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Commit f5defe19 authored by Tobias Schmidt's avatar Tobias Schmidt
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added option to rotate all atoms of a torsion or just specified one; removed... 

added option to rotate all atoms of a torsion or just specified one; removed legacy Set/RotateAngle from TorsionHandle which is in ICSEditor
parent 1e7a150d
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with 180 additions and 57 deletions
modules/mol/base/pymod/export_editors.cc
+ 14
− 8
View file @ f5defe19
......@@ -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)
;
......
modules/mol/base/pymod/export_torsion.cc
+ 1
− 7
View file @ f5defe19
......@@ -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))
;
......
modules/mol/base/src/ics_editor.cc
+ 16
− 8
View file @ f5defe19
......@@ -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
modules/mol/base/src/ics_editor.hh
+ 7
− 4
View file @ f5defe19
......@@ -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();
......
modules/mol/base/src/impl/dihedral.hh
+ 1
− 1
View file @ f5defe19
......@@ -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;
......
modules/mol/base/src/impl/torsion_impl.cc
+ 4
− 4
View file @ f5defe19
......@@ -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
modules/mol/base/src/torsion_handle.cc
+ 0
− 12
View file @ f5defe19
......@@ -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_)
......
modules/mol/base/src/torsion_handle.hh
+ 0
− 12
View file @ f5defe19
......@@ -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_;
}
......
modules/mol/base/tests/test_ics.cc
+ 137
− 1
View file @ f5defe19
......@@ -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()
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