ignore bulge option in dssp calculation

src/modules/molanl/MolAnlManager.cpp

@@ -584,8 +584,7 @@ namespace {
   }
 }
 
-
-void MolAnlManager::calcProt2ndry(MolCoordPtr pMol, double hbmax)
+void MolAnlManager::calcProt2ndry(MolCoordPtr pMol, double hbmax, bool bignb)
 {
   // Record undo info
   Prot2ndryEditInfo *pPEI = NULL;
@@ -596,7 +595,7 @@ void MolAnlManager::calcProt2ndry(MolCoordPtr pMol, double hbmax)
     pPEI->saveBefore(pMol);
   }
 
-  pMol->calcProt2ndry(hbmax);
+  pMol->calcProt2ndry(hbmax, bignb);
 
   // Record redo info
   if (pPEI!=NULL && uu.isOK()) {

src/modules/molanl/MolAnlManager.hpp

@@ -83,7 +83,7 @@ namespace molanl {
                                  double r_min, double r_max, bool hbond,
                                  int nMax);
 
-    void calcProt2ndry(MolCoordPtr pMol, double hbmax);
+    void calcProt2ndry(MolCoordPtr pMol, double hbmax, bool bignb);
 
     void setProt2ndry(MolCoordPtr pMol, SelectionPtr pSel, int nSecType);
 

src/modules/molanl/MolAnlManager.qif

@@ -43,7 +43,7 @@ runtime_class MolAnlManager
   //////////////////////////
   // protein secondary structure
 
-  void calcProt2ndry(object<MolCoord$> pmol, real hbmax);
+  void calcProt2ndry(object<MolCoord$> pmol, real hbmax, boolean ignb);
 
   void setProt2ndry(object<MolCoord$> pmol, object<MolSelection$> pSel, integer nSecType);
 

src/modules/molstr/MolBond.cpp

@@ -38,9 +38,9 @@ namespace {
 
       MolAtomPtr pBonAtm1 = pMol->getAtom(pb->getAtom1());
       MolAtomPtr pBonAtm2 = pMol->getAtom(pb->getAtom2());
-      MB_DPRINTLN("Bond %s <--> %s",
-                  pBonAtm1->toString().c_str(),
-                  pBonAtm2->toString().c_str());
+      //MB_DPRINTLN("Bond %s <--> %s",
+      //pBonAtm1->toString().c_str(),
+      //pBonAtm2->toString().c_str());
       if (pb->getAtom1()==aid1)
         atoms1.push_back(pBonAtm2->getPos());
       else if (pb->getAtom2()==aid1)
@@ -64,7 +64,7 @@ namespace {
 
     bOK = true;
 
-    MB_DPRINTLN("DblBon nbon=%d, nv=%s", nbon1, nv1.toString().c_str());
+    //MB_DPRINTLN("DblBon nbon=%d, nv=%s", nbon1, nv1.toString().c_str());
     return nv1;
   }
 }

src/modules/molstr/MolCoord.hpp

@@ -281,7 +281,7 @@ namespace molstr {
     ///
     /// Calculate secondary structure (impl: Prot2ndry.cpp)
     ///
-    void calcProt2ndry(double hb_high = -500.0);
+    void calcProt2ndry(double hb_high = -500.0, bool bIgnoreBulge=false);
 
     void calcBasePair(double cutoff, double tilt);
 

src/modules/molstr/MolCoord.qif

@@ -69,7 +69,7 @@ runtime_class MolCoord extends Object
   integer appendAtom1(object<MolAtom$> pAtom, string chain, integer resid, string resn) => appendAtomScr1;
 
   void applyTopology();
-  void calcProt2ndry(real hb_high);
+  void calcProt2ndry(real hb_high, boolean bIgnoreBulge);
   void calcBasePair(real cutoff, real tilt);
 };
 

src/modules/molstr/Prot2ndry.cpp

@@ -347,6 +347,10 @@ namespace {
     /// HBHIGH - HIGHEST ALLOWED ENERGY OF A HYDROGEN BOND IN CAL/MOL
     double m_hbhigh;
 
+    /// Ignore-bulge flag
+    /// Do not link beta strand connected by a bulge
+    bool m_bIgnoreBulge;
+
     //////////////////////////////////
 
     ///
@@ -680,12 +684,12 @@ namespace {
 	MB_DPRINTLN("%s sheet", (with.btyp==parallel)?"parallel":"antiparallel");
 
 	MB_DPRINTLN("  %s%d (%d) <--> %s%d (%d)",
-		    pr_ib->getChainName().c_str(), pr_ib->getIndex(), with.ib,
-		    pr_jb->getChainName().c_str(), pr_jb->getIndex(), with.jb);
+		    pr_ib->getChainName().c_str(), pr_ib->getIndex().toInt(), with.ib,
+		    pr_jb->getChainName().c_str(), pr_jb->getIndex().toInt(), with.jb);
 
 	MB_DPRINTLN("  %s%d (%d) <--> %s%d (%d)",
-		    pr_ie->getChainName().c_str(), pr_ie->getIndex(), with.ie,
-		    pr_je->getChainName().c_str(), pr_je->getIndex(), with.je);
+		    pr_ie->getChainName().c_str(), pr_ie->getIndex().toInt(), with.ie,
+		    pr_je->getChainName().c_str(), pr_je->getIndex().toInt(), with.je);
       }
 #endif
     }
@@ -783,9 +787,9 @@ namespace {
     }
 
     /*
-      link the two bridges connected by a buldge
+      link the two bridges connected by a bulge
      */
-    void linkBuldge(Bridge &Abr, Bridge &Bbr)
+    void linkBulge(Bridge &Abr, Bridge &Bbr)
     {
       if (Abr.btyp==parallel) {
 	MB_DPRINTLN("linking par: (%d:%d) --> (%d:%d)",
@@ -809,7 +813,7 @@ namespace {
        If two the same b-type bridges are separated 1 and 4 residues,
        they are defined to be connected by a buldge region.
     */
-    bool checkBuldge(Bridge &Abr, Bridge &Bbr)
+    bool checkBulge(Bridge &Abr, Bridge &Bbr)
     {
       int idiff, jdiff;
 
@@ -820,7 +824,7 @@ namespace {
 	if (1<=idiff && 1<=jdiff) {
 	  if ((idiff<=2 && jdiff<=5) ||
 	      (idiff<=5 && jdiff<=2)) {
-	    linkBuldge(Abr, Bbr);
+	    linkBulge(Abr, Bbr);
 	    return true;
 	  }
 	}
@@ -831,7 +835,7 @@ namespace {
 	if (1<=idiff && 1<=jdiff) {
 	  if ((idiff<=2 && jdiff<=5) ||
 	      (idiff<=5 && jdiff<=2)) {
-	    linkBuldge(Bbr, Abr);
+	    linkBulge(Bbr, Abr);
 	    return true;
 	  }
 	}
@@ -843,7 +847,7 @@ namespace {
 	if (1<=idiff && 1<=jdiff) {
 	  if ((idiff<=2 && jdiff<=5) ||
 	      (idiff<=5 && jdiff<=2)) {
-	    linkBuldge(Abr, Bbr);
+	    linkBulge(Abr, Bbr);
 	    return true;
 	  }
 	}
@@ -854,7 +858,7 @@ namespace {
 	if (1<=idiff && 1<=jdiff) {
 	  if ((idiff<=2 && jdiff<=5) ||
 	      (idiff<=5 && jdiff<=2)) {
-	    linkBuldge(Bbr, Abr);
+	    linkBulge(Bbr, Abr);
 	    return true;
 	  }
 	}
@@ -879,13 +883,18 @@ namespace {
 	if (iwith.ib!=iwith.ie)
 	  iwith.bIsolated = false;
 
-        BridgeList::iterator jter = iter; //m_bridges.begin();
-	++jter;
-        for (; jter!=eiter; ++jter) {
-          Bridge &jwith = *jter;
-	  if (!checkBuldge(iwith, jwith)) continue;
-	  iwith.bIsolated = false;
-	  jwith.bIsolated = false;
+        if (!m_bIgnoreBulge) {
+          BridgeList::iterator jter = iter;
+          ++jter;
+          for (; jter!=eiter; ++jter) {
+            Bridge &jwith = *jter;
+            if (!checkBulge(iwith, jwith)) continue;
+            MB_DPRINTLN("Buldge detected for %d:%d/%d:%d - %d:%d/%d:%d",
+                        iwith.ib, iwith.ie, iwith.jb, iwith.je,
+                        jwith.ib, jwith.ie, jwith.jb, jwith.je);
+            iwith.bIsolated = false;
+            jwith.bIsolated = false;
+          }
 	}	
       }
 
@@ -1224,13 +1233,14 @@ namespace {
 
 //////////////////////////////////////
 
-void MolCoord::calcProt2ndry(double hb_high)
+void MolCoord::calcProt2ndry(double hb_high /*= -500.0*/, bool bIgnoreBulge /*=false*/)
 {
   MolCoordPtr pMol(this);
 
   Prot2ndry ps;
   ps.init(pMol);
   ps.m_hbhigh = hb_high;
+  ps.m_bIgnoreBulge = bIgnoreBulge;
   if (ps.m_chains.size()<=0) {
     MB_DPRINTLN("calcProt2ndry> no amino acid residues in %d/%s",
                 getUID(), getName().c_str());

src/modules/molvis/RibbonRenderer.cpp

@@ -19,37 +19,37 @@ using gfx::ColorPtr;
 /////////////////////////////////////////////////////
 
 namespace molvis {
-// Specialized evaluator for ribbon smoothness values
-class RibbonSmoothEval : public RealNumEvaluator
-{
-public:
-  double m_helix;
-  double m_sheet;
-  double m_coil;
-
-  RibbonSmoothEval() : m_helix(0.0), m_sheet(0.5), m_coil(0.0) {}
-  virtual ~RibbonSmoothEval() {}
+  // Specialized evaluator for ribbon smoothness values
+  class RibbonSmoothEval : public RealNumEvaluator
+  {
+  public:
+    double m_helix;
+    double m_sheet;
+    double m_coil;
+
+    RibbonSmoothEval() : m_helix(0.0), m_sheet(0.5), m_coil(0.0) {}
+    virtual ~RibbonSmoothEval() {}
+
+    virtual bool getAtomValue(MolAtom *pAtom, double &value) {
+      // not used
+      return false;
+    }
 
-  virtual bool getAtomValue(MolAtom *pAtom, double &value) {
-    // not used
-    return false;
-  }
+    virtual bool getResidValue(MolResidue *pRes, double &value) {
+      if (pRes==NULL) return false;
+      LString sec("coil");
+      pRes->getPropStr("secondary", sec);
+      if (sec.equals("helix"))
+        value = m_helix;
+      else if (sec.equals("sheet"))
+        value = m_sheet;
+      else
+        value = m_coil;
 
-  virtual bool getResidValue(MolResidue *pRes, double &value) {
-    if (pRes==NULL) return false;
-    LString sec("coil");
-    pRes->getPropStr("secondary", sec);
-    if (sec.equals("helix"))
-      value = m_helix;
-    else if (sec.equals("sheet"))
-      value = m_sheet;
-    else
-      value = m_coil;
+      return true;
+    }
 
-    return true;
-  }
-
-};
+  };
 }
 
 /////////////////////////////////////////////////////

src/version.hpp

@@ -2,12 +2,12 @@
 // Version info
 //
 
-#define FILEVER       2,2,2,393
-#define PRODUCTVER    2,2,2,393
-#define STRFILEVER    "2.2.2.393"
-#define STRPRODUCTVER "2.2.2.393"
-#define BUILD_ID 20160722103849
-#define STRBUILD_ID "20160722103849"
+#define FILEVER       2,2,2,394
+#define PRODUCTVER    2,2,2,394
+#define STRFILEVER    "2.2.2.394"
+#define STRPRODUCTVER "2.2.2.394"
+#define BUILD_ID 20160809180044
+#define STRBUILD_ID "20160809180044"
 
 #define QUE_VERSION_STRING "Version " STRPRODUCTVER " build " STRBUILD_ID
 

src/xpcom/XPCTimerImpl.cpp

@@ -23,7 +23,7 @@
 #  include <xmlrpc_bridge/XmlRpcMgr.hpp>
 #endif
 
-#define USE_PERFTIMER 1
+// #define USE_PERFTIMER 1
 
 #ifdef USE_PERFTIMER
 #  include <boost/timer/timer.hpp>

src/xul_gui/application.ini

@@ -8,11 +8,11 @@ Vendor=BKR-LAB
 Name=CueMol2_GUI
 ;
 ; This field specifies your application's version.  This field is optional.
-Version=2.2.2.393
+Version=2.2.2.394
 ;
 ; This field specifies your application's build ID (timestamp).  This field is
 ; required.
-BuildID=20160722103849
+BuildID=20160809180044
 ;
 ; This field specifies a compact copyright notice for your application.  This
 ; field is optional.

src/xul_gui/chrome/content/tools/prot2ndry-tool-dlg.xul

@@ -33,6 +33,8 @@
 	  <radio label="Recalc secondry str" id="radio_recalc" selected="true"/>
 	</caption>
 
+	<checkbox id="ign_bulge" label="Ignore &#0946; bulge" checked="false"/>
+
 	<hbox align="center">
 	  <label value="Max hbond energy (cal/mol):"/>
 	  <textbox id="hbmax" type="number"

src/xul_gui/chrome/content/tools/prot2ndry-tool.js

@@ -59,6 +59,7 @@ if (!("Prot2ndryTool" in cuemolui)) {
       let that = this;
 
       this.mHbMax = document.getElementById('hbmax');
+      this.mIgnBlg = document.getElementById('ign_bulge');
 
       this.mTargMol.addSelChanged(function(aEvent) {
 	try { that.onTargMolChanged(aEvent);}
@@ -133,11 +134,13 @@ if (!("Prot2ndryTool" in cuemolui)) {
       dd("onRadioSelChanged: "+tgtid);
       if (tgtid=="radio_recalc") {
 	this.mHbMax.disabled = false;
+	this.mIgnBlg.disabled = false;
 	this.mTargSel.disabled = true;
 	this.mSecTypeSel.disabled = true;
       }
       else if (tgtid=="radio_assign") {
 	this.mHbMax.disabled = true;
+	this.mIgnBlg.disabled = true;
 	this.mTargSel.disabled = false;
 	this.mSecTypeSel.disabled = false;
       }
@@ -195,6 +198,8 @@ if (!("Prot2ndryTool" in cuemolui)) {
       if (isNaN(hbmax))
 	return false;
 
+      let bIgnBlg = this.mIgnBlg.checked;
+
       /////////////////////////////////////
 
       let mgr = cuemol.getService("MolAnlManager");
@@ -203,7 +208,7 @@ if (!("Prot2ndryTool" in cuemolui)) {
       scene.startUndoTxn("Recalc protein secondary str");
 
       try {
-	mgr.calcProt2ndry(tgtmol, hbmax);
+	mgr.calcProt2ndry(tgtmol, hbmax, bIgnBlg);
       }
       catch (e) {
 	dd("calcProt2ndry Error!!");

winbuild/cuemol2.sln

@@ -133,7 +133,4 @@ Global
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
-	GlobalSection(Performance) = preSolution
-		HasPerformanceSessions = true
-	EndGlobalSection
 EndGlobal