From 949c8e2090ca1095aa77c183617bbfc65933c8cb Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Mon, 3 Jan 2011 16:00:46 +0100
Subject: [PATCH] forward GetCAlphaCBetaPos
---
modules/qa/src/impl/reduced_impl.cc | 57 +++++++++++++++--------------
modules/qa/src/impl/reduced_impl.hh | 5 ++-
modules/qa/src/reduced_potential.cc | 7 ++++
modules/qa/src/reduced_potential.hh | 5 +++
4 files changed, 44 insertions(+), 30 deletions(-)
diff --git a/modules/qa/src/impl/reduced_impl.cc b/modules/qa/src/impl/reduced_impl.cc
index 0efa531b3..8994fada4 100644
--- a/modules/qa/src/impl/reduced_impl.cc
+++ b/modules/qa/src/impl/reduced_impl.cc
@@ -58,34 +58,35 @@ bool ReducedPotentialImpl::VisitResidue(const mol::ResidueHandle& res)
bool ReducedPotentialImpl::GetCAlphaCBetaPos(const mol::ResidueHandle& res,
geom::Vec3& ca_pos,
geom::Vec3& cb_pos)
- {
- const static Real bond_length=1.5;
- mol::AtomHandle ca=res.FindAtom("CA");
- if (!ca.IsValid()) {
- return false;
- }
- ca_pos=ca.GetPos();
- mol::AtomHandle cb=res.FindAtom("CB");
- if (cb.IsValid()) {
- cb_pos=cb.GetPos();
- return true;
- }
- mol::AtomHandle n=res.FindAtom("N");
- mol::AtomHandle c=res.FindAtom("C");
- if (!(ca.IsValid() && c.IsValid() && n.IsValid())) {
- LOG_WARNING("residue " << res.GetQualifiedName()
- << " doesn't have enough atoms to reconstruct Cbeta position");
- return false;
- }
- geom::Vec3 v1=geom::Normalize(ca.GetPos()-n.GetPos());
- geom::Vec3 v2=geom::Normalize(ca.GetPos()-c.GetPos());
- geom::Vec3 in_plane_v=geom::Normalize(v1+v2);
- geom::Plane p(ca.GetPos() ,n.GetPos(), c.GetPos());
- // rotate around vector perpendicular to p and in_plane_v
- geom::Vec3 axis=geom::Normalize(geom::Cross(p.GetNormal(), in_plane_v));
- geom::Mat3 rot_mat=geom::AxisRotation(axis, (-54/180.0)*M_PI);
- cb_pos=ca.GetPos()+rot_mat*in_plane_v*bond_length;
+{
+ const static Real bond_length=1.5;
+ mol::AtomHandle ca=res.FindAtom("CA");
+ if (!ca.IsValid()) {
+ return false;
+ }
+ ca_pos=ca.GetPos();
+ mol::AtomHandle cb=res.FindAtom("CB");
+ if (cb.IsValid()) {
+ cb_pos=cb.GetPos();
return true;
- }
+ }
+ mol::AtomHandle n=res.FindAtom("N");
+ mol::AtomHandle c=res.FindAtom("C");
+ if (!(ca.IsValid() && c.IsValid() && n.IsValid())) {
+ LOG_WARNING("residue " << res.GetQualifiedName()
+ << " doesn't have enough atoms to reconstruct Cbeta position");
+ return false;
+ }
+ geom::Vec3 v1=geom::Normalize(ca.GetPos()-n.GetPos());
+ geom::Vec3 v2=geom::Normalize(ca.GetPos()-c.GetPos());
+ geom::Vec3 in_plane_v=geom::Normalize(v1+v2);
+ geom::Plane p(ca.GetPos() ,n.GetPos(), c.GetPos());
+ // rotate around vector perpendicular to p and in_plane_v
+ geom::Vec3 axis=geom::Normalize(geom::Cross(p.GetNormal(), in_plane_v));
+ geom::Mat3 rot_mat=geom::AxisRotation(axis, (-54/180.0)*M_PI);
+ cb_pos=ca.GetPos()+rot_mat*in_plane_v*bond_length;
+ return true;
+}
+
}}}
diff --git a/modules/qa/src/impl/reduced_impl.hh b/modules/qa/src/impl/reduced_impl.hh
index e10ef2c38..98651360b 100644
--- a/modules/qa/src/impl/reduced_impl.hh
+++ b/modules/qa/src/impl/reduced_impl.hh
@@ -38,8 +38,9 @@ public:
virtual bool VisitResidue(const mol::ResidueHandle& res);
- bool GetCAlphaCBetaPos(const mol::ResidueHandle& res, geom::Vec3& ca_pos,
- geom::Vec3& cb_pos);
+ static bool GetCAlphaCBetaPos(const mol::ResidueHandle& res,
+ geom::Vec3& ca_pos,
+ geom::Vec3& cb_pos);
virtual void OnInteraction(AminoAcid aa_one, AminoAcid aa_two,
Real dist, Real angle)=0;
diff --git a/modules/qa/src/reduced_potential.cc b/modules/qa/src/reduced_potential.cc
index e2bbc2bbd..78df5c902 100644
--- a/modules/qa/src/reduced_potential.cc
+++ b/modules/qa/src/reduced_potential.cc
@@ -61,6 +61,13 @@ private:
}
+bool ReducedPotential::GetCAlphaCBetaPos(const mol::ResidueHandle& res,
+ geom::Vec3& ca_pos,
+ geom::Vec3& cb_pos)
+{
+ return impl::ReducedPotentialImpl::GetCAlphaCBetaPos(res, ca_pos, cb_pos);
+}
+
ReducedPotentialPtr ReducedPotential::Load(const String& filename)
{
std::ifstream stream(filename.c_str(), std::ios_base::binary);
diff --git a/modules/qa/src/reduced_potential.hh b/modules/qa/src/reduced_potential.hh
index a85698ffe..534892678 100644
--- a/modules/qa/src/reduced_potential.hh
+++ b/modules/qa/src/reduced_potential.hh
@@ -49,6 +49,11 @@ public:
Real GetTotalEnergy(ost::mol::EntityHandle ent, bool normalize=true);
+
+ static bool GetCAlphaCBetaPos(const mol::ResidueHandle& res,
+ geom::Vec3& ca_pos,
+ geom::Vec3& cb_pos);
+
Real GetEnergy(AminoAcid aa_one, AminoAcid aa_two,
Real ca_dist, Real angle) const
{
--
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