diff --git a/modules/mol/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 22c485bc0ec5a20295348afad99a0b2be299c231..5e7861c2521f05cfb875c168cbf8a6b51f3303e4 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -32,4 +32,4 @@ def MergeCoordGroups(*coord_groups):
cg=CreateCoordGroup(coord_groups[0].atoms)
for coord_group in coord_groups:
cg.AddFrames(coord_group)
- return cg
\ No newline at end of file
+ return cg
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 87c19665b6f50e7231d5088061980443ca6e8de1..e411bc30a9dbb4d4dc24f273ec461ed5019b08af 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -58,10 +58,6 @@ 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)
@@ -70,12 +66,12 @@ void set_pos2_nc_t(XCSEditor& e, const AtomHandleList& alist, PyArrayObject* na)
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)))));
+ 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)))));
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,1))),
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,2)))));
}
}
}
@@ -84,46 +80,46 @@ 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) {
+
+ if(PyArray_NDIM(na)!=2 || PyArray_DIM(na,0)!=int(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)));
+ e.SetAtomOriginalPos(alist,reinterpret_cast<float*>(PyArray_DATA(na)));
} else {
- e.SetAtomTransformedPos(alist,reinterpret_cast<float*>(PyArray_DATA(na)));
+ 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)));
+ e.SetAtomOriginalPos(alist,reinterpret_cast<double*>(PyArray_DATA(na)));
} else {
- e.SetAtomTransformedPos(alist,reinterpret_cast<double*>(PyArray_DATA(na)));
+ e.SetAtomTransformedPos(alist,reinterpret_cast<double*>(PyArray_DATA(na)));
}
} else {
- throw std::runtime_error("excpected a numpy array of type float or double");
+ throw std::runtime_error("expected a numpy array of type float or double");
return;
}
} else {
// non-contiguous
#if 0
- throw std::runtime_error("excpected contiguous numpy array");
+ throw std::runtime_error("expected 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");
+ throw std::runtime_error("expected a numpy array of type float or double");
return;
}
#endif
@@ -131,27 +127,63 @@ void set_pos2_t(XCSEditor& e, const AtomHandleList& alist, object pyobj)
}
#endif
-void set_t_pos2(XCSEditor& e, const AtomHandleList& alist, object pyobj)
+void set_pos(XCSEditor& e, object o1, object o2, bool trans)
{
+ extract<AtomHandle> eah(o1);
+ extract<geom::Vec3> ev3(o2);
+ if(eah.check() && ev3.check()) {
+ if(trans) {
+ e.SetAtomTransformedPos(eah(),ev3());
+ } else {
+ e.SetAtomOriginalPos(eah(),ev3());
+ }
+ return;
+ }
+
#if OST_NUMPY_SUPPORT_ENABLED
- set_pos2_t<false>(e,alist,pyobj);
+
+ extract<AtomHandleList> eal(o1);
+ if(eal.check()) {
+ if(trans) {
+ set_pos2_t<false>(e,eal(),o2);
+ } else {
+ set_pos2_t<true>(e,eal(),o2);
+ }
+ return;
+ }
+
+ std::map<unsigned long,AtomHandle> amap;
+ EntityHandle eh=e.GetEntity();
+ for(AtomHandleIter ait=eh.AtomsBegin(), aite=eh.AtomsEnd(); ait!=aite; ++ait) {
+ amap[(*ait).GetIndex()]=*ait;
+ }
+
+ AtomHandleList alist;
+ for(int i=0;i<len(o1);++i) {
+ int gid = extract<int>(o1[i]);
+ std::map<unsigned long,AtomHandle>::iterator ait=amap.find(static_cast<unsigned long>(gid));
+ alist.push_back(ait==amap.end() ? AtomHandle() : ait->second);
+ }
+
+ if(trans) {
+ set_pos2_t<false>(e,alist,o2);
+ } else {
+ set_pos2_t<true>(e,alist,o2);
+ }
+
#else
- throw std::runtime_error("SetAtomTransformedPos(alist,ndarray) disabled, since numpy support is not compiled in");
+ throw std::runtime_error("SetAtom*Pos(...,ndarray) not available, because numpy support not compiled in");
#endif
}
-void set_o_pos2(XCSEditor& e, const AtomHandleList& alist, object pyobj)
+void set_o_pos(XCSEditor& e, object o1, object o2)
{
-#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
+ set_pos(e,o1,o2,false);
}
-void set_pos2(XCSEditor& e, const AtomHandleList& alist, object pyobj)
+void set_t_pos(XCSEditor& e, object o1, object o2)
{
- set_t_pos2(e,alist,pyobj);
+ set_pos(e,o1,o2,true);
}
}
@@ -186,12 +218,9 @@ void export_Editors()
;
class_<XCSEditor, bases<EditorBase> >("XCSEditor", no_init)
- .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("SetAtomPos", set_t_pos)
+ .def("SetAtomTransformedPos", set_t_pos)
+ .def("SetAtomOriginalPos", set_o_pos)
.def("ApplyTransform", &XCSEditor::ApplyTransform)
.def("SetTransform", &XCSEditor::SetTransform)
.def("UpdateICS", &XCSEditor::UpdateICS)
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 5ab540f31087e2e6dd18a2161b3525a100d48890..3c1e071ee56b34e4cf90f17acf86f4ef46af6f67 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -196,11 +196,6 @@ TorsionHandle EditorBase::AddTorsion(const String& name, const AtomHandle& a1,
}
-EditMode EditorBase::GetMode() const
-{
- return mode_;
-}
-
void EditorBase::UpdateTrace()
{
if (mode_==UNBUFFERED_EDIT) {
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index fd6c63d2a718715ee14fd44128ef88c25a2eff0b..b62aa96252165e0a897d4bc21f6d2dca2ee756bc 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -190,8 +190,11 @@ public:
void ReorderAllResidues();
/// \brief Get edit mode of editor
- EditMode GetMode() const;
+ EditMode GetMode() const {return mode_;}
+ /// \ brief return entity this editor works on
+ EntityHandle GetEntity() const {return ent_;}
+
/// \brief change the name of the atom to the new name
void RenameAtom(AtomHandle atom, const String& new_name);
protected:
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 559a2cf109fd1a1089d38ead2b60bc4781249584..fff9f6efc306b77df8ca9aa6f6b804f1480329c0 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -137,7 +137,7 @@ public:
///
/// The two iterators returned by ResiduesBegin() and ResiduesEnd() form a
/// half-closed range. It is cheaper to cache the iterator returned by
- /// ResiduesEnd() than to call ResiduesEnd() after very loop, i.e. like
+ /// ResiduesEnd() than to call ResiduesEnd() after every loop, i.e. like
/// \code
/// // e is an instance of EntityHandle
/// for (ResidueHandleIter i=e.ResiduesBegin(), x=e.ResiduesEnd(); i!=x; ++i) {
diff --git a/modules/mol/base/src/xcs_editor.cc b/modules/mol/base/src/xcs_editor.cc
index 41d6be611684698acffeb0775d865e64ef31c8e0..5a4a6063d92dcf4c58df294a2924baa1b2dbbb23 100644
--- a/modules/mol/base/src/xcs_editor.cc
+++ b/modules/mol/base/src/xcs_editor.cc
@@ -68,7 +68,7 @@ XCSEditor& XCSEditor::operator=(const XCSEditor& rhs)
}
void XCSEditor::SetAtomTransformedPos(const AtomHandle& atom,
- const geom::Vec3& position)
+ const geom::Vec3& position)
{
CheckHandleValidity(atom);
atom.Impl()->TransformedPos()=position;
@@ -88,15 +88,17 @@ namespace {
{
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()));
+ if(ait->IsValid()) {
+ 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]);
+ if(has_tf) {
+ ait->Impl()->OriginalPos()=ait->Impl()->TransformedPos();
+ } else {
+ ait->Impl()->OriginalPos() = geom::Vec3(ent->GetInvTransfMatrix()*geom::Vec4(ait->Impl()->TransformedPos()));
+ }
}
+ positions+=3;
}
ent->MarkICSDirty();
ent->MarkOrganizerDirty();
@@ -116,7 +118,7 @@ void XCSEditor::SetAtomTransformedPos(const AtomHandleList& alist, double *posit
}
void XCSEditor::SetAtomOriginalPos(const AtomHandle& atom,
- const geom::Vec3& position)
+ const geom::Vec3& position)
{
CheckHandleValidity(atom);
atom.Impl()->OriginalPos()=position;
@@ -136,15 +138,17 @@ namespace {
{
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()));
+ if(ait->IsValid()) {
+ 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]);
+ if(has_tf) {
+ ait->Impl()->TransformedPos()=ait->Impl()->OriginalPos();
+ } else {
+ ait->Impl()->TransformedPos() = geom::Vec3(ent->GetTransfMatrix()*geom::Vec4(ait->Impl()->OriginalPos()));
+ }
}
+ positions+=3;
}
ent->MarkICSDirty();
ent->MarkOrganizerDirty();
diff --git a/modules/mol/base/tests/test_numpy.py b/modules/mol/base/tests/test_numpy.py
index cad6f764f3308fd26cc702686e6c7575aee877b6..1255425f85ad0bfed89b238f7264d7ec394b367d 100644
--- a/modules/mol/base/tests/test_numpy.py
+++ b/modules/mol/base/tests/test_numpy.py
@@ -7,6 +7,9 @@ import numpy
def v2v(v):
return geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
+def dd(v1,v2):
+ return geom.Distance(v1,v2)<1e-8
+
class TestNumpy(unittest.TestCase):
def setUp(self):
pass
@@ -17,32 +20,41 @@ 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)
+ self.assertEqual(a0.GetIndex(),0)
a1=ed.InsertAtom(re,"B",geom.Vec3(1,0,0))
- self.assertTrue(a1.GetIndex()==1)
+ self.assertEqual(a1.GetIndex(),1)
a2=ed.InsertAtom(re,"C",geom.Vec3(2,0,0))
- self.assertTrue(a2.GetIndex()==2)
+ self.assertEqual(a2.GetIndex(),2)
a3=ed.InsertAtom(re,"D",geom.Vec3(3,0,0))
- self.assertTrue(a3.GetIndex()==3)
+ self.assertEqual(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)
+ self.assertTrue(dd(a0.pos,geom.Vec3(0,0,0)))
+ self.assertTrue(dd(a1.pos,geom.Vec3(1,0,0)))
+ self.assertTrue(dd(a2.pos,geom.Vec3(2,0,0)))
+ self.assertTrue(dd(a3.pos,geom.Vec3(3,0,0)))
- ed.SetAtomTransformedPos(entity.GetAtomList(),numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]], dtype=numpy.float32))
+ 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)
- self.assertTrue(geom.Distance(a2.pos,geom.Vec3(0,3,0))<1e-10)
- self.assertTrue(geom.Distance(a3.pos,geom.Vec3(0,4,0))<1e-10)
+ self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+ self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+ self.assertTrue(dd(a2.pos,geom.Vec3(0,3,0)))
+ self.assertTrue(dd(a3.pos,geom.Vec3(0,4,0)))
na=entity.positions
- 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)
+ self.assertTrue(dd(v2v(na[0]),geom.Vec3(0,1,0)))
+ self.assertTrue(dd(v2v(na[1]),geom.Vec3(0,2,0)))
+ self.assertTrue(dd(v2v(na[2]),geom.Vec3(0,3,0)))
+ self.assertTrue(dd(v2v(na[3]),geom.Vec3(0,4,0)))
+
+ ed.SetAtomTransformedPos([3,99,2],
+ numpy.array([[0,0,-3],[-1,-1,-1],[0,0,-2]], dtype=numpy.float32))
+
+ self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+ self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+ self.assertTrue(dd(a2.pos,geom.Vec3(0,0,-2)))
+ self.assertTrue(dd(a3.pos,geom.Vec3(0,0,-3)))
if __name__== '__main__':
unittest.main()