diff --git a/sidechain/doc/reconstruct.rst b/sidechain/doc/reconstruct.rst
index d5361b7bf072b9a8582184314ab6ecbb310161fa..69ba71554fb7ada1006a4b7abf6037b9db3d40b6 100644
--- a/sidechain/doc/reconstruct.rst
+++ b/sidechain/doc/reconstruct.rst
@@ -20,7 +20,8 @@ SidechainReconstructor Class
--------------------------------------------------------------------------------
.. class:: SidechainReconstructor(keep_sidechains=True, build_disulfids=True, \
- cutoff=20, graph_max_complexity=100000000, \
+ optimize_subrotamers=False, cutoff=20, \
+ graph_max_complexity=100000000, \
graph_intial_epsilon=0.02, \
disulfid_score_thresh=45)
@@ -41,6 +42,11 @@ SidechainReconstructor Class
the result.
:type build_disulfids: :class:`bool`
+ :param optimize_subrotamers: Flag, whether the :func:`SubrotamerOptimizer`
+ with default parametrization should be called
+ if we're dealing with FRM rotamers.
+ :type optimize_subrotamers: :class:`bool`
+
:param cutoff: Cutoff used to search relevant residues surrounding the loop.
:type cutoff: :class:`float`
diff --git a/sidechain/pymod/export_sidechain_reconstructor.cc b/sidechain/pymod/export_sidechain_reconstructor.cc
index 4f97d55a4cf714539b90dba820d96c625e5ca61e..b550dd262b642207b070d661a8aa1b3413e7c514 100644
--- a/sidechain/pymod/export_sidechain_reconstructor.cc
+++ b/sidechain/pymod/export_sidechain_reconstructor.cc
@@ -91,8 +91,9 @@ void export_SidechainReconstructor() {
class_<SidechainReconstructor, SidechainReconstructorPtr>
("SidechainReconstructor", no_init)
- .def(init<bool, bool, Real, uint64_t, Real, Real>(
+ .def(init<bool, bool, bool, Real, uint64_t, Real, Real>(
(arg("keep_sidechains")=true, arg("build_disulfids")=true,
+ arg("optimize_subrotamers")=false,
arg("cutoff")=20, arg("graph_max_complexity")=100000000,
arg("graph_intial_epsilon")=0.02,
arg("disulfid_score_thresh")=45)))
diff --git a/sidechain/src/sidechain_reconstructor.cc b/sidechain/src/sidechain_reconstructor.cc
index b82b7ce621848cff410e84701ddaf3624f6ca7ec..e1f9dd10c3d5e5bd4a478bd9c909c4a5753023ff 100644
--- a/sidechain/src/sidechain_reconstructor.cc
+++ b/sidechain/src/sidechain_reconstructor.cc
@@ -1,6 +1,7 @@
#include <promod3/sidechain/sidechain_reconstructor.hh>
#include <promod3/sidechain/disulfid.hh>
#include <promod3/sidechain/rotamer_graph.hh>
+#include <promod3/sidechain/subrotamer_optimizer.hh>
#include <promod3/core/message.hh>
#include <promod3/core/runtime_profiling.hh>
@@ -321,6 +322,24 @@ void SidechainReconstructor::CollectRotamerGroups_(
}
}
+void ApplySubrotamerOptimization(std::vector<FRMRotamerGroupPtr>& rotamer_groups,
+ const std::vector<int>& solution) {
+
+ uint num_rotamer_groups = rotamer_groups.size();
+
+ std::vector<FRMRotamerPtr> rotamers(rotamer_groups.size());
+ for(uint i = 0; i < num_rotamer_groups; ++i){
+ rotamers[i] = (*rotamer_groups[i])[solution[i]];
+ }
+ SubrotamerOptimizer(rotamers);
+}
+
+void ApplySubrotamerOptimization(std::vector<RRMRotamerGroupPtr>& rotamer_groups,
+ const std::vector<int>& solution) {
+ //there's nothing to do...
+}
+
+
template<typename RotamerGroup>
void SidechainReconstructor::SolveSystem_(
SidechainReconstructionDataPtr res) const {
@@ -377,6 +396,11 @@ void SidechainReconstructor::SolveSystem_(
std::pair<std::vector<int>,Real> solution =
graph->TreeSolve(graph_max_complexity_, graph_intial_epsilon_);
+ // do subrotamer optimization if required
+ if(optimize_subrotamers_){
+ ApplySubrotamerOptimization(rotamer_groups, solution.first);
+ }
+
// apply solution to subset of data
for (uint i = 0; i < res->rotamer_res_indices.size(); ++i) {
const uint res_idx = res->rotamer_res_indices[i];
diff --git a/sidechain/src/sidechain_reconstructor.hh b/sidechain/src/sidechain_reconstructor.hh
index 2e052b386fbec9bbc8cf1492a40a3cf8d4ca3ec0..bd405ec35454703603f16a38cd1015ecf5fd369c 100644
--- a/sidechain/src/sidechain_reconstructor.hh
+++ b/sidechain/src/sidechain_reconstructor.hh
@@ -38,12 +38,15 @@ class SidechainReconstructor {
public:
SidechainReconstructor(bool keep_sidechains = true,
- bool build_disulfids = true, Real cutoff = 20,
+ bool build_disulfids = true,
+ bool optimize_subrotamers = false,
+ Real cutoff = 20,
uint64_t graph_max_complexity = 100000000,
Real graph_intial_epsilon = 0.02,
Real disulfid_score_thresh = 45)
: keep_sidechains_(keep_sidechains)
, build_disulfids_(build_disulfids)
+ , optimize_subrotamers_(optimize_subrotamers)
, cutoff_(cutoff)
, graph_max_complexity_(graph_max_complexity)
, graph_intial_epsilon_(graph_intial_epsilon)
@@ -104,6 +107,7 @@ private:
// reconstruction parameters
bool keep_sidechains_;
bool build_disulfids_;
+ bool optimize_subrotamers_;
Real cutoff_;
uint64_t graph_max_complexity_;
Real graph_intial_epsilon_;
diff --git a/sidechain/src/subrotamer_optimizer.hh b/sidechain/src/subrotamer_optimizer.hh
index 594d3ffd7aa87b07d95569aa2729b6b27022c28b..df415f00cadbaebca42f393dce66c7bb8e620d80 100644
--- a/sidechain/src/subrotamer_optimizer.hh
+++ b/sidechain/src/subrotamer_optimizer.hh
@@ -9,7 +9,7 @@
namespace promod3{ namespace sidechain{
void SubrotamerOptimizer(std::vector<FRMRotamerPtr>& rotamers,
- Real active_internal_energy = -0.5,
+ Real active_internal_energy = -2.0,
Real inactive_internal_energy = 0.0,
uint max_complexity = 100000000,
Real initial_epsilon = 0.02);
diff --git a/sidechain/tests/test_sidechain.py b/sidechain/tests/test_sidechain.py
index 5ddc769a14c443860d098eb239e5ee17202f5d4e..fad4df490211a73d089ab1b73ab8496b190b1ae8 100644
--- a/sidechain/tests/test_sidechain.py
+++ b/sidechain/tests/test_sidechain.py
@@ -23,17 +23,20 @@ class SidechainTests(unittest.TestCase):
self.assertLessEqual(geom.Length(a.pos - a_ref.pos), max_dist)
def CheckEnvVsPy(self, ent, env, keep_sidechains, build_disulfids,
+ optimize_subrotamers,
rotamer_model, rotamer_library):
# reconstruct sidechains for full OST entity
ent_py = ent.Copy()
sidechain.Reconstruct(ent_py, keep_sidechains=keep_sidechains,
build_disulfids=build_disulfids,
+ optimize_subrotamers=optimize_subrotamers,
rotamer_model=rotamer_model,
rotamer_library=rotamer_library)
# same with SidechainReconstructor
sc_rec = sidechain.SidechainReconstructor(keep_sidechains=keep_sidechains,
- build_disulfids=build_disulfids)
+ build_disulfids=build_disulfids,
+ optimize_subrotamers=optimize_subrotamers)
sc_rec.AttachEnvironment(env, use_frm=(rotamer_model=="frm"),
rotamer_library=rotamer_library)
res = sc_rec.Reconstruct(1, ent.residue_count)
@@ -63,28 +66,33 @@ class SidechainTests(unittest.TestCase):
env = loop.AllAtomEnv(seqres_str)
env.SetInitialEnvironment(ent)
self.CheckEnvVsPy(ent, env, keep_sidechains=False,
- build_disulfids=False, rotamer_model="rrm",
- rotamer_library=self.rotamer_library)
+ build_disulfids=False, optimize_subrotamers=False,
+ rotamer_model="rrm", rotamer_library=self.rotamer_library)
# reuse env with keep_sidechains=True
self.CheckEnvVsPy(ent, env, keep_sidechains=True,
- build_disulfids=False, rotamer_model="rrm",
- rotamer_library=self.rotamer_library)
+ build_disulfids=False, optimize_subrotamers=False,
+ rotamer_model="rrm", rotamer_library=self.rotamer_library)
# vary one by one (need to reset env to get new stuff)
env = loop.AllAtomEnv(seqres_str)
env.SetInitialEnvironment(ent)
self.CheckEnvVsPy(ent, env, keep_sidechains=True,
- build_disulfids=False, rotamer_model="frm",
- rotamer_library=self.rotamer_library)
+ build_disulfids=False, optimize_subrotamers=False,
+ rotamer_model="frm", rotamer_library=self.rotamer_library)
env = loop.AllAtomEnv(seqres_str)
env.SetInitialEnvironment(ent)
self.CheckEnvVsPy(ent, env, keep_sidechains=True,
- build_disulfids=False, rotamer_model="rrm",
- rotamer_library=self.rotamer_library)
+ build_disulfids=False, optimize_subrotamers=False,
+ rotamer_model="rrm", rotamer_library=self.rotamer_library)
env = loop.AllAtomEnv(seqres_str)
env.SetInitialEnvironment(ent)
self.CheckEnvVsPy(ent, env, keep_sidechains=True,
- build_disulfids=False, rotamer_model="rrm",
- rotamer_library=self.bbdep_rotamer_library)
+ build_disulfids=False, optimize_subrotamers=False,
+ rotamer_model="rrm", rotamer_library=self.bbdep_rotamer_library)
+ env = loop.AllAtomEnv(seqres_str)
+ env.SetInitialEnvironment(ent)
+ self.CheckEnvVsPy(ent, env, keep_sidechains=False,
+ build_disulfids=True, optimize_subrotamers=True,
+ rotamer_model="frm", rotamer_library=self.bbdep_rotamer_library)
# crn needed to check for disulfid bridges
ent = io.LoadPDB(os.path.join('data', '1crn_sc_test.pdb'))
@@ -92,8 +100,8 @@ class SidechainTests(unittest.TestCase):
env = loop.AllAtomEnv(seqres_str)
env.SetInitialEnvironment(ent)
self.CheckEnvVsPy(ent, env, keep_sidechains=True,
- build_disulfids=True, rotamer_model="rrm",
- rotamer_library=self.rotamer_library)
+ build_disulfids=True, optimize_subrotamers=False,
+ rotamer_model="rrm", rotamer_library=self.rotamer_library)
if __name__ == "__main__":
from ost import testutils