6x.mtz
+residem -r dark/5b6v.pdb -m dark/5b6v.mtz -t dark/5b6x.mtz --scale aniso/iso/no -w ursby/ren/hekstra/default -sm cctbx/ccp4 
 ~~~
 In the above example, DED map is calculated for 760ns triggered structure (pdb id: 5b6x) with respect to dark state structure (pdb id: 5b6v).
 
 
 ## Inputs 
 
-It requires a reference state pdb `-r`, an reference state `-m` and triggered state `-t` mtz file containing 
+It requires a reference state pdb `-r`, an reference state `-m` and triggered state `-t` mtz files containing 
 structure factor amplitudes or intensities. The reference state,triggered state
 mtz should also have a column associated with structure factor amplitudes and its associated sigma "FP,SIGFP" or 
 intensities with column name "I,SIGI". 
@@ -33,16 +34,16 @@ Isomorphous difference density map rely on proper scaling of the  reference stat
 and triggered state observed structure factor {math}`|F_{obs}^{t}|` .
 This is done through resolution dependent scaling which can be either isotropic or anisotropic. 
 The tool has a few options to scale the reference and triggered state structure factor. 
-This consists of scaling using either cctbx scaling method or using ccp4 based scaleit method. 
-There are three options such as `--scale no` scaling, `--scale iso` isotropic scaling or `--scale aniso`. 
+This consists of scaling using either cctbx based scaling method or using ccp4 based scaleit method. 
+There are three options such as `--scale no` scaling, `--scale iso` isotropic scaling or `--scale aniso` which can be applied for scaling. 
 The scaling can be done either using inbuilt method using `-sm cctbx` library or using `-sm ccp4` scaleit.
-After scaling, the time dependent intensities,  Wilson Plots of {math}`|F_{obs}^{t}|^2` and 
-the {math}`|F_{obs}^{ref}|^2` have the approximately same slopes.
+After scaling, the time dependent intensities and its Wilson Plots corresponding to {math}`|F_{obs}^{t}|^2` and 
+the {math}`|F_{obs}^{ref}|^2` should have approximately same slopes.
 
 ![Wilson plot scaling](images/Wilson_plot_comparison.jpg)
 Figure 1: Wilson plot of 760ns bR Intensities before and after anisotropic scaling. 
 
-## Isomorphism idicators
+## Isomorphism indicators
 ### Cross -R-Factor ( {math}`R_{iso}`) and  Isomorphism indicating correlation coefficient ({math}`CC_{iso}`).
 
 After scaling, an estimate can be obtained quantitatively to identify how similar the reference state data is 
@@ -153,19 +154,19 @@ where the term {math}`\frac{ω_{hkl}}{\langle ω \rangle}` may correspond weight
 
 
 
- [Nango et al.](https://www.science.org/doi/10.1126/science.aah3497) for Bacteriorhodopsin(bR) did not use any weights.
- So, to discuss more about the weight, test case of Photoactive yellow protein (PYP) published by [Pandey et al.,](https://doi.org/10.1038/s41592-019-0628-z) is discussed below. 
+ [Nango et al.](https://www.science.org/doi/10.1126/science.aah3497) for Bacteriorhodopsin(bR) dataset did not use any weights.
+ In order to discuss more about the weights, another test dataset of Photoactive yellow protein (PYP) published by [Pandey et al.,](https://doi.org/10.1038/s41592-019-0628-z) is discussed below. 
 
 ![Distribution DSF](images/Distribution_DSF.png)
 
-Figure 3: Plot showing distribution of amplitude of difference structure factor as a function of signal-to-noise ratio. 
+Figure 3: Plot showing distribution of amplitude of difference structure factor as a function of signal-to-noise ratio for various weights. 
 Clearer PDF file for the image can be found [here](images/Difference_structure_factor_distribution.pdf).
 
-In Figure 3,  we see the distribution of difference Fourier coefficients plotted with signal-to-noise ratios with and without weight. 
-We can see the distribution of the difference structure factor. In the first distribution we can see the {math}`|\Delta F|` 
-as a function of signal-to-noise  ratio {math}`|\Delta F|/ σ_{| \Delta F|} `, in the inset of the plot is the distribution of
+In Figure 3,  we see the distribution of difference Fourier coefficients is plotted against signal-to-noise ratios with and without weight. 
+The image gives an overview about the distribution of the difference structure factor and experimental error(sigma) in inset plot. In the first distribution we can see the {math}`|\Delta F|` 
+as a function of signal-to-noise  ratio {math}`|\Delta F|/ σ_{| \Delta F|} `, the inset of the plot is the distribution of
 {math}`|\Delta F| ` vs  {math}`σ_{| \Delta F|}`. It can be seen that by using modified Ren weight or `hekstra` weight with alpha=1 by [Schmidt et al.,](https://doi.org/10.1016/S0006-3495(03)75018-8)
-is the one which satisfies the condition. This denotes that there are no large amplitudes with large experimental errors (sigma) values, 
+is the one which has the least errors, which satisfies the condition. This denotes that there are no large amplitudes with large experimental errors (sigma) values, 
 and hence is chosen as best weight for PYP. 
 
 The obtained isomorphous difference map (DED) without and with weight is shown in the following figure. 

diff --git a/docs/Result.md b/docs/Result.md
@@ -20,9 +20,9 @@ more details of which can be found in [command line options](command.md).
 ~~~bash
 mkdir bR
 cd bR
-# download the reference and 760ns triggered pdb 
-residem_pdb_mtz -r 5b6v; residem_pdb_mtz -r 5b6x # pdb code of dark and 760ns respectively
-
+# copy the data associated with 760ns given the current working directory 
+# is test_data available in tests directory of the repository
+cp ../dark/5b6v.* . ;cp  ../05_760ns/5b6x.* .
 ~~~
 ```bash
 tree # If you see the file in the folder we see the following

diff --git a/docs/SVD_unit_test.py b/docs/SVD_unit_test.py
diff --git a/docs/_build/doctrees/About.doctree b/docs/_build/doctrees/About.doctree
diff --git a/docs/_build/doctrees/Algorithm.doctree b/docs/_build/doctrees/Algorithm.doctree
diff --git a/docs/_build/doctrees/DBSCAN.doctree b/docs/_build/doctrees/DBSCAN.doctree
diff --git a/docs/_build/doctrees/Installation.doctree b/docs/_build/doctrees/Installation.doctree
diff --git a/docs/_build/doctrees/Limitation.doctree b/docs/_build/doctrees/Limitation.doctree
diff --git a/docs/_build/doctrees/Quickstart.doctree b/docs/_build/doctrees/Quickstart.doctree
diff --git a/docs/_build/doctrees/Result.doctree b/docs/_build/doctrees/Result.doctree
diff --git a/docs/_build/doctrees/Usage.doctree b/docs/_build/doctrees/Usage.doctree
diff --git a/docs/_build/doctrees/command.doctree b/docs/_build/doctrees/command.doctree
diff --git a/docs/_build/doctrees/distribution_dsf.doctree b/docs/_build/doctrees/distribution_dsf.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 89fb2952db4c7f8d2657d4dd9d7e3f08
+config: e4838d10fffc4bb31f9edeb09d2dc302
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/About.html b/docs/_build/html/About.html
@@ -7,7 +7,7 @@
   <title>About ResiDEM &mdash; Residem</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/custom.css" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=e9b4edf4" />
 
 
     <link rel="shortcut icon" href="_static/Resi-DEM_icon.png"/>
@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=a1637f0b"></script>
+        <script src="_static/documentation_options.js?v=01f34227"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -72,7 +72,7 @@
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">About ResiDEM</li>
       <li class="wy-breadcrumbs-aside">
-            <a href="_sources/About.md" rel="nofollow"> View page source</a>
+            <a href="_sources/About.md.txt" rel="nofollow"> View page source</a>
       </li>
   </ul>
   <hr/>
@@ -107,7 +107,7 @@ <h1>About ResiDEM<a class="headerlink" href="#about-residem" title="Link to this
 <p>For more information, kindly please see the <a class="reference external" href="https://doi.org/10.1021/acs.jcim.4c00858">published paper</a>.</p>
 <p>If the tool was useful please cite us: Sriram Srinivasa Raghavan, Osamu Miyashita.ResiDEM: <a class="reference external" href="https://doi.org/10.1021/acs.jcim.4c00858">Analytical Tool for Isomorphous Difference Electron
 Density Maps Utilizing Dynamic Residue Identification via Density Clustering</a>. Journal of chemical information and modelling, <strong>2024</strong>.</p>
-<p>For any help or quires with respect to the tool contact <a class="reference external" href="mailto:hypowergravity&#37;&#52;&#48;gmail&#46;com">me</a>.</p>
+<p>For any help or queries with respect to the tool, contact <a class="reference external" href="mailto:hypowergravity&#37;&#52;&#48;gmail&#46;com">me</a>.</p>
 <script>
 document.querySelectorAll('a[href^="http"]').forEach(link => {
     link.setAttribute('target', '_blank');

diff --git a/docs/_build/html/Algorithm.html b/docs/_build/html/Algorithm.html
@@ -7,7 +7,7 @@
   <title>Algorithm &mdash; Residem</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/custom.css" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=0db739f3" />
 
 
     <link rel="shortcut icon" href="_static/Resi-DEM_icon.png"/>
@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=a1637f0b"></script>
+        <script src="_static/documentation_options.js?v=01f34227"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script>window.MathJax = {"options": {"processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
@@ -79,7 +79,7 @@
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Algorithm</li>
       <li class="wy-breadcrumbs-aside">
-            <a href="_sources/Algorithm.md" rel="nofollow"> View page source</a>
+            <a href="_sources/Algorithm.md.txt" rel="nofollow"> View page source</a>
       </li>
   </ul>
   <hr/>

diff --git a/docs/_build/html/DBSCAN.html b/docs/_build/html/DBSCAN.html
@@ -7,7 +7,7 @@
   <title>Work Flow of DBSCAN implemented in ResiDEM &mdash; Residem</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/custom.css" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=0db739f3" />
 
 
     <link rel="shortcut icon" href="_static/Resi-DEM_icon.png"/>
@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=a1637f0b"></script>
+        <script src="_static/documentation_options.js?v=01f34227"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="https://unpkg.com/[email protected]/dist/mermaid.min.js"></script>
@@ -73,7 +73,7 @@
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Work Flow of DBSCAN implemented in ResiDEM</li>
       <li class="wy-breadcrumbs-aside">
-            <a href="_sources/DBSCAN.md" rel="nofollow"> View page source</a>
+            <a href="_sources/DBSCAN.md.txt" rel="nofollow"> View page source</a>
       </li>
   </ul>
   <hr/>