diff --git a/modules/mol/base/pymod/export_bond.cc b/modules/mol/base/pymod/export_bond.cc
index 5f7ab1154ad0c785cca591fd5ee47c5b01ee700c..da2a31509575f4a80de3104667cfa18a8a7d89ac 100644
--- a/modules/mol/base/pymod/export_bond.cc
+++ b/modules/mol/base/pymod/export_bond.cc
@@ -21,7 +21,6 @@
using namespace boost::python;
-
#include <ost/mol/mol.hh>
using namespace ost;
@@ -61,4 +60,5 @@ void export_Bond()
.def(vector_indexing_suite<BondHandleList>())
.def(geom::VectorAdditions<BondHandleList>());
def("BondExists", &BondExists);
+
}
diff --git a/modules/mol/base/src/CMakeLists.txt b/modules/mol/base/src/CMakeLists.txt
index 8d206d3c61b193deb48942e563baadb31c4c5aa4..0a399125f5bbc75f3af8f7868d80cbff07dab30e 100644
--- a/modules/mol/base/src/CMakeLists.txt
+++ b/modules/mol/base/src/CMakeLists.txt
@@ -30,6 +30,7 @@ residue_handle.cc
residue_view.cc
surface_builder.cc
surface_handle.cc
+transfer_connectivity.cc
torsion_handle.cc
query_view_wrapper.cc
view_op.cc
@@ -87,6 +88,7 @@ builder.hh
surface_handle.hh
surface_prop.hh
torsion_handle.hh
+transfer_connectivity.hh
query_view_wrapper.hh
view_op.hh
view_type_fw.hh
diff --git a/modules/mol/base/src/builder.hh b/modules/mol/base/src/builder.hh
index 0a652a8b010ac97182a50e79591c00f6c3c6b81d..d46ed485bbe0c8ebf3d2ccf54e62347034b66915 100644
--- a/modules/mol/base/src/builder.hh
+++ b/modules/mol/base/src/builder.hh
@@ -26,6 +26,7 @@
#include "residue_handle.hh"
#include "chain_handle.hh"
#include "entity_handle.hh"
+#include "bond_handle.hh"
#include "xcs_editor.hh"
@@ -62,6 +63,27 @@ public:
edi_.InsertAtom(res_, name, pos);
return *this;
}
+ Builder& Gly(bool connect=true) {
+ this->Residue("GLY");
+ this->Atom("N");
+ this->Atom("CA");
+ this->Atom("C");
+ this->Atom("O");
+ if (connect) {
+ edi_.Connect(res_.FindAtom("N"), res_.FindAtom("CA"));
+ edi_.Connect(res_.FindAtom("CA"), res_.FindAtom("C"));
+ edi_.Connect(res_.FindAtom("C"), res_.FindAtom("O"));
+ }
+ return *this;
+ }
+ Builder& ConnectToPrev() {
+ AtomHandle ah = res_.FindAtom("N");
+ AtomHandle pa = res_.GetPrev().FindAtom("C");
+ if (pa) {
+ edi_.Connect(pa, ah);
+ }
+ return *this;
+ }
private:
EntityHandle ent_;
ChainHandle chain_;
diff --git a/modules/mol/base/src/transfer_connectivity.cc b/modules/mol/base/src/transfer_connectivity.cc
new file mode 100644
index 0000000000000000000000000000000000000000..38b1d6f151043611eac09762f9fcf4ec2f00272c
--- /dev/null
+++ b/modules/mol/base/src/transfer_connectivity.cc
@@ -0,0 +1,119 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include "transfer_connectivity.hh"
+#include "entity_visitor.hh"
+#include "residue_handle.hh"
+#include "atom_handle.hh"
+#include "bond_handle.hh"
+#include "xcs_editor.hh"
+
+
+namespace ost { namespace mol {
+
+namespace {
+
+class ConnectivityTransferVisitor : public EntityVisitor {
+public:
+ ConnectivityTransferVisitor(EntityHandle dst,
+ const std::map<ResidueHandle, ResidueHandle>* to_from):
+ edi_(dst.EditXCS(mol::BUFFERED_EDIT)), to_from_(to_from) {
+ }
+
+ bool VisitResidue(const ResidueHandle& dest_res) {
+ std::map<ResidueHandle, ResidueHandle>::const_iterator i = to_from_->find(dest_res);
+ if (i == to_from_->end()) {
+ return false;
+ }
+ const std::pair<ResidueHandle, ResidueHandle>& ft = *i;
+ if (!ft.second.IsValid()) {
+ return false;
+ }
+
+ // define a map from atom name to atom handle for the dest residue.
+ std::map<String, AtomHandle> name_to_handle;
+ AtomHandleList dest_atoms = dest_res.GetAtomList();
+ for (AtomHandleList::iterator j = dest_atoms.begin(), e = dest_atoms.end(); j !=e ; ++j) {
+ name_to_handle[j->GetName()] = *j;
+ }
+
+ AtomHandleList src_atoms = ft.second.GetAtomList();
+ for (AtomHandleList::iterator j = src_atoms.begin(), e = src_atoms.end(); j !=e ; ++j) {
+ BondHandleList bonds = j->GetBondList();
+ for (BondHandleList::iterator k = bonds.begin(), e2 = bonds.end(); k !=e2; ++k) {
+ AtomHandle first = k->GetFirst();
+ AtomHandle second = k->GetSecond();
+ AtomHandle dst_frst = this->GetDestAtomForSrcAtom(first, ft.second, ft.first,
+ name_to_handle);
+ AtomHandle dst_scnd = this->GetDestAtomForSrcAtom(second, ft.second, ft.first,
+ name_to_handle);
+ // add bond...
+ if (!dst_frst || !dst_scnd) {
+ continue;
+ }
+ edi_.Connect(dst_frst, dst_scnd);
+ }
+ }
+ return false;
+ }
+
+ AtomHandle GetDestAtomForSrcAtom(AtomHandle src_atom, ResidueHandle src_res,
+ ResidueHandle dst_res,
+ const std::map<String, AtomHandle>& name_to_atom) {
+ ResidueHandle r = src_atom.GetResidue();
+ if (r == src_res) {
+ // fast track...
+ std::map<String, AtomHandle>::const_iterator i = name_to_atom.find(src_atom.GetName());
+ return i == name_to_atom.end() ? AtomHandle() : i->second;
+ }
+ // educated guess: we are trying to connect to the previous/next residue
+ std::map<ResidueHandle, ResidueHandle>::const_iterator j;
+ j = to_from_->find(dst_res.GetPrev());
+ if (j != to_from_->end()) {
+ if (j->second == r) {
+ return j->first.FindAtom(src_atom.GetName());
+ }
+ }
+ j = to_from_->find(dst_res.GetNext());
+ if (j != to_from_->end()) {
+ if (j->second == r) {
+ return j->first.FindAtom(src_atom.GetName());
+ }
+ }
+ // still nothing. scan linearly through all residues.
+ for ( j = to_from_->begin(); j != to_from_->end(); ++j) {
+ if (j->second == r) {
+ return j->first.FindAtom(src_atom.GetName());
+ }
+ }
+ return AtomHandle();
+ }
+private:
+ XCSEditor edi_;
+ const std::map<ResidueHandle, ResidueHandle>* to_from_;
+};
+
+}
+void TransferConnectivity(EntityHandle dest,
+ const std::map<ResidueHandle, ResidueHandle>& to_from) {
+ ConnectivityTransferVisitor visitor(dest, &to_from);
+ dest.Apply(visitor);
+}
+
+}}
diff --git a/modules/mol/base/src/transfer_connectivity.hh b/modules/mol/base/src/transfer_connectivity.hh
new file mode 100644
index 0000000000000000000000000000000000000000..e46691cd25d920ff1268f52d730ef70f2662d464
--- /dev/null
+++ b/modules/mol/base/src/transfer_connectivity.hh
@@ -0,0 +1,37 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_MOL_TRANSFER_CONNECTIVITY_HH
+#define OST_MOL_TRANSFER_CONNECTIVITY_HH
+
+
+#include "module_config.hh"
+#include "entity_handle.hh"
+#include "residue_handle.hh"
+
+namespace ost { namespace mol {
+
+void DLLEXPORT_OST_MOL
+TransferConnectivity(EntityHandle dest, const std::map<ResidueHandle, ResidueHandle>& to_from);
+
+
+bool operator<(const ResidueHandle& lhs, const ResidueHandle& rhs) {
+ return lhs.GetHashCode()<rhs.GetHashCode();
+}
+}}
+#endif
diff --git a/modules/mol/base/tests/CMakeLists.txt b/modules/mol/base/tests/CMakeLists.txt
index 176f6ad2421f1d381eaf4800c4f2ec3ad2419325..20f039557801f6a0c672550fb230306f59b418ba 100644
--- a/modules/mol/base/tests/CMakeLists.txt
+++ b/modules/mol/base/tests/CMakeLists.txt
@@ -12,6 +12,7 @@ set(OST_MOL_BASE_UNIT_TESTS
test_surface.cc
test_residue.cc
test_view.cc
+ test_transfer_connectivity.cc
test_view_op.cc
tests.cc
)
diff --git a/modules/mol/base/tests/test_transfer_connectivity.cc b/modules/mol/base/tests/test_transfer_connectivity.cc
new file mode 100644
index 0000000000000000000000000000000000000000..2f5dff1439bf64099a9e109d6336ac6dc54b8737
--- /dev/null
+++ b/modules/mol/base/tests/test_transfer_connectivity.cc
@@ -0,0 +1,78 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+/*
+ * Authors: Marco Biasini
+ */
+
+#include <ost/mol/builder.hh>
+#include <ost/mol/transfer_connectivity.hh>
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
+using namespace ost;
+using namespace ost::mol;
+
+BOOST_AUTO_TEST_SUITE( mol_transfer_conn );
+
+BOOST_AUTO_TEST_CASE(test_transfer_conn)
+{
+ EntityHandle ent = Builder()
+ .Chain("A")
+ .Gly()
+ .Gly()
+ .ConnectToPrev()
+ .Gly()
+ .ConnectToPrev()
+ ;
+
+ ent.EditXCS().Connect(ent.FindAtom("A", 1, "O"), ent.FindAtom("A", 3, "O"));
+
+ EntityHandle ent2 = Builder()
+ .Chain("A")
+ .Gly(false)
+ .Gly(false)
+ .Gly(false)
+ ;
+ std::map<ResidueHandle, ResidueHandle> to_from;
+ ResidueHandleList r1 = ent.GetResidueList();
+ ResidueHandleList r2 = ent2.GetResidueList();
+ for (size_t i = 0;i<r1.size(); ++i) {
+ to_from[r2[i]] = r1[i];
+ }
+ TransferConnectivity(ent2, to_from);
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 1, "N"), ent2.FindAtom("A", 1, "CA")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 1, "CA"), ent2.FindAtom("A", 1, "C")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 1, "C"), ent2.FindAtom("A", 1, "O")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 1, "C"), ent2.FindAtom("A", 2, "N")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 2, "N"), ent2.FindAtom("A", 2, "CA")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 2, "CA"), ent2.FindAtom("A", 2, "C")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 2, "C"), ent2.FindAtom("A", 2, "O")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 2, "C"), ent2.FindAtom("A", 3, "N")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 3, "N"), ent2.FindAtom("A", 3, "CA")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 3, "CA"), ent2.FindAtom("A", 3, "C")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 3, "C"), ent2.FindAtom("A", 3, "O")));
+ BOOST_CHECK(BondExists(ent2.FindAtom("A", 1, "O"), ent2.FindAtom("A", 3, "O")));
+ BOOST_CHECK_EQUAL(12, ent2.GetBondCount());
+}
+
+
+
+BOOST_AUTO_TEST_SUITE_END();