From 378d6c4f0379358d6ccc9c9519dadb2d045aed99 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Fri, 18 May 2012 17:14:27 -0400
Subject: [PATCH] Added a function to fit a cylinder to a selection on the
CoordFrame level
---
modules/mol/base/pymod/export_coord_frame.cc | 3 ++-
modules/mol/base/src/coord_frame.cc | 12 +++++++++++-
modules/mol/base/src/coord_frame.hh | 1 +
3 files changed, 14 insertions(+), 2 deletions(-)
diff --git a/modules/mol/base/pymod/export_coord_frame.cc b/modules/mol/base/pymod/export_coord_frame.cc
index e4c02c926..1f417064d 100644
--- a/modules/mol/base/pymod/export_coord_frame.cc
+++ b/modules/mol/base/pymod/export_coord_frame.cc
@@ -41,7 +41,7 @@ Real (CoordFrame::*get_alpha)(const mol::EntityView& segment) = &CoordFrame::Get
geom::Line3 (CoordFrame::*get_odr_line)(const mol::EntityView& view1) = &CoordFrame::GetODRLine;
geom::Line3 (CoordFrame::*get_odr_line2)() = &geom::Vec3List::GetODRLine;
geom::Plane (CoordFrame::*get_odr_plane)(const mol::EntityView& view1) = &CoordFrame::GetODRPlane;
-
+geom::Line3 (CoordFrame::*fit_cylinder)(const mol::EntityView& view1) = &CoordFrame::FitCylinder;
void export_CoordFrame()
{
@@ -61,6 +61,7 @@ void export_CoordFrame()
.def("GetODRLine",get_odr_line)
.def("GetODRLine",get_odr_line2)
.def("GetAlphaHelixContent",get_alpha)
+ .def("FitCylinder",fit_cylinder)
;
def("CreateCoordFrame",CreateCoordFrame);
}
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 5e2e7812b..71b9ed9a6 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -325,7 +325,17 @@ namespace ost { namespace mol {
center/=atoms_pos_list.size();
return atoms_pos_list.FitCylinder(initial_axis,center);
}
-
+
+ geom::Line3 CoordFrame::FitCylinder(const mol::EntityView& view1){
+ // Return a lin which is the axis of the best fit cylinder to the CA atoms
+ // of the EntityView.
+ // It is assumed that we fit an alpha-helix and that the CA atoms are oredered sequentially
+ CheckHandleValidity(view1);
+ std::vector<unsigned long> indices_ca;
+ GetCaIndices(view1, indices_ca);
+ return CoordFrame::FitCylinder(indices_ca);
+ }
+
Real CoordFrame::GetAlphaHelixContent(const mol::EntityView& segment){
//Returns the percentage of residues in the EntityView (segment) that are in an alpha-helix
//Each residue is assigned as being in an alpha-helix or not, based on and backbone torsion angles
diff --git a/modules/mol/base/src/coord_frame.hh b/modules/mol/base/src/coord_frame.hh
index 5458f4cef..98eb0c25c 100644
--- a/modules/mol/base/src/coord_frame.hh
+++ b/modules/mol/base/src/coord_frame.hh
@@ -78,6 +78,7 @@ public:
geom::Line3 GetODRLine(const mol::EntityView& view1);
geom::Plane GetODRPlane(const mol::EntityView& view1);
geom::Line3 FitCylinder(std::vector<unsigned long>& indices_ca);
+ geom::Line3 FitCylinder(const mol::EntityView& view1);
Real GetAlphaHelixContent(std::vector<unsigned long>& indices_ca, std::vector<unsigned long>& indices_c,
std::vector<unsigned long>& indices_o, std::vector<unsigned long>& indices_n);
Real GetAlphaHelixContent(const mol::EntityView& segment);
--
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