From 54cd6e1d5ddfde7997eaaacb3e83f4f09a4cbb16 Mon Sep 17 00:00:00 2001
From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Fri, 26 Jan 2018 00:39:52 +0100
Subject: [PATCH] NGL Viewer for min and md

---
 TODO                                      |    5 +-
 django_simple/todo/templates/about.html   |    1 +
 django_simple/todo/templates/details.html |  241 ++++++++++++++++++++++++++++-
 files/fluct_plot.py                       |   13 ++
 4 files changed, 253 insertions(+), 7 deletions(-)

diff --git a/TODO b/TODO
index ebd4d57..3e98406 100644
--- a/TODO
+++ b/TODO
@@ -9,7 +9,7 @@ add javascript instead of separate forms
 
 check input pdb for: 
 #        missing residues (chain breaks) - done
-	unknown residues, 
+#	unknown residues - done
 	max length (1000), 
 	max number of dissulfides (30),
 	etc,
@@ -17,7 +17,8 @@ check input pdb for:
 
 check input for other errors (sequence ?)
 
-add web viewer NGL WebGL
+# add web viewer NGL WebGL
+# done
 
 # add BOXX BOXY BOXZ in advanced md and mremd
 # done
diff --git a/django_simple/todo/templates/about.html b/django_simple/todo/templates/about.html
index 8f9ce85..72262df 100644
--- a/django_simple/todo/templates/about.html
+++ b/django_simple/todo/templates/about.html
@@ -118,6 +118,7 @@ License terms of UNRES package implemented in the server
 
 Third party software employed in the server
 <ul> 
+<li> <a href="https://github.com/arose/ngl"> NGL Viewer </a>
 <li> <a href="http://pymol.org"> pymol </a>
 <li> convpdb.pl from <a href="http://www.mmtsb.org/">MMTSB Tool Set</a>
 <li> tleap, sander and ambpdb from <a href="http://ambermd.org">Amber Tools</a>
diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html
index 3484627..44f5e62 100644
--- a/django_simple/todo/templates/details.html
+++ b/django_simple/todo/templates/details.html
@@ -355,15 +355,26 @@ Created {{ task.created_date  }}
 			  width="500"></a> </div>
 			</li>
 
-
+<!--
 			<li class="list-group-item task-item">
 			  <div class="col-md-2"> Structure overlap </div>
 			  <div class="col-md-10"> <img 
 			  src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
 			  width="500"> </div>
 			</li>
-
-
+-->
+			<li class="list-group-item task-item">
+			  <div class="col-md-2"> Structure overlap NGL viewer</div>
+			  <div class="col-md-10" id="viewport_min"
+			  style="width:500px;height:500px;"> 
+			  </div>
+			</li>
+                        <li class="list-group-item task-item">
+               <div class="col-md-12">
+               <button id="toggleAllatom">Input structure on/off</button>
+               <button id="toggleSidechains2">Side-chains on/off</button>
+               </div>
+                        </li>
                         {% endif %}
 
 		        <li class="list-group-item task-item">
@@ -399,6 +410,25 @@ Created {{ task.created_date  }}
 			  
 			    </div>
 			    </li>
+
+{% if task.md_mdpdb %}
+			<li class="list-group-item task-item">
+			  <div class="col-md-2"> Trajectory NGL viewer</div>
+			  <div class="col-md-10" id="viewport_traj"
+			  style="width:500px;height:500px;"> 
+			  </div>
+			</li>
+                        <li class="list-group-item task-item">
+               <div class="col-md-6">
+<input id="clipRange" type="range" value=0 min=0 max= {% widthratio task.md_nstep task.md_ntwx 1 %} step=1 ></input><span id="clipRange_val">0</span> frame
+</div>
+<div class="col-md-6">
+<button id="toggleRunMDs">run/pause MD</button>  
+<button id="toggleSidechains1">side-chains on/off</button>			  
+</div>
+                        </li>
+
+{% endif %}
 			    
 			<li class="list-group-item task-item">
 			  <div class="col-md-2"> Radius of gyration based
@@ -435,7 +465,7 @@ Created {{ task.created_date  }}
 			  src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
 			  width="500"> </div>
 			</li>
-
+<!--
 			<li class="list-group-item task-item">
 			  <div class="col-md-2"> fluctuations putty on
 			  starting structure</div>
@@ -446,6 +476,15 @@ Created {{ task.created_date  }}
 			  src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
 			  width="500"></a> </div>
 			</li>
+-->
+			<li class="list-group-item task-item">
+			  <div class="col-md-2"> fluctuations putty on
+			  starting structure NGL viewer</div>
+			  <div class="col-md-10" id="viewport_putty"
+			  style="width:500px;height:500px;"> 
+			  </div>
+			</li>
+
 			
 			   {% endif %}
 
@@ -621,6 +660,7 @@ $('.majorpointslegend').click(function(){
 });
 </script>
 
+{% if task.type == "remd" %}
 <script>
 var slideIndex = 1;
 showDivs(slideIndex);
@@ -640,6 +680,7 @@ function showDivs(n) {
   x[slideIndex-1].style.display = "block";
 }
 </script>
+{% endif %}
 
 {% if not task.done %}
 <script>
@@ -664,5 +705,195 @@ $(document).ready(function() {
 </script>
 {% endif %} 
 	
-	
+<script src="https://unpkg.com/ngl"></script>
+{% if task.type == "min" %}
+<script>
+window.addEventListener("resize",
+     function (event) {
+     stage.handleResize();
+     },false);
+               
+var stage = new NGL.Stage("viewport_min");
+stage.setParameters( { backgroundColor: "white" } );
+Promise.all([
+  stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
+     o.addRepresentation( "backbone",{ color:
+       "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+     })
+     o.addRepresentation( "licorice",{ color:
+       "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
+     })    
+     return o
+  }),
+      
+  stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
+     o.addRepresentation( "backbone",{ name: "allatom", color:
+       "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
+     })
+     o.addRepresentation( "line",{ name: "allatomsc", color:
+       "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+       ,sele:"not hydrogen and sidechainAttached" 
+     })    
+     return o
+  })
+]).then(function (ol) {
+   ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
+   ol[ 0 ].autoView()
+})             
+
+var allatom=true;
+var side=true;
+var toggleAll = document.getElementById( "toggleAllatom" );
+toggleAll.addEventListener( "click", function(){
+                        allatom=! allatom;                                
+			stage.getRepresentationsByName(
+				"allatom" ).list.forEach( function( repre ){
+				repre.setVisibility( !repre.visible );
+			} );
+            if (side) {
+			stage.getRepresentationsByName(
+				"allatomsc" ).list.forEach( function( repre ){
+				repre.setVisibility( !repre.visible );
+			} );
+            }
+} );
+var toggleSidechains = document.getElementById("toggleSidechains2" );
+toggleSidechains.addEventListener( "click", function(){
+          side=!side;
+          if (allatom) {
+		stage.getRepresentationsByName(
+			"allatomsc" ).list.forEach( function( repre ){
+				repre.setVisibility( !repre.visible );
+		} );
+					              
+	  }
+	  stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
+		repre.setVisibility( !repre.visible );
+	  } );
+
+} );
+</script>
+{% endif %}
+
+{% if task.type == "md" and task.md_start == "pdbstart" %}
+<script>
+window.addEventListener("resize",
+     function (event) {
+     stage.handleResize();
+     },false);
+
+var stage = new NGL.Stage("viewport_putty");
+stage.setParameters( { backgroundColor: "white" } );
+
+var tooltip = document.createElement("div")
+Object.assign(tooltip.style, {
+  display: "none",
+  position: "fixed",
+  zIndex: 10,
+  pointerEvents: "none",
+  backgroundColor: "rgba( 0, 0, 0, 0.6 )",
+  color: "lightgrey",
+  padding: "8px",
+  fontFamily: "sans-serif"
+})
+document.body.appendChild(tooltip)
+
+stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then 
+       (function ( o ){
+       o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
+       sele: "backbone",
+       radius:"bfactor",
+       colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
+       o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
+       o.autoView();
+})
+
+// remove default hoverPick mouse action
+stage.mouseControls.remove("hoverPick")
+
+stage.signals.hovered.add(function (pickingProxy) {
+  if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
+    var atom = pickingProxy.atom || pickingProxy.closestBondAtom
+    var mp = pickingProxy.mouse.position
+    var bf= atom.bfactor.toFixed(2)
+    tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
+    tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
+    tooltip.style.left = mp.x + 3 + "px"
+    tooltip.style.display = "block"
+  } else {
+    tooltip.style.display = "none"
+  }
+})
+</script>
+{% endif %}	
+
+{% if task.type == "md" and task.md_mdpdb %}
+<script>
+window.addEventListener("resize",
+     function (event) {
+     stage.handleResize();
+     },false);
+
+      var stage = new NGL.Stage("viewport_traj");
+      stage.setParameters( { backgroundColor: "white" } );
+      stage.setParameters( { cameraType: "orthographic" } ); 
+      var traj;
+      var player;
+      stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", { 
+       asTrajectory: true } ) .then( function( o ){
+        o.setName ("unres_md");
+        o.addRepresentation( "backbone",{ color:
+       "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+        });
+        o.addRepresentation( "licorice",{ color:
+       "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+        });        
+        o.autoView();
+        o.addTrajectory();
+      });
+
+            var toggleSidechains = document.getElementById( "toggleSidechains1" );
+            toggleSidechains.addEventListener( "click", function(){
+							stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
+									repre.setVisibility( !repre.visible );
+							} );
+            } );
+
+
+      function numberWithCommas(x) {
+                return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
+      }
+      var toggleRunMDs = document.getElementById( "toggleRunMDs" );
+      var isRunning = false;
+      toggleRunMDs.addEventListener( "click", function(){
+         var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
+         var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
+				if( !isRunning ){
+					player.play();
+					isRunning = true;
+
+                    trajComp.signals.frameChanged.add(function(){
+                      var fnum=trajComp.trajectory.currentFrame;                   
+                      clipRange.value = fnum;
+                      clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
+                    });
+
+				}else{
+			   	        player.play();
+					player.pause();
+					isRunning = false;
+				}
+      } );      
+      var clipRange = document.getElementById( "clipRange" );
+      var clipRange_val = document.getElementById( "clipRange_val" );
+      clipRange.oninput = function( e ){
+                var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
+                trajComp.setFrame(e.target.value)
+                clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));
+      };      
+
+</script>
+{% endif %}	
+
+
 {% endblock %}
diff --git a/files/fluct_plot.py b/files/fluct_plot.py
index 7719b2f..1064e90 100755
--- a/files/fluct_plot.py
+++ b/files/fluct_plot.py
@@ -7,6 +7,7 @@ import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import os.path
+from itertools import cycle
 
 iatom=0
 nmol=0
@@ -74,4 +75,16 @@ if len(b)!=0:
  plt.plot(x,b,'-',c='red')
  plt.legend(['fluctuations','sqrt(3*bfactor/8*pi^2)'])
 plt.savefig('fluct_plot.png')
+
+ycycle=cycle(y)
+with open('plik.pdb') as f, open ('plik_bf.pdb','w') as fw:
+  prev_ires=None
+  for line in f:
+     if line[0:4]=='ATOM':
+          if line[22:26] != prev_ires:
+             prev_ires=line[22:26]
+             bf=next(ycycle)
+          fw.write(line[0:60]+'{:6.2f}'.format(bf)+line[66:])
+     elif line[0:3] == 'TER' or line[0:6] == 'CONECT':
+          fw.write(line)
                                
\ No newline at end of file
-- 
1.7.9.5