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Update gh-pages to output generated at 9b66523
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@rvhonorato
rvhonorato committed Aug 30, 2024
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2 changes: 1 addition & 1 deletion CNS.html
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Expand Up @@ -285,7 +285,7 @@ <h3>3. Makefile<a class="headerlink" href="#makefile" title="Permalink to this h

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2 changes: 1 addition & 1 deletion INSTALL.html
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Expand Up @@ -282,7 +282,7 @@ <h2><code class="docutils literal notranslate"><span class="pre">gdock</span></c

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2 changes: 1 addition & 1 deletion USAGE.html
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Expand Up @@ -141,7 +141,7 @@ <h2>Run HADDOCK3<a class="headerlink" href="#run-haddock3" title="Permalink to t

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2 changes: 1 addition & 1 deletion _modules/haddock.html
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Expand Up @@ -140,7 +140,7 @@ <h1>Source code for haddock</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli.html
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Expand Up @@ -295,7 +295,7 @@ <h1>Source code for haddock.clis.cli</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_analyse.html
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Expand Up @@ -756,7 +756,7 @@ <h1>Source code for haddock.clis.cli_analyse</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_bm.html
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Expand Up @@ -794,7 +794,7 @@ <h1>Source code for haddock.clis.cli_bm</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_cfg.html
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Expand Up @@ -286,7 +286,7 @@ <h1>Source code for haddock.clis.cli_cfg</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_clean.html
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Expand Up @@ -211,7 +211,7 @@ <h1>Source code for haddock.clis.cli_clean</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_cp.html
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Expand Up @@ -274,7 +274,7 @@ <h1>Source code for haddock.clis.cli_cp</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_dmn.html
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Expand Up @@ -428,7 +428,7 @@ <h1>Source code for haddock.clis.cli_dmn</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_mpi.html
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Expand Up @@ -218,7 +218,7 @@ <h1>Source code for haddock.clis.cli_mpi</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_pp.html
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Expand Up @@ -263,7 +263,7 @@ <h1>Source code for haddock.clis.cli_pp</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_re.html
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Expand Up @@ -155,7 +155,7 @@ <h1>Source code for haddock.clis.cli_re</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_restraints.html
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Expand Up @@ -179,7 +179,7 @@ <h1>Source code for haddock.clis.cli_restraints</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_score.html
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Expand Up @@ -383,7 +383,7 @@ <h1>Source code for haddock.clis.cli_score</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_traceback.html
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Expand Up @@ -465,7 +465,7 @@ <h1>Source code for haddock.clis.cli_traceback</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/cli_unpack.html
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Expand Up @@ -233,7 +233,7 @@ <h1>Source code for haddock.clis.cli_unpack</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/re/clustfcc.html
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Expand Up @@ -313,7 +313,7 @@ <h1>Source code for haddock.clis.re.clustfcc</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/re/clustrmsd.html
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Expand Up @@ -383,7 +383,7 @@ <h1>Source code for haddock.clis.re.clustrmsd</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/re/score.html
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Expand Up @@ -243,7 +243,7 @@ <h1>Source code for haddock.clis.re.score</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/restraints/active_passive_to_ambig.html
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Expand Up @@ -164,7 +164,7 @@ <h1>Source code for haddock.clis.restraints.active_passive_to_ambig</h1><div cla

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/restraints/calc_accessibility.html
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Expand Up @@ -509,7 +509,7 @@ <h1>Source code for haddock.clis.restraints.calc_accessibility</h1><div class="h

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/restraints/passive_from_active.html
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Expand Up @@ -162,7 +162,7 @@ <h1>Source code for haddock.clis.restraints.passive_from_active</h1><div class="

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2 changes: 1 addition & 1 deletion _modules/haddock/clis/restraints/restrain_bodies.html
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2 changes: 1 addition & 1 deletion _modules/haddock/clis/restraints/validate_tbl.html
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Expand Up @@ -153,7 +153,7 @@ <h1>Source code for haddock.clis.restraints.validate_tbl</h1><div class="highlig

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2 changes: 1 addition & 1 deletion _modules/haddock/core/cns_paths.html
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Expand Up @@ -183,7 +183,7 @@ <h1>Source code for haddock.core.cns_paths</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/core/exceptions.html
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Expand Up @@ -150,7 +150,7 @@ <h1>Source code for haddock.core.exceptions</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/core/supported_molecules.html
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Expand Up @@ -578,7 +578,7 @@ <h1>Source code for haddock.core.supported_molecules</h1><div class="highlight">

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2 changes: 1 addition & 1 deletion _modules/haddock/core/typing.html
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Expand Up @@ -292,7 +292,7 @@ <h1>Source code for haddock.core.typing</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/clean_steps.html
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2 changes: 1 addition & 1 deletion _modules/haddock/gear/config.html
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Expand Up @@ -434,7 +434,7 @@ <h1>Source code for haddock.gear.config</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/expandable_parameters.html
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Expand Up @@ -1020,7 +1020,7 @@ <h1>Source code for haddock.gear.expandable_parameters</h1><div class="highlight

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/extend_run.html
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Expand Up @@ -378,7 +378,7 @@ <h1>Source code for haddock.gear.extend_run</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/greetings.html
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Expand Up @@ -168,7 +168,7 @@ <h1>Source code for haddock.gear.greetings</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/haddockmodel.html
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Expand Up @@ -158,7 +158,7 @@ <h1>Source code for haddock.gear.haddockmodel</h1><div class="highlight"><pre>

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10 changes: 8 additions & 2 deletions _modules/haddock/gear/prepare_run.html
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Expand Up @@ -1049,9 +1049,15 @@ <h1>Source code for haddock.gear.prepare_run</h1><div class="highlight"><pre>
<span class="c1"># Check if the limiting parameter is present in the parameters</span>
<span class="k">if</span> <span class="n">limiting_param</span> <span class="ow">in</span> <span class="n">params</span><span class="p">:</span>
<span class="c1"># Check each incompatibility for the limiting parameter</span>
<span class="n">incompatible_value_of_limiting_param</span> <span class="o">=</span> <span class="n">incompatibilities</span><span class="p">[</span><span class="s2">&quot;value&quot;</span><span class="p">]</span>
<span class="k">for</span> <span class="n">incompatible_param</span><span class="p">,</span> <span class="n">incompatible_value</span> <span class="ow">in</span> <span class="n">incompatibilities</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">incompatible_param</span> <span class="o">==</span> <span class="s2">&quot;value&quot;</span><span class="p">:</span>
<span class="k">continue</span>
<span class="c1"># Check if the incompatible parameter is present and has the incompatible value</span>
<span class="k">if</span> <span class="n">params</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">incompatible_param</span><span class="p">)</span> <span class="o">==</span> <span class="n">incompatible_value</span><span class="p">:</span>
<span class="k">if</span> <span class="p">(</span>
<span class="n">params</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">incompatible_param</span><span class="p">)</span> <span class="o">==</span> <span class="n">incompatible_value</span>
<span class="ow">and</span> <span class="n">params</span><span class="p">[</span><span class="n">limiting_param</span><span class="p">]</span> <span class="o">==</span> <span class="n">incompatible_value_of_limiting_param</span>
<span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;Parameter `</span><span class="si">{</span><span class="n">limiting_param</span><span class="si">}</span><span class="s2">` is incompatible with `</span><span class="si">{</span><span class="n">incompatible_param</span><span class="si">}</span><span class="s2">=</span><span class="si">{</span><span class="n">incompatible_value</span><span class="si">}</span><span class="s2">`.&quot;</span>
<span class="p">)</span></div>
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<p>&#169; Copyright 2024, BonvinLab.
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</span></p>
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2 changes: 1 addition & 1 deletion _modules/haddock/gear/preprocessing.html
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Expand Up @@ -1185,7 +1185,7 @@ <h1>Source code for haddock.gear.preprocessing</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/restart_run.html
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Expand Up @@ -162,7 +162,7 @@ <h1>Source code for haddock.gear.restart_run</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/validations.html
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Expand Up @@ -109,7 +109,7 @@ <h1>Source code for haddock.gear.validations</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/yaml2cfg.html
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Expand Up @@ -341,7 +341,7 @@ <h1>Source code for haddock.gear.yaml2cfg</h1><div class="highlight"><pre>

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2 changes: 1 addition & 1 deletion _modules/haddock/gear/zerofill.html
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Expand Up @@ -230,7 +230,7 @@ <h1>Source code for haddock.gear.zerofill</h1><div class="highlight"><pre>

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