diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index 4194cac02880ea0d4fb7d3cd1fd528c247dacec9..3066deef9a85a45d42fc6a77641d673667a7e89f 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -101,6 +101,14 @@ Real Angle(const Vec3& v1, const Vec3& v2)
return std::acos(dot_product);
}
+Real SignedAngle(const Vec3& v1, const Vec3& v2, const Vec3& ref_normal )
+{
+ Vec3 a=Normalize(v1);
+ Vec3 b=Normalize(v2);
+ Vec3 c=Normalize(ref_normal);
+ return std::atan2(Dot(c,Cross(a,b)), Dot(a,b));
+}
+
Mat3 EulerTransformation(Real theta, Real phi, Real xi)
{
Real costheta=cos(theta);
diff --git a/modules/geom/src/vecmat3_op.hh b/modules/geom/src/vecmat3_op.hh
index 76bd719d282ffc4261fdcc15d3104c9f2e4ff079..94c3c77b32d2fe7cb45a34d0a66c5bc001a9a3fe 100644
--- a/modules/geom/src/vecmat3_op.hh
+++ b/modules/geom/src/vecmat3_op.hh
@@ -151,9 +151,12 @@ Real DLLEXPORT_OST_GEOM Minor(const Mat3& m, unsigned int i, unsigned int j);
// determinant
Real DLLEXPORT_OST_GEOM Det(const Mat3& m);
-// angle between zwo vectors
+// angle between two vectors
Real DLLEXPORT_OST_GEOM Angle(const Vec3& v1, const Vec3& v2);
+// signed angle between two vectors, based on a reference normal
+Real DLLEXPORT_OST_GEOM SignedAngle(const Vec3& v1, const Vec3& v2, const Vec3& ref);
+
Mat3 DLLEXPORT_OST_GEOM EulerTransformation(Real theta, Real phi, Real xi);
Mat3 DLLEXPORT_OST_GEOM AxisRotation(const Vec3& axis, Real angle);
diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index e3a14b7a7106414d3fb98cdfbab962b8a0a34c95..235ad226b232465e037342333493de62063343b9 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -83,7 +83,7 @@ public:
NodeEntry entry={ca, GfxObj::Ele2Color(ca.GetElement()),
GfxObj::Ele2Color(ca.GetElement()),
geom::Vec3(), // this will be set by the gfx trace obj
- res.GetCentralNormal(),
+ geom::Normalize(res.GetCentralNormal()),
1.0,
geom::Vec3(),geom::Vec3(),geom::Vec3(), // for later use in NA rendering
false,id_counter_++};
@@ -159,46 +159,36 @@ void BackboneTrace::AddNodeEntryList(const NodeEntryList& l)
void BackboneTrace::PrepList(NodeEntryList& nelist)
{
- // assign direction and normal vectors for each entry
- // they are composed of the i-1 -> i and i->i+1 directions
- //
- // this same algorithm is used in the spline generation, so
- // perhaps all of this here is not necessary ?!
- //
+ // orthogonalize the residue normals with
+ // twist detection; important for later
+ // spline generation
+ if(nelist.size()<3) return;
NodeEntry* e0=&nelist[0];
NodeEntry* e1=&nelist[1];
NodeEntry* e2=&nelist[2];
geom::Vec3 p0 = e0->atom.GetPos();
geom::Vec3 p1 = e1->atom.GetPos();
geom::Vec3 p2 = e2->atom.GetPos();
-
+
+ geom::Vec3 dir=geom::Normalize(p1-p0);
e0->direction=geom::Normalize(p1-p0);
- // e0->normal is set afterwards to normal of second one
- // backup residue normal
- e0->v1 = e0->normal;
-
- //reference normal to avoid twisting
- geom::Vec3 nref=geom::Normalize(geom::Cross(p0-p1,p2-p1));
-
- // start loop with the second
+ geom::Vec3 orth=geom::Normalize(geom::Cross(e0->direction,e0->normal));
+ geom::Vec3 norm=geom::Normalize(geom::Cross(orth,dir));
+ e0->normal=norm;
+ // start loop with the second residue
unsigned int i=1;
for(;i<nelist.size()-1;++i) {
- geom::Vec3 p10 = p0-p1;
- geom::Vec3 p12 = p2-p1;
- if(p10==-p12 || p10==p12) p12+=geom::Vec3(0.001,0.001,0.001);
- e1->v1=e1->normal;
- // twist avoidance
- if(geom::Dot(e0->v1,e1->v1)<0.0) {
- e1->v1=-e1->v1;
+ geom::Vec3 p10=p0-p1;
+ geom::Vec3 p12=p2-p1;
+ dir=geom::Normalize(p2-p0);
+ e1->direction = dir;
+ orth=geom::Normalize(geom::Cross(dir,e1->normal));
+ norm=geom::Normalize(geom::Cross(orth,dir));
+ // twist check
+ if(geom::Dot(geom::Cross(e0->normal,dir),geom::Cross(norm,dir))<0.0) {
+ norm=-norm;
}
- e1->normal=geom::Normalize(geom::Cross(p10,p12));
- float omega=0.5*acos(geom::Dot(geom::Normalize(p10),geom::Normalize(p12)));
- geom::Vec3 orth=geom::AxisRotation(e1->normal, -omega)*p12;
- e1->direction=geom::Normalize(geom::Cross(e1->normal,orth));
-
- // align normals to avoid twisting
- //if(geom::Dot(e1->normal,nref)<0.0) e1->normal=-e1->normal;
- //nref=e1->normal;
+ e1->normal=norm;
// skip over shift for the last iteration
if(i==nelist.size()-2) break;
// shift to i+1 for next iteration
@@ -209,16 +199,14 @@ void BackboneTrace::PrepList(NodeEntryList& nelist)
p1 = e1->atom.GetPos();
p2 = e2->atom.GetPos();
}
- // finish remaining values
- // i is at size-2 due to break statement above
- nelist[0].normal=nelist[1].normal;
- nelist[i+1].direction=geom::Normalize(p2-p1);
- nelist[i+1].v1=nelist[i+1].normal;
- if (geom::Dot(nelist[i].v1,
- nelist[i+1].v1)<0.0) {
- nelist[i+1].v1=-nelist[i+1].v1;
+ dir=geom::Normalize(p2-p1);
+ e2->direction=dir;
+ orth=geom::Normalize(geom::Cross(dir,e2->normal));
+ norm=geom::Normalize(geom::Cross(orth,dir));
+ if(geom::Dot(geom::Cross(e1->normal,dir),geom::Cross(norm,dir))<0.0) {
+ norm=-norm;
}
- nelist[i+1].normal=nelist[i].normal;
+ e2->normal=norm;
}
BackboneTrace BackboneTrace::CreateSubset(const mol::EntityView& subview)
diff --git a/modules/gfx/src/impl/cartoon_renderer.cc b/modules/gfx/src/impl/cartoon_renderer.cc
index 1c5bc481bc2d574f62b35aa18aab155a3b02b01b..b1ec4dad4f0f0cbe5092a16a9f3e654c348b14fb 100644
--- a/modules/gfx/src/impl/cartoon_renderer.cc
+++ b/modules/gfx/src/impl/cartoon_renderer.cc
@@ -389,33 +389,33 @@ void CartoonRenderer::RebuildSplineObj(IndexedVertexArray& va,
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
}
@@ -447,14 +447,23 @@ void CartoonRenderer::RebuildSplineObj(IndexedVertexArray& va,
TraceProfile tprof1=TransformAndAddProfile(profiles,slist[0],va);
CapProfile(tprof1,slist[0],true,va);
TraceProfile tprof2;
- unsigned int sc=1;
+ size_t sc=1;
+ size_t psize=tprof1.size()-1;
+ double psized=static_cast<double>(psize);
+ float of=static_cast<float>(psize)/(2.0*M_PI);
for (; sc<slist.size(); ++sc) {
+ //double dd=geom::Dot(slist.at(sc-1).normal,slist.at(sc).normal);
+ geom::Vec3 dir=slist.at(sc).position-slist.at(sc-1).position;
+ double ang=-geom::SignedAngle(geom::Cross(slist.at(sc-1).normal,dir),
+ geom::Cross(slist.at(sc).normal,dir),
+ dir);
+ size_t offset=psize+static_cast<size_t>(round(ang*of)+psized);
if(slist.at(sc).type==3) {
if(slist.at(sc-1).type!=3) {
// boundary to arrow
SplineEntry se(slist[sc]);
tprof2=TransformAndAddProfile(profiles,se, va);
- AssembleProfile(tprof1,tprof2,va);
+ AssembleProfile(tprof1,tprof2,va,offset);
tprof1=tprof2;
se.type=2;
se.type1=4;
@@ -469,7 +478,7 @@ void CartoonRenderer::RebuildSplineObj(IndexedVertexArray& va,
} else {
tprof2=TransformAndAddProfile(profiles,slist.at(sc), va);
}
- AssembleProfile(tprof1,tprof2,va);
+ AssembleProfile(tprof1,tprof2,va,offset);
tprof1=tprof2;
}
CapProfile(tprof1,slist.at(sc-1),false,va);
@@ -551,49 +560,22 @@ namespace {
void CartoonRenderer::AssembleProfile(const TraceProfile& prof1,
const TraceProfile& prof2,
- IndexedVertexArray& va)
+ IndexedVertexArray& va,
+ size_t offset)
{
/*
the wrap around algorithm used here needs to take into account
that the TraceProfile has a duplicate entry for prof*[0] and
prof*[N-1], which fall onto the same point except and have
the same normal but a different texture coordinate. Hence
- all the mods are done with size()-1, but in the assembly
- routine prof*[0] is turned into prof*[N-1] if necessary
+ size()-1
*/
size_t size=prof1.size()-1;
-
- // first get the best correction offset
- float accum[]={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) {
- 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);
- }
- }
-
- float best_spread=accum[0];
- int best_off=-2;
- for(int k=-1;k<=2;++k) {
- if(accum[k+2]<best_spread) {
- best_spread=accum[k+2];
- best_off=k;
- }
- }
- best_off=(best_off+(size))%(size);
-
// now assemble the triangles
for(unsigned int i1=0;i1<size;++i1) {
- unsigned int i2=(i1+1)%(size);
- unsigned int i3=(i1+best_off)%(size);
- unsigned int i4=(i1+best_off+1)%(size);
+ size_t i2=(i1+1)%(size);
+ size_t i3=(i1+offset)%(size);
+ size_t i4=(i1+offset+1)%(size);
// wrap around correction for proper texture coordinates
i2 = (i2==0) ? size : i2;
diff --git a/modules/gfx/src/impl/cartoon_renderer.hh b/modules/gfx/src/impl/cartoon_renderer.hh
index 95a7b3844802e14c9f3fd087b4f67b3021c47ab4..475c1db2b110055f73e0275bea73dcb5373114f9 100644
--- a/modules/gfx/src/impl/cartoon_renderer.hh
+++ b/modules/gfx/src/impl/cartoon_renderer.hh
@@ -66,7 +66,8 @@ private:
void AssembleProfile(const TraceProfile& prof1,
const TraceProfile& prof2,
- IndexedVertexArray& va);
+ IndexedVertexArray& va,
+ size_t offset);
TraceProfile TransformAndAddProfile(const std::vector<TraceProfile>& profiles,
const SplineEntry& se,
diff --git a/modules/gfx/src/impl/entity_detail.cc b/modules/gfx/src/impl/entity_detail.cc
index 40ba7351876fbf25ea823b383fdaca532fef41d6..55fab9f53d8b7553dbb1d8bd4fa20ed3ea6327a2 100644
--- a/modules/gfx/src/impl/entity_detail.cc
+++ b/modules/gfx/src/impl/entity_detail.cc
@@ -296,76 +296,37 @@ SplineEntryList Spline::Generate(const SplineEntryList& entry_list, int nsub, ui
// interpolate position and helper vectors
for(int k=0;k<3;++k) {
SPLINE_ENTRY_INTERPOLATE(position[k]);
- //SPLINE_ENTRY_INTERPOLATE(v0[k]);
- SPLINE_ENTRY_INTERPOLATE(v1[k]);
- //SPLINE_ENTRY_INTERPOLATE(v2[k]);
+ SPLINE_ENTRY_INTERPOLATE(normal[k]);
}
SPLINE_ENTRY_INTERPOLATE(rad);
LOG_DEBUG("SplineGenerate: assigning direction and normal components");
- // assign direction and normal
- // entity trace has the same algorithm
+ // assign direction and then re-assign normal
geom::Vec3 p0 = sublist.at(0).position;
geom::Vec3 p1 = sublist.at(1).position;
- geom::Vec3 p2 = ipsize>2 ? sublist.at(2).position : p1+(p1-p0);
- // normal of 0 is set at the end
+ geom::Vec3 p2 = sublist.size()>2 ? sublist.at(2).position : p1+p1-p0;
sublist.at(0).direction=geom::Normalize(p1-p0);
- sublist.at(0).v1=geom::Normalize(sublist.at(0).v1);
- geom::Vec3 orth = geom::Cross(sublist.at(0).direction,sublist.at(0).v1);
- sublist.at(0).v0 = geom::Normalize(geom::Cross(orth,sublist.at(0).direction));
-
- // reference normal to avoid twisting
- //geom::Vec3 nref=geom::Normalize(geom::Cross(p0-p1,p2-p1));
unsigned int i=1;
for(;i<sublist.size()-1;++i) {
geom::Vec3 p10 = p0-p1;
geom::Vec3 p12 = p2-p1;
- // correction for perfectly aligned consecutive directions
- if(p10==-p12 || p10==p12) p12+=geom::Vec3(0.001,0.001,0.001);
- sublist.at(i).normal=geom::Normalize(geom::Cross(p10,p12));
- // paranoid error checking due to occasional roundoff troubles
- float cosw = geom::Dot(geom::Normalize(p10),geom::Normalize(p12));
- cosw = std::min(float(1.0),std::max(float(-1.0),cosw));
- float omega=0.5*acos(cosw);
- orth=geom::AxisRotation(sublist.at(i).normal, -omega)*p12;
- sublist.at(i).direction=geom::Normalize(geom::Cross(sublist.at(i).normal,orth));
- // twist avoidance
- sublist.at(i).v1=geom::Normalize(sublist.at(i).v1);
- orth = geom::Cross(sublist.at(i).direction,sublist.at(i).v1);
- sublist.at(i).v0 = geom::Normalize(geom::Cross(orth,sublist.at(i).direction));
- if(geom::Dot(sublist.at(i-1).v0,sublist.at(i).v0)<0.0) {
- sublist.at(i).v0=-sublist.at(i).v0;
- //sublist.at(i).nflip = !sublist.at(i).nflip;
- }
-
- // avoid twisting
- //if(geom::Dot(sublist.at(i).normal,nref)<0.0) sublist.at(i).normal=-sublist.at(i).normal;
- //nref=sublist.at(i).normal;
- // skip over shift for the last iteration
+ geom::Vec3 dir=geom::Normalize(p2-p0);
+ sublist.at(i).direction=dir;
+ geom::Vec3 orth=geom::Normalize(geom::Cross(dir,sublist[i].normal));
+ geom::Vec3 norm=geom::Normalize(geom::Cross(orth,dir));
+ sublist[i].normal=norm;
if(i==sublist.size()-2) break;
// shift to i+1 for next iteration
p0 = sublist.at(i).position;
p1 = sublist.at(i+1).position;
p2 = sublist.at(i+2).position;
}
- // assign remaining ones
- sublist.at(0).normal=sublist.at(1).normal;
- sublist.at(i+1).direction=geom::Normalize(p2-p1);
- sublist.at(i+1).normal=sublist.at(i).normal;
- sublist.at(i+1).v1=geom::Normalize(sublist.at(i+1).v1);
- orth = geom::Cross(sublist.at(i+1).direction,sublist.at(i+1).v1);
- sublist.at(i+1).v0 = geom::Normalize(geom::Cross(orth,sublist.at(i+1).direction));
- if(geom::Dot(sublist.at(i).v0,sublist.at(i+1).v0)<0.0) {
- sublist.at(i+1).v0=-sublist.at(i+1).v0;
- }
+ sublist[0].normal=sublist[0].normal;
+ sublist[i+1].direction=geom::Normalize(p2-p1);
+ sublist[i+1].normal=sublist[i].normal;
- // hack
- // TODO: merge this with above routine
- for(unsigned int i=0;i<sublist.size();++i) {
- sublist.at(i).normal = sublist.at(i).v0;
- }
LOG_DEBUG("SplineGenerate: assigning non-interpolated entry components");
// finally the non-interpolated type
diff --git a/modules/gfx/src/impl/line_trace_renderer.cc b/modules/gfx/src/impl/line_trace_renderer.cc
index f183c6b5b0439696f8fa357baaeb24951c65dc49..abf91fcad5c3bfafd27f5a093ea88951eccb9136 100644
--- a/modules/gfx/src/impl/line_trace_renderer.cc
+++ b/modules/gfx/src/impl/line_trace_renderer.cc
@@ -88,43 +88,51 @@ void LineTraceRenderer::PrepareRendering(const BackboneTrace& trace_subset,
va.SetAALines(options_->GetAALines());
if(is_sel) {
for (int node_list=0; node_list<trace_subset.GetListCount(); ++node_list) {
- const NodeEntryList& nl=trace_subset.GetList(node_list);
- if(nl.size()<1) continue;
- for(unsigned int i=0;i<nl.size();++i) {
- const NodeEntry& entry=nl[i];
- if(sel_.FindAtom(entry.atom).IsValid()) {
- geom::Vec3 apos = entry.atom.GetPos();
- VertexID p0=va.Add(apos, geom::Vec3(),sel_clr);
- if(i>0) {
- VertexID p1 =va.Add(apos+0.5*(nl[i-1].atom.GetPos()-apos), geom::Vec3(), sel_clr);
- va.AddLine(p0, p1);
- }
- if(i<nl.size()-1) {
- VertexID p1 =va.Add(apos+0.5*(nl[i+1].atom.GetPos()-apos), geom::Vec3(), sel_clr);
- va.AddLine(p0, p1);
- }
- }
- }
+ const NodeEntryList& nl=trace_subset.GetList(node_list);
+ if(nl.size()<1) continue;
+ for(unsigned int i=0;i<nl.size();++i) {
+ const NodeEntry& entry=nl[i];
+ if(sel_.FindAtom(entry.atom).IsValid()) {
+ geom::Vec3 apos = entry.atom.GetPos();
+ VertexID p0=va.Add(apos, geom::Vec3(),sel_clr);
+ if(i>0) {
+ VertexID p1 =va.Add(apos+0.5*(nl[i-1].atom.GetPos()-apos), geom::Vec3(), sel_clr);
+ va.AddLine(p0, p1);
+ }
+ if(i<nl.size()-1) {
+ VertexID p1 =va.Add(apos+0.5*(nl[i+1].atom.GetPos()-apos), geom::Vec3(), sel_clr);
+ va.AddLine(p0, p1);
+ }
+ }
+ }
}
} else {
for (int node_list=0; node_list<trace_subset.GetListCount(); ++node_list) {
- const NodeEntryList& nl=trace_subset.GetList(node_list);
-
- if (nl.size()<2) continue;
-
- VertexID p0=va.Add(nl[0].atom.GetPos(), geom::Vec3(),
- nl[0].color1);
- for (unsigned int i=1; i<nl.size()-1;++i) {
- const NodeEntry& entry=nl[i];
- VertexID p1 =va.Add(entry.atom.GetPos(), geom::Vec3(),
- entry.color1);
- va.AddLine(p0, p1);
- p0=p1;
- }
- const NodeEntry& entry=nl.back();
- VertexID p1 =va.Add(entry.atom.GetPos(), geom::Vec3(),
- entry.color1);
- va.AddLine(p0, p1);
+ const NodeEntryList& nl=trace_subset.GetList(node_list);
+
+ if (nl.size()<2) continue;
+
+ VertexID p0=va.Add(nl[0].atom.GetPos(), geom::Vec3(),
+ nl[0].color1);
+ for (unsigned int i=1; i<nl.size()-1;++i) {
+ const NodeEntry& entry=nl[i];
+ VertexID p1 =va.Add(entry.atom.GetPos(), geom::Vec3(),
+ entry.color1);
+ va.AddLine(p0, p1);
+ p0=p1;
+#if 1
+ VertexID p2 =va.Add(entry.atom.GetPos()+entry.direction, geom::Vec3(),
+ Color(1,0,0));
+ VertexID p3 =va.Add(entry.atom.GetPos()+entry.normal, geom::Vec3(),
+ Color(0,1,1));
+ va.AddLine(p0,p2);
+ va.AddLine(p0,p3);
+#endif
+ }
+ const NodeEntry& entry=nl.back();
+ VertexID p1 =va.Add(entry.atom.GetPos(), geom::Vec3(),
+ entry.color1);
+ va.AddLine(p0, p1);
}
}
}
diff --git a/modules/gfx/src/impl/sline_renderer.cc b/modules/gfx/src/impl/sline_renderer.cc
index 2b54046dd634acc1da4413aa9d69b7f4960889a9..92aa0f4836b4b8d603d0279fd655c37206789652 100644
--- a/modules/gfx/src/impl/sline_renderer.cc
+++ b/modules/gfx/src/impl/sline_renderer.cc
@@ -72,7 +72,7 @@ void SlineRenderer::PrepareRendering(const BackboneTrace& trace_subset,
entry.normal, entry.rad,
is_sel ? sel_clr : entry.color1,
is_sel ? sel_clr : entry.color2,
- 0, entry.id);
+ 0, entry.id);
ee.v1 = entry.v1;
spl.push_back(ee);
}
@@ -83,13 +83,11 @@ void SlineRenderer::PrepareRendering(const BackboneTrace& trace_subset,
VertexID p1 = va.Add(sit->position, geom::Vec3(),sit->color1);
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));
+#if 1
+ VertexID p2 = va.Add(sit->position+sit->direction,geom::Vec3(),Color(1,0,0));
+ VertexID p3 = va.Add(sit->position+sit->normal,geom::Vec3(),Color(0,1,1));
va.AddLine(p0,p2);
va.AddLine(p0,p3);
- va.AddLine(p0,p4);
#endif
}
}
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index 75590b1fea096169c76226df15442543fafd697e..6d0856b111c071316e4604b7c6d9a18d1c953085 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -212,24 +212,28 @@ ChainImplPtr ResidueImpl::GetChain() const
geom::Vec3 ResidueImpl::GetCentralNormal() const
{
+ geom::Vec3 nrvo(1,0,0);
if (chem_class_.IsPeptideLinking()) {
AtomImplPtr a1 = FindAtom("C");
AtomImplPtr a2 = FindAtom("O");
- geom::Vec3 nrvo;
if(a1 && a2) {
- nrvo = geom::Normalize(a1->GetPos()-a2->GetPos());
+ nrvo = geom::Normalize(a2->GetPos()-a1->GetPos());
} else {
- geom::Vec3 v0=GetCentralAtom()->GetPos();
- nrvo=geom::Cross(geom::Normalize(v0),
- geom::Normalize(geom::Vec3(-v0[2],v0[0],v0[1])));
- LOG_VERBOSE("warning: could not find atoms for proper central normal calculation");
+ a1 = FindAtom("CB");
+ a2 = FindAtom("CA");
+ if(a1 && a2) {
+ nrvo = geom::Normalize(a2->GetPos()-a1->GetPos());
+ } else {
+ geom::Vec3 v0=GetCentralAtom()->GetPos();
+ nrvo=geom::Cross(geom::Normalize(v0),
+ geom::Normalize(geom::Vec3(-v0[2],v0[0],v0[1])));
+ LOG_VERBOSE("warning: could not find atoms for proper central normal calculation");
+ }
}
- return nrvo;
} else if (chem_class_.IsNucleotideLinking()) {
AtomImplPtr a1 = FindAtom("P");
AtomImplPtr a2 = FindAtom("OP1");
AtomImplPtr a3 = FindAtom("OP2");
- geom::Vec3 nrvo;
if(a1 && a2 && a3) {
nrvo = geom::Normalize(a1->GetPos()-(a2->GetPos()+a3->GetPos())*.5);
} else {
@@ -238,9 +242,8 @@ geom::Vec3 ResidueImpl::GetCentralNormal() const
geom::Normalize(geom::Vec3(-v0[2],v0[0],v0[1])));
LOG_VERBOSE("warning: could not find atoms for proper central normal calculation");
}
- return nrvo;
}
- return geom::Vec3();
+ return nrvo;
}