diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 6146858baa5abc0236ea248db849fa8b6d7bcb5e..c156af92fd1d0b71eae164a9e627f13d6faaebc1 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -1712,7 +1712,7 @@ class Table(object):
- def GaussianSmooth(self, col, std=1.0, na_value=0.0):
+ def GaussianSmooth(self, col, std=1.0, na_value=0.0, padding='reflect', cval=0.0):
'''
In place gaussian smooth of a column in the table with a given standard deviation.
@@ -1727,13 +1727,22 @@ class Table(object):
:param na_value: all na (None) values of the speciefied column are set to na_value before smoothing
:type na_value: `scalar`
+ :param padding: allows to handle padding behaviour see scipy ndimage.gaussian_filter1d documentation for more information. standard is reflect
+ :type padding: :class:`str`
+
+ :param cval: constant value used for padding if padding mode is constant
+ :type cval: `scalar`
+
+
+
:warning: The function depends on *scipy*
'''
try:
from scipy import ndimage
+ import numpy as np
except ImportError:
- LogError("Function needs scipy.ndimage, but I could no import it")
+ LogError("I need scipy.ndimage and numpy, but could not import it")
raise
idx = self.GetColIndex(col)
@@ -1748,7 +1757,8 @@ class Table(object):
else:
vals.append(na_value)
- smoothed_values_ndarray=ndimage.gaussian_filter1d(vals,std)
+
+ smoothed_values_ndarray=ndimage.gaussian_filter1d(vals,std, mode=padding, cval=cval)
result=[]
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 241fd007e47ec1da465feeb4ec869a4dc5127c18..c9d7873982ee0b33a51403090dfb8b758fe9922f 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -54,18 +54,6 @@ ResidueHandle (EditorBase::*append_b)(ChainHandle ch, const ResidueKey&,
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,
@@ -240,12 +228,8 @@ void export_Editors()
.def("DeleteResidue", &EditorBase::DeleteResidue)
.def("DeleteChain", &EditorBase::DeleteChain)
.def("DeleteAtom", &EditorBase::DeleteAtom)
- .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("InsertResidueBefore", &EditorBase::InsertResidueBefore)
+ .def("InsertResidueAfter", &EditorBase::InsertResidueAfter)
.def("AppendResidue", append_a)
.def("AppendResidue", append_b)
.def("AppendResidue", append_c, (arg("chain"), arg("residue"),
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 49c1311b2f4ccdfb5ea5c4a650836c1a17f57cc6..ebf30627eaf9bf892b2838644789995a80b54c38 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -42,47 +42,9 @@ ChainHandle EditorBase::InsertChain(const String& chain_name)
ChainHandle EditorBase::InsertChain(const String& chain_name, ChainHandle chain, bool deep)
{
-
- impl::ChainImplPtr inserted_chain=ent_.Impl()->InsertChain(chain.Impl());
+ impl::ChainImplPtr inserted_chain=ent_.Impl()->InsertChain(chain.Impl(), deep);
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)
@@ -103,17 +65,7 @@ ResidueHandle EditorBase::AppendResidue(ChainHandle chain, ResidueHandle residue
{
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);
- }
- }
+ impl::ResidueImplPtr inserted_residue=chain.Impl()->AppendResidue(residue.Impl(),deep);
return inserted_residue;
}
@@ -125,34 +77,6 @@ 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)
@@ -161,30 +85,6 @@ 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);
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 7e969b9101a604d8e45b2270c5843a0317d38518..524849941a691f5b54060ced818e4c45821241aa 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -101,8 +101,6 @@ public:
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
@@ -111,9 +109,6 @@ 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
//@{
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 009f436a5406a42caeda27605574587d48decbe3..91261db8e74cd0b9bbd5358c0dfb7892f5a68aa3 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -61,7 +61,7 @@ bool ChainImpl::InSequence() const {
return in_sequence_;
}
-ResidueImplPtr ChainImpl::AppendResidue(const ResidueImplPtr& res)
+ResidueImplPtr ChainImpl::AppendResidue(const ResidueImplPtr& res, bool deep)
{
ResidueImplPtr dst_res=this->AppendResidue(res->GetKey(), res->GetNumber());
dst_res->Assign(*res.get());
@@ -70,6 +70,16 @@ ResidueImplPtr ChainImpl::AppendResidue(const ResidueImplPtr& res)
dst_res->SetChemClass(res->GetChemClass());
dst_res->SetProtein(res->IsProtein());
dst_res->SetIsLigand(res->IsLigand());
+ if(deep)
+ {
+ AtomImplList::iterator it=res->GetAtomList().begin(),
+ it_end=res->GetAtomList().end();
+ for(;it!=it_end;++it)
+ {
+ AtomHandle atom=*it;
+ dst_res->InsertAtom(atom.Impl());
+ }
+ }
return dst_res;
}
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 5c11bde4b14c9ba2244c3b40537757ef0b9ba1a1..446c74052937d6947f6a6a4a4b04f0a733730cf7 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -105,7 +105,7 @@ public:
/// \brief append new residue with exactly the same parameters as res, but
/// no atoms and bonds
- ResidueImplPtr AppendResidue(const ResidueImplPtr& res);
+ ResidueImplPtr AppendResidue(const ResidueImplPtr& res, bool deep=true);
ResidueImplPtr InsertResidueBefore(int index, const ResNum& n,
const ResidueKey& k);
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 6942ce00fee8b3a93f45e31c083b90c51c80bdd3..6bdbd835c01b12f48930f2c89ce448a618a0328b 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -125,10 +125,19 @@ EntityImplPtr EntityImpl::Copy()
return ent_p;
}
-ChainImplPtr EntityImpl::InsertChain(const ChainImplPtr& chain)
+ChainImplPtr EntityImpl::InsertChain(const ChainImplPtr& chain, bool deep)
{
ChainImplPtr dst_chain=this->InsertChain(chain->GetName());
dst_chain->Assign(*chain.get());
+ if(deep)
+ {
+ ResidueImplList::iterator it=chain->GetResidueList().begin(),
+ it_end=chain->GetResidueList().end();
+ for(;it!=it_end;++it){
+ ResidueImplPtr res=*it;
+ dst_chain->AppendResidue(res, true);
+ }
+ }
return dst_chain;
}
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index ccbf85b449cdf035493096c73157a485dc9baea8..209858644faa69c8fd61628cd90d04803f899f8e 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -109,7 +109,7 @@ public:
/// \brief insert a new chain based on parameters of the given chain
///
/// The chain will have no residues and atoms
- ChainImplPtr InsertChain(const ChainImplPtr& chain);
+ ChainImplPtr InsertChain(const ChainImplPtr& chain, bool deep=false);
ConnectorImplP Connect(const AtomImplPtr& first, const AtomImplPtr& second,
Real len, Real theta, Real phi,
unsigned char bond_order);