From c41e3f4e20ded2169d515526aeb5351885fb307b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 18 Jan 2017 07:54:58 +0100
Subject: [PATCH] Implement a ToFrameResidue function for Rotamers
---
sidechain/doc/rotamer.rst | 23 ++++++++++++++++++++--
sidechain/pymod/_reconstruct_sidechains.py | 3 +--
sidechain/pymod/export_rotamer.cc | 2 ++
sidechain/src/rotamer.cc | 18 +++++++++++++++++
sidechain/src/rotamer.hh | 5 +++++
sidechain/src/sidechain_reconstructor.cc | 9 ++-------
6 files changed, 49 insertions(+), 11 deletions(-)
diff --git a/sidechain/doc/rotamer.rst b/sidechain/doc/rotamer.rst
index b8dd468e..de974604 100644
--- a/sidechain/doc/rotamer.rst
+++ b/sidechain/doc/rotamer.rst
@@ -184,6 +184,15 @@ Rotamers
:raises: :exc:`~exceptions.RuntimeError` if *res_idx* is invalid
+ .. method:: ToFrameResidue(res_idx)
+
+ Generates and returns a :class:`FrameResidue` based on the internal
+ particles.
+
+ :param res_idx: Idx passed over to :class:`FrameResidue` constructor
+ :type res_idx: :class:`int`
+
+ :returns: The constructed :class:`FrameResidue`
.. method:: GetInternalEnergyPrefactor()
@@ -331,6 +340,16 @@ Rotamers
:raises: :exc:`~exceptions.RuntimeError` if *res_idx* is invalid
+ .. method:: ToFrameResidue(res_idx)
+
+ Generates and returns a :class:`FrameResidue` based on the internal
+ particles of the active subrotamer.
+
+ :param res_idx: Idx passed over to :class:`FrameResidue` constructor
+ :type res_idx: :class:`int`
+
+ :returns: The constructed :class:`FrameResidue`
+
.. method:: GetSubrotamerDefinition(index)
:param index: Index of subrotamer
@@ -441,8 +460,8 @@ Rotamers
The provided **idx** relates to the subrotamer definitions added at the
rotamer buildup. This idx controls which subrotamer is used when
- :func:`ApplyOnResidue` gets called. By default, the value is 0
- => first added subrotamer definition gets used.
+ :func:`ApplyOnResidue` of :func:`ToFrameResidue` gets called.
+ By default, the value is 0 => first added subrotamer definition gets used.
:param idx: Index of subrotamer definition applied on residues
diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py
index ac41d155..c6b49bf0 100644
--- a/sidechain/pymod/_reconstruct_sidechains.py
+++ b/sidechain/pymod/_reconstruct_sidechains.py
@@ -184,8 +184,7 @@ def _AddCysteinFrameResidues(frame_residues, incomplete_sidechains,
# handle cysteins participating in a disulfid bond
for cys_idx, cys_rot in zip(disulfid_indices, disulfid_rotamers):
# add FrameResidue
- frame_residue = sidechain.FrameResidue([cys_rot[0]], cys_idx)
- frame_residues.append(frame_residue)
+ frame_residues.append(cys_rot.ToFrameResidue(cys_idx))
# set the position in the proteins residues
cys_rot.ApplyOnResidue(res_list[cys_idx].handle,
consider_hydrogens=False)
diff --git a/sidechain/pymod/export_rotamer.cc b/sidechain/pymod/export_rotamer.cc
index 47f99e55..f2bf1e87 100644
--- a/sidechain/pymod/export_rotamer.cc
+++ b/sidechain/pymod/export_rotamer.cc
@@ -157,6 +157,7 @@ void export_Rotamer()
(arg("res"), arg("consider_hydrogens")=false, arg("new_res_name")=""))
.def("ApplyOnResidue", WrapRRMApplyOnResAA,
(arg("all_atom"), arg("res_idx")))
+ .def("ToFrameResidue", &RRMRotamer::ToFrameResidue, (arg("res_idx")))
.def("GetInternalEnergyPrefactor",&RRMRotamer::GetInternalEnergyPrefactor)
.def("GetInternalEnergy",&RRMRotamer::GetInternalEnergy)
.def("GetFrameEnergy",&RRMRotamer::GetFrameEnergy)
@@ -184,6 +185,7 @@ void export_Rotamer()
(arg("res"), arg("consider_hydrogens")=false, arg("new_res_name")=""))
.def("ApplyOnResidue", WrapFRMApplyOnResAA,
(arg("all_atom"), arg("res_idx")))
+ .def("ToFrameResidue", &FRMRotamer::ToFrameResidue, (arg("res_idx")))
.def("GetInternalEnergyPrefactor",&FRMRotamer::GetInternalEnergyPrefactor)
.def("GetInternalEnergy",&FRMRotamer::GetInternalEnergy)
.def("GetFrameEnergy",&GetFRMFrameEnergyOne)
diff --git a/sidechain/src/rotamer.cc b/sidechain/src/rotamer.cc
index 3cf238f3..4143480d 100644
--- a/sidechain/src/rotamer.cc
+++ b/sidechain/src/rotamer.cc
@@ -55,6 +55,12 @@ void RRMRotamer::ApplyOnResidue(loop::AllAtomPositions& all_atom,
}
}
+FrameResiduePtr RRMRotamer::ToFrameResidue(uint res_idx) const {
+
+ FrameResiduePtr frame_res(new FrameResidue(particles_, res_idx));
+ return frame_res;
+}
+
FRMRotamer::FRMRotamer(const std::vector<Particle>& particles, Real T,
Real probability, Real internal_e_prefactor):
particles_(particles), n_particles_(particles.size()),
@@ -140,4 +146,16 @@ void FRMRotamer::ApplyOnResidue(loop::AllAtomPositions& all_atom,
}
}
+
+FrameResiduePtr FRMRotamer::ToFrameResidue(uint res_idx) const {
+
+ const std::vector<int>& sub_def = subrotamer_definitions_[active_subrotamer_];
+ std::vector<Particle> particles(sub_def.size());
+ for(uint i = 0; i < sub_def.size(); ++i){
+ particles[i] = particles_[sub_def[i]];
+ }
+ FrameResiduePtr frame_res(new FrameResidue(particles, res_idx));
+ return frame_res;
+}
+
}}//ns
diff --git a/sidechain/src/rotamer.hh b/sidechain/src/rotamer.hh
index fd984f57..1e7d3297 100644
--- a/sidechain/src/rotamer.hh
+++ b/sidechain/src/rotamer.hh
@@ -7,6 +7,7 @@
#include <boost/make_shared.hpp>
#include <promod3/sidechain/particle.hh>
+#include <promod3/sidechain/frame.hh>
#include <promod3/loop/all_atom_positions.hh>
#include <promod3/core/message.hh>
@@ -34,6 +35,8 @@ public:
void ApplyOnResidue(loop::AllAtomPositions& all_atom, uint res_idx) const;
+ FrameResiduePtr ToFrameResidue(uint res_idx) const;
+
Real GetInternalEnergyPrefactor() const { return internal_e_prefactor_; }
Real GetInternalEnergy() const { return internal_energy_; }
@@ -97,6 +100,8 @@ public:
void ApplyOnResidue(loop::AllAtomPositions& all_atom, uint res_idx) const;
+ FrameResiduePtr ToFrameResidue(uint res_idx) const;
+
void AddSubrotamerDefinition(const std::vector<int>& definition);
void SetActiveSubrotamer(uint idx);
diff --git a/sidechain/src/sidechain_reconstructor.cc b/sidechain/src/sidechain_reconstructor.cc
index 92ff3157..b82b7ce6 100644
--- a/sidechain/src/sidechain_reconstructor.cc
+++ b/sidechain/src/sidechain_reconstructor.cc
@@ -259,23 +259,18 @@ template<typename RotamerGroup> void SidechainReconstructor::BuildDisulfids_(
uint idx_two = cys_with_rot_groups[bond_pair.second];
uint global_idx_one = res_indices[idx_one];
uint global_idx_two = res_indices[idx_two];
- std::vector<Particle> particles(1);
// update the rotamer groups participating in disulfid bonds
is_bonded[bond_pair.first] = 1;
is_bonded[bond_pair.second] = 1;
// do first disulfid bond partner
- particles[0] = *(r_one->begin());
- FrameResiduePtr frame_res_one(new FrameResidue(particles, global_idx_one));
- frame_residues.push_back(frame_res_one);
+ frame_residues.push_back(r_one->ToFrameResidue(global_idx_one));
r_one->ApplyOnResidue(out_pos, idx_one);
has_sidechain[idx_one] = true;
// do second disulfid bond partner
- particles[0] = *(r_two->begin());
- FrameResiduePtr frame_res_two(new FrameResidue(particles, global_idx_two));
- frame_residues.push_back(frame_res_two);
+ frame_residues.push_back(r_two->ToFrameResidue(global_idx_two));
r_two->ApplyOnResidue(out_pos, idx_two);
has_sidechain[idx_two] = true;
--
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