From 9d02e0991a4364ed09a3c2ba623c74378dde1e1e Mon Sep 17 00:00:00 2001
From: Ansgar Philippsen <ansgar.philippsen@gmail.com>
Date: Mon, 21 Feb 2011 17:32:00 -0500
Subject: [PATCH] moved and expanded numpy setpos to xcs editor various related
cleanups and optimizations: - removed superfluous sort in load_dcd - added
explicit *TransformedPos() methods to complement *Pos() methods
(XCSEditor, AtomHandle, AtomImpl) - changed getter/setter logic for AtomImpl
Name, TransformedPos and OriginalPos to direct access, deprecated GetName
and removed Get*Pos and Set*Pos
---
modules/io/src/mol/dcd_io.cc | 6 +-
modules/mol/base/pymod/export_editors.cc | 116 +++++++++++++++++++-
modules/mol/base/pymod/export_entity.cc | 100 +++++------------
modules/mol/base/src/atom_base.cc | 8 +-
modules/mol/base/src/editor_base.cc | 2 +-
modules/mol/base/src/impl/atom_impl.cc | 12 +-
modules/mol/base/src/impl/atom_impl.hh | 20 ++--
modules/mol/base/src/impl/chain_impl.cc | 8 +-
modules/mol/base/src/impl/connector_impl.cc | 8 +-
modules/mol/base/src/impl/dihedral.cc | 4 +-
modules/mol/base/src/impl/entity_impl.cc | 31 +++---
modules/mol/base/src/impl/residue_impl.cc | 49 +++++----
modules/mol/base/src/query_state.cc | 10 +-
modules/mol/base/src/xcs_editor.cc | 106 ++++++++++++++++--
modules/mol/base/src/xcs_editor.hh | 39 ++++++-
modules/mol/base/tests/test_numpy.py | 17 ++-
16 files changed, 364 insertions(+), 172 deletions(-)
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index 3fdb02f55..e5f48a93d 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -184,7 +184,7 @@ bool read_frame(std::istream& istream, const DCDHeader& header,
}
-mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
+mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom list is already sorted!
const String& trj_fn,
unsigned int stride)
{
@@ -196,10 +196,6 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
}
Profile profile_load("LoadCHARMMTraj");
- mol::AtomHandleList alist(alist2);
- std::sort(alist.begin(),alist.end(),less_index);
-
-
DCDHeader header;
bool swap_flag=false, skip_flag=false, gap_flag=false;
read_dcd_header(istream, header, swap_flag, skip_flag, gap_flag);
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 9976b0d8f..87c19665b 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -26,6 +26,10 @@ using namespace boost::python;
using namespace ost;
using namespace ost::mol;
+#if OST_NUMPY_SUPPORT_ENABLED
+#include <numpy/arrayobject.h>
+#endif
+
namespace {
BondHandle (EditorBase::*connect_a)(const AtomHandle&,
@@ -53,11 +57,111 @@ void (ICSEditor::*rotate_torsion_a)(TorsionHandle, Real)=&ICSEditor::RotateTorsi
void (ICSEditor::*rotate_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
Real)=&ICSEditor::RotateTorsionAngle;
-
+
+void (XCSEditor::*set_pos1)(const AtomHandle&, const geom::Vec3&) = &XCSEditor::SetAtomPos;
+void (XCSEditor::*set_t_pos1)(const AtomHandle&, const geom::Vec3&) = &XCSEditor::SetAtomTransformedPos;
+void (XCSEditor::*set_o_pos1)(const AtomHandle&, const geom::Vec3&) = &XCSEditor::SetAtomOriginalPos;
+
+#if OST_NUMPY_SUPPORT_ENABLED
+template<typename T, bool O>
+void set_pos2_nc_t(XCSEditor& e, const AtomHandleList& alist, PyArrayObject* na)
+{
+ size_t count=0;
+ for(AtomHandleList::const_iterator ait=alist.begin();ait!=alist.end();++ait,++count) {
+ if(O) {
+ e.SetAtomOriginalPos(*ait,geom::Vec3(static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,0))),
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,1))),
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,2)))));
+ } else {
+ e.SetAtomTransformedPos(*ait,geom::Vec3(static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,0))),
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,1))),
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,2)))));
+ }
+ }
+}
+
+template<bool O>
+void set_pos2_t(XCSEditor& e, const AtomHandleList& alist, object pyobj)
+{
+ size_t acount = alist.size();
+
+ if(!PyArray_Check(pyobj.ptr())) {
+ throw std::runtime_error("expected a numpy array");
+ return;
+ }
+ PyArrayObject* na=reinterpret_cast<PyArrayObject*>(pyobj.ptr());
+
+ if(PyArray_NDIM(na)!=2 || PyArray_DIM(na,0)!=acount || PyArray_DIM(na,1)!=3) {
+ throw std::runtime_error("excpected a numpy array of shape (NAtoms, 3)");
+ return;
+ }
+
+ if(PyArray_ISCONTIGUOUS(na)) {
+ if(PyArray_TYPE(na)==NPY_FLOAT) {
+ if(O) {
+ e.SetAtomOriginalPos(alist,reinterpret_cast<float*>(PyArray_DATA(na)));
+ } else {
+ e.SetAtomTransformedPos(alist,reinterpret_cast<float*>(PyArray_DATA(na)));
+ }
+ } else if(PyArray_TYPE(na)==NPY_DOUBLE) {
+ if(O) {
+ e.SetAtomOriginalPos(alist,reinterpret_cast<double*>(PyArray_DATA(na)));
+ } else {
+ e.SetAtomTransformedPos(alist,reinterpret_cast<double*>(PyArray_DATA(na)));
+ }
+ } else {
+ throw std::runtime_error("excpected a numpy array of type float or double");
+ return;
+ }
+ } else {
+ // non-contiguous
+#if 0
+ throw std::runtime_error("excpected contiguous numpy array");
+#else
+ if(PyArray_TYPE(na)==NPY_FLOAT) {
+ set_pos2_nc_t<float,O>(e,alist,na);
+ } else if(PyArray_TYPE(na)==NPY_DOUBLE) {
+ set_pos2_nc_t<double,O>(e,alist,na);
+ } else {
+ throw std::runtime_error("excpected a numpy array of type float or double");
+ return;
+ }
+#endif
+ }
+}
+#endif
+
+void set_t_pos2(XCSEditor& e, const AtomHandleList& alist, object pyobj)
+{
+#if OST_NUMPY_SUPPORT_ENABLED
+ set_pos2_t<false>(e,alist,pyobj);
+#else
+ throw std::runtime_error("SetAtomTransformedPos(alist,ndarray) disabled, since numpy support is not compiled in");
+#endif
+}
+
+void set_o_pos2(XCSEditor& e, const AtomHandleList& alist, object pyobj)
+{
+#if OST_NUMPY_SUPPORT_ENABLED
+ set_pos2_t<true>(e,alist,pyobj);
+#else
+ throw std::runtime_error("SetAtomOriginalPos(alist,ndarray) disabled, since numpy support is not compiled in");
+#endif
+}
+
+void set_pos2(XCSEditor& e, const AtomHandleList& alist, object pyobj)
+{
+ set_t_pos2(e,alist,pyobj);
+}
+
}
void export_Editors()
-{
+{
+#if OST_NUMPY_SUPPORT_ENABLED
+ import_array();
+#endif
+
class_<EditorBase>("EditorBase", no_init)
.def("InsertChain", &EditorBase::InsertChain)
.def("InsertAtom", &EditorBase::InsertAtom,
@@ -82,8 +186,12 @@ void export_Editors()
;
class_<XCSEditor, bases<EditorBase> >("XCSEditor", no_init)
- .def("SetAtomPos", &XCSEditor::SetAtomPos)
- .def("SetAtomOriginalPos", &XCSEditor::SetAtomOriginalPos)
+ .def("SetAtomPos", set_pos1)
+ .def("SetAtomPos", set_pos2)
+ .def("SetAtomTransformedPos", set_t_pos1)
+ .def("SetAtomTransformedPos", set_t_pos2)
+ .def("SetAtomOriginalPos", set_o_pos1)
+ .def("SetAtomOriginalPos", set_o_pos2)
.def("ApplyTransform", &XCSEditor::ApplyTransform)
.def("SetTransform", &XCSEditor::SetTransform)
.def("UpdateICS", &XCSEditor::UpdateICS)
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index 36ab544f1..826a07bb0 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -68,18 +68,34 @@ ICSEditor depr_request_ics_editor(EntityHandle e, EditMode m)
return e.EditICS(m);
}
+bool less_index(const mol::AtomHandle& a1, const mol::AtomHandle& a2)
+{
+ return a1.GetIndex()<a2.GetIndex();
+}
-PyObject* get_pos(EntityHandle& entity)
+
+PyObject* get_pos2(EntityHandle& entity, bool id_sorted)
{
#if OST_NUMPY_SUPPORT_ENABLED
npy_intp dims[]={entity.GetAtomCount(),3};
- PyObject* na = PyArray_SimpleNew(2,dims,NPY_DOUBLE);
- npy_double* nad = reinterpret_cast<npy_double*>(PyArray_DATA(na));
- for(AtomHandleIter it=entity.AtomsBegin();it!=entity.AtomsEnd();++it,nad+=3) {
- geom::Vec3 pos=(*it).GetPos();
- nad[0]=static_cast<npy_double>(pos[0]);
- nad[1]=static_cast<npy_double>(pos[1]);
- nad[2]=static_cast<npy_double>(pos[2]);
+ PyObject* na = PyArray_SimpleNew(2,dims,NPY_FLOAT);
+ npy_float* nad = reinterpret_cast<npy_float*>(PyArray_DATA(na));
+ if(id_sorted) {
+ AtomHandleList alist = entity.GetAtomList();
+ std::sort(alist.begin(),alist.end(),less_index);
+ for(AtomHandleList::const_iterator it=alist.begin();it!=alist.end();++it,nad+=3) {
+ geom::Vec3 pos=(*it).GetPos();
+ nad[0]=static_cast<npy_float>(pos[0]);
+ nad[1]=static_cast<npy_float>(pos[1]);
+ nad[2]=static_cast<npy_float>(pos[2]);
+ }
+ } else {
+ for(AtomHandleIter it=entity.AtomsBegin();it!=entity.AtomsEnd();++it,nad+=3) {
+ geom::Vec3 pos=(*it).GetPos();
+ nad[0]=static_cast<npy_float>(pos[0]);
+ nad[1]=static_cast<npy_float>(pos[1]);
+ nad[2]=static_cast<npy_float>(pos[2]);
+ }
}
return na;
#else
@@ -88,67 +104,9 @@ PyObject* get_pos(EntityHandle& entity)
#endif
}
-
-#if OST_NUMPY_SUPPORT_ENABLED
-template <typename T>
-void set_pos_t(PyArrayObject* na, EntityHandle& entity)
+PyObject* get_pos1(EntityHandle& entity)
{
- XCSEditor ed=entity.EditXCS(BUFFERED_EDIT);
-
- if(PyArray_ISCONTIGUOUS(na)) {
- T* data = reinterpret_cast<T*>(PyArray_DATA(na));
- size_t count=0;
- for(AtomHandleIter it=entity.AtomsBegin();it!=entity.AtomsEnd();++it,++count) {
- ed.SetAtomPos(*it,geom::Vec3(static_cast<Real>(data[count*3+0]),
- static_cast<Real>(data[count*3+1]),
- static_cast<Real>(data[count*3+2])));
- }
- } else {
- size_t count=0;
- for(AtomHandleIter it=entity.AtomsBegin();it!=entity.AtomsEnd();++it,++count) {
- ed.SetAtomPos(*it,geom::Vec3(static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,0))),
- static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,1))),
- static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,2)))));
- }
- }
-}
-#endif
-
-void set_pos(EntityHandle& entity, object& pyobj)
-{
-#if OST_NUMPY_SUPPORT_ENABLED
- size_t acount = entity.GetAtomCount();
-
- if(!PyArray_Check(pyobj.ptr())) {
- throw std::runtime_error(std::string("expected a numpy array"));
- return;
- }
- PyArrayObject* na=reinterpret_cast<PyArrayObject*>(pyobj.ptr());
-
- if(PyArray_NDIM(na)!=2 || PyArray_DIM(na,0)!=acount || PyArray_DIM(na,1)!=3) {
- throw std::runtime_error("excpected a numpy array of shape (NAtoms, 3)");
- return;
- }
-
- switch(PyArray_TYPE(na)) {
- case NPY_FLOAT:
- set_pos_t<float>(na,entity); break;
- case NPY_DOUBLE:
- set_pos_t<double>(na,entity); break;
- case NPY_INT:
- set_pos_t<int>(na,entity); break;
- case NPY_LONG:
- set_pos_t<long>(na,entity); break;
- case NPY_SHORT:
- set_pos_t<short>(na,entity); break;
- default:
- throw std::runtime_error("excpected a numpy array of type float, double, int, long or short");
- return;
- };
-
-#else
- throw std::runtime_error("SetPositions disabled, since numpy support is not compiled in");
-#endif
+ return get_pos2(entity,true);
}
} // ns
@@ -230,9 +188,9 @@ void export_Entity()
.def(self==self)
.def(self!=self)
#if OST_NUMPY_SUPPORT_ENABLED
- .def("SetPositions",set_pos)
- .def("GetPositions",get_pos)
- .add_property("positions",get_pos,set_pos)
+ .def("GetPositions",get_pos1)
+ .def("GetPositions",get_pos2)
+ .add_property("positions",get_pos1)
#endif
;
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index f25d40135..642ea5aa9 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -42,25 +42,25 @@ const GenericPropContainerImpl* AtomBase::GpImpl() const
const String& AtomBase::GetName() const
{
this->CheckValidity();
- return impl_->GetName();
+ return impl_->Name();
}
void AtomBase::SetName(const String& atom_name)
{
this->CheckValidity();
- return impl_->SetName(atom_name);
+ impl_->Name()=atom_name;
}
const geom::Vec3& AtomBase::GetPos() const
{
this->CheckValidity();
- return impl_->GetPos();
+ return impl_->TransformedPos();
}
const geom::Vec3& AtomBase::GetOriginalPos() const
{
this->CheckValidity();
- return impl_->GetOriginalPos();
+ return impl_->OriginalPos();
}
geom::Vec3 AtomBase::GetAltPos(const String& alt_group) const
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 01eaf549d..5ab540f31 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -143,7 +143,7 @@ void EditorBase::ReorderAllResidues()
void EditorBase::RenameAtom(AtomHandle atom, const String& new_name)
{
CheckHandleValidity(atom);
- atom.Impl()->SetName(new_name);
+ atom.Impl()->Name()=new_name;
}
BondHandle EditorBase::Connect(const AtomHandle& first,
diff --git a/modules/mol/base/src/impl/atom_impl.cc b/modules/mol/base/src/impl/atom_impl.cc
index a04f4ce1e..73123d538 100644
--- a/modules/mol/base/src/impl/atom_impl.cc
+++ b/modules/mol/base/src/impl/atom_impl.cc
@@ -95,11 +95,11 @@ void AtomImpl::TraceDirectionality(FragmentImplP frag, ConnectorImplP conn,
#if !defined(NDEBUG)
if (conn->GetFirst()==shared_from_this()) {
LOG_TRACE("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
- << "." << GetName() << " [" << conn->GetSecond()->GetQualifiedName()
+ << "." << Name() << " [" << conn->GetSecond()->GetQualifiedName()
<< " ]");
} else {
LOG_TRACE("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
- << "." << GetName() << " [" << conn->GetFirst()->GetQualifiedName()
+ << "." << Name() << " [" << conn->GetFirst()->GetQualifiedName()
<< " ]");
}
@@ -107,7 +107,7 @@ void AtomImpl::TraceDirectionality(FragmentImplP frag, ConnectorImplP conn,
#endif
} else {
LOG_TRACE("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
- << "." << GetName() << " [ ]");
+ << "." << Name() << " [ ]");
}
// presence of a primary connector indicates ring closure
@@ -196,7 +196,7 @@ void AtomImpl::UpdateFromXCS()
// stack before calling UpdateFromICS() on the next atom.
{
// Derive direction and length of connector from atom positions.
- geom::Vec3 global_d=((*i)->GetSecond()->GetOriginalPos()-this->GetOriginalPos());
+ geom::Vec3 global_d=((*i)->GetSecond()->OriginalPos()-this->OriginalPos());
// Set direction and length of connector. Direction is relative to
// local coordinate system of this atom.
// Note the order of arguments for the matrix multiplication. This is the
@@ -225,7 +225,7 @@ std::ostream& operator<<(std::ostream& o, const AtomImplPtr ap)
{
o << ap->GetResidue()->GetChain()->GetName() << ".";
o << ap->GetResidue()->GetKey() << ap->GetResidue()->GetNumber() << ".";
- o << ap->GetName();
+ o << ap->Name();
return o;
}
@@ -258,7 +258,7 @@ ConnectorImplP GetConnector(const AtomImplPtr& a, const AtomImplPtr& b) {
}
String AtomImpl::GetQualifiedName() const {
- return this->GetResidue()->GetQualifiedName()+"."+this->GetName();
+ return this->GetResidue()->GetQualifiedName()+"."+this->Name();
}
void AtomImpl::DeleteAllConnectors() {
diff --git a/modules/mol/base/src/impl/atom_impl.hh b/modules/mol/base/src/impl/atom_impl.hh
index 963f5ab60..b342c526a 100644
--- a/modules/mol/base/src/impl/atom_impl.hh
+++ b/modules/mol/base/src/impl/atom_impl.hh
@@ -56,21 +56,21 @@ public:
~AtomImpl();
void Apply(EntityVisitor& h);
- const String& GetName() const {return name_;}
-
- void SetName(const String& atom_name) {
- name_=atom_name;
- }
+ // for efficiency reasons, the simple setter/getter methods are
+ // replaced by direct access - this is the impl layer after all
+ const String& Name() const {return name_;}
+ String& Name() {return name_;}
- const geom::Vec3& GetPos() const {return tf_pos_;}
+ // DEPRECATED
+ const String& GetName() const {return name_;}
- const geom::Vec3& GetOriginalPos() const {return pos_;}
+ const geom::Vec3& TransformedPos() const {return tf_pos_;}
+ geom::Vec3& TransformedPos() {return tf_pos_;}
- void SetTransformedPos(const geom::Vec3& pos) { tf_pos_=pos; }
+ const geom::Vec3& OriginalPos() const {return pos_;}
+ geom::Vec3& OriginalPos() {return pos_;}
- void SetOriginalPos(const geom::Vec3& pos) { pos_=pos; }
-
ResidueImplPtr GetResidue() const;
void SetPrimaryConnector(const ConnectorImplP& bp) {
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 456255c3c..ea0f4cce8 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -387,8 +387,8 @@ geom::AlignedCuboid ChainImpl::GetBounds() const
ResidueImplPtr r=*i;
for (AtomImplList::iterator j=r->GetAtomList().begin();
j!=r->GetAtomList().end(); ++j) {
- mmin=geom::Min(mmin, (*j)->GetPos());
- mmax=geom::Max(mmax, (*j)->GetPos());
+ mmin=geom::Min(mmin, (*j)->TransformedPos());
+ mmax=geom::Max(mmax, (*j)->TransformedPos());
atoms=true;
}
}
@@ -408,7 +408,7 @@ geom::Vec3 ChainImpl::GetCenterOfAtoms() const
ResidueImplPtr r=*i;
for (AtomImplList::iterator j=r->GetAtomList().begin();
j!=r->GetAtomList().end(); ++j) {
- sum+=(*j)->GetPos();
+ sum+=(*j)->TransformedPos();
}
}
sum/=this->GetAtomCount();
@@ -426,7 +426,7 @@ geom::Vec3 ChainImpl::GetCenterOfMass() const
ResidueImplPtr r=*i;
for (AtomImplList::iterator j=r->GetAtomList().begin();
j!=r->GetAtomList().end(); ++j) {
- center+=(*j)->GetPos() * (*j)->GetMass();
+ center+=(*j)->TransformedPos() * (*j)->GetMass();
}
}
center/=mass;
diff --git a/modules/mol/base/src/impl/connector_impl.cc b/modules/mol/base/src/impl/connector_impl.cc
index b244bc000..7598fdf6f 100644
--- a/modules/mol/base/src/impl/connector_impl.cc
+++ b/modules/mol/base/src/impl/connector_impl.cc
@@ -77,14 +77,14 @@ geom::Mat3 find_rotation(const geom::Vec3& d) {
geom::Vec3 ConnectorImpl::GetPos() const
{
- return (GetFirst()->GetPos()+GetSecond()->GetPos())*0.5;
+ return (GetFirst()->TransformedPos()+GetSecond()->TransformedPos())*0.5;
}
Real ConnectorImpl::GetLength() const
{
Real length;
if (this->GetFirst()->GetEntity()->HasICS()==false) {
- length=geom::Distance(this->GetFirst()->GetOriginalPos(),this->GetSecond()->GetOriginalPos());
+ length=geom::Distance(this->GetFirst()->OriginalPos(),this->GetSecond()->OriginalPos());
} else {
length=len_;
}
@@ -110,8 +110,8 @@ bool ConnectorImpl::IsConnectorOf(const AtomImplPtr& a,
geom::Vec3 ConnectorImpl::GetOriginalPos() const
{
- return (this->GetFirst()->GetOriginalPos()+
- this->GetSecond()->GetOriginalPos())*0.5;
+ return (this->GetFirst()->OriginalPos()+
+ this->GetSecond()->OriginalPos())*0.5;
}
void ConnectorImpl::Switch()
diff --git a/modules/mol/base/src/impl/dihedral.cc b/modules/mol/base/src/impl/dihedral.cc
index 3580829b1..cac771039 100644
--- a/modules/mol/base/src/impl/dihedral.cc
+++ b/modules/mol/base/src/impl/dihedral.cc
@@ -46,8 +46,8 @@ Dihedral::Dihedral(const AtomImplList& atoms)
Real Dihedral::GetAngleXCS() const {
- return geom::DihedralAngle(atoms_[0]->GetPos(), atoms_[1]->GetPos(),
- atoms_[2]->GetPos(), atoms_[3]->GetPos());
+ return geom::DihedralAngle(atoms_[0]->TransformedPos(), atoms_[1]->TransformedPos(),
+ atoms_[2]->TransformedPos(), atoms_[3]->TransformedPos());
}
Real Dihedral::GetAngleICS() const {
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index eb85cef79..622e06b1a 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -268,10 +268,10 @@ geom::AlignedCuboid EntityImpl::GetBounds() const
if (this->GetAtomCount()>0) {
geom::Vec3 mmin, mmax;
AtomImplMap::const_iterator it=atom_map_.begin();
- mmin=mmax=it->second->GetPos();
+ mmin=mmax=it->second->TransformedPos();
for (++it; it!=atom_map_.end();++it) {
- mmin=geom::Min(mmin,it->second->GetPos());
- mmax=geom::Max(mmax,it->second->GetPos());
+ mmin=geom::Min(mmin,it->second->TransformedPos());
+ mmax=geom::Max(mmax,it->second->TransformedPos());
}
return geom::AlignedCuboid(mmin, mmax);
} else {
@@ -285,7 +285,7 @@ geom::Vec3 EntityImpl::GetCenterOfAtoms() const {
if (this->GetAtomCount()>0) {
for (AtomImplMap::const_iterator it = atom_map_.begin();
it!=atom_map_.end();++it) {
- center+=it->second->GetPos();
+ center+=it->second->TransformedPos();
}
center/=static_cast<Real>(atom_map_.size());
}
@@ -297,7 +297,7 @@ geom::Vec3 EntityImpl::GetCenterOfMass() const {
Real mass = this->GetMass();
if (this->GetAtomCount()>0 && mass>0) {
for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
- center+=it->second->GetPos()*it->second->GetMass();
+ center+=it->second->TransformedPos()*it->second->GetMass();
}
center/=mass;
}
@@ -324,12 +324,12 @@ AtomImplPtr EntityImpl::CreateAtom(const ResidueImplPtr& rp,
#else
AtomImplPtr ap(new AtomImpl(shared_from_this(), rp, name, pos, ele, next_index_++));
#endif
- if (identity_transf_ == false) {
+ if (!identity_transf_) {
geom::Vec3 transformed_pos = geom::Vec3(transformation_matrix_*geom::Vec4(pos));
- ap->SetTransformedPos(transformed_pos);
+ ap->TransformedPos()=transformed_pos;
atom_organizer_.Add(ap,transformed_pos);
} else {
- ap->SetTransformedPos(pos);
+ ap->TransformedPos()=pos;
atom_organizer_.Add(ap,pos);
}
atom_map_.insert(AtomImplMap::value_type(ap.get(),ap));
@@ -496,8 +496,8 @@ Real EntityImpl::GetAngleXCS(const AtomImplPtr& a1, const AtomImplPtr& a2,
ConnectorImplP c23=GetConnector(a2, a3);
if (c12 && c12->GetFirst() && c12->GetSecond()) {
if (c23 && c23->GetFirst() && c23->GetSecond()) {
- return Angle(a2->GetPos()-a1->GetPos(),
- a2->GetPos()-a3->GetPos());
+ return Angle(a2->TransformedPos()-a1->TransformedPos(),
+ a2->TransformedPos()-a3->TransformedPos());
} else {
AtomHandle ah2(a2), ah3(a3);
throw NotConnectedError(ah2, ah3);
@@ -763,12 +763,7 @@ void EntityImpl::SetTransform(const geom::Mat4 transfmat)
{
transformation_matrix_=transfmat;
inverse_transformation_matrix_=Invert(transformation_matrix_);
- geom::Mat4 identity = geom::Mat4();
- if (transformation_matrix_ == identity) {
- identity_transf_ = true;
- } else {
- identity_transf_ = false;
- }
+ identity_transf_ = (transformation_matrix_==geom::Mat4());
this->UpdateTransformedPos();
this->MarkXCSDirty();
}
@@ -1047,7 +1042,7 @@ void EntityImpl::UpdateOrganizer()
atom_organizer_.Clear();
for (AtomImplMap::const_iterator i=atom_map_.begin(),
e=atom_map_.end(); i!=e; ++i) {
- atom_organizer_.Add(i->second, i->second->GetPos());
+ atom_organizer_.Add(i->second, i->second->TransformedPos());
}
}
@@ -1186,7 +1181,7 @@ void EntityImpl::RenameChain(ChainImplPtr chain, const String& new_name)
void EntityImpl::UpdateTransformedPos(){
for(AtomImplMap::iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
- it->second->SetTransformedPos(geom::Vec3(transformation_matrix_*geom::Vec4(it->second->GetOriginalPos())));
+ it->second->TransformedPos()=geom::Vec3(transformation_matrix_*geom::Vec4(it->second->OriginalPos()));
}
}
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index 3b8bd2ace..af7012825 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -60,8 +60,8 @@ AtomImplPtr ResidueImpl::InsertAtom(const String& name,
AtomImplPtr ResidueImpl::InsertAtom(const AtomImplPtr& atom)
{
- AtomImplPtr dst_atom=this->InsertAtom(atom->GetName(),
- atom->GetPos(),
+ AtomImplPtr dst_atom=this->InsertAtom(atom->Name(),
+ atom->TransformedPos(),
atom->GetElement());
dst_atom->Assign(*atom.get());
@@ -166,12 +166,12 @@ AtomImplPtr ResidueImpl::GetCentralAtom() const
if (chem_class_.IsNucleotideLinking()) {
for (AtomImplList::const_iterator it=atom_list_.begin();
it!=atom_list_.end();++it) {
- if((*it)->GetName()=="P") return *it;
+ if((*it)->Name()=="P") return *it;
}
} else if (chem_class_.IsPeptideLinking()) {
for (AtomImplList::const_iterator it=atom_list_.begin();
it!=atom_list_.end();++it) {
- if((*it)->GetName()=="CA") return *it;
+ if((*it)->Name()=="CA") return *it;
}
}
@@ -217,14 +217,14 @@ geom::Vec3 ResidueImpl::GetCentralNormal() const
AtomImplPtr a1 = FindAtom("C");
AtomImplPtr a2 = FindAtom("O");
if(a1 && a2) {
- nrvo = geom::Normalize(a2->GetPos()-a1->GetPos());
+ nrvo = geom::Normalize(a2->TransformedPos()-a1->TransformedPos());
} else {
a1 = FindAtom("CB");
a2 = FindAtom("CA");
if(a1 && a2) {
- nrvo = geom::Normalize(a2->GetPos()-a1->GetPos());
+ nrvo = geom::Normalize(a2->TransformedPos()-a1->TransformedPos());
} else {
- geom::Vec3 v0=GetCentralAtom()->GetPos();
+ geom::Vec3 v0=GetCentralAtom()->TransformedPos();
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");
@@ -235,9 +235,9 @@ geom::Vec3 ResidueImpl::GetCentralNormal() const
AtomImplPtr a2 = FindAtom("OP1");
AtomImplPtr a3 = FindAtom("OP2");
if(a1 && a2 && a3) {
- nrvo = geom::Normalize(a1->GetPos()-(a2->GetPos()+a3->GetPos())*.5);
+ nrvo = geom::Normalize(a1->TransformedPos()-(a2->TransformedPos()+a3->TransformedPos())*.5);
} else {
- geom::Vec3 v0=GetCentralAtom()->GetPos();
+ geom::Vec3 v0=GetCentralAtom()->TransformedPos();
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");
@@ -251,7 +251,7 @@ AtomImplPtr ResidueImpl::FindAtom(const String& aname) const
{
for (AtomImplList::const_iterator it=atom_list_.begin();
it!=atom_list_.end();++it) {
- if ((*it)->GetName()==aname) {
+ if ((*it)->Name()==aname) {
return *it;
}
}
@@ -366,18 +366,25 @@ void ResidueImpl::DeleteAtom(const AtomImplPtr& atom) {
}
}
+namespace {
+ struct aname_matcher {
+ aname_matcher(const String& n): aname(n) {}
+ bool operator()(AtomImplPtr& a) {return a->Name()==aname;}
+ String aname;
+ };
+}
+
void ResidueImpl::DeleteAtoms(const String& atom_name) {
AtomImplList::iterator i=atom_list_.begin();
for (; i!=atom_list_.end(); ++i) {
- if ((*i)->GetName()==atom_name) {
+ if ((*i)->Name()==atom_name) {
(*i)->DeleteAllTorsions();
(*i)->DeleteAllConnectors();
this->GetEntity()->DeleteAtom(*i);
}
}
AtomImplList::iterator new_end;
- new_end=std::remove_if(atom_list_.begin(), atom_list_.end(),
- bind(&AtomImpl::GetName, _1)==atom_name);
+ new_end=std::remove_if(atom_list_.begin(), atom_list_.end(), aname_matcher(atom_name));
atom_list_.erase(new_end, atom_list_.end());
}
@@ -452,10 +459,10 @@ geom::AlignedCuboid ResidueImpl::GetBounds() const
if (atom_list_.size()>0) {
AtomImplList::const_iterator i=atom_list_.begin();
- mmin=mmax=(*i)->GetPos();
+ mmin=mmax=(*i)->TransformedPos();
for (++i; i!=atom_list_.end(); ++i) {
- mmax=geom::Max(mmax,(*i)->GetPos());
- mmin=geom::Min(mmin,(*i)->GetPos());
+ mmax=geom::Max(mmax,(*i)->TransformedPos());
+ mmin=geom::Min(mmin,(*i)->TransformedPos());
}
return geom::AlignedCuboid(mmin, mmax);
} else {
@@ -469,7 +476,7 @@ geom::Vec3 ResidueImpl::GetCenterOfAtoms() const
if (!atom_list_.empty()) {
for (AtomImplList::const_iterator i=atom_list_.begin();
i!=atom_list_.end(); ++i) {
- sum+=(*i)->GetPos();
+ sum+=(*i)->TransformedPos();
}
sum/=atom_list_.size();
}
@@ -483,7 +490,7 @@ geom::Vec3 ResidueImpl::GetCenterOfMass() const
if (this->GetAtomCount() > 0 && mass > 0) {
for (AtomImplList::const_iterator i=atom_list_.begin();
i!=atom_list_.end(); ++i) {
- center+=(*i)->GetPos()*(*i)->GetMass();
+ center+=(*i)->TransformedPos()*(*i)->GetMass();
}
}
return center/mass;
@@ -565,7 +572,7 @@ bool ResidueImpl::SwitchAtomPos(const String& group) {
for (; k!=gr.atoms.end(); ++k) {
AtomGroupEntry& entry=*k;
assert(!entry.atom.expired());
- entry.pos=entry.atom.lock()->GetOriginalPos();
+ entry.pos=entry.atom.lock()->OriginalPos();
}
}
AtomGroup& agr=i->second;
@@ -574,11 +581,11 @@ bool ResidueImpl::SwitchAtomPos(const String& group) {
AtomGroupEntry& entry=*j;
assert(!entry.atom.expired());
- entry.atom.lock()->SetOriginalPos(entry.pos);
+ entry.atom.lock()->OriginalPos()=entry.pos;
EntityHandle ent = entry.atom.lock()->GetEntity();
geom::Mat4 transf_matrix = ent.GetTransformationMatrix();
geom::Vec3 transf_pos = geom::Vec3(transf_matrix*geom::Vec4(entry.pos));
- entry.atom.lock()->SetTransformedPos(transf_pos);
+ entry.atom.lock()->TransformedPos()=transf_pos;
}
curr_group_=group;
return true;
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index 2f04aeecc..4e5c86403 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -318,22 +318,22 @@ boost::logic::tribool QueryState::EvalAtom(const impl::AtomImplPtr& a) {
int int_value;
switch (ss.sel_id) {
case Prop::ANAME:
- str_value = a->GetName();
+ str_value = a->Name();
s_[*i] = cmp_string(ss.comp_op,str_value,
boost::get<String>(ss.param));
break;
case Prop::AX:
- float_value=(a->GetPos())[0];
+ float_value=(a->TransformedPos())[0];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::AY:
- float_value=(a->GetPos())[1];
+ float_value=(a->TransformedPos())[1];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::AZ:
- float_value=(a->GetPos())[2];
+ float_value=(a->TransformedPos())[2];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
@@ -353,7 +353,7 @@ boost::logic::tribool QueryState::EvalAtom(const impl::AtomImplPtr& a) {
boost::get<float>(ss.param));
break;
case Prop::WITHIN:
- s_[*i]= this->do_within(a->GetPos(),
+ s_[*i]= this->do_within(a->TransformedPos(),
boost::get<WithinParam>(ss.param),
ss.comp_op);
break;
diff --git a/modules/mol/base/src/xcs_editor.cc b/modules/mol/base/src/xcs_editor.cc
index 88d8bbcd4..41d6be611 100644
--- a/modules/mol/base/src/xcs_editor.cc
+++ b/modules/mol/base/src/xcs_editor.cc
@@ -67,33 +67,117 @@ XCSEditor& XCSEditor::operator=(const XCSEditor& rhs)
return *this;
}
-void XCSEditor::SetAtomPos(const AtomHandle& atom,
- const geom::Vec3& position)
+void XCSEditor::SetAtomTransformedPos(const AtomHandle& atom,
+ const geom::Vec3& position)
{
CheckHandleValidity(atom);
- atom.Impl()->SetTransformedPos(position);
- geom::Mat4 inv_transformation_matrix = ent_.Impl()->GetInvTransfMatrix();
- geom::Vec3 original_pos = geom::Vec3(inv_transformation_matrix*geom::Vec4(position));
- atom.Impl()->SetOriginalPos(original_pos);
+ atom.Impl()->TransformedPos()=position;
+ if(ent_.Impl()->IsTransfIdentity()) {
+ atom.Impl()->OriginalPos()=position;
+ } else {
+ atom.Impl()->OriginalPos() = geom::Vec3(ent_.Impl()->GetInvTransfMatrix()*geom::Vec4(position));
+ }
ent_.Impl()->MarkICSDirty();
ent_.Impl()->MarkOrganizerDirty();
this->Update();
}
+namespace {
+ template<typename T>
+ void set_transformed_pos(impl::EntityImpl* ent, const AtomHandleList& alist, T *positions)
+ {
+ bool has_tf=ent->IsTransfIdentity();
+ for(AtomHandleList::const_iterator ait=alist.begin();ait!=alist.end();++ait) {
+ ait->Impl()->TransformedPos()[0]=static_cast<Real>(positions[0]);
+ ait->Impl()->TransformedPos()[1]=static_cast<Real>(positions[1]);
+ ait->Impl()->TransformedPos()[2]=static_cast<Real>(positions[2]);
+ positions+=3;
+ if(has_tf) {
+ ait->Impl()->OriginalPos()=ait->Impl()->TransformedPos();
+ } else {
+ ait->Impl()->OriginalPos() = geom::Vec3(ent->GetInvTransfMatrix()*geom::Vec4(ait->Impl()->TransformedPos()));
+ }
+ }
+ ent->MarkICSDirty();
+ ent->MarkOrganizerDirty();
+ }
+} // anon ns
+
+void XCSEditor::SetAtomTransformedPos(const AtomHandleList& alist, float *positions)
+{
+ set_transformed_pos<float>(ent_.Impl().get(),alist,positions);
+ this->Update();
+}
+
+void XCSEditor::SetAtomTransformedPos(const AtomHandleList& alist, double *positions)
+{
+ set_transformed_pos<double>(ent_.Impl().get(),alist,positions);
+ this->Update();
+}
void XCSEditor::SetAtomOriginalPos(const AtomHandle& atom,
- const geom::Vec3& position)
+ const geom::Vec3& position)
{
CheckHandleValidity(atom);
- atom.Impl()->SetOriginalPos(position);
- geom::Mat4 transformation_matrix = atom.GetEntity().GetTransformationMatrix();
- geom::Vec3 transformed_pos = geom::Vec3(transformation_matrix*geom::Vec4(position));
- atom.Impl()->SetTransformedPos(transformed_pos);
+ atom.Impl()->OriginalPos()=position;
+ if(ent_.Impl()->IsTransfIdentity()) {
+ atom.Impl()->TransformedPos()=position;
+ } else {
+ atom.Impl()->TransformedPos() = geom::Vec3(ent_.Impl()->GetTransfMatrix()*geom::Vec4(position));
+ }
ent_.Impl()->MarkICSDirty();
ent_.Impl()->MarkOrganizerDirty();
this->Update();
}
+namespace {
+ template<typename T>
+ void set_original_pos(impl::EntityImpl* ent, const AtomHandleList& alist, T *positions)
+ {
+ bool has_tf=ent->IsTransfIdentity();
+ for(AtomHandleList::const_iterator ait=alist.begin();ait!=alist.end();++ait) {
+ ait->Impl()->OriginalPos()[0]=static_cast<Real>(positions[0]);
+ ait->Impl()->OriginalPos()[1]=static_cast<Real>(positions[1]);
+ ait->Impl()->OriginalPos()[2]=static_cast<Real>(positions[2]);
+ positions+=3;
+ if(has_tf) {
+ ait->Impl()->TransformedPos()=ait->Impl()->OriginalPos();
+ } else {
+ ait->Impl()->TransformedPos() = geom::Vec3(ent->GetTransfMatrix()*geom::Vec4(ait->Impl()->OriginalPos()));
+ }
+ }
+ ent->MarkICSDirty();
+ ent->MarkOrganizerDirty();
+ }
+} // anon ns
+
+void XCSEditor::SetAtomOriginalPos(const AtomHandleList& alist, float *positions)
+{
+ set_original_pos<float>(ent_.Impl().get(),alist,positions);
+ this->Update();
+}
+
+void XCSEditor::SetAtomOriginalPos(const AtomHandleList& alist, double *positions)
+{
+ set_original_pos<double>(ent_.Impl().get(),alist,positions);
+ this->Update();
+}
+
+void XCSEditor::SetAtomPos(const AtomHandle& atom, const geom::Vec3& position)
+{
+ this->SetAtomTransformedPos(atom,position);
+}
+
+void XCSEditor::SetAtomPos(const AtomHandleList& alist, float *positions)
+{
+ this->SetAtomTransformedPos(alist,positions);
+}
+
+void XCSEditor::SetAtomPos(const AtomHandleList& alist, double *positions)
+{
+ this->SetAtomTransformedPos(alist,positions);
+}
+
void XCSEditor::ApplyTransform(const geom::Mat4& transform)
{
ent_.Impl()->ApplyTransform(transform);
diff --git a/modules/mol/base/src/xcs_editor.hh b/modules/mol/base/src/xcs_editor.hh
index 4b89083c6..73d96a652 100644
--- a/modules/mol/base/src/xcs_editor.hh
+++ b/modules/mol/base/src/xcs_editor.hh
@@ -51,11 +51,47 @@ public:
void SetAtomOriginalPos(const AtomHandle& atom,
const geom::Vec3& position);
+ /// \brief numpy float interface
+ ///
+ /// the passed in float array must have a length of 3*alist.size()
+ void SetAtomOriginalPos(const AtomHandleList& alist,
+ float *positions);
+
+ /// \brief numpy double interface
+ ///
+ /// the passed in double array must have a length of 3*alist.size()
+ void SetAtomOriginalPos(const AtomHandleList& alist,
+ double *positions);
+
/// \brief set transformed position of atom
///
/// This function also updates the original coordinates
+ void SetAtomTransformedPos(const AtomHandle& atom,
+ const geom::Vec3& position);
+
+ /// \brief numpy float interface
+ ///
+ /// the passed in float array must have a length of 3*alist.size()
+ void SetAtomTransformedPos(const AtomHandleList& alist,
+ float *positions);
+
+ /// \brief numpy double interface
+ ///
+ /// the passed in double array must have a length of 3*alist.size()
+ void SetAtomTransformedPos(const AtomHandleList& alist,
+ double *positions);
+
+ /// \brief same as SetAtomTransformedPos(AtomHandle, geom::Vec3)
void SetAtomPos(const AtomHandle& atom,
- const geom::Vec3& position);
+ const geom::Vec3& position);
+
+ /// \brief same as SetTransformedPos(AtomHandleList,float*)
+ void SetAtomPos(const AtomHandleList& alist,
+ float *positions);
+
+ /// \brief same as SetTransformedPos(AtomHandleList,double*)
+ void SetAtomPos(const AtomHandleList& alist,
+ double *positions);
/// \brief apply additional transformation to all atoms
///
@@ -69,6 +105,7 @@ public:
/// \brief immediately update internal coordinate system
void UpdateICS();
+
protected:
XCSEditor(const EntityHandle& ent, EditMode mode);
diff --git a/modules/mol/base/tests/test_numpy.py b/modules/mol/base/tests/test_numpy.py
index 8dc14835a..cad6f764f 100644
--- a/modules/mol/base/tests/test_numpy.py
+++ b/modules/mol/base/tests/test_numpy.py
@@ -4,6 +4,9 @@ sys.path.append("../../../../stage/lib64/openstructure")
from ost import *
import numpy
+def v2v(v):
+ return geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
+
class TestNumpy(unittest.TestCase):
def setUp(self):
pass
@@ -14,16 +17,20 @@ class TestNumpy(unittest.TestCase):
ch=ed.InsertChain("X")
re=ed.AppendResidue(ch,"ALA")
a0=ed.InsertAtom(re,"A",geom.Vec3(0,0,0))
+ self.assertTrue(a0.GetIndex()==0)
a1=ed.InsertAtom(re,"B",geom.Vec3(1,0,0))
+ self.assertTrue(a1.GetIndex()==1)
a2=ed.InsertAtom(re,"C",geom.Vec3(2,0,0))
+ self.assertTrue(a2.GetIndex()==2)
a3=ed.InsertAtom(re,"D",geom.Vec3(3,0,0))
+ self.assertTrue(a3.GetIndex()==3)
self.assertTrue(geom.Distance(a0.pos,geom.Vec3(0,0,0))<1e-10)
self.assertTrue(geom.Distance(a1.pos,geom.Vec3(1,0,0))<1e-10)
self.assertTrue(geom.Distance(a2.pos,geom.Vec3(2,0,0))<1e-10)
self.assertTrue(geom.Distance(a3.pos,geom.Vec3(3,0,0))<1e-10)
- entity.positions=numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]])
+ ed.SetAtomTransformedPos(entity.GetAtomList(),numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]], dtype=numpy.float32))
self.assertTrue(geom.Distance(a0.pos,geom.Vec3(0,1,0))<1e-10)
self.assertTrue(geom.Distance(a1.pos,geom.Vec3(0,2,0))<1e-10)
@@ -32,10 +39,10 @@ class TestNumpy(unittest.TestCase):
na=entity.positions
- self.assertTrue(geom.Distance(geom.Vec3(na[0][0],na[0][1],na[0][2]),geom.Vec3(0,1,0))<1e-10)
- self.assertTrue(geom.Distance(geom.Vec3(na[1][0],na[1][1],na[1][2]),geom.Vec3(0,2,0))<1e-10)
- self.assertTrue(geom.Distance(geom.Vec3(na[2][0],na[2][1],na[2][2]),geom.Vec3(0,3,0))<1e-10)
- self.assertTrue(geom.Distance(geom.Vec3(na[3][0],na[3][1],na[3][2]),geom.Vec3(0,4,0))<1e-10)
+ self.assertTrue(geom.Distance(v2v(na[0]),geom.Vec3(0,1,0))<1e-10)
+ self.assertTrue(geom.Distance(v2v(na[1]),geom.Vec3(0,2,0))<1e-10)
+ self.assertTrue(geom.Distance(v2v(na[2]),geom.Vec3(0,3,0))<1e-10)
+ self.assertTrue(geom.Distance(v2v(na[3]),geom.Vec3(0,4,0))<1e-10)
if __name__== '__main__':
unittest.main()
--
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