Merge branch 'upstream-objcryst'

* upstream-objcryst:
  SpaceGroupExplorer: allow keeping or not the tested spacegroup, or the best solution
  Add Crystal.GetFormula(). Fix same function in Molecule to use symbol and not ScatteringPower name for sorting. Use formula to automatically name Crystal and DiffractionDataSingleCrystal when imported from CIF and no name is given.
  Rename SpacegroupExplorer to SpaceGroupExplorer for consistency
  Move Spacegroup explorer in a separate class along PowderPattern, for non-GUI access
  Correct EstimateCellVolume estimation for orthorombic F
  Better format for ObjRegistry::Print()

# Conflicts:
#	ObjCryst/wxCryst/wxPowderPattern.cpp

Author: vincefn

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

@@ -2180,8 +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);