Merge pull request #9 from vincefn/master

Update from upstream

Author: sbillinge

src/ObjCryst/ObjCryst/Atom.cpp

@@ -169,16 +169,23 @@ string Atom::GetComponentName(const int i) const{ return this->GetName();}
 void Atom::Print() const
 {
    VFN_DEBUG_MESSAGE("Atom::Print()",1)
-   cout << "Atom ("
-        << FormatString(mpScattPowAtom->GetSymbol(),4) << ") :"
-        << FormatString(this->GetName(),16)  << " at : "
-        << FormatFloat(this->GetX())
-        << FormatFloat(this->GetY())
-        << FormatFloat(this->GetZ());
-   if(this->IsDummy()) cout << " DUMMY! ";
+   if(this->IsDummy())
+   {
+      cout << "Atom (DUMMY) :"
+           << FormatString(this->GetName(),16)  << " at : "
+           << FormatFloat(this->GetX())
+           << FormatFloat(this->GetY())
+           << FormatFloat(this->GetZ());
+   }
    else
    {
-      cout << ", Biso="
+      cout << "Atom ("
+           << FormatString(mpScattPowAtom->GetSymbol(),4) << ") :"
+           << FormatString(this->GetName(),16)  << " at : "
+           << FormatFloat(this->GetX())
+           << FormatFloat(this->GetY())
+           << FormatFloat(this->GetZ())
+           << ", Biso="
            << FormatFloat(mpScattPowAtom->GetBiso())
            << ", Popu=" << FormatFloat(this->GetOccupancy());
    }
@@ -303,6 +310,7 @@ void Atom::GLInitDisplayList(const bool onlyIndependentAtoms,
                              const bool fullMoleculeInLimits)const
 {
    VFN_DEBUG_MESSAGE("Atom::GLInitDisplayList():"<<this->GetName(),5)
+   if(this->IsDummy()) return ;
    REAL en=1;
    if(displayEnantiomer==true) en=-1;
 
@@ -323,7 +331,6 @@ void Atom::GLInitDisplayList(const bool onlyIndependentAtoms,
    const REAL bb=this->GetCrystal().GetLatticePar(1);
    const REAL cc=this->GetCrystal().GetLatticePar(2);
 
-   if(this->IsDummy()) return ;
    if(hideHydrogens  && (mpScattPowAtom->GetForwardScatteringFactor(RAD_XRAY)<1.5)) return;
    GLUquadricObj* pQuadric = gluNewQuadric();
    if(true==onlyIndependentAtoms)

src/ObjCryst/ObjCryst/CIF.cpp

@@ -1171,8 +1171,10 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
             if(verbose) cout<<endl<<"Finally using spacegroup name:"<<bestsymbol<<endl;
             pCryst->GetSpaceGroup().ChangeSpaceGroup(bestsymbol);
          }
+         // Try to set name from CIF. If that fails, the computed formula will be used at the end
          if(pos->second.mName!="") pCryst->SetName(pos->second.mName);
          else if(pos->second.mFormula!="") pCryst->SetName(pos->second.mFormula);
+         
          const float t1=chrono.seconds();
          (*fpObjCrystInformUser)((boost::format("CIF: Create Crystal:%s(%s)(dt=%6.3fs)")%pCryst->GetName() % pCryst->GetSpaceGroup().GetName() % t1).str());
 
@@ -1277,6 +1279,7 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
             }
             (*fpObjCrystInformUser)((boost::format("CIF: finished connecting atoms (%u isolated atoms, %u molecules) (Crystal creation=%6.3fs total)") % ctat % ctmol % chrono.seconds()).str());
          }
+         if(pCryst->GetName()=="") pCryst->SetName(pCryst->GetFormula());
       }
    return pCryst;
 }
@@ -1299,6 +1302,7 @@ PowderPattern* CreatePowderPatternFromCIF(CIF &cif)
 DiffractionDataSingleCrystal* CreateSingleCrystalDataFromCIF(CIF &cif, Crystal *pcryst)
 {
    DiffractionDataSingleCrystal* pData=NULL;
+   std::string name("");
    for(map<string,CIFData>::iterator pos=cif.mvData.begin();pos!=cif.mvData.end();++pos)
    {
       if(pos->second.mH.numElements()>0)
@@ -1310,6 +1314,7 @@ DiffractionDataSingleCrystal* CreateSingleCrystalDataFromCIF(CIF &cif, Crystal *
             {  // Use last Crystal created
                pcryst=&(gCrystalRegistry.GetObj(gCrystalRegistry.GetNb()-1));
                (*fpObjCrystInformUser)((boost::format("CIF: Importing SINGLE CRYSTAL DIFFRACTION data: using last Crystal structure as corresponding crystal [%s]") % pcryst->GetName().c_str()).str());
+               name = pcryst->GetName();
             }
             else
             {
@@ -1320,6 +1325,7 @@ DiffractionDataSingleCrystal* CreateSingleCrystalDataFromCIF(CIF &cif, Crystal *
          }
          pData=new DiffractionDataSingleCrystal(*pcryst);
          pData->SetHklIobs(pos->second.mH,pos->second.mK,pos->second.mL,pos->second.mIobs,pos->second.mSigma);
+         if(pData->GetName()=="") pData->SetName(name);
          (*fpObjCrystInformUser)((boost::format("CIF: Imported SINGLE CRYSTAL DIFFRACTION data, with %d reflections") % pData->GetNbRefl()).str());
       }
    }

src/ObjCryst/ObjCryst/Crystal.cpp

@@ -380,11 +380,41 @@ void Crystal::Print(ostream &os)const
    const long genMult=this->GetSpaceGroup().GetNbSymmetrics();
    for(int i=0;i<mScattCompList.GetNbComponent();i++)
       nbAtoms += genMult * mScattCompList(i).mOccupancy * mScattCompList(i).mDynPopCorr;
-   os << " Total number of components (atoms) in one unit cell : " << nbAtoms<<endl<<endl;
+   os << " Total number of components (atoms) in one unit cell : " << nbAtoms<<endl
+      << " Chemical formula: "<< this->GetFormula() <<endl;
 
    VFN_DEBUG_MESSAGE("Crystal::Print():End",5)
 }
 
+std::string Crystal::GetFormula() const
+{
+   this->GetScatteringComponentList();
+   if(mScattCompList.GetNbComponent() == 0) return "";
+   std::map<std::string,float> velts;
+   for(unsigned int i=0; i<mScattCompList.GetNbComponent(); ++i)
+   {
+      const ScatteringComponent* psi = &mScattCompList(i);
+      if(psi->mpScattPow == 0) continue;
+      if(psi->mpScattPow->GetClassName().compare("ScatteringPowerAtom")!=0) continue;
+      const ScatteringPowerAtom *pat=dynamic_cast<const ScatteringPowerAtom*>(psi->mpScattPow);
+      string p=pat->GetSymbol();
+      if(velts.count(p)==0)
+         velts[p] = psi->mOccupancy * psi->mDynPopCorr ;
+      else velts[p] += psi->mOccupancy * psi->mDynPopCorr;
+   }
+   stringstream s;
+   s<<std::setprecision(2);
+   for(std::map<std::string,float>::const_iterator pos=velts.begin();pos!=velts.end();++pos)
+   {
+      if(pos!=velts.begin()) s<<" ";
+      float nb=pos->second;
+      if((abs(nb)-nb)<0.01) s<<pos->first<<int(round(nb));
+      else s<<pos->first<<nb;
+   }
+   return s.str();
+}
+   
+
 CrystMatrix_REAL Crystal::GetMinDistanceTable(const REAL minDistance) const
 {
    VFN_DEBUG_MESSAGE("Crystal::MinDistanceTable()",5)

src/ObjCryst/ObjCryst/Crystal.h

@@ -189,6 +189,9 @@ class Crystal:public UnitCell
       /// \todo one function to print on one line and a PrintLong() function
       /// \param os the stream to which the information is outputed (default=cout)
       void Print(ostream &os=cout) const;
+   
+      /// Formula with atoms in alphabetic order
+      std::string GetFormula() const;
 
       /** \brief Minimum interatomic distance between all scattering components (atoms) in
       * the crystal.

src/ObjCryst/ObjCryst/Indexing.h

@@ -30,6 +30,7 @@
 #include <time.h>
 #include "ObjCryst/RefinableObj/RefinableObj.h"
 #include "ObjCryst/RefinableObj/LSQNumObj.h"
+#include "ObjCryst/ObjCryst/PowderPattern.h"
 namespace ObjCryst
 {
 /** Different lattice types.

src/ObjCryst/ObjCryst/Molecule.cpp

@@ -937,6 +937,9 @@ void MolBondAngle::SetAtom3(MolAtom& at){mvpAtom[2]=&at;}
 //MolAtom& MolBondAngle::GetAtom1(){return *(mvpAtom[0]);}
 //MolAtom& MolBondAngle::GetAtom2(){return *(mvpAtom[1]);}
 //MolAtom& MolBondAngle::GetAtom3(){return *(mvpAtom[2]);}
+std::size_t MolBondAngle::size() const {return mvpAtom.size();}
+vector<MolAtom*>::const_iterator MolBondAngle::begin() const {return mvpAtom.begin();}
+vector<MolAtom*>::const_iterator MolBondAngle::end() const  {return mvpAtom.end();}
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolBondAngle::WXCreate(wxWindow* parent)
 {
@@ -1294,6 +1297,9 @@ MolAtom& MolDihedralAngle::GetAtom1(){return *(mvpAtom[0]);}
 MolAtom& MolDihedralAngle::GetAtom2(){return *(mvpAtom[1]);}
 MolAtom& MolDihedralAngle::GetAtom3(){return *(mvpAtom[2]);}
 MolAtom& MolDihedralAngle::GetAtom4(){return *(mvpAtom[3]);}
+std::size_t MolDihedralAngle::size() const {return mvpAtom.size();}
+vector<MolAtom*>::const_iterator MolDihedralAngle::begin() const {return mvpAtom.begin();}
+vector<MolAtom*>::const_iterator MolDihedralAngle::end() const  {return mvpAtom.end();}
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolDihedralAngle::WXCreate(wxWindow* parent)
 {
@@ -2174,8 +2180,8 @@ std::string Molecule::GetFormula() const
       if((*pos)->IsDummy()) continue;
       string p=(*pos)->GetScatteringPower().GetSymbol();
       if(velts.count(p)==0)
-         velts[(*pos)->GetScatteringPower().GetName()]=(*pos)->GetOccupancy();
-      else velts[(*pos)->GetScatteringPower().GetName()]+=(*pos)->GetOccupancy();
+         velts[p]=(*pos)->GetOccupancy();
+      else velts[p]+=(*pos)->GetOccupancy();
    }
    stringstream s;
    s<<std::setprecision(2);

src/ObjCryst/ObjCryst/Molecule.h

@@ -229,6 +229,7 @@ class MolBond:public Restraint
       void SetBondOrder(const REAL length);
       bool IsFreeTorsion()const;
       void SetFreeTorsion(const bool isInRing);
+   
   private:
       pair<MolAtom*,MolAtom*> mAtomPair;
       REAL mLength0,mDelta,mSigma;
@@ -316,6 +317,9 @@ class MolBondAngle:public Restraint
       MolAtom& GetAtom3();
       bool IsFlexible()const;
       void SetFlexible(const bool isInRing);
+      std::size_t size() const;
+      vector<MolAtom*>::const_iterator begin() const;
+      vector<MolAtom*>::const_iterator end() const;
    private:
       /// The vector of the 3 atoms involved in the bond angle.
       vector<MolAtom*> mvpAtom;
@@ -408,6 +412,9 @@ class MolDihedralAngle:public Restraint
       MolAtom& GetAtom2();
       MolAtom& GetAtom3();
       MolAtom& GetAtom4();
+      std::size_t size() const;
+      vector<MolAtom*>::const_iterator begin() const;
+      vector<MolAtom*>::const_iterator end() const;
    private:
       /// The vector of the 4 atoms involved in the bond angle.
       vector<MolAtom*> mvpAtom;