diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 8af2ab6cc20f088401c9e80038d8bc98e31f8561..6146858baa5abc0236ea248db849fa8b6d7bcb5e 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -641,7 +641,7 @@ class Table(object):
for row, d in zip(self.rows, data):
row.append(d)
- elif data!=None:
+ elif data!=None and len(self.cols)==0:
if IsScalar(data):
self.AddRow({col_name : data})
else:
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index e53a02d35ffc39d35e826c9f34938dfd2821c4a1..241fd007e47ec1da465feeb4ec869a4dc5127c18 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -42,11 +42,45 @@ BondHandle (EditorBase::*connect_b)(const AtomHandle&, const AtomHandle&,
BondHandle (EditorBase::*connect_d)(const AtomHandle&, const AtomHandle&,
Real, Real, Real,
unsigned char)=&EditorBase::Connect;
+
+ChainHandle (EditorBase::*insert_chain_a)(const String& chain_name)=&EditorBase::InsertChain;
+ChainHandle (EditorBase::*insert_chain_b)(const String& chain_name,
+ ChainHandle chain, bool deep)=&EditorBase::InsertChain;
ResidueHandle (EditorBase::*append_a)(ChainHandle ch,
const ResidueKey&)=&EditorBase::AppendResidue;
ResidueHandle (EditorBase::*append_b)(ChainHandle ch, const ResidueKey&,
const ResNum&)=&EditorBase::AppendResidue;
+ResidueHandle (EditorBase::*append_c)(ChainHandle ch, ResidueHandle residue,
+ bool deep)=&EditorBase::AppendResidue;
+
+ResidueHandle (EditorBase::*insert_residue_before_a)(ChainHandle chain, int index,
+ const ResNum& num,
+ const ResidueKey& k)=&EditorBase::InsertResidueBefore;
+ResidueHandle (EditorBase::*insert_residue_before_b)(ChainHandle chain, ResidueHandle residue,
+ int index,bool deep)=&EditorBase::InsertResidueBefore;
+
+ResidueHandle (EditorBase::*insert_residue_after_a)(ChainHandle chain, int index,
+ const ResNum& num,
+ const ResidueKey& k)=&EditorBase::InsertResidueAfter;
+ResidueHandle (EditorBase::*insert_residue_after_b)(ChainHandle chain, ResidueHandle residue,
+ int index, bool deep)=&EditorBase::InsertResidueAfter;
+
+AtomHandle (EditorBase::*insert_atom_a)(ResidueHandle residue, const String& name,
+ const geom::Vec3& pos, const String& ele,
+ Real occupancy, Real b_factor,
+ bool is_hetatm)=&EditorBase::InsertAtom;
+AtomHandle (EditorBase::*insert_atom_b)(ResidueHandle residue, AtomHandle atom)=&EditorBase::InsertAtom;
+
+
+AtomHandle (EditorBase::*insert_alt_atom_a)(ResidueHandle residue, const String& name,
+ const String& alt_group, const geom::Vec3& pos,
+ const String& ele, Real occ,
+ Real b_factor)=&EditorBase::InsertAltAtom;
+AtomHandle (EditorBase::*insert_alt_atom_b)(ResidueHandle residue, AtomHandle atom,
+ const String& alt_group)=&EditorBase::InsertAltAtom;
+
+
void (ICSEditor::*set_torsion_a)(TorsionHandle, Real, bool)=&ICSEditor::SetTorsionAngle;
void (ICSEditor::*set_torsion_b)(const AtomHandle&, const AtomHandle&,
@@ -195,18 +229,27 @@ void export_Editors()
#endif
class_<EditorBase>("EditorBase", no_init)
- .def("InsertChain", &EditorBase::InsertChain)
- .def("InsertAtom", &EditorBase::InsertAtom,
+ .def("InsertChain", insert_chain_a)
+ .def("InsertChain", insert_chain_b,(arg("chain_name"),arg("chain"), arg("deep")=false))
+ .def("InsertAtom", insert_atom_a,
(arg("residue"), arg("name"), arg("pos"), arg("element")="",
arg("occupancy")=1.0, arg("b_factor")=0.0, arg("is_hetatm")=false))
- .def("InsertAltAtom", &EditorBase::InsertAltAtom)
+ .def("InsertAtom", insert_atom_b)
+ .def("InsertAltAtom", insert_alt_atom_a)
+ .def("InsertAltAtom", insert_alt_atom_b)
.def("DeleteResidue", &EditorBase::DeleteResidue)
.def("DeleteChain", &EditorBase::DeleteChain)
.def("DeleteAtom", &EditorBase::DeleteAtom)
- .def("InsertResidueBefore", &EditorBase::InsertResidueBefore)
- .def("InsertResidueAfter", &EditorBase::InsertResidueAfter)
+ .def("InsertResidueBefore", insert_residue_before_a)
+ .def("InsertResidueBefore", insert_residue_before_b, (arg("chain"), arg("residue"),
+ arg("index"), arg("deep")=false))
+ .def("InsertResidueAfter", insert_residue_after_a)
+ .def("InsertResidueAfter", insert_residue_after_b, (arg("chain"), arg("residue"),
+ arg("index"), arg("deep")=false))
.def("AppendResidue", append_a)
- .def("AppendResidue", append_b)
+ .def("AppendResidue", append_b)
+ .def("AppendResidue", append_c, (arg("chain"), arg("residue"),
+ arg("deep")=false))
.def("Connect", connect_a)
.def("Connect", connect_b)
.def("Connect", connect_c)
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index d75827806359c8dc5036fa7cf819abb0ce7ffcc6..49c1311b2f4ccdfb5ea5c4a650836c1a17f57cc6 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -40,6 +40,51 @@ ChainHandle EditorBase::InsertChain(const String& chain_name)
return ent_.Impl()->InsertChain(chain_name);
}
+ChainHandle EditorBase::InsertChain(const String& chain_name, ChainHandle chain, bool deep)
+{
+
+ impl::ChainImplPtr inserted_chain=ent_.Impl()->InsertChain(chain.Impl());
+ inserted_chain->SetName(chain_name);
+
+ if(deep){
+ ResidueHandleIter it=chain.ResiduesBegin(),
+ it_end=chain.ResiduesEnd();
+ for(;it!=it_end;++it){
+ ResidueHandle res=*it;
+ this->AppendResidue(inserted_chain, res, true);
+ }
+ }
+
+ return inserted_chain;
+
+
+
+ /*
+ impl::ChainImplPtr new_chain=chain.Impl();
+ new_chain->SetName(chain_name);
+ if(!deep) new_chain->DeleteAllResidues();
+ return ent_.Impl()->InsertChain(new_chain);
+ */
+ /*
+ if(deep){
+
+ ChainHandle inserted_chain=ent_.Impl()->InsertChain(chain_name);
+
+ ResidueHandleIter it=chain.ResiduesBegin(),
+ it_end=chain.ResiduesEnd();
+ for(;it!=it_end;++it){
+ ResidueHandle res=*it;
+ this->AppendResidue(inserted_chain, res, true);
+ }
+ return inserted_chain;
+ }
+
+ else{
+ return ent_.Impl()->InsertChain(chain.GetName());
+ }
+ */
+}
+
ResidueHandle EditorBase::AppendResidue(ChainHandle chain, const ResidueKey& k)
{
CheckHandleValidity(chain);
@@ -54,6 +99,24 @@ ResidueHandle EditorBase::AppendResidue(ChainHandle chain, const ResidueKey& k,
return ResidueHandle(chain.Impl()->AppendResidue(k, num));
}
+ResidueHandle EditorBase::AppendResidue(ChainHandle chain, ResidueHandle residue, bool deep)
+{
+ CheckHandleValidity(chain);
+
+ impl::ResidueImplPtr inserted_residue=chain.Impl()->AppendResidue(residue.Impl());
+ if(deep)
+ {
+ AtomHandleIter it=residue.AtomsBegin(),
+ it_end=residue.AtomsEnd();
+ for(;it!=it_end;++it)
+ {
+ AtomHandle atom=*it;
+ this->InsertAtom(inserted_residue,atom);
+ }
+ }
+ return inserted_residue;
+}
+
ResidueHandle EditorBase::InsertResidueBefore(ChainHandle chain, int index,
const ResNum& num,
const ResidueKey& k)
@@ -62,6 +125,34 @@ ResidueHandle EditorBase::InsertResidueBefore(ChainHandle chain, int index,
return ResidueHandle(chain.Impl()->InsertResidueBefore(index, num, k));
}
+ResidueHandle EditorBase::InsertResidueBefore(ChainHandle chain,
+ ResidueHandle residue,
+ int index, bool deep)
+{
+ CheckHandleValidity(chain);
+
+ if(deep)
+ {
+ ResidueHandle inserted_residue=chain.Impl()->InsertResidueBefore(index,
+ residue.GetNumber(),
+ residue.GetKey());
+ AtomHandleIter it=inserted_residue.AtomsBegin(),
+ it_end=inserted_residue.AtomsEnd();
+ for(;it!=it_end;++it)
+ {
+ AtomHandle atom=*it;
+ this->InsertAtom(inserted_residue, atom);
+ }
+ return inserted_residue;
+ }
+ else
+ {
+ return ResidueHandle(chain.Impl()->InsertResidueBefore(index,
+ residue.GetNumber(),
+ residue.GetKey()));
+ }
+}
+
ResidueHandle EditorBase::InsertResidueAfter(ChainHandle chain, int index,
const ResNum& num,
const ResidueKey& k)
@@ -70,6 +161,30 @@ ResidueHandle EditorBase::InsertResidueAfter(ChainHandle chain, int index,
return ResidueHandle(chain.Impl()->InsertResidueAfter(index, num, k));
}
+ResidueHandle EditorBase::InsertResidueAfter(ChainHandle chain, ResidueHandle residue,
+ int index, bool deep)
+{
+ if(deep)
+ {
+ ResidueHandle inserted_residue=chain.Impl()->InsertResidueAfter(index,
+ residue.GetNumber(),
+ residue.GetKey());
+ AtomHandleIter it=inserted_residue.AtomsBegin(),
+ it_end=inserted_residue.AtomsEnd();
+ for(;it!=it_end;++it)
+ {
+ this->InsertAtom(inserted_residue, *it);
+ }
+ return inserted_residue;
+ }
+ else
+ {
+ return ResidueHandle(chain.Impl()->InsertResidueAfter(index,
+ residue.GetNumber(),
+ residue.GetKey()));
+ }
+}
+
void EditorBase::RenameResidue(ResidueHandle res, const String& new_name)
{
CheckHandleValidity(res);
@@ -116,6 +231,14 @@ AtomHandle EditorBase::InsertAtom(ResidueHandle res, const String& name,
return atom;
}
+AtomHandle EditorBase::InsertAtom(ResidueHandle res, AtomHandle atom)
+{
+ CheckHandleValidity(res);
+ ent_.Impl()->MarkTraceDirty();
+ AtomHandle a(res.Impl()->InsertAtom(atom.Impl()));
+ return a;
+}
+
AtomHandle EditorBase::InsertAltAtom(ResidueHandle res, const String& name,
const String& alt_group,
const geom::Vec3& pos,
@@ -130,6 +253,18 @@ AtomHandle EditorBase::InsertAltAtom(ResidueHandle res, const String& name,
return atom;
}
+AtomHandle EditorBase::InsertAltAtom(ResidueHandle res, AtomHandle atom,
+ const String& alt_group)
+{
+ CheckHandleValidity(res);
+ ent_.Impl()->MarkTraceDirty();
+ AtomHandle a(res.Impl()->InsertAltAtom(atom.GetName(), alt_group,
+ atom.GetPos(), atom.GetElement(),
+ atom.GetOccupancy(), atom.GetBFactor()));
+ this->UpdateTrace();
+ return a;
+}
+
void EditorBase::AddAltAtomPos(const String& group,
const AtomHandle& atom,
const geom::Vec3& position, Real occ,
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 504311d547cf00f43e11fb5b1c49925a16564e34..7e969b9101a604d8e45b2270c5843a0317d38518 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -57,6 +57,9 @@ public:
/// \return The newly created chain handle
ChainHandle InsertChain(const String& chain_name);
+ //ChainHandle InsertChain(ChainHandle chain, bool deep=false);
+ ChainHandle InsertChain(const String& chain_name, ChainHandle chain, bool deep=false);
+
/// \name Inserting, removing and modifying order of residues
///@{
/// \brief Append residue to the end of the chain
@@ -76,6 +79,9 @@ public:
ResidueHandle AppendResidue(ChainHandle chain, const ResidueKey& k,
const ResNum& num);
+
+ ResidueHandle AppendResidue(ChainHandle chain, ResidueHandle residue, bool deep=false);
+
/// \brief Insert residue into chain
///
/// Insert residue with residue number \var num and key \var k into the
@@ -94,6 +100,9 @@ public:
ResidueHandle InsertResidueBefore(ChainHandle chain, int index,
const ResNum& num,
const ResidueKey& k);
+
+ ResidueHandle InsertResidueBefore(ChainHandle chain, ResidueHandle residue,
+ int index, bool deep=false);
/// \brief insert residue into chain
///
/// This method is identical to InsertResidueBefore() but inserts the
@@ -102,6 +111,9 @@ public:
ResidueHandle InsertResidueAfter(ChainHandle chain, int index,
const ResNum& num,
const ResidueKey& k);
+
+ ResidueHandle InsertResidueAfter(ChainHandle chain, ResidueHandle residue,
+ int index, bool deep=false);
/// \name Adding/removing atoms
//@{
@@ -120,12 +132,19 @@ public:
Real occupancy=1.0, Real b_factor=0.0,
bool is_hetatm=false);
+ AtomHandle InsertAtom(ResidueHandle residue, AtomHandle atom);
+
/// \brief Insert new atom with alternative position indicator
/// \sa EditorBase::AddAltAtomPos(), ResidueHandle
AtomHandle InsertAltAtom(ResidueHandle residue, const String& name,
const String& alt_group, const geom::Vec3& pos,
const String& ele="", Real occ=1.0,
Real b_factor=0.0);
+
+ AtomHandle InsertAltAtom(ResidueHandle residue, AtomHandle atom,
+ const String& alt_group);
+
+
/// \brief Add alternative atom position
/// \param group is the name of the alternative atom position group. If no
/// group of that name exists, it will be created.
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index bcb3436e2bc463dadcfe1ca6af4e1bbac48af24b..5c11bde4b14c9ba2244c3b40537757ef0b9ba1a1 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -119,6 +119,7 @@ public:
/// \brief Append residue at end of chain.
ResidueImplPtr AppendResidue(const ResidueKey& k, const ResNum& n);
+
// next residue, not necessarily in sequence
ResidueImplPtr GetPrev(const ResidueImplPtr& r) const;