diff --git a/doc/contributing.rst b/doc/contributing.rst
index 6b01d03e3ba02f1c5c5c41da13f53015428348db..417eafe2646dfdfc5bee95773a5be8007bb12ec5 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -251,7 +251,8 @@ lines:
Afterwards, you should be able to compile and run small sample codes that use
|project| and |ost_s| as in the :file:`test.cc` example. You can compile your
-code by executing ``make`` and run it with ``make run``.
+code by executing ``make`` and run it with ``make run``. Also, remember to set
+the ``PROMOD3_SHARED_DATA_PATH`` variable if you moved the stage folder.
--------------------------------------------------------------------------------
Unit Tests
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
index 70f7c40272d77b1773c94fc9b92397e4b9a8b86e..52436a0066f1c265292bb03d974a1e56f30b16e6 100644
--- a/doc/html/_modules/promod3.html
+++ b/doc/html/_modules/promod3.html
@@ -62,8 +62,18 @@
<span class="n">compound_lib</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">CompoundLib</span><span class="o">.</span><span class="n">Load</span><span class="p">(</span><span class="n">compound_lib_path</span><span class="p">)</span>
<span class="n">conop</span><span class="o">.</span><span class="n">SetDefaultLib</span><span class="p">(</span><span class="n">compound_lib</span><span class="p">)</span>
<span class="n">io</span><span class="o">.</span><span class="n">profiles</span><span class="p">[</span><span class="s">'DEFAULT'</span><span class="p">]</span><span class="o">.</span><span class="n">processor</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">RuleBasedProcessor</span><span class="p">(</span><span class="n">compound_lib</span><span class="p">)</span>
+</div>
+<span class="k">def</span> <span class="nf">GetProMod3SharedDataPath</span><span class="p">():</span>
+ <span class="sd">"""Get path to the shared data folder. Used for binaries.</span>
+<span class="sd"> Returns None if not set.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s">"PROMOD3_SHARED_DATA_PATH"</span><span class="p">)</span>
-<span class="c"># check if we already have an OST PrefixPath</span></div>
+<span class="k">def</span> <span class="nf">SetProMod3SharedDataPath</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+ <span class="sd">"""Set path to the shared data folder. Used for binaries."""</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s">"PROMOD3_SHARED_DATA_PATH"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span>
+
+<span class="c"># check if we already have an OST PrefixPath</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">GetSharedDataPath</span><span class="p">()</span>
<span class="k">except</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">rt_err</span><span class="p">:</span>
@@ -75,10 +85,20 @@
<span class="k">if</span> <span class="ow">not</span> <span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">():</span>
<span class="n">SetCompoundsChemlib</span><span class="p">()</span>
+<span class="c"># ensure that PROMOD3_SHARED_DATA_PATH env. var. set and override if needed</span>
+<span class="k">if</span> <span class="n">GetProMod3SharedDataPath</span><span class="p">()</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="c"># module_path = PROMOD3_ROOT/lib64/python2.7/site-packages/promod3</span>
+ <span class="n">module_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">__file__</span><span class="p">))</span>
+ <span class="c"># get PROMOD3_ROOT</span>
+ <span class="n">promod3_lib</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">module_path</span><span class="p">)))</span>
+ <span class="n">promod3_root</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">promod3_lib</span><span class="p">)</span>
+ <span class="n">SetProMod3SharedDataPath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">promod3_root</span><span class="p">,</span> <span class="s">"share"</span><span class="p">,</span> <span class="s">"promod3"</span><span class="p">))</span>
+
<span class="c"># set version</span>
-<span class="n">__version__</span> <span class="o">=</span> <span class="s">"0.1.0"</span>
+<span class="n">__version__</span> <span class="o">=</span> <span class="s">"1.0.0"</span>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'SetCompoundsChemlib'</span><span class="p">,)</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'SetCompoundsChemlib'</span><span class="p">,</span> <span class="s">'GetProMod3SharedDataPath'</span><span class="p">,</span>
+ <span class="s">'SetProMod3SharedDataPath'</span><span class="p">)</span>
<span class="c"># LocalWords: OST os ost conop io SetCompoundsChemlib CHEMLIB param chemlib</span>
<span class="c"># LocalWords: str SetDefaultLib RuleBasedProcessor PrefixPath RuntimeError</span>
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index 6b01d03e3ba02f1c5c5c41da13f53015428348db..417eafe2646dfdfc5bee95773a5be8007bb12ec5 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -251,7 +251,8 @@ lines:
Afterwards, you should be able to compile and run small sample codes that use
|project| and |ost_s| as in the :file:`test.cc` example. You can compile your
-code by executing ``make`` and run it with ``make run``.
+code by executing ``make`` and run it with ``make run``. Also, remember to set
+the ``PROMOD3_SHARED_DATA_PATH`` variable if you moved the stage folder.
--------------------------------------------------------------------------------
Unit Tests
diff --git a/doc/html/_sources/portableIO.txt b/doc/html/_sources/portableIO.txt
index 38f288cb88d782edbed6fc7a8a976c77eb6f22ed..26044c63e75fd61dd8f0766ab4a5107828a0b134 100644
--- a/doc/html/_sources/portableIO.txt
+++ b/doc/html/_sources/portableIO.txt
@@ -378,5 +378,11 @@ During the ``make`` process, portable versions of the files (stored in the
:file:`<MODULE>/data` folder) are converted and corresponding raw binary files
are stored in the :file:`stage/share/promod3/<MODULE>_data` folder.
+If the stage folder is moved after compilation (e.g. ``make install``), the
+location of the :file:`share/promod3` folder is to be stored in an environment
+variable called ``PROMOD3_SHARED_DATA_PATH``. This variable is automatically set
+if you load any |python| module from ``promod3`` or if you use the ``pm``
+script or if you use a well-setup module on a cluster.
+
Code for the generation of the binary files and their portable versions are
in the :file:`extras/data_generation` folder (provided as-is).
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 62890bd4f5f6b3b947fa12c05879582fff6a8f65..4fe0ba21fce9eec9c31fe7d386479b534a420c1e 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -252,7 +252,8 @@ lines:</p>
</div>
<p>Afterwards, you should be able to compile and run small sample codes that use
ProMod3 and OST as in the <code class="file docutils literal"><span class="pre">test.cc</span></code> example. You can compile your
-code by executing <code class="docutils literal"><span class="pre">make</span></code> and run it with <code class="docutils literal"><span class="pre">make</span> <span class="pre">run</span></code>.</p>
+code by executing <code class="docutils literal"><span class="pre">make</span></code> and run it with <code class="docutils literal"><span class="pre">make</span> <span class="pre">run</span></code>. Also, remember to set
+the <code class="docutils literal"><span class="pre">PROMOD3_SHARED_DATA_PATH</span></code> variable if you moved the stage folder.</p>
</div>
<div class="section" id="unit-tests">
<h2>Unit Tests<a class="headerlink" href="#unit-tests" title="Permalink to this headline">ΒΆ</a></h2>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 569c2d76daf9465ec245857590e3a184eb0830b9..3b1433795f7e946480615f1553be4ad1f551c390 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index d76786e29b9ca0991e3560f1c8efa685779105c0..7513d9e6441e4c78f1e3baff462f4ede7b407239 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -398,6 +398,11 @@ and non-portable I/O:</p>
<p>During the <code class="docutils literal"><span class="pre">make</span></code> process, portable versions of the files (stored in the
<code class="file docutils literal"><span class="pre"><MODULE>/data</span></code> folder) are converted and corresponding raw binary files
are stored in the <code class="file docutils literal"><span class="pre">stage/share/promod3/<MODULE>_data</span></code> folder.</p>
+<p>If the stage folder is moved after compilation (e.g. <code class="docutils literal"><span class="pre">make</span> <span class="pre">install</span></code>), the
+location of the <code class="file docutils literal"><span class="pre">share/promod3</span></code> folder is to be stored in an environment
+variable called <code class="docutils literal"><span class="pre">PROMOD3_SHARED_DATA_PATH</span></code>. This variable is automatically set
+if you load any Python module from <code class="docutils literal"><span class="pre">promod3</span></code> or if you use the <code class="docutils literal"><span class="pre">pm</span></code>
+script or if you use a well-setup module on a cluster.</p>
<p>Code for the generation of the binary files and their portable versions are
in the <code class="file docutils literal"><span class="pre">extras/data_generation</span></code> folder (provided as-is).</p>
</div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index cd9cc0a46d7a84bb90a7dde3f49650f2244c30a5..13b041078b7562efabc597f1b42897b35c412bf3 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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oil:[19,22],torsion_sampler_extend:[19,22],torsion_sampler_hel:22,torsion_sampler_helix:19,torsion_sampler_list:19,torsion_scor:14,torsion_weight:19,torsionprob:19,torsionsampl:[12,13,14,16,17,18,19,20,21,22],torsionscor:13,total:[13,19],touch:[0,4],toward:[4,13,17,21],tpl:21,tpr:[29,30],track:[5,26],tradit:7,tradition:5,train:16,trajectori:18,tran:[13,29,30],transform:[12,28,30],transformation_matrix:12,translat:[3,29,30],transofrm:12,transomegators:13,treat:[4,21,22,30],tree:[0,3,4,25],trg:[7,21],tri:[21,30],trick:[0,4],trigger:[0,3,4,27],tripeptid:20,tripl:5,triplet:[],trp:29,trustworthi:4,tryptophan:29,ttccpsivarsnfnvcrlpgtpea:21,ttccpsivarsnfnvcrlpgtpeaicatgytciiipgatcpgdyan:21,ttccpsivarsnfnvcrlpgtpeaicatytgciiipgatcpgdyan:21,tupl:[5,12,21],turn:[0,4,5,21],tutori:4,tweak:21,two:[0,4,12,13,14,17,19,21,22,23,26,28,29,30,31],txt:[0,1,3,4],type:[5,7,22],typedef:22,typenam:22,typic:[12,18,26,28],tyr:[28,29,30,31],tyrosin:29,uint32_t:22,uint:22,ultra:19,uncertain:4,under:[3,4],undergo:[17,18],underli:[14,21],underscor:0,understand:4,unexpect:1,unfavor:13,unfavour:[17,18,23],unfortun:4,uniqu:[13,14,18,30],unittest:[0,4],unix:4,unlik:[26,31],unrecognis:[5,7],unsupport:22,until:[4,13,17,21,25,28],untrack:0,unus:4,updat:[4,17,21],updatedistribut:20,upon:[17,18],usabl:4,usag:[16,19,24,26],use_full_extend:21,use_scoring_extend:21,user:[],userlevel:0,usr:4,usual:[0,1,3,4,7,15,21],utilis:4,v_size:22,val:[20,29],valid:[4,13,18,21,27],valin:29,valu:[1,5,7,12,13,14,18,19,21,22,24,25,26,27,28,29,30],valueerror:19,varadarajan:19,vari:[3,22],variabl:[0,1,4,10,21,31],variant:[7,21],variou:[0,1,3,4],vec3:[12,21,23,24,28],vector:[20,22],verbos:0,veri:[0,4,5,21,22,31],verif:7,verifi:[0,4,5],version:[1,4,13,19,20,22,27,29,30],vertex:19,via:[0,4,7,8],view:[4,20],virtual:4,visual:10,wai:[0,1,3,4,7,12,15,19,24,26,27,29],wait:4,walk:[0,4],want:[0,1,4,8,13,15,17,19,21,28,30],warn:[4,21],watch:4,web:[1,4],weight:[14,18,19],weird:[17,26],well:[1,3,4,13,19,20,21,26,28,30],went:4,were:[4,19,21],wether:25,what:[0,4,5,7,15],when:[0,3,4,7,12,13,18,19,20,21,22,23,24,26,27,28,30,31],whenev:13,where:[0,3,4,5,12,13,19,20,22,27,30],wherea:19,whether:[5,12,13,14,17,18,19,24,26,28,30],which:[0,3,4,5,6,7,10,12,13,14,18,19,20,21,22,24,28],whistl:4,who:[25,26],whole:[0,4,19,21],why:[0,4],width:22,wild:3,wise:3,wish:[9,13,20,21],within:[1,3,4,13,21,30],without:[0,3,4,5,16,17,19,21,27],won:[24,26,27],word:[3,27],work:[0,1,3,4,7,21,22,27],worst:4,would:[0,1,4,5,20,23,28],wrapper:[0,3,4,8,21],writebasetyp:22,writemagicnumb:22,writetypes:22,writeversionnumb:22,written:[4,22],wrong:[1,7],xlabel:20,xlim:20,xml:4,xxx:29,year:0,yet:[13,19],ylabel:20,ylim:20,you:[0,1,3,4,5,7,8,10,13,14,15,17,18,19,20,21,22,24,26,27,28,30],your:3,your_modul:4,yourself:[1,4],zero:[19,21,30],zhou2005:19,zhou:19,zip:26},titles:["<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Contributing","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","Documentation For Developers","Getting Started","Welcome To ProMod3’s Documentation!","Backbone","Loop Scoring","Helper Classes","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Modelling","Load Loop Objects","Loop Closing","Monte Carlo Sampling","Structural Database","Torsion Sampler","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein 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class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Contributing","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","Documentation For Developers","Getting Started","Welcome To ProMod3’s Documentation!","Backbone","Loop Scoring","Helper Classes","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Modelling","Load Loop Objects","Loop Closing","Monte Carlo Sampling","Structural Database","Torsion Sampler","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Using binary files in ProMod3","Disulfid Bond Evaluation","Frame","Coming to a solution","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Load Rotamer Libraries","Rotamers","RotamerID","Rotamer Library","Rotamer Settings","Documentation For Users"],titleterms:{"class":[14,20,21],"function":[3,5,6,24,26,28],acid:20,action:[0,3,4],actiontestcas:0,amino:20,api:0,argument:7,backbon:[12,17,30],backboneloopscor:13,base:19,basic:12,binari:22,block:[12,28],bond:23,branch:4,build:[1,12,28],can:29,carlo:18,ccd:17,chain:19,changelog:2,close:[17,21],closer:18,cmake:[0,1,3,4],code:22,come:25,command:7,construct:[24,28],contribut:4,conveni:[24,28],cooler:18,core:6,creat:0,data:22,databas:19,defin:[19,20],definit:3,depend:[1,30],detect:21,develop:9,directori:4,disulfid:23,document:[3,4,9,11,32],edit:12,entri:30,evalu:23,everyth:5,exampl:22,execut:0,exisit:22,extend:21,featur:[4,19],file:[5,22],find:19,fragment:19,frame:24,full:12,gap:21,geometr:19,get:[10,29],git:4,graph:25,group:28,handl:[14,21],have:0,header:22,helper:[5,14],hook:4,how:[4,29],indic:11,integr:0,interact:25,introduct:[3,5,7],issu:4,kic:17,librari:[27,30],licens:4,line:7,load:[16,27],loop:[13,14,15,16,17],mainten:3,make:[0,1],messag:5,model:[10,15,21,26],modul:[3,4,26],mont:18,must:0,non:30,object:[16,18,24],onc:14,output:0,own:4,pars:7,parser:7,parti:4,particl:28,pipelin:[10,21],pm3argpars:7,portabl:22,promod3:[1,3,4,6,10,11,22],protein:21,psipr:14,punch:21,quick:4,reconstruct:26,relax:17,releas:2,residu:[12,24],ring:21,rotam:[27,28,30,31],rotamerid:29,run:[0,1,10],sampl:18,sampler:[18,20],score:13,scorer:18,script:0,sequenc:19,set:31,setcompoundschemlib:8,sever:14,share:[3,5],sidechain:26,smallest:28,solut:25,stage:4,start:[4,10],stretch:12,structur:[4,19],subclass:0,tabl:11,test:[0,3,4,5],test_act:0,third:4,torsion:20,triplet:20,type:30,unit:[0,3,4],user:32,welcom:11,write:4,your:4}})
\ No newline at end of file
diff --git a/doc/portableIO.rst b/doc/portableIO.rst
index 38f288cb88d782edbed6fc7a8a976c77eb6f22ed..26044c63e75fd61dd8f0766ab4a5107828a0b134 100644
--- a/doc/portableIO.rst
+++ b/doc/portableIO.rst
@@ -378,5 +378,11 @@ During the ``make`` process, portable versions of the files (stored in the
:file:`<MODULE>/data` folder) are converted and corresponding raw binary files
are stored in the :file:`stage/share/promod3/<MODULE>_data` folder.
+If the stage folder is moved after compilation (e.g. ``make install``), the
+location of the :file:`share/promod3` folder is to be stored in an environment
+variable called ``PROMOD3_SHARED_DATA_PATH``. This variable is automatically set
+if you load any |python| module from ``promod3`` or if you use the ``pm``
+script or if you use a well-setup module on a cluster.
+
Code for the generation of the binary files and their portable versions are
in the :file:`extras/data_generation` folder (provided as-is).