From a23842e399f1a7c07c0047d519651ac07498e886 Mon Sep 17 00:00:00 2001
From: Ansgar Philippsen <ansgar.philippsen@gmail.com>
Date: Fri, 13 Jul 2012 11:45:02 -0400
Subject: [PATCH] added in-place coord group transform; fixed
Transform::ApplyAxisRotation
---
modules/mol/base/src/coord_group.cc | 11 ++++++++++-
modules/mol/base/src/coord_group.hh | 6 +++++-
modules/mol/base/src/coord_source.cc | 21 ++++++++++++++++-----
modules/mol/base/src/coord_source.hh | 4 ++++
modules/mol/base/src/transform.cc | 2 +-
modules/mol/base/tests/test_coord_group.cc | 12 ++++++++++++
6 files changed, 48 insertions(+), 8 deletions(-)
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index bd56a4e00..4fe6677ee 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -254,6 +254,15 @@ CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected, int first,
}
return filtered_cg;
}
-
+
+void CoordGroupHandle::ApplyTransform(const mol::Transform& tf)
+{
+ this->CheckValidity();
+ if (source_->IsMutable()) {
+ source_->ApplyTransform(tf);
+ } else {
+ throw IntegrityError("Cannot apply transform, CoordGroup is immutable");
+ }
+}
}} // ns
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index bf049aadd..74fffcb6c 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -30,6 +30,8 @@
namespace ost { namespace mol {
+class Transform;
+
/// \brief coordinate group, for trajectories and such
class DLLEXPORT_OST_MOL CoordGroupHandle {
public:
@@ -105,7 +107,9 @@ public:
/// \brief return a filtered coord group, containing only the atoms in the
/// view
CoordGroupHandle Filter(const EntityView& selected,int first=0,int last=-1) const;
-
+
+ /// \brief apply in-place transform to each coordinate in each frame
+ void ApplyTransform(const Transform& tf);
private:
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index 335117423..06b7864b7 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -21,13 +21,12 @@
Author: Marco Biasini
*/
#include <ost/log.hh>
-#include <ost/mol/atom_handle.hh>
-#include <ost/mol/xcs_editor.hh>
-#include <ost/mol/in_mem_coord_source.hh>
-
+#include "atom_handle.hh"
+#include "xcs_editor.hh"
+#include "in_mem_coord_source.hh"
+#include "transform.hh"
#include "coord_source.hh"
-
namespace ost { namespace mol {
@@ -166,4 +165,16 @@ geom::Vec3 CoordSource::GetAtomPos(uint frame, AtomHandle atom) const
return geom::Vec3();
}
+void CoordSource::ApplyTransform(const Transform& tf)
+{
+ if(!mutable_) return;
+ size_t frame_count=GetFrameCount();
+ for(size_t n=0;n<frame_count;++n) {
+ CoordFramePtr cfp=GetFrame(n);
+ for(CoordFrame::iterator it=cfp->begin();it!=cfp->end();++it) {
+ *it=tf.Apply(*it);
+ }
+ }
+}
+
}} // ns
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index a50f256a1..a33162abc 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -31,6 +31,7 @@
namespace ost { namespace mol {
class CoordSource;
+class Transform;
typedef boost::shared_ptr<CoordSource> CoordSourcePtr;
@@ -80,6 +81,9 @@ public:
virtual void AddFrame(const std::vector<geom::Vec3>& coords) = 0;
virtual void AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& cell_size,const geom::Vec3& cell_angles) = 0;
virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords) = 0;
+
+ void ApplyTransform(const Transform& tf);
+
protected:
void SetMutable(bool flag);
private:
diff --git a/modules/mol/base/src/transform.cc b/modules/mol/base/src/transform.cc
index cb76e7196..ba1e59258 100644
--- a/modules/mol/base/src/transform.cc
+++ b/modules/mol/base/src/transform.cc
@@ -122,7 +122,7 @@ void Transform::ApplyZAxisRotation(float delta)
void Transform::ApplyAxisRotation(float delta, const Vec3& axis)
{
- rot_=rot_*AxisRotation(rot_*axis, delta*P_180);
+ rot_=rot_*AxisRotation(axis, delta*P_180);
update_tm();
}
diff --git a/modules/mol/base/tests/test_coord_group.cc b/modules/mol/base/tests/test_coord_group.cc
index 7e3d38598..3c0cdc18f 100644
--- a/modules/mol/base/tests/test_coord_group.cc
+++ b/modules/mol/base/tests/test_coord_group.cc
@@ -80,6 +80,18 @@ BOOST_AUTO_TEST_CASE(coord_group)
BOOST_CHECK(ab.GetPos()==geom::Vec3(-14,-15,-16));
BOOST_CHECK(ac.GetPos()==geom::Vec3(-17,-18,-19));
BOOST_CHECK(ad.GetPos()==geom::Vec3(9,10,11));
+
+ Transform tf;
+ tf.ApplyXAxisRotation(17.0);
+ tf.ApplyYAxisRotation(-135.0);
+ tf.ApplyZAxisRotation(234.0);
+ tf.SetCenter(geom::Vec3(-7.3,1.2,5.5));
+ tf.SetTrans(geom::Vec3(14.5,-87.1,22.2));
+
+ cg.ApplyTransform(tf);
+ for(size_t i=0;i<3;++i) {
+ BOOST_CHECK_CLOSE(geom::Distance(cg.GetAtomPos(1,alist[i]),tf.Apply(clist[i])),Real(0),1e-6);
+ }
}
BOOST_AUTO_TEST_SUITE_END();
--
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