diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 4d3b42197fcc22a8d98a6d4e2e1b58e2d34bfdb7..2a59feef9f8527366fdb3cd122d8e01fc87abf38 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -48,15 +48,15 @@ ResidueHandle (EditorBase::*append_a)(ChainHandle ch,
ResidueHandle (EditorBase::*append_b)(ChainHandle ch, const ResidueKey&,
const ResNum&)=&EditorBase::AppendResidue;
-void (ICSEditor::*set_torsion_a)(TorsionHandle, Real)=&ICSEditor::SetTorsionAngle;
+void (ICSEditor::*set_torsion_a)(TorsionHandle, Real, bool)=&ICSEditor::SetTorsionAngle;
void (ICSEditor::*set_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
- Real)=&ICSEditor::SetTorsionAngle;
+ Real, bool)=&ICSEditor::SetTorsionAngle;
-void (ICSEditor::*rotate_torsion_a)(TorsionHandle, Real)=&ICSEditor::RotateTorsionAngle;
+void (ICSEditor::*rotate_torsion_a)(TorsionHandle, Real, bool)=&ICSEditor::RotateTorsionAngle;
void (ICSEditor::*rotate_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
- Real)=&ICSEditor::RotateTorsionAngle;
+ Real, bool)=&ICSEditor::RotateTorsionAngle;
#if OST_NUMPY_SUPPORT_ENABLED
template<typename T, bool O>
@@ -234,10 +234,16 @@ void export_Editors()
class_<ICSEditor, bases<EditorBase> >("ICSEditor", no_init)
.def("SetAngle", &ICSEditor::SetAngle)
.def("SetBondLength", &ICSEditor::SetBondLength)
- .def("SetTorsionAngle", set_torsion_a)
- .def("SetTorsionAngle", set_torsion_b)
- .def("RotateTorsionAngle", rotate_torsion_a)
- .def("RotateTorsionAngle", rotate_torsion_b)
+ .def("SetTorsionAngle", set_torsion_a,
+ (arg("torsion"),arg("angle"), arg("update_others")=true))
+ .def("SetTorsionAngle", set_torsion_b,
+ (arg("atom_a"), arg("atom_b"), arg("atom_c"), arg("atom_d"),
+ arg("angle"), arg("update_others")))
+ .def("RotateTorsionAngle", rotate_torsion_a,
+ (arg("torsion"),arg("angle"), arg("update_others")=true))
+ .def("RotateTorsionAngle", rotate_torsion_b,
+ (arg("atom_a"), arg("atom_b"), arg("atom_c"), arg("atom_d"),
+ arg("angle"), arg("update_others")))
.def("UpdateXCS", &ICSEditor::UpdateXCS)
.def("__exit__", &ICSEditor::UpdateXCS)
;
diff --git a/modules/mol/base/pymod/export_torsion.cc b/modules/mol/base/pymod/export_torsion.cc
index e7b45e0fd4c3afb385410f688267e05406351250..fbf9e2b726880b9e56a430e3def0aa50f0c1fd7b 100644
--- a/modules/mol/base/pymod/export_torsion.cc
+++ b/modules/mol/base/pymod/export_torsion.cc
@@ -49,14 +49,8 @@ void export_Torsion()
.add_property("third", &TorsionHandle::GetThird)
.add_property("fourth", &TorsionHandle::GetFourth)
.def("IsValid", &TorsionHandle::IsValid)
- .def("SetAngle", &TorsionHandle::SetAngle)
.def("GetAngle", &TorsionHandle::GetAngle)
- .def("RotateAngle", &TorsionHandle::RotateAngle,
- X_rotate_angle_overloads(args("angle", "up")))
- .add_property("angle", &TorsionHandle::GetAngle,
- &TorsionHandle::SetAngle)
- .def("SetAngle", &TorsionHandle::SetAngle,
- X_set_angle_overloads(args("angle", "up")))
+ .add_property("angle", &TorsionHandle::GetAngle)
.def(self_ns::str(self))
;
diff --git a/modules/mol/base/src/ics_editor.cc b/modules/mol/base/src/ics_editor.cc
index c374a0f09697accb0f56fee925200d3b03df4879..910c7fd85365f747e12eed613147bde49b2a4fdb 100644
--- a/modules/mol/base/src/ics_editor.cc
+++ b/modules/mol/base/src/ics_editor.cc
@@ -23,6 +23,7 @@
#include "impl/torsion_impl.hh"
#include "impl/entity_impl.hh"
#include "impl/connector_impl.hh"
+#include "impl/atom_impl.hh"
/*
Author: Marco Biasini
*/
@@ -96,18 +97,20 @@ bool ICSEditor::SetAngle(const AtomHandle& atom_a, const AtomHandle& atom_b,
return return_value;
}
-void ICSEditor::SetTorsionAngle(TorsionHandle torsion, Real angle)
+void ICSEditor::SetTorsionAngle(TorsionHandle torsion, Real angle,
+ bool update_others)
{
CheckHandleValidity(torsion);
- torsion.Impl()->SetAngle(angle, false);
+ torsion.Impl()->SetAngle(angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
-void ICSEditor::RotateTorsionAngle(TorsionHandle torsion, Real angle)
+void ICSEditor::RotateTorsionAngle(TorsionHandle torsion, Real angle,
+ bool update_others)
{
CheckHandleValidity(torsion);
- torsion.Impl()->RotateAngle(angle, false);
+ torsion.Impl()->RotateAngle(angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
@@ -116,7 +119,9 @@ void ICSEditor::RotateTorsionAngle(TorsionHandle torsion, Real angle)
void ICSEditor::RotateTorsionAngle(const AtomHandle& atom_a,
const AtomHandle& atom_b,
const AtomHandle& atom_c,
- const AtomHandle& atom_d, Real angle)
+ const AtomHandle& atom_d,
+ Real angle,
+ bool update_others)
{
CheckHandleValidity(atom_a);
CheckHandleValidity(atom_b);
@@ -124,7 +129,7 @@ void ICSEditor::RotateTorsionAngle(const AtomHandle& atom_a,
CheckHandleValidity(atom_d);
impl::Dihedral d(atom_a.Impl(), atom_b.Impl(), atom_c.Impl(), atom_d.Impl());
Real cur_angle=d.GetAngleICS();
- d.SetAngleICS(cur_angle+angle);
+ d.SetAngleICS(cur_angle+angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
@@ -133,16 +138,19 @@ void ICSEditor::RotateTorsionAngle(const AtomHandle& atom_a,
void ICSEditor::SetTorsionAngle(const AtomHandle& atom_a,
const AtomHandle& atom_b,
const AtomHandle& atom_c,
- const AtomHandle& atom_d, Real angle)
+ const AtomHandle& atom_d,
+ Real angle,
+ bool update_others)
{
CheckHandleValidity(atom_a);
CheckHandleValidity(atom_b);
CheckHandleValidity(atom_c);
CheckHandleValidity(atom_d);
impl::Dihedral d(atom_a.Impl(), atom_b.Impl(), atom_c.Impl(), atom_d.Impl());
- d.SetAngleICS(angle, false);
+ d.SetAngleICS(angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
+
}} // ns
diff --git a/modules/mol/base/src/ics_editor.hh b/modules/mol/base/src/ics_editor.hh
index 9643336949dbf2fe700187feee372f5baca235cc..eb51807432d2a9aa3f2ddeb08b48c5a8ea88d073 100644
--- a/modules/mol/base/src/ics_editor.hh
+++ b/modules/mol/base/src/ics_editor.hh
@@ -74,19 +74,22 @@ public:
/// bonds untouched, use the SetDihedralAngle() function
///
/// \sa RotateTorsionAngle
- void SetTorsionAngle(TorsionHandle torsion, Real angle);
+ void SetTorsionAngle(TorsionHandle torsion, Real angle,
+ bool update_others=true);
/// \brief rotate torsion angle
- void RotateTorsionAngle(TorsionHandle torsion, Real delta);
+ void RotateTorsionAngle(TorsionHandle torsion, Real delta,
+ bool update_others=true);
void RotateTorsionAngle(const AtomHandle& atom_a,
const AtomHandle& atom_b,
const AtomHandle& atom_c,
const AtomHandle& atom_d,
- Real angle);
+ Real angle,
+ bool update_others=true);
void SetTorsionAngle(const AtomHandle& atom_a, const AtomHandle& atom_b,
const AtomHandle& atom_c, const AtomHandle& atom_d,
- Real angle);
+ Real angle, bool update_others=true);
/// \brief immediately update external coordinate system
void UpdateXCS();
diff --git a/modules/mol/base/src/impl/dihedral.hh b/modules/mol/base/src/impl/dihedral.hh
index 2996205ba7e06cfd53c2a45829335c365a034d28..a722c93e60ff4b8d015d5f5bb97bc7d1b3a9709c 100644
--- a/modules/mol/base/src/impl/dihedral.hh
+++ b/modules/mol/base/src/impl/dihedral.hh
@@ -52,7 +52,7 @@ public:
/// \param update_other
/// If true, connectors of atom3 are updated accordingly, otherwise
/// they will be left untouched
- void SetAngleICS(Real angle, bool update_other=false);
+ void SetAngleICS(Real angle, bool update_other);
geom::Vec3 GetPos() const;
geom::Vec3 GetOriginalPos() const;
diff --git a/modules/mol/base/src/impl/torsion_impl.cc b/modules/mol/base/src/impl/torsion_impl.cc
index 744d648f33f3139d1bb03c7327f8ef0a9a77b7f1..9f9ffcdd9b74fa46969ed70f934b1c0a434e4602 100644
--- a/modules/mol/base/src/impl/torsion_impl.cc
+++ b/modules/mol/base/src/impl/torsion_impl.cc
@@ -48,8 +48,8 @@ Real TorsionImpl::GetAngle() const {
}
}
-void TorsionImpl::SetAngle(Real angle, bool up) {
- this->SetAngleICS(angle, true);
+void TorsionImpl::SetAngle(Real angle, bool update_others) {
+ this->SetAngleICS(angle, update_others);
}
void TorsionImpl::Apply(EntityVisitor& v) {
@@ -57,8 +57,8 @@ void TorsionImpl::Apply(EntityVisitor& v) {
v.VisitTorsion(TorsionHandle(shared_from_this()));
}
-void TorsionImpl::RotateAngle(Real angle, bool up) {
- this->SetAngle(this->GetAngleICS()+angle, up);
+void TorsionImpl::RotateAngle(Real angle, bool update_others) {
+ this->SetAngle(this->GetAngleICS()+angle, update_others);
}
}}} // ns
diff --git a/modules/mol/base/src/torsion_handle.cc b/modules/mol/base/src/torsion_handle.cc
index c4bac5ff1455e70cf4ba5f3ba51c650d9cea3334..2830bc8211ef30477693f3610b76b46fdf79d27e 100644
--- a/modules/mol/base/src/torsion_handle.cc
+++ b/modules/mol/base/src/torsion_handle.cc
@@ -95,18 +95,6 @@ Real TorsionHandle::GetAngle() const
this->CheckValidity();
return impl_->GetAngle();
}
-
-void TorsionHandle::SetAngle(Real a, bool up)
-{
- this->CheckValidity();
- impl_->SetAngle(a, up);
-}
-
-void TorsionHandle::RotateAngle(Real angle, bool up)
-{
- this->CheckValidity();
- impl_->RotateAngle(angle, up);
-}
void TorsionHandle::CheckValidity() const {
if (!impl_)
diff --git a/modules/mol/base/src/torsion_handle.hh b/modules/mol/base/src/torsion_handle.hh
index 856cd67e731983ee898213101d52764b214ddb07..06f7e7bf0eb7283318617f8fd0a4f222718f87ad 100644
--- a/modules/mol/base/src/torsion_handle.hh
+++ b/modules/mol/base/src/torsion_handle.hh
@@ -87,18 +87,6 @@ public:
/// \brief get position, i.e midpoint between the second and third atom (original coordinates)
geom::Vec3 GetOriginalPos() const;
- /// \brief set absolute torsion angle
- ///
- /// All connectors at the third atom (A3) will be adjusted accordingly. If
- /// you only want to adjust the bond between A3 and A4, and leave the other
- /// bonds untouched, use the ost::SetDihedralAngle() function
- ///
- /// \sa RotateAngle
- void SetAngle(Real a, bool up=true);
-
- /// relative rotation, either upstream or downstream
- void RotateAngle(Real angle, bool up=true);
-
impl::TorsionImplP& Impl() {
return impl_;
}
diff --git a/modules/mol/base/tests/test_ics.cc b/modules/mol/base/tests/test_ics.cc
index 8c26db5d96c1738e8454487366989ca1041255c1..f7ffd372289be951b9ecdec7968e375c15a8ab0a 100644
--- a/modules/mol/base/tests/test_ics.cc
+++ b/modules/mol/base/tests/test_ics.cc
@@ -59,6 +59,37 @@ struct Structure {
AtomHandle a5;
};
+struct TorsionStructure {
+ TorsionStructure()
+ {
+ e=CreateEntity();
+ ICSEditor editor=e.EditICS();
+ c=editor.InsertChain("A");
+ r=editor.AppendResidue(c, "TORSTIN");
+ a1=editor.InsertAtom(r, "X1", geom::Vec3( 0.0, -1.0, 0.0));
+ a2=editor.InsertAtom(r, "X2", geom::Vec3( 1.0, 0.0, 0.0));
+ a3=editor.InsertAtom(r, "X3", geom::Vec3( 2.0, 0.0, 0.0));
+ a4=editor.InsertAtom(r, "X4", geom::Vec3( 3.0, 1.0, 0.0));
+ a5=editor.InsertAtom(r, "X5", geom::Vec3( 3.0, -1.0, 0.0));
+ editor.Connect(a1, a2);
+ editor.Connect(a2, a3);
+ editor.Connect(a3, a4);
+ editor.Connect(a3, a5);
+ t1 = editor.AddTorsion("T1", a1, a2, a3, a4);
+ t2 = editor.AddTorsion("T2", a1, a2, a3, a5);
+ }
+ EntityHandle e;
+ ChainHandle c;
+ ResidueHandle r;
+ AtomHandle a1;
+ AtomHandle a2;
+ AtomHandle a3;
+ AtomHandle a4;
+ AtomHandle a5;
+ TorsionHandle t1;
+ TorsionHandle t2;
+};
+
const static Real EPSILON=0.000001;
Real angle_xcs(AtomHandle a1, AtomHandle a2, AtomHandle a3) {
@@ -72,6 +103,111 @@ bool test_angle(Real a, Real e) {
BOOST_AUTO_TEST_SUITE( mol_base )
+BOOST_AUTO_TEST_CASE(ics_settorsion_unbuffered)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::UNBUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), M_PI, eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI, eps);
+ e.SetTorsionAngle(s.t2,M_PI/4);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), -M_PI+M_PI/4, eps);
+ e.SetTorsionAngle(s.t1,-M_PI/4);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), -M_PI/4, eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), 3/4.*M_PI, eps);
+ e.RotateTorsionAngle(s.t1, M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(std::abs(s.t2.GetAngle()), M_PI, eps);
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_buffered)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::BUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), M_PI, eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI, eps);
+ e.SetTorsionAngle(s.t2,M_PI/4);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), -M_PI+M_PI/4, eps);
+ e.SetTorsionAngle(s.t1,-M_PI/4);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), -M_PI/4, eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), 3/4.*M_PI, eps);
+ e.RotateTorsionAngle(s.t1, M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(std::abs(s.t2.GetAngle()), M_PI, eps);
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_unbuffered_update_others)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::UNBUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), M_PI, eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t2,M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,-M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), -M_PI/4, eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+ e.RotateTorsionAngle(s.t1, M_PI/4,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_buffered_update_others)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::BUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), M_PI, eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t2,M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,-M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), -M_PI/4, eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+ e.RotateTorsionAngle(s.t1, M_PI/4,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_linear_unbuffered)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::UNBUFFERED_EDIT);
+ e.SetAngle(s.a2,s.a3,s.a4,M_PI);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t2,M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+ e.SetTorsionAngle(s.t1,-M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.RotateTorsionAngle(s.t1, M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), M_PI/4, eps);
+}
BOOST_AUTO_TEST_CASE(ics_angle_trivia)
{
@@ -147,4 +283,4 @@ BOOST_AUTO_TEST_CASE(ics_get_angle)
<< " found");
}
-BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
+BOOST_AUTO_TEST_SUITE_END()