Merge pull request #15 from vincefn/master

Update libobjcryst
diffpy · Jun 21, 2021 · 8382a88 · 8382a88
2 parents 4bb5517 + 2f81f37
commit 8382a88
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Showing 5 changed files with 36 additions and 2 deletions.
diff --git a/src/ObjCryst/ObjCryst/CIF.cpp b/src/ObjCryst/ObjCryst/CIF.cpp
@@ -1014,7 +1014,8 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
 
    bool import_multiple = true;
    if(pCryst!=NULL) import_multiple = false;
-
+   bool crystal_found = false;
+
    for(map<string,CIFData>::iterator pos=cif.mvData.begin();pos!=cif.mvData.end();++pos)
       if(pos->second.mvLatticePar.size()==6)
       {
@@ -1102,6 +1103,7 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
          else
             pCryst->Init(pos->second.mvLatticePar[0],pos->second.mvLatticePar[1],pos->second.mvLatticePar[2],
                          pos->second.mvLatticePar[3],pos->second.mvLatticePar[4],pos->second.mvLatticePar[5],spg, "");
+         crystal_found = true;
          if(  (pos->second.mSpacegroupSymbolHall=="")
             &&(pos->second.mvSymmetry_equiv_pos_as_xyz.size()>0)
             &&(pos->second.mSpacegroupHermannMauguin!="")
@@ -1290,6 +1292,7 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
          if(pCryst->GetName()=="") pCryst->SetName(pCryst->GetFormula());
          if(!import_multiple) return pCryst;
       }
+   if(!crystal_found) throw ObjCrystException("CreateCrystalFromCIF: no structure found");
    return pCryst;
 }
 

diff --git a/src/ObjCryst/ObjCryst/Molecule.cpp b/src/ObjCryst/ObjCryst/Molecule.cpp
@@ -355,6 +355,8 @@ bool MolAtom::IsNonFlipAtom() const
    return mIsNonFlipAtom;
 }
 
+size_t MolAtom::int_ptr() const {return (size_t)this;}
+
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolAtom::WXCreate(wxWindow* parent)
 {
@@ -634,6 +636,9 @@ void MolBond::SetFreeTorsion(const bool isFreeTorsion)
    mIsFreeTorsion=isFreeTorsion;
    mpMol->GetBondListClock().Click();
 }
+
+size_t MolBond::int_ptr() const {return (size_t)this;}
+
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolBond::WXCreate(wxWindow* parent)
 {
@@ -941,6 +946,9 @@ void MolBondAngle::SetAtom3(MolAtom& at){mvpAtom[2]=&at;}
 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();}
+
+size_t MolBondAngle::int_ptr() const {return (size_t)this;}
+
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolBondAngle::WXCreate(wxWindow* parent)
 {
@@ -1301,6 +1309,9 @@ 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();}
+
+size_t MolDihedralAngle::int_ptr() const {return (size_t)this;}
+
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolDihedralAngle::WXCreate(wxWindow* parent)
 {
@@ -1325,6 +1336,9 @@ string RigidGroup::GetName()const
    for(;at!=this->end();++at) name+=", "+(*at)->GetName();
    return name;
 }
+
+size_t RigidGroup::int_ptr() const {return (size_t)this;}
+
 //######################################################################
 //
 //      MolRing
@@ -1338,6 +1352,9 @@ const std::list<MolAtom*>& MolRing::GetAtomList()const
 
 std::list<MolAtom*>& MolRing::GetAtomList()
 {return mvpAtom;}
+
+size_t MolRing::int_ptr() const {return (size_t)this;}
+
 //######################################################################
 //
 //      Quaternion

diff --git a/src/ObjCryst/ObjCryst/Molecule.h b/src/ObjCryst/ObjCryst/Molecule.h
@@ -117,6 +117,8 @@ class MolAtom
       void SetNonFlipAtom(const bool nonflip);
       /// Can this atom be flipped (return=false) or should its absolute configuration be kept (return=true)
       bool IsNonFlipAtom() const;
+      /// Access to the integer address of this object, for unique identification from python
+      size_t int_ptr() const;
    private:
       /// Name for this atom
       string mName;
@@ -229,7 +231,8 @@ class MolBond:public Restraint
       void SetBondOrder(const REAL length);
       bool IsFreeTorsion()const;
       void SetFreeTorsion(const bool isInRing);
-
+      /// Access to the integer address of this object, for unique identification from python
+      size_t int_ptr() const;
   private:
       pair<MolAtom*,MolAtom*> mAtomPair;
       REAL mLength0,mDelta,mSigma;
@@ -320,6 +323,8 @@ class MolBondAngle:public Restraint
       std::size_t size() const;
       vector<MolAtom*>::const_iterator begin() const;
       vector<MolAtom*>::const_iterator end() const;
+      /// Access to the integer address of this object, for unique identification from python
+      size_t int_ptr() const;
    private:
       /// The vector of the 3 atoms involved in the bond angle.
       vector<MolAtom*> mvpAtom;
@@ -415,6 +420,8 @@ class MolDihedralAngle:public Restraint
       std::size_t size() const;
       vector<MolAtom*>::const_iterator begin() const;
       vector<MolAtom*>::const_iterator end() const;
+      /// Access to the integer address of this object, for unique identification from python
+      size_t int_ptr() const;
    private:
       /// The vector of the 4 atoms involved in the bond angle.
       vector<MolAtom*> mvpAtom;
@@ -454,6 +461,8 @@ class MolRing
       MolRing();
       const std::list<MolAtom*>& GetAtomList()const;
       std::list<MolAtom*>& GetAtomList();
+      /// Access to the integer address of this object, for unique identification from python
+      size_t int_ptr() const;
    private:
       std::list<MolAtom*> mvpAtom;
 };
@@ -529,6 +538,8 @@ class RigidGroup:public std::set<MolAtom *>
       /// Temporary list of the atoms indices in the molecule, used during optimization
       /// This is created in Molecule::BeginOptimization()
       mutable std::set<unsigned int> mvIdx;
+      /// Access to the integer address of this object, for unique identification from python
+      size_t int_ptr() const;
 };
 
 /** Abstract base Stretch Mode for Molecule objects

diff --git a/src/ObjCryst/RefinableObj/RefinableObj.cpp b/src/ObjCryst/RefinableObj/RefinableObj.cpp
@@ -1981,6 +1981,7 @@ void RefinableObj::TagNewBestConfig()const
 }
 const RefinableObjClock& RefinableObj::GetClockMaster()const{return mClockMaster;}
 
+size_t RefinableObj::int_ptr() const {return (size_t)this;}
 
 void RefinableObj::UpdateDisplay()const
 {

diff --git a/src/ObjCryst/RefinableObj/RefinableObj.h b/src/ObjCryst/RefinableObj/RefinableObj.h
@@ -1238,6 +1238,8 @@ class RefinableObj
       virtual void TagNewBestConfig()const;
       /// This clocks records _any_ change in the object. See refinableObj::mClockMaster
       const RefinableObjClock& GetClockMaster()const;
+      /// Access to the integer address of this object, for unique identification from python
+      size_t int_ptr() const;
    protected:
       /// Find a refinable parameter with a given name
       long FindPar(const string &name) const;