diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index c99508826de934526fcb3ee659a3f41bf9cae09f..53b66b59ddada4d7f18c542a1275d030424cd6d0 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -38,6 +38,8 @@ bool in_sequence(const mol::ResidueHandle& r1, const mol::ResidueHandle& r2)
if(n2.GetInsCode()!='\0') {
if(n1.NextInsertionCode()==n2) return true;
}
+ if(mol::InSequence(r1,r2)) return true;
+ // fallback, perhaps the wrong thing to do
if(n1.GetNum()+1==n2.GetNum()) return true;
return false;
}
@@ -176,7 +178,7 @@ void BackboneTrace::PrepList(NodeEntryList& nelist)
e0->v1 = e0->normal;
//reference normal to avoid twisting
- geom::Vec3 nref=geom::Normalize(geom::Cross(p0-p1,p2-p1));
+ //geom::Vec3 nref=geom::Normalize(geom::Cross(p0-p1,p2-p1));
// start loop with the second
unsigned int i=1;
diff --git a/modules/gfx/src/impl/cartoon_renderer.cc b/modules/gfx/src/impl/cartoon_renderer.cc
index 0f9b5bb5a87327e61e05ca75e38e8f009c3b199b..e3a2cff52367934889c591635911e6292ef1ab07 100644
--- a/modules/gfx/src/impl/cartoon_renderer.cc
+++ b/modules/gfx/src/impl/cartoon_renderer.cc
@@ -79,19 +79,19 @@ void CartoonRenderer::PrepareRendering(const BackboneTrace& subset,
int type=0;
const NodeEntry& entry=nl[i];
if(!force_tube_) {
- mol::ResidueHandle resh = entry.atom.GetResidue();
- mol::SecStructure sst=resh.GetSecStructure();
- if(sst.IsHelical()) {
- type=1;
- } else if(sst.IsExtended()) {
- type=2;
- }
+ mol::ResidueHandle resh = entry.atom.GetResidue();
+ mol::SecStructure sst=resh.GetSecStructure();
+ if(sst.IsHelical()) {
+ type=1;
+ } else if(sst.IsExtended()) {
+ type=2;
+ }
}
SplineEntry ee(entry.atom.GetPos(),entry.direction,
- entry.normal, entry.rad,
- entry.color1,
- entry.color2,
- type, entry.id);
+ entry.normal, entry.rad,
+ entry.color1,
+ entry.color2,
+ type, entry.id);
ee.v1 = entry.v1;
spl.push_back(ee);
}
@@ -147,28 +147,28 @@ void CartoonRenderer::PrepareRendering()
SplineEntryList nlist;
unsigned int sc=0;
while(sc<slist.size()) {
- int curr_id=slist.at(sc).id;
- if(id_set.count(curr_id)>0) {
- // if a match is found, add all until a new id is found
- while(sc<slist.size() && slist.at(sc).id==curr_id) {
- nlist.push_back(slist[sc++]);
- // override with the selection color
- nlist.back().color1=sel_color;
- nlist.back().color2=sel_color;
- }
- } else {
- // introduce break
- if(!nlist.empty()) {
- sel_spline_list_list_.push_back(nlist);
- nlist.clear();
- }
- // and advance to the next id
- while(sc<slist.size() && slist.at(sc).id==curr_id) ++sc;
- }
+ int curr_id=slist.at(sc).id;
+ if(id_set.count(curr_id)>0) {
+ // if a match is found, add all until a new id is found
+ while(sc<slist.size() && slist.at(sc).id==curr_id) {
+ nlist.push_back(slist[sc++]);
+ // override with the selection color
+ nlist.back().color1=sel_color;
+ nlist.back().color2=sel_color;
+ }
+ } else {
+ // introduce break
+ if(!nlist.empty()) {
+ sel_spline_list_list_.push_back(nlist);
+ nlist.clear();
+ }
+ // and advance to the next id
+ while(sc<slist.size() && slist.at(sc).id==curr_id) ++sc;
+ }
}
if(!nlist.empty()) {
- sel_spline_list_list_.push_back(nlist);
- nlist.clear();
+ sel_spline_list_list_.push_back(nlist);
+ nlist.clear();
}
}
RebuildSplineObj(sel_va_, sel_spline_list_list_, true);
@@ -287,17 +287,17 @@ void CartoonRenderer::FudgeSplineObj(SplineEntryListList& olistlist)
nlistlist.push_back(nlist);
nlist.clear();
}
-
- // make a two entry list with the cyl type
- nlist.push_back(SplineEntry(cyl.first,geom::Vec3(),geom::Vec3(),0.0,
- olist[lstart].color1,olist[lstart].color1,
- 6,olist[lstart].id));
- nlist.push_back(SplineEntry(cyl.second,geom::Vec3(),geom::Vec3(),0.0,
- olist[lend].color1,olist[lend].color1,
- 6,olist[lend].id));
- nlistlist.push_back(nlist);
- nlist.clear();
-
+
+ // make a two entry list with the cyl type
+ nlist.push_back(SplineEntry(cyl.first,geom::Vec3(),geom::Vec3(),0.0,
+ olist[lstart].color1,olist[lstart].color1,
+ 6,olist[lstart].id));
+ nlist.push_back(SplineEntry(cyl.second,geom::Vec3(),geom::Vec3(),0.0,
+ olist[lend].color1,olist[lend].color1,
+ 6,olist[lend].id));
+ nlistlist.push_back(nlist);
+ nlist.clear();
+
if(lend+1<olist.size()) {
// and get going with an entry at the end of the cylinder
SplineEntry tmp_start(olist[lend]);
@@ -329,42 +329,42 @@ void CartoonRenderer::FudgeSplineObj(SplineEntryListList& olistlist)
for(;lc<olist.size() && olist.at(lc).type==2;++lc,++kend) {
nlist.push_back(olist.at(lc));
}
- if(kend-kstart<2) {
- // dont bother with too short strands
- for(unsigned int i=kstart;i<kend;++i) {
- nlist.at(i).type=0;
- }
- } else {
- kend-=1;
- // these magic numbers are used in RebuildSplineObj for proper arrow rendering
- nlist.at(kend-1).type=3;
- nlist.at(kend).type=5;
-
- if(options_->GetStrandMode()==1) {
- // smooth the strands for mode 1
- nlist.at(kstart).direction = geom::Normalize(nlist.at(kend).position-nlist.at(kstart).position);
- nlist.at(kend).direction=nlist.at(kstart).direction;
- float invf=1.0/static_cast<float>(kend-kstart);
- for(unsigned int k=kstart;k<=kend;++k) {
- float f = static_cast<float>(k-kstart)*invf;
- nlist.at(k).position=nlist.at(kstart).position+f*(nlist.at(kend).position-nlist.at(kstart).position);
- nlist.at(k).direction=nlist.at(kstart).direction;
- geom::Vec3 tmpn=geom::Normalize(nlist.at(kstart).normal+f*(nlist.at(kend).normal-nlist.at(kstart).normal));
- geom::Vec3 tmpx=geom::Normalize(geom::Cross(nlist.at(kstart).direction,tmpn));
- nlist.at(k).normal=geom::Normalize(geom::Cross(tmpx,nlist.at(kstart).direction));
- }
- }
-
- // break nodelist, re-start at arrow tip for both modes
- if(lc+1<olist.size()) {
- nlistlist.push_back(nlist);
- nlist.clear();
- nlist.push_back(nlistlist.back().back());
- nlist.back().type=0;
- nlist.back().color1=olist[lc+1].color1;
- nlist.back().color2=olist[lc+1].color2;
- }
- }
+ if(kend-kstart<2) {
+ // dont bother with too short strands
+ for(unsigned int i=kstart;i<kend;++i) {
+ nlist.at(i).type=0;
+ }
+ } else {
+ kend-=1;
+ // these magic numbers are used in RebuildSplineObj for proper arrow rendering
+ nlist.at(kend-1).type=3;
+ nlist.at(kend).type=5;
+
+ if(options_->GetStrandMode()==1) {
+ // smooth the strands for mode 1
+ nlist.at(kstart).direction = geom::Normalize(nlist.at(kend).position-nlist.at(kstart).position);
+ nlist.at(kend).direction=nlist.at(kstart).direction;
+ float invf=1.0/static_cast<float>(kend-kstart);
+ for(unsigned int k=kstart;k<=kend;++k) {
+ float f = static_cast<float>(k-kstart)*invf;
+ nlist.at(k).position=nlist.at(kstart).position+f*(nlist.at(kend).position-nlist.at(kstart).position);
+ nlist.at(k).direction=nlist.at(kstart).direction;
+ geom::Vec3 tmpn=geom::Normalize(nlist.at(kstart).normal+f*(nlist.at(kend).normal-nlist.at(kstart).normal));
+ geom::Vec3 tmpx=geom::Normalize(geom::Cross(nlist.at(kstart).direction,tmpn));
+ nlist.at(k).normal=geom::Normalize(geom::Cross(tmpx,nlist.at(kstart).direction));
+ }
+ }
+
+ // break nodelist, re-start at arrow tip for both modes
+ if(lc+1<olist.size()) {
+ nlistlist.push_back(nlist);
+ nlist.clear();
+ nlist.push_back(nlistlist.back().back());
+ nlist.back().type=0;
+ nlist.back().color1=olist[lc+1].color1;
+ nlist.back().color2=olist[lc+1].color2;
+ }
+ }
}
if(lc<olist.size()) {
nlist.push_back(olist.at(lc));
@@ -385,40 +385,40 @@ void CartoonRenderer::RebuildSplineObj(IndexedVertexArray& va,
LOG_DEBUG("CartoonRenderer: starting profile assembly");
unsigned int detail = std::min(MAX_ARC_DETAIL,
std::max(options_->GetArcDetail(),
- (unsigned int)1));
+ (unsigned int)1));
std::vector<TraceProfile> profiles;
float factor=is_sel ? 0.2 : 0.0;
profiles.push_back(GetCircProfile(detail,
- options_->GetTubeRadius()*options_->GetTubeRatio()+factor,
- options_->GetTubeRadius()+factor,
- options_->GetTubeProfileType(),
- 1.0)); // profile 0 = tube
+ options_->GetTubeRadius()*options_->GetTubeRatio()+factor,
+ options_->GetTubeRadius()+factor,
+ options_->GetTubeProfileType(),
+ 1.0)); // profile 0 = tube
if (!force_tube_) {
profiles.push_back(GetCircProfile(detail,
- options_->GetHelixWidth()+factor,
- options_->GetHelixThickness()+factor,
- options_->GetHelixProfileType(),
- options_->GetHelixEcc())); // profile 1 = helix
+ options_->GetHelixWidth()+factor,
+ options_->GetHelixThickness()+factor,
+ options_->GetHelixProfileType(),
+ options_->GetHelixEcc())); // profile 1 = helix
profiles.push_back(GetCircProfile(detail,
- options_->GetStrandWidth()+factor,
- options_->GetStrandThickness()+factor,
- options_->GetStrandProfileType(),
- options_->GetStrandEcc())); // profile 2 = strand
+ options_->GetStrandWidth()+factor,
+ options_->GetStrandThickness()+factor,
+ options_->GetStrandProfileType(),
+ options_->GetStrandEcc())); // profile 2 = strand
profiles.push_back(profiles.back()); // profile 3==2, strand
-
+
profiles.push_back(GetCircProfile(detail,
- 1.7*options_->GetStrandWidth()+factor,
- 1.1*options_->GetStrandThickness()+factor,
- options_->GetStrandProfileType(),
- options_->GetStrandEcc())); // profile 4 = arrow start
+ 1.7*options_->GetStrandWidth()+factor,
+ 1.1*options_->GetStrandThickness()+factor,
+ options_->GetStrandProfileType(),
+ options_->GetStrandEcc())); // profile 4 = arrow start
profiles.push_back(GetCircProfile(detail,
- 0.01*options_->GetStrandWidth()+factor,
- 1.1*options_->GetStrandThickness()+factor,
- options_->GetStrandProfileType(),
- options_->GetStrandEcc())); // profile 5 = arrow end
-
+ 0.01*options_->GetStrandWidth()+factor,
+ 1.1*options_->GetStrandThickness()+factor,
+ options_->GetStrandProfileType(),
+ options_->GetStrandEcc())); // profile 5 = arrow end
+
}
-
+
// iterate over all spline segments
#if !defined(NDEBUG)
@@ -434,13 +434,13 @@ void CartoonRenderer::RebuildSplineObj(IndexedVertexArray& va,
SplineEntryList slist=*it;
if(slist.empty()) continue;
LOG_DEBUG("CartoonRenderer: assembling fragment " << tmp_count << " with " << slist.size() << " spline segments");
-
+
if(slist.size()==2 && slist[0].type==6) {
// make a cylinder
va.AddCylinder(CylinderPrim(slist[0].position,slist[1].position,
- options_->GetHelixWidth(),
- slist[0].color1,slist[1].color1),
- options_->GetArcDetail(),true);
+ options_->GetHelixWidth(),
+ slist[0].color1,slist[1].color1),
+ options_->GetArcDetail(),true);
continue;
}
@@ -564,25 +564,25 @@ void CartoonRenderer::AssembleProfile(const TraceProfile& prof1,
size_t size=prof1.size()-1;
// first get the best correction offset
- float accum[]={0.0,0.0,0.0,0.0,0.0};
+ float accum[]={0.0,0.0,0.0,0.0,0.0,0.0,0.0};
for(size_t i=0;i<size;++i) {
int i1=(i+0)%(size);
int i2=(i+1)%(size);
geom::Vec3 v1=va.GetVert(prof1[i1].id);
geom::Vec3 v2=va.GetVert(prof1[i2].id);
- for(int k=-2;k<=2;++k) {
+ for(int k=-3;k<=3;++k) {
int i3=(i+k+0+size)%(size);
int i4=(i+k+1+size)%(size);
geom::Vec3 v3=va.GetVert(prof2[i3].id);
geom::Vec3 v4=va.GetVert(prof2[i4].id);
- accum[k+2]+=spread(v1,v2,v3,v4);
+ accum[k+3]+=spread(v1,v2,v3,v4);
}
}
float best_spread=accum[0];
- int best_off=-2;
- for(int k=-1;k<=2;++k) {
- if(accum[k+2]<best_spread) {
+ int best_off=-3;
+ for(int k=-2;k<=3;++k) {
+ if(accum[k+3]<best_spread) {
best_spread=accum[k+2];
best_off=k;
}
diff --git a/modules/gfx/src/impl/sline_renderer.cc b/modules/gfx/src/impl/sline_renderer.cc
index 92cf81bd54184bb5a005c5d514a71b786f9b0ddd..2b54046dd634acc1da4413aa9d69b7f4960889a9 100644
--- a/modules/gfx/src/impl/sline_renderer.cc
+++ b/modules/gfx/src/impl/sline_renderer.cc
@@ -81,14 +81,16 @@ void SlineRenderer::PrepareRendering(const BackboneTrace& trace_subset,
VertexID p0=va.Add(sit->position, geom::Vec3(),sit->color1);
for (++sit; sit!=sel.end(); ++sit) {
VertexID p1 = va.Add(sit->position, geom::Vec3(),sit->color1);
- //va.AddLine(p0,p1);
+ va.AddLine(p0,p1);
p0=p1;
+#if 0
VertexID p2 = va.Add(sit->position+sit->direction,geom::Vec3(),Color(0,1,0));
VertexID p3 = va.Add(sit->position+sit->normal,geom::Vec3(),Color(1,0,0));
VertexID p4 = va.Add(sit->position+sit->v2,geom::Vec3(),Color(1,0,1));
va.AddLine(p0,p2);
va.AddLine(p0,p3);
va.AddLine(p0,p4);
+#endif
}
}
}
diff --git a/modules/gfx/src/impl/trace_renderer.cc b/modules/gfx/src/impl/trace_renderer.cc
index e0827989db551a74180065c70ae0244fca080278..a6b442ee63540e9dd9c20aa0615282a5d313e65d 100644
--- a/modules/gfx/src/impl/trace_renderer.cc
+++ b/modules/gfx/src/impl/trace_renderer.cc
@@ -61,55 +61,55 @@ void TraceRenderer::PrepareRendering(BackboneTrace& trace_subset,
if(is_sel) {
va.SetOpacity(GetSelectionColor().Alpha());
for (int node_list=0; node_list<trace_subset.GetListCount(); ++node_list) {
- const NodeEntryList& nl=trace_subset.GetList(node_list);
- for(unsigned int i=0;i<nl.size();++i) {
- mol::AtomHandle ah=nl[i].atom;
- if(sel_.FindAtom(ah).IsValid()) {
- geom::Vec3 apos = ah.GetPos();
- va.AddSphere(SpherePrim(apos,
- options_->GetTubeRadius()+0.05,
- sel_clr),
- options_->GetArcDetail());
- if(i>0) {
- va.AddCylinder(CylinderPrim(apos+0.5*(nl[i-1].atom.GetPos()-apos),
- apos,
- options_->GetTubeRadius()+0.05,
- sel_clr),
- options_->GetArcDetail());
- }
- if(i<nl.size()-1) {
- va.AddCylinder(CylinderPrim(apos,
- apos+0.5*(nl[i+1].atom.GetPos()-apos),
- options_->GetTubeRadius()+0.05,
- sel_clr),
- options_->GetArcDetail());
- }
- }
- }
+ const NodeEntryList& nl=trace_subset.GetList(node_list);
+ for(unsigned int i=0;i<nl.size();++i) {
+ mol::AtomHandle ah=nl[i].atom;
+ if(sel_.FindAtom(ah).IsValid()) {
+ geom::Vec3 apos = ah.GetPos();
+ va.AddSphere(SpherePrim(apos,
+ options_->GetTubeRadius()+0.05,
+ sel_clr),
+ options_->GetArcDetail());
+ if(i>0) {
+ va.AddCylinder(CylinderPrim(apos+0.5*(nl[i-1].atom.GetPos()-apos),
+ apos,
+ options_->GetTubeRadius()+0.05,
+ sel_clr),
+ options_->GetArcDetail());
+ }
+ if(i<nl.size()-1) {
+ va.AddCylinder(CylinderPrim(apos,
+ apos+0.5*(nl[i+1].atom.GetPos()-apos),
+ options_->GetTubeRadius()+0.05,
+ sel_clr),
+ options_->GetArcDetail());
+ }
+ }
+ }
}
} else {
for (int node_list=0; node_list<trace_subset.GetListCount(); ++node_list) {
- const NodeEntryList& nl=trace_subset.GetList(node_list);
- mol::AtomHandle a1=nl[0].atom;
- va.AddSphere(SpherePrim(a1.GetPos(),
- options_->GetTubeRadius(),
- nl[0].color1),
- options_->GetArcDetail());
- for(unsigned int i=1;i<nl.size();++i) {
- mol::AtomHandle a2=nl[i].atom;
- va.AddSphere(SpherePrim(a2.GetPos(),
- options_->GetTubeRadius(),
- nl[i].color1),
- options_->GetArcDetail());
- const geom::Vec3& p0=a1.GetPos();
- const geom::Vec3& p2=a2.GetPos();
- geom::Vec3 p1=(p0+p2)*0.5;
- va.AddCylinder(CylinderPrim(p0,p1,options_->GetTubeRadius(),nl[i-1].color1),
- options_->GetArcDetail());
- va.AddCylinder(CylinderPrim(p1,p2,options_->GetTubeRadius(),nl[i].color1),
- options_->GetArcDetail());
- a1=a2;
- }
+ const NodeEntryList& nl=trace_subset.GetList(node_list);
+ mol::AtomHandle a1=nl[0].atom;
+ va.AddSphere(SpherePrim(a1.GetPos(),
+ options_->GetTubeRadius(),
+ nl[0].color1),
+ options_->GetArcDetail());
+ for(unsigned int i=1;i<nl.size();++i) {
+ mol::AtomHandle a2=nl[i].atom;
+ va.AddSphere(SpherePrim(a2.GetPos(),
+ options_->GetTubeRadius(),
+ nl[i].color1),
+ options_->GetArcDetail());
+ const geom::Vec3& p0=a1.GetPos();
+ const geom::Vec3& p2=a2.GetPos();
+ geom::Vec3 p1=(p0+p2)*0.5;
+ va.AddCylinder(CylinderPrim(p0,p1,options_->GetTubeRadius(),nl[i-1].color1),
+ options_->GetArcDetail());
+ va.AddCylinder(CylinderPrim(p1,p2,options_->GetTubeRadius(),nl[i].color1),
+ options_->GetArcDetail());
+ a1=a2;
+ }
}
}
}
diff --git a/modules/gfx/src/prim_list.cc b/modules/gfx/src/prim_list.cc
index 72047addeb091fbec674ae9372f1c98125ee67ee..c48abf97955178245c2b79ff6b2acb0f50ea2824 100644
--- a/modules/gfx/src/prim_list.cc
+++ b/modules/gfx/src/prim_list.cc
@@ -23,6 +23,7 @@
#include "scene.hh"
#include "prim_list.hh"
+#include "povray.hh"
namespace ost { namespace gfx {
@@ -31,7 +32,6 @@ PrimList::PrimList(const String& name):
points_(),
lines_(),
radius_(0.5),
- diameter_(0.5),
sphere_detail_(4),
arc_detail_(4)
{}
@@ -136,7 +136,18 @@ void PrimList::CustomRenderGL(RenderPass pass)
void PrimList::CustomRenderPov(PovState& pov)
{
- // TODO: add primlist pov export
+ if(points_.empty() && lines_.empty()) return;
+ pov.write_merge_or_union(GetName());
+
+ for(PointEntryList::const_iterator it=points_.begin();it!=points_.end();++it) {
+ pov.write_sphere(it->pos,radius_,it->color,GetName());
+ }
+ for(LineEntryList::const_iterator it=lines_.begin();it!=lines_.end();++it) {
+ pov.write_sphere(it->pos1,radius_,it->color,GetName());
+ pov.write_sphere(it->pos2,radius_,it->color,GetName());
+ pov.write_cyl(it->pos1,it->pos2,radius_,it->color,GetName(),true);
+ }
+ pov.inc() << " }\n";
}
void PrimList::AddPoint(geom::Vec3& p, const Color& col)
@@ -155,7 +166,7 @@ void PrimList::AddLine(geom::Vec3& p1, geom::Vec3& p2, const Color& col)
void PrimList::SetDiameter(float d)
{
- diameter_=d;
+ radius_=d*0.5;
Scene::Instance().RequestRedraw();
FlagRebuild();
}
@@ -229,11 +240,11 @@ void PrimList::render_custom()
}
for(LineEntryList::const_iterator it=lines_.begin();it!=lines_.end();++it) {
- va_.AddSphere(SpherePrim(it->pos1, diameter_/2.0, it->color),
+ va_.AddSphere(SpherePrim(it->pos1, radius_, it->color),
GetSphereDetail());
- va_.AddSphere(SpherePrim(it->pos2, diameter_/2.0, it->color),
+ va_.AddSphere(SpherePrim(it->pos2, radius_, it->color),
GetSphereDetail());
- va_.AddCylinder(CylinderPrim(it->pos1,it->pos2,diameter_/2.0,it->color),
+ va_.AddCylinder(CylinderPrim(it->pos1,it->pos2,radius_,it->color),
GetArcDetail());
}
}
diff --git a/modules/gfx/src/prim_list.hh b/modules/gfx/src/prim_list.hh
index fbac2cffc2f633bdf5bfe4ef8fc20ce6658c72d4..b4aa65b98a3c601b913376b4c857c8d4aedda18d 100644
--- a/modules/gfx/src/prim_list.hh
+++ b/modules/gfx/src/prim_list.hh
@@ -74,6 +74,7 @@ class DLLEXPORT_OST_GFX PrimList: public GfxObj
const mol::Transform& tf) const;
/// \brief get center
virtual geom::Vec3 GetCenter() const;
+
virtual void CustomRenderPov(PovState& pov);
virtual void CustomRenderGL(RenderPass pass);