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vincefnvincefn
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Merge branch 'upstream-objcryst'
* upstream-objcryst: Move ZScatterer2Molecule to Molecule.h and Molecule.cpp, so it can be used from python
2 parents 068ff56 + 9cf94a7 commit b9794dd

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‎src/ObjCryst/ObjCryst/Molecule.cpp‎

Lines changed: 144 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -28,6 +28,7 @@
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#include "ObjCryst/Quirks/VFNStreamFormat.h"
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#include "ObjCryst/ObjCryst/Molecule.h"
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#include "ObjCryst/ObjCryst/ZScatterer.h"
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#include "ObjCryst/RefinableObj/GlobalOptimObj.h"
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#ifdef OBJCRYST_GL
@@ -7904,4 +7905,147 @@ WXCrystObjBasic* Molecule::WXCreate(wxWindow* parent)
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}
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#endif
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Molecule *ZScatterer2Molecule(ZScatterer *scatt)
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{
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VFN_DEBUG_ENTRY("ZScatterer2Molecule()",6)
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Molecule *mol=new Molecule(scatt->GetCrystal(),scatt->GetName());
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const unsigned long nb=scatt->GetZAtomRegistry().GetNb();
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REAL x0=0,y0=0,z0=0;
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for(unsigned int i=0;i<nb;++i)
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{
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const REAL x=scatt->GetZAtomX(i);
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const REAL y=scatt->GetZAtomY(i);
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const REAL z=scatt->GetZAtomZ(i);
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x0+=x;
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y0+=y;
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z0+=z;
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mol->AddAtom(x,y,z,scatt->GetZAtomRegistry().GetObj(i).GetScatteringPower(),
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scatt->GetZAtomRegistry().GetObj(i).GetName());
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#if 0
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if(i>0)
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{
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const RefinablePar* pLength=&(scatt->GetPar(&(scatt->GetZAtomRegistry()
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.GetObj(i).GetZBondLength())));
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if(pLength->IsFixed())
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mol->AddBond(mol->GetAtom(i),mol->GetAtom(scatt->GetZBondAtom(i)),
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pLength->GetValue(),.01,.02,false);
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else
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if(pLength->IsLimited())
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mol->AddBond(mol->GetAtom(i),mol->GetAtom(scatt->GetZBondAtom(i)),
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(pLength->GetMin()+pLength->GetMax())/2.,.01,.02,false);
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}
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if(i>1)
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{
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const RefinablePar* pAngle=&(scatt->GetPar(&(scatt->GetZAtomRegistry()
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.GetObj(i).GetZAngle())));
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if(pAngle->IsFixed())
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mol->AddBondAngle(mol->GetAtom(i),mol->GetAtom(scatt->GetZBondAtom(i)),
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mol->GetAtom(scatt->GetZAngleAtom(i)),
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pAngle->GetValue(),.01,.02,false);
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else
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if(pAngle->IsLimited())
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mol->AddBondAngle(mol->GetAtom(i),mol->GetAtom(scatt->GetZBondAtom(i)),
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mol->GetAtom(scatt->GetZAngleAtom(i)),
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(pAngle->GetMin()+pAngle->GetMax())/2.,.01,.02,false);
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}
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if(i>2)
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{
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const RefinablePar* pDihed=&(scatt->GetPar(&(scatt->GetZAtomRegistry()
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.GetObj(i).GetZDihedralAngle())));
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MolAtom *p1=&(mol->GetAtom(i));
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MolAtom *p2=&(mol->GetAtom(scatt->GetZBondAtom(i)));
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MolAtom *p3=&(mol->GetAtom(scatt->GetZAngleAtom(i)));
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MolAtom *p4=&(mol->GetAtom(scatt->GetZDihedralAngleAtom(i)));
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if( (fabs(GetBondAngle(*p1,*p2,*p3)-M_PI)>0.3)
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&&(fabs(GetBondAngle(*p1,*p2,*p4)-M_PI)>0.3)
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&&(fabs(GetBondAngle(*p1,*p3,*p4)-M_PI)>0.3)
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&&(fabs(GetBondAngle(*p2,*p3,*p4)-M_PI)>0.3))
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{
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if(pDihed->IsFixed())
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mol->AddDihedralAngle(*p1,*p2,*p3,*p4,pDihed->GetValue(),.01,.02,false);
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else
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if(((pDihed->GetMax()-pDihed->GetMax())<0.3)&&(i>2)&&(pDihed->IsLimited()))
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mol->AddDihedralAngle(*p1,*p2,*p3,*p4,
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(pDihed->GetMin()+pDihed->GetMax())/2.,.01,.02,false);
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}
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}
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#endif
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mol->GetAtom(i).SetOccupancy(scatt->GetZAtomRegistry().GetObj(i).GetOccupancy());
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}
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CrystVector_REAL x(nb),y(nb),z(nb),radius(nb);
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vector<pair<const ScatteringPowerAtom *,long> > scattpow(nb);
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for(unsigned int i=0;i<nb;++i)
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{
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x(i)=mol->GetAtom(i).GetX();
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y(i)=mol->GetAtom(i).GetY();
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z(i)=mol->GetAtom(i).GetZ();
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if(mol->GetAtom(i).IsDummy())
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{
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radius(i)=-1;
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scattpow[i].first=0;
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}
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else
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{
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radius(i)=mol->GetAtom(i).GetScatteringPower().GetRadius();
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scattpow[i].first=dynamic_cast<const ScatteringPowerAtom *>
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(&(mol->GetAtom(i).GetScatteringPower()));
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scattpow[i].second=scattpow[i].first->GetAtomicNumber();
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}
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}
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for(unsigned int i=0;i<nb;++i)
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{
8000+
if(scattpow[i].first==0) continue;
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const REAL x1=x(i),y1=y(i),z1=z(i);
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x += -x1;
8003+
y += -y1;
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z += -z1;
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for(unsigned int j=i+1;j<nb;++j)
8006+
{
8007+
if(scattpow[j].first==0) continue;
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const REAL dist=sqrt(x(j)*x(j)+y(j)*y(j)+z(j)*z(j));
8009+
//cout<<" -> d="<<dist<<"("<<radius(i)<<","<<radius(j)<<"):"<<scattpow[i].second<<","<<scattpow[j].second<<endl;
8010+
if(dist<(1.10*(radius(i)+radius(j))))
8011+
{
8012+
if((1!=scattpow[i].second)||(1!=scattpow[j].second))
8013+
{
8014+
mol->AddBond(mol->GetAtom(i),mol->GetAtom(j),dist,.01,.02,false);
8015+
}
8016+
}
8017+
}
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x += x1;
8019+
y += y1;
8020+
z += z1;
8021+
}
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mol->BuildConnectivityTable();
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for(map<MolAtom*,set<MolAtom*> >::const_iterator pos=mol->GetConnectivityTable().begin();
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pos!=mol->GetConnectivityTable().end();++pos)
8025+
{
8026+
for(set<MolAtom*>::const_iterator pos1=pos->second.begin();
8027+
pos1!=pos->second.end();++pos1)
8028+
{
8029+
for(set<MolAtom*>::const_iterator pos2=pos1;
8030+
pos2!=pos->second.end();++pos2)
8031+
{
8032+
if(pos2==pos1) continue;
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if(mol->FindBondAngle(**pos1,*(pos->first),**pos2)== mol->GetBondAngleList().end())
8034+
mol->AddBondAngle(**pos1,*(pos->first),**pos2,
8035+
GetBondAngle(**pos1,*(pos->first),**pos2),0.01,0.02,false);
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}
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}
8038+
}
8039+
x0 /= nb;
8040+
y0 /= nb;
8041+
z0 /= nb;
8042+
mol->GetCrystal().OrthonormalToFractionalCoords(x0,y0,z0);
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mol->SetX(x0);
8044+
mol->SetY(y0);
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mol->SetZ(z0);
8046+
mol->UpdateDisplay();
8047+
VFN_DEBUG_EXIT("ZScatterer2Molecule()",6)
8048+
return mol;
8049+
}
8050+
79078051
}//namespace

‎src/ObjCryst/ObjCryst/Molecule.h‎

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Original file line numberDiff line numberDiff line change
@@ -1432,6 +1432,11 @@ void ExpandAtomGroupRecursive(MolAtom* atom,
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const map<MolAtom*,set<MolAtom*> > &connect,
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map<MolAtom*,unsigned long> &atomlist,const unsigned long maxdepth, unsigned long depth=0);
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// Forward declaration
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class ZScatterer;
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/// Converter from ZScatterer to a Molecule object
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Molecule *ZScatterer2Molecule(ZScatterer *scatt);
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}//namespace
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#endif

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