Added possibility to keep all polar hydrogens after sidechain reconstruction

sidechain/pymod/export_frame.cc

@@ -133,6 +133,8 @@ void export_Frame()
     .def("__init__",make_constructor(&WrapFrameResidueInit))
     .def("__len__", &FrameResidue::size)
     .def("__getitem__", &WrapGetItem, (arg( "index" )))
+    .def("ApplyOnResidue",&FrameResidue::ApplyOnResidue)
+    .def("GetResidueIndex",&FrameResidue::GetResidueIndex)
   ;
 
   register_ptr_to_python<FrameResiduePtr>();

sidechain/pymod/reconstruct_sidechains.py

@@ -3,7 +3,7 @@ from ost import geom
 
 def Reconstruct(ent, keep_sidechains = False, build_disulfids = True, 
                 rotamer_model = "frm", consider_hbonds = True,
-                rotamer_library = None):
+                rotamer_library = None,add_all_polar_hydrogens=False):
 
     name_id_mapper = dict()
     name_id_mapper["ARG"] = sidechain.ARG
@@ -320,3 +320,11 @@ def Reconstruct(ent, keep_sidechains = False, build_disulfids = True,
         except:
             print "there is a backbone atom missing... ",prot.residues[i].GetQualifiedName()
 
+    if add_all_polar_hydrogens:
+        for r in frame_residues:
+            i=r.GetResidueIndex()
+            if i==100000:continue#These are cysteins that were already handled
+            rh=prot.residues[i].GetHandle()
+            r.ApplyOnResidue(rh,True)
+
+

sidechain/src/frame.cc

@@ -37,6 +37,21 @@ FrameResiduePtr FrameResidue::GetTransformedCopy(const geom::Transform& t, uint
 
 } 
 
+void FrameResidue::ApplyOnResidue(ost::mol::ResidueHandle& res, bool consider_hydrogens) const{
+  ost::mol::XCSEditor ed = res.GetEntity().EditXCS(ost::mol::BUFFERED_EDIT);
+  for(uint i = 0; i < n_particles_; ++i){
+    Particle p=particles_[i];
+    String particle_name =p.GetName();
+    if(particle_name[0] == 'H' && !consider_hydrogens) continue;
+    ost::mol::AtomHandle a=res.FindAtom(particle_name);
+    if (a.IsValid()){
+      ed.SetAtomPos(a,p.GetPos());
+    }
+    else {
+      ed.InsertAtom(res,p.GetName(),p.GetPos(),particle_name.substr(0,1));
+    }
+  }
+}
 
 Frame::Frame(const std::vector<FrameResiduePtr>& frame_residues,
              const std::vector<geom::Transform>& rt_operators): 

sidechain/src/frame.hh

@@ -46,6 +46,7 @@ public:
   iterator end() const { return particles_ + n_particles_; }
 
   uint GetResidueIndex() const { return residue_index_; }
+  void ApplyOnResidue(ost::mol::ResidueHandle& res, bool consider_hydrogens) const;
 
 private:
   Particle* particles_;