diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py
index 7bc30c0b280171fc62d64771a0b9ecce717ecca3..8a2ced98b9dc1ffe58177726e788b39358cdf7f6 100644
--- a/sidechain/pymod/_reconstruct_sidechains.py
+++ b/sidechain/pymod/_reconstruct_sidechains.py
@@ -376,43 +376,48 @@ def _GetDisulfidBridges(frame_residues, cystein_indices, res_list, rotamer_libra
def Reconstruct(ent, keep_sidechains=False, build_disulfids=True,
rotamer_model="frm", consider_ligands=True,
- rotamer_library=None):
+ rotamer_library=None, graph_max_complexity=100000000,
+ graph_intial_epsilon=0.02):
'''Reconstruct sidechains for the given structure.
- :param ent: Structure for sidechain reconstruction. Note, that the
- sidechain reconstruction gets directly applied on the
- structure itself.
+ :param ent: Structure for sidechain reconstruction. Note, that the sidechain
+ reconstruction gets directly applied on the structure itself.
+ :type ent: :class:`ost.mol.EntityHandle`
:param keep_sidechains: Flag, whether complete sidechains in *ent* (i.e.
containing all required atoms) should be kept rigid
and directly be added to the frame.
+ :type keep_sidechains: :class:`bool`
:param build_disulfids: Flag, whether possible disulfid bonds should be
searched. If a disulfid bond is found, the two
participating cysteins are fixed and added to
the frame.
+ :type build_disulfids: :class:`bool`
:param rotamer_model: Rotamer model to be used, can either be "frm" or "rrm"
+ :type rotamer_model: :class:`str`
:param consider_hbonds: Flag, whether hbonds should be evaluated in the
energy function. If set to False, no hydrogens will
be built when building rotamers and frame.
+ :type consider_hbonds: :class:`bool`
:param consider_ligands: Flag, whether to add ligands (anything in chain
'_') as static objects.
+ :type consider_ligands: :class:`bool`
:param rotamer_library: A rotamer library to extract the rotamers from. The
default is the :meth:`Dunbrack <LoadDunbrackLib>`
library.
-
-
- :type ent: :class:`ost.mol.EntityHandle`
- :type keep_sidechains: :class:`bool`
- :type build_disulfids: :class:`bool`
- :type rotamer_model: :class:`str`
- :type consider_hbonds: :class:`bool`
- :type consider_ligands: :class:`bool`
- :type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
+ :type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
+
+ :param graph_max_complexity: Max. complexity for
+ :meth:`RotamerGraph.TreeSolve`.
+ :type graph_max_complexity: :class:`int`
+ :param graph_intial_epsilon: Initial epsilon for
+ :meth:`RotamerGraph.TreeSolve`.
+ :type graph_intial_epsilon: :class:`float`
'''
prof_name = 'sidechain::Reconstruct'
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
@@ -495,16 +500,19 @@ def Reconstruct(ent, keep_sidechains=False, build_disulfids=True,
else:
graph = sidechain.RotamerGraph.CreateFromRRMList(rotamer_groups)
- solution = graph.TreeSolve(100000000,0.02)[0]
+ solution = graph.TreeSolve(max_complexity=graph_max_complexity,
+ initial_epsilon=graph_intial_epsilon)[0]
# update structure
- for i,rot_group,sol in zip(residues_with_rotamer_group,rotamer_groups,solution):
+ for i, rot_group, sol in zip(residues_with_rotamer_group, rotamer_groups,
+ solution):
try:
res_handle = prot.residues[i].handle
rot_group[sol].ApplyOnResidue(res_handle, consider_hydrogens=False)
sidechain.ConnectSidechain(res_handle, rotamer_ids[i])
except:
- print "there is a backbone atom missing... ", res_handle.GetQualifiedName()
+ print "there is a backbone atom missing... ", \
+ res_handle.GetQualifiedName()
# these methods will be exported into module
__all__ = ('Reconstruct',)
diff --git a/sidechain/pymod/export_graph.cc b/sidechain/pymod/export_graph.cc
index fb78d8fe3468409f85206303d404cbf17e4103e7..d572fcbcbc4bbe5a067d5ebd8ba91cd18746bfd5 100644
--- a/sidechain/pymod/export_graph.cc
+++ b/sidechain/pymod/export_graph.cc
@@ -59,17 +59,23 @@ boost::python::tuple WrapAStarSolve(RotamerGraphPtr graph,
void export_Graph()
{
- class_<RotamerGraph,boost::noncopyable>("RotamerGraph", no_init)
- .def("CreateFromRRMList",&WrapRRMList,(arg("rotamer_groups"))).staticmethod("CreateFromRRMList")
- .def("CreateFromFRMList",&WrapFRMList,(arg("rotamer_groups"))).staticmethod("CreateFromFRMList")
- .def("Prune",&RotamerGraph::Prune,(arg("epsilon"),arg("e_cut")=0.0,arg("consider_all_nodes")=false))
+ class_<RotamerGraph, boost::noncopyable>("RotamerGraph", no_init)
+ .def("CreateFromRRMList", &WrapRRMList, (arg("rotamer_groups")))
+ .staticmethod("CreateFromRRMList")
+ .def("CreateFromFRMList", &WrapFRMList, (arg("rotamer_groups")))
+ .staticmethod("CreateFromFRMList")
+ .def("Prune", &RotamerGraph::Prune,
+ (arg("epsilon"), arg("e_cut")=0.0, arg("consider_all_nodes")=false))
.def("Reset", &RotamerGraph::Reset)
.def("GetNumNodes", &RotamerGraph::GetNumNodes)
.def("GetNumEdges", &RotamerGraph::GetNumEdges)
.def("GetNumActiveNodes", &RotamerGraph::GetNumActiveNodes)
.def("GetNumActiveEdges", &RotamerGraph::GetNumActiveEdges)
- .def("TreeSolve",&WrapTreeSolve,(arg("max_complexity")=std::numeric_limits<uint64_t>::max(),arg("initial_epsilon")=0.02))
- .def("AStarSolve",&WrapAStarSolve,(arg("e_thresh"),arg("max_n")=100,arg("max_visited_nodes")=100000000))
+ .def("TreeSolve", &WrapTreeSolve,
+ (arg("max_complexity")=std::numeric_limits<uint64_t>::max(),
+ arg("initial_epsilon")=0.02))
+ .def("AStarSolve", &WrapAStarSolve,
+ (arg("e_thresh"), arg("max_n")=100, arg("max_visited_nodes")=100000000))
;
register_ptr_to_python<RotamerGraphPtr>();