diff --git a/modules/base/tests/test_generic_property.cc b/modules/base/tests/test_generic_property.cc
index 9fad50c49e5e876868e995518cf8419975987120..8b946685cbb0da482e024adf87c0901a09217119 100644
--- a/modules/base/tests/test_generic_property.cc
+++ b/modules/base/tests/test_generic_property.cc
@@ -29,7 +29,7 @@ BOOST_AUTO_TEST_SUITE( base )
BOOST_AUTO_TEST_CASE( test_generic_property )
{
EntityHandle eh=CreateEntity();
- XCSEditor editor=eh.RequestXCSEditor();
+ XCSEditor editor=eh.EditXCS();
ChainHandle ch=editor.InsertChain("A");
ResidueHandle res = editor.AppendResidue(ch, "X");
AtomHandle atom = editor.InsertAtom(res, "Y",geom::Vec3());
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 9405a31df86e42656ac449db07679968af097928..04db235931de9885850cc2c412cb8ed7038c6399 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -120,10 +120,12 @@ def _RunTmScore(tmscore, tmp_dir):
model2_filename=os.path.join(tmp_dir, 'model02.pdb')
if platform.system() == "Windows":
tmscore_path=settings.Locate('tmscore.exe', explicit_file_name=tmscore)
- command="\"%s\" %s %s" %(os.path.normpath(tmscore_path), model1_filename, model2_filename)
+ command="\"%s\" %s %s" %(os.path.normpath(tmscore_path), model1_filename,
+ model2_filename)
else:
tmscore_path=settings.Locate('tmscore', explicit_file_name=tmscore)
- command="\"%s\" \"%s\" \"%s\"" %(tmscore_path, model1_filename, model2_filename)
+ command="\"%s\" \"%s\" \"%s\"" % (tmscore_path, model1_filename,
+ model2_filename)
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
ps.wait()
lines=ps.stdout.readlines()
@@ -137,7 +139,7 @@ def TMAlign(model1, model2, tmalign=None):
"""
tmp_dir_name=_SetupFiles((model1, model2))
result=_RunTmAlign(tmalign, tmp_dir_name)
- model1.handle.RequestXCSEditor().ApplyTransform(result.transform)
+ model1.handle.EditXCS().ApplyTransform(result.transform)
_CleanupFiles(tmp_dir_name)
return result
def TMScore(model1, model2, tmscore=None):
@@ -146,6 +148,6 @@ def TMScore(model1, model2, tmscore=None):
"""
tmp_dir_name=_SetupFiles((model1, model2))
result=_RunTmScore(tmscore, tmp_dir_name)
- model1.handle.RequestXCSEditor().ApplyTransform(result.transform)
+ model1.handle.EditXCS().ApplyTransform(result.transform)
_CleanupFiles(tmp_dir_name)
return result
diff --git a/modules/conop/src/builder.cc b/modules/conop/src/builder.cc
index 9fce604d833a0d25508c231360a95642a48e5152..60bf273a5d08b374707c93afdbaccb84741364d9 100644
--- a/modules/conop/src/builder.cc
+++ b/modules/conop/src/builder.cc
@@ -168,7 +168,7 @@ void Builder::AssignBackBoneTorsionsToResidue(mol::ResidueHandle res)
mol::ResidueHandle prev=res.GetPrev();
mol::ResidueHandle next=res.GetNext();
- mol::XCSEditor e=res.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor e=res.GetEntity().EditXCS(mol::BUFFERED_EDIT);
//psi
if (next.IsValid() && next.IsPeptideLinking()){
mol::AtomHandle ca_this=res.FindAtom("CA");
@@ -209,7 +209,7 @@ void Builder::AssignBackBoneTorsionsToResidue(mol::ResidueHandle res)
void Builder::DistanceBasedConnect(mol::AtomHandle atom)
{
mol::EntityHandle ent=atom.GetEntity();
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
mol::AtomHandleList alist = ent.FindWithin(atom.GetPos(),4.0);
mol::ResidueHandle res_a=atom.GetResidue();
for (mol::AtomHandleList::const_iterator it=alist.begin(),
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index e992fd7d5ca8667afe8b2738e25173e0c120119b..f546f520459dc072f1095fabd2d484da7d1e0b9a 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -262,7 +262,7 @@ void Conopology::ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flag)
{
Profile profile_connect("ConnectAll");
LOG_DEBUG("Conopology: ConnectAll: building internal coordinate system");
- mol::XCSEditor xcs_e=eh.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor xcs_e=eh.EditXCS(mol::BUFFERED_EDIT);
PropAssigner a(b);
eh.Apply(a);
LOG_DEBUG("Conopology: ConnectAll: connecting all bonds");
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 55f548ae37b97fa43eb564d8a1f93cec8d1da5d7..c808dbd083f43204855c10c9dd24ff768d312508 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -195,7 +195,7 @@ void HeuristicBuilder::ConnectivityFromAtomNames(const mol::ResidueHandle& res,
mol::AtomHandleList& unknown_atoms) {
unknown_atoms.clear();
mol::AtomHandleList atomlist=res.GetAtomList();
- mol::XCSEditor editor=res.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=res.GetEntity().EditXCS(mol::BUFFERED_EDIT);
for (mol::AtomHandleList::iterator it1=atomlist.begin();it1!=atomlist.end();++it1) {
if (centry.HasAtom(it1->GetName())) {
mol::AtomHandleList::iterator it2=it1;
@@ -265,7 +265,7 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
{
static String fname=flag ? "HeuristicBuilder: ConnectNextXCS" : "HeuristicBuilder: ConnectPrevXCS";
if(!res0) return; // return if invalid
- mol::XCSEditor editor=res0.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=res0.GetEntity().EditXCS(mol::BUFFERED_EDIT);
LOG_DEBUG(fname << " on " << res0.GetKey() << " " << res0.GetNumber());
if(!res1) {
@@ -333,7 +333,7 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
void HeuristicBuilder::AssignTorsionsToResidue(mol::ResidueHandle res)
{
- mol::XCSEditor editor=res.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=res.GetEntity().EditXCS(mol::BUFFERED_EDIT);
mol::ChainHandle chain=res.GetChain();
std::pair<detail::ConnResEntry,bool> centry2 = LookupResEntry(res.GetKey());
if (centry2.second) {
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index bd7b5cfcade5f2b814f0f5fc4da5bd3e9a399660..03bfb13a25deba48e28b5f24aa46a44a7954b757 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -202,7 +202,7 @@ void RuleBasedBuilder::ConnectAtomsOfResidue(mol::ResidueHandle rh)
dist_connect(this, rh.GetAtomList());
return;
}
- mol::XCSEditor e=rh.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor e=rh.GetEntity().EditXCS(mol::BUFFERED_EDIT);
BondSpecList::const_iterator j=last_compound_->GetBondSpecs().begin();
mol::AtomHandleList atoms=rh.GetAtomList();
for(; j!=last_compound_->GetBondSpecs().end(); ++j) {
@@ -232,7 +232,7 @@ void RuleBasedBuilder::ConnectResidueToNext(mol::ResidueHandle rh,
return;
}
Compound::Dialect dialect=this->GetDialect()==PDB_DIALECT ? Compound::PDB : Compound::CHARMM;
- mol::XCSEditor e=rh.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor e=rh.GetEntity().EditXCS(mol::BUFFERED_EDIT);
CompoundPtr mc=compound_lib_->FindCompound(rh.GetName(), dialect);
CompoundPtr nc=compound_lib_->FindCompound(next.GetName(), dialect);
if (!(mc && nc))
diff --git a/modules/conop/tests/test_heuristic_builder.cc b/modules/conop/tests/test_heuristic_builder.cc
index 473ff46dd7c1addd82403eeebdfd09e15793ccdb..33a1aaa7606a8fcfce335c28102293b83f98b48e 100644
--- a/modules/conop/tests/test_heuristic_builder.cc
+++ b/modules/conop/tests/test_heuristic_builder.cc
@@ -33,7 +33,7 @@ namespace {
ResidueHandle make_arg(ChainHandle chain)
{
- XCSEditor e=chain.GetEntity().RequestXCSEditor();
+ XCSEditor e=chain.GetEntity().EditXCS();
ResidueHandle res = e.AppendResidue(chain, "ARG");
e.InsertAtom(res, "N",geom::Vec3(20.202,33.112,58.011));
e.InsertAtom(res, "CA",geom::Vec3(19.396,31.903,58.033));
@@ -51,7 +51,7 @@ ResidueHandle make_arg(ChainHandle chain)
ResidueHandle make_leu(ChainHandle chain)
{
- XCSEditor e=chain.GetEntity().RequestXCSEditor();
+ XCSEditor e=chain.GetEntity().EditXCS();
ResidueHandle res=e.AppendResidue(chain, "LEU");
e.InsertAtom(res, "N", geom::Vec3(19.003,32.473,60.366));
@@ -146,7 +146,7 @@ BOOST_AUTO_TEST_SUITE( conop )
BOOST_AUTO_TEST_CASE(name_based_connect)
{
EntityHandle e=CreateEntity();
- ChainHandle c=e.RequestXCSEditor().InsertChain("A");
+ ChainHandle c=e.EditXCS().InsertChain("A");
ResidueHandle ile=make_leu(c);
ResidueHandle arg=make_arg(c);
HeuristicBuilder heuristic_builder;
@@ -164,7 +164,7 @@ BOOST_AUTO_TEST_CASE(name_based_connect)
BOOST_AUTO_TEST_CASE(test_assign_torsions){
EntityHandle e=CreateEntity();
- ChainHandle c=e.RequestXCSEditor().InsertChain("A");
+ ChainHandle c=e.EditXCS().InsertChain("A");
ResidueHandle l1=make_leu(c);
ResidueHandle a2=make_arg(c);
ResidueHandle l3=make_leu(c);
@@ -178,7 +178,7 @@ BOOST_AUTO_TEST_CASE(test_assign_torsions){
heuristic_builder.ConnectAtomsOfResidue(l1);
heuristic_builder.ConnectAtomsOfResidue(a2);
heuristic_builder.ConnectAtomsOfResidue(l3);
- XCSEditor edi=e.RequestXCSEditor();
+ XCSEditor edi=e.EditXCS();
edi.Connect(l1.FindAtom("C"), a2.FindAtom("N"));
edi.Connect(a2.FindAtom("C"), l3.FindAtom("N"));
heuristic_builder.AssignTorsions(c);
diff --git a/modules/gui/src/file_loader.cc b/modules/gui/src/file_loader.cc
index a874742bce365399da8a5c89328fd2d19436a1e3..ac35f1a6a0bc03873dc1bdcebbdcde023b4df2eb 100644
--- a/modules/gui/src/file_loader.cc
+++ b/modules/gui/src/file_loader.cc
@@ -245,7 +245,7 @@ gfx::GfxObjP FileLoader::TryLoadEntity(const QString& filename, io::EntityIOHand
else{
QFileInfo file_info(filename);
mol::EntityHandle eh=mol::CreateEntity();
- mol::XCSEditor xcs_lock=eh.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor xcs_lock=eh.EditXCS(mol::BUFFERED_EDIT);
handler->Import(eh,filename.toStdString());
if(handler->RequiresBuilder()) {
conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index 88286b78e628d869a96ee89456c8070374545c53..02817c2a990252481528e0451b88cb9c8df67b0b 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -87,7 +87,7 @@ void CRDReader::Import(mol::EntityHandle& ent)
void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
{
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
LOG_TRACE( "line: [" << line << "]" );
@@ -257,7 +257,7 @@ mol::EntityHandle LoadCRD(const String& file_name)
conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
CRDReader reader(file_name);
mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
reader.Import(ent);
conop::Conopology::Instance().ConnectAll(builder,ent);
return ent;
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index f5def7a3e0e6c944fd3bd8652fc376d4e8f9fd0b..b48cdd551bc4279f02668ab682e90a6f346f2f04 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -119,7 +119,7 @@ void MAEReader::Import(mol::EntityHandle& ent)
int i_res_num=-1;
int i_chain_name=-1;
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
while(std::getline(in_,line)) {
line = boost::trim_copy(line);
@@ -325,7 +325,7 @@ mol::EntityHandle LoadMAE(const String& file_name)
conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
MAEReader reader(file_name);
mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
reader.Import(ent);
conop::Conopology::Instance().ConnectAll(builder,ent);
return ent;
diff --git a/modules/io/src/mol/load_entity.cc b/modules/io/src/mol/load_entity.cc
index 4eda99b4a01acb435819e0a9f3905e5e01db9a39..f35178546f766148e7d5317a1c1286969ca90198 100644
--- a/modules/io/src/mol/load_entity.cc
+++ b/modules/io/src/mol/load_entity.cc
@@ -60,7 +60,7 @@ mol::EntityHandle LoadEntity(const String& filename, int flag)
{
LOG_DEBUG("creating emtpy entity");
mol::EntityHandle eh=mol::CreateEntity();
- mol::XCSEditor xcs_lock=eh.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor xcs_lock=eh.EditXCS(mol::BUFFERED_EDIT);
Import(eh,filename,flag);
return eh;
}
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 969d9ffa158269e26a8e885b64d3b37121b4fbc3..b3059d49f3ac9f01a39e1c4a3ec082b3712488b4 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -411,7 +411,7 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
if (!this->EnsureLineLength(line, 54)) {
return;
}
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
char alt_loc=0;
String chain_name;
StringRef res_name, atom_name;
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index a7f70c916adf46b04133aca145d0809b721c3836..09dea4696191fd9e0c7878b20776d3ba8aaf6cfa 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -54,7 +54,7 @@ SDFReader::SDFReader(std::istream& instream)
void SDFReader::Import(mol::EntityHandle& ent)
{
String line;
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
while (std::getline(instream_,line)) {
++line_num;
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index fe1abe329fcb5b408dbcc397583cd462ff119a88..292495a1de60d07b195da26d54a81e132c3e6eb5 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -221,7 +221,7 @@ BOOST_AUTO_TEST_CASE(write_atom)
PDBWriter writer(out);
mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor edi=ent.RequestXCSEditor();
+ mol::XCSEditor edi=ent.EditXCS();
mol::ChainHandle ch=edi.InsertChain("A");
mol::ResidueHandle r=edi.AppendResidue(ch, "GLY");
@@ -242,7 +242,7 @@ BOOST_AUTO_TEST_CASE(write_hetatom)
PDBWriter writer(out);
mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor edi=ent.RequestXCSEditor();
+ mol::XCSEditor edi=ent.EditXCS();
mol::ChainHandle ch=edi.InsertChain("A");
mol::ResidueHandle r=edi.AppendResidue(ch, "CA");
mol::AtomHandle a=edi.InsertAtom(r, "CA", geom::Vec3(32.0, -128.0, -2.5),
@@ -380,7 +380,7 @@ BOOST_AUTO_TEST_CASE(res_name_too_long)
PDBWriter writer(out);
mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor edi=ent.RequestXCSEditor();
+ mol::XCSEditor edi=ent.EditXCS();
mol::ChainHandle ch=edi.InsertChain("A");
mol::ResidueHandle r=edi.AppendResidue(ch, "CALCIUM");
mol::AtomHandle a=edi.InsertAtom(r, "CA", geom::Vec3(32.0, -128.0, -2.5));
@@ -393,7 +393,7 @@ BOOST_AUTO_TEST_CASE(chain_name_too_long)
PDBWriter writer(out);
mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor edi=ent.RequestXCSEditor();
+ mol::XCSEditor edi=ent.EditXCS();
mol::ChainHandle ch=edi.InsertChain("AB");
mol::ResidueHandle r=edi.AppendResidue(ch, "CA");
mol::AtomHandle a=edi.InsertAtom(r, "CA", geom::Vec3(32.0, -128.0, -2.5));
@@ -406,7 +406,7 @@ BOOST_AUTO_TEST_CASE(atom_name_too_long)
PDBWriter writer(out);
mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor edi=ent.RequestXCSEditor();
+ mol::XCSEditor edi=ent.EditXCS();
mol::ChainHandle ch=edi.InsertChain("A");
mol::ResidueHandle r=edi.AppendResidue(ch, "CA");
mol::AtomHandle a=edi.InsertAtom(r, "CALCIUM", geom::Vec3(32.0, -128.0, -2.5));
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
index bd88902b0e181bb29f62da86ae41367137b23ded..cea1ea47d1e37140b7920814e27e5aa830388457 100644
--- a/modules/mol/alg/src/local_dist_test.cc
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -121,7 +121,7 @@ Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
// Residues with symmetric side-chains require special treatment as there are
// two possible ways to name the atoms. We calculate the overlap with the
// fixed atoms and take the solution that gives bigger scores.
- XCSEditor edi=ref.GetHandle().RequestXCSEditor(BUFFERED_EDIT);
+ XCSEditor edi=ref.GetHandle().EditXCS(BUFFERED_EDIT);
for (ResidueViewList::iterator
i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
const String rname=i->GetName();
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index 191871a9c888eca76ef2672def7d08e71281523c..90b6a8c04a6adbddbcd63cc9859ea579ad95d374 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -354,7 +354,7 @@ SuperpositionResult SuperposeAtoms(const mol::AtomViewList& atoms1,
res.ncycles=1;
mol::AtomView jv=atoms1.front();
if (apply_transform){
- mol::XCSEditor ed=jv.GetResidue().GetChain().GetEntity().GetHandle().RequestXCSEditor();
+ mol::XCSEditor ed=jv.GetResidue().GetChain().GetEntity().GetHandle().EditXCS();
ed.ApplyTransform(res.transformation);
}
return res;
@@ -381,7 +381,7 @@ SuperpositionResult SuperposeSVD(const mol::EntityView& ev1,
//save rmsd info
res.rmsd=CalculateRMSD(ev1, ev2, res.transformation);
if (apply_transform){
- mol::XCSEditor ed=ev1.GetHandle().RequestXCSEditor();
+ mol::XCSEditor ed=ev1.GetHandle().EditXCS();
ed.ApplyTransform(res.transformation);
}
return res;
@@ -457,7 +457,7 @@ SuperpositionResult IterativeSuperposition(mol::EntityView& ev1,
result.entity_view2=CreateViewFromAtomList(atoms_b);
if (apply_transform){
- mol::XCSEditor ed=ev1.GetHandle().RequestXCSEditor();
+ mol::XCSEditor ed=ev1.GetHandle().EditXCS();
ed.ApplyTransform(result.transformation);
}
return result;
diff --git a/modules/mol/alg/tests/test_superposition.cc b/modules/mol/alg/tests/test_superposition.cc
index 599e0e31ca8461a1302b6f9ec8b77131a66cbcb6..0d18b1aa8cb623655c332a7305de485307112d5a 100644
--- a/modules/mol/alg/tests/test_superposition.cc
+++ b/modules/mol/alg/tests/test_superposition.cc
@@ -34,7 +34,7 @@ struct Fixture {
Fixture() {
e=CreateEntity();
- XCSEditor ed=e.RequestXCSEditor();
+ XCSEditor ed=e.EditXCS();
c=ed.InsertChain("A");
r=ed.AppendResidue(c, "XXX");
ab=ed.InsertAtom(r, "A", geom::Vec3(-5,-5,-5), "C");
@@ -84,7 +84,7 @@ BOOST_AUTO_TEST_CASE(superposition_svd)
{
Fixture f1, f2;
EntityView ev1 = f1.e.CreateFullView();
- XCSEditor ed=f1.e.RequestXCSEditor();
+ XCSEditor ed=f1.e.EditXCS();
EntityView ev2 = f2.e.CreateFullView();
ChainHandle ch1=f1.e.GetChainList()[0];
ResidueHandleIter rit=ch1.ResiduesBegin();
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index e6bebee7c94e7f83b8fba0c83685cc930e039002..8099919ae73b3c596c77256d0a746d5d3edabf33 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -143,7 +143,7 @@ The Handle Classes
See :attr:`atoms`
- .. method:: RequestXCSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+ .. method:: EditXCS([edit_mode=mol.EditMode.BUFFERED_EDIT])
Request :class:`XCSEditor` for editing the external coordinate system. This
call will fail when there are pending changes of the internal coordinate
@@ -156,7 +156,7 @@ The Handle Classes
:returns: :class:`XCSEditor`
- .. method:: RequestICSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+ .. method:: EditICS([edit_mode=mol.EditMode.BUFFERED_EDIT])
Request :class:`ICSEditor` for editing the internal coordinate system, such
as torsions, bond lengths and angle between two bonds. This call will fail
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 91926f2e797135940d00faeb1f544b07b0d89542..8c485cb7f0d2c52bbf08ea99c92d6d7d9fb1f39a 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -59,12 +59,7 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_insert_atom_overloads,
}
void export_Editors()
-{
- enum_<EditMode>("EditMode")
- .value("BUFFERED_EDIT", BUFFERED_EDIT)
- .value("UNBUFFERED_EDIT", UNBUFFERED_EDIT)
- ;
-
+{
class_<EditorBase>("EditorBase", no_init)
.def("InsertChain", &EditorBase::InsertChain)
.def("InsertAtom", &EditorBase::InsertAtom,
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index b0df16c0c9065f8084127b48a1055cd29090d849..b8fcff8a959679f64573b905cb9880737d703549 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -49,11 +49,20 @@ StringMethod select_string=&EntityHandle::Select;
Real (EntityHandle::*get_angle1)(const AtomHandle&, const AtomHandle&, const AtomHandle&) const = &EntityHandle::GetAngle;
Real (EntityHandle::*get_angle2)(const AtomView&, const AtomView&, const AtomView&) const = &EntityHandle::GetAngle;
+
+XCSEditor depr_request_xcs_editor(EntityHandle e, EditMode m)
+{
+ WARN_DEPRECATED("EntityHandle::RequestXCSEditor is deprecated. Use "
+ "EntityHandle::EditXCS instead");
+ return e.EditXCS(m);
+}
-BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_xcs_editor_overloads,
- EntityHandle::RequestXCSEditor, 0, 1)
-BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_ics_editor_overloads,
- EntityHandle::RequestICSEditor, 0, 1)
+ICSEditor depr_request_ics_editor(EntityHandle e, EditMode m)
+{
+ WARN_DEPRECATED("EntityHandle::RequestICSEditor is deprecated. Use "
+ "EntityHandle::EditICS instead");
+ return e.EditICS(m);
+}
}
@@ -121,10 +130,11 @@ void export_Entity()
.add_property("transform",
make_function(&EntityHandle::GetTransformationMatrix,
return_value_policy<copy_const_reference>()))
- .def("RequestICSEditor", &EntityHandle::RequestICSEditor,
- X_ics_editor_overloads(args("mode")))
- .def("RequestXCSEditor", &EntityHandle::RequestXCSEditor,
- X_xcs_editor_overloads(args("mode")))
+
+ .def("EditXCS", &EntityHandle::EditXCS, arg("mode")=UNBUFFERED_EDIT)
+ .def("EditICS", &EntityHandle::EditICS, arg("mode")=UNBUFFERED_EDIT)
+ .def("RequestXCSEditor", &depr_request_xcs_editor, arg("mode")=UNBUFFERED_EDIT)
+ .def("RequestICSEditor", &depr_request_ics_editor, arg("mode")=UNBUFFERED_EDIT)
.def("IsTransformationIdentity",&EntityHandle::IsTransformationIdentity)
.def(self==self)
.def(self!=self)
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index 6885a79020eb5a667a498766a7ae6c07df7c54e8..800af3a1ce108e979faaa9f50180b4f5fa0f0740 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -18,6 +18,7 @@
//------------------------------------------------------------------------------
#include <boost/python.hpp>
#include <ost/mol/transform.hh>
+#include <ost/mol/editor_base.hh>
#include <ost/info/info.hh>
using namespace boost::python;
@@ -44,6 +45,10 @@ void export_QueryViewWrapper();
void export_EntityPropertyMapper();
BOOST_PYTHON_MODULE(_mol)
{
+ enum_<EditMode>("EditMode")
+ .value("BUFFERED_EDIT", BUFFERED_EDIT)
+ .value("UNBUFFERED_EDIT", UNBUFFERED_EDIT)
+ ;
export_Entity();
export_Surface();
export_Query();
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index 6de12176fc090aa013d084ecf1bd178153778011..a8719ab960b8e367aca7be53590d025f182de08b 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -188,7 +188,7 @@ void AtomBase::SetCharge(Real charge)
void AtomBase::SetRadius(Real radius)
{
this->CheckValidity();
- Impl()->SetCharge(radius);
+ Impl()->SetRadius(radius);
}
const geom::Mat3& AtomBase::GetAnisou() const
diff --git a/modules/mol/base/src/chain_handle.hh b/modules/mol/base/src/chain_handle.hh
index 6337818deeebc8356c1a08421173edc39da076ee..514188612bd03e31fea1556dfa4856924223f046 100644
--- a/modules/mol/base/src/chain_handle.hh
+++ b/modules/mol/base/src/chain_handle.hh
@@ -46,7 +46,7 @@ namespace ost { namespace mol {
/// the residue numbers are in ascending order.
///
/// New residues are inserted via one of the editors obtained from
-/// EntityHandle::RequestXCSEditor() or EntityHandle::RequestICSEditor(). To
+/// EntityHandle::EditXCS() or EntityHandle::EditICS(). To
/// append a residue to the C-terminal end, use EditorBase::AppendResidue, to
/// insert after or before a specific residue, EditorBase::InsertResidueAfter
/// and ditorBase::InsertResidueABefore will do the job, respectively.
diff --git a/modules/mol/base/src/chem_class.hh b/modules/mol/base/src/chem_class.hh
index f9c0f8279666df6fee4f2370b2ed40ba29432203..43bdef9a85cbcfc623c95eda4de7314071378fbc 100644
--- a/modules/mol/base/src/chem_class.hh
+++ b/modules/mol/base/src/chem_class.hh
@@ -18,16 +18,13 @@
//------------------------------------------------------------------------------
#ifndef OST_BASE_CHEM_CLASS_HI
#define OST_BASE_CHEM_CLASS_HI
-#include <vector>
-
-#include <boost/shared_ptr.hpp>
#include <ost/mol/module_config.hh>
namespace ost { namespace mol {
-struct ChemClass {
+struct DLLEXPORT ChemClass {
const static char PeptideLinking ='P';
const static char DPeptideLinking ='D';
const static char LPeptideLinking ='L';
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index 37d1fbd91cf9ce4dba16bb3614909cf77f064111..db02718fd5bec7c2721ddf11ec3eca4bc55e0932 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -63,7 +63,7 @@ void CoordSource::CopyFrame(uint frame_id)
return;
}
assert(frame->size()==atoms_.size());
- XCSEditor edi=atoms_.front().GetEntity().RequestXCSEditor(BUFFERED_EDIT);
+ XCSEditor edi=atoms_.front().GetEntity().EditXCS(BUFFERED_EDIT);
CoordFrame::const_iterator c=frame->begin();
for (AtomHandleList::iterator i=atoms_.begin(),
e=atoms_.end(); i!=e; ++i, ++c) {
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index e8a11272657de25b909201a73eca6fb2bb42e64e..c0ee9135024a7b0cfb28d3e15ab0f3784c7c6727 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -39,8 +39,8 @@ namespace ost { namespace mol {
/// Editors are usually used as one of the concrete subclasses of EditorBase:
/// XCSEditor and ICSEditor. The former operates on the external carthesian
/// coordinate system while the latter operates on the internal coordinate
-/// system. To create a new editor, use EntityHandle::RequestXCSEditor() and
-/// EntityHandle::RequestICSEditor(), respectively.
+/// system. To create a new editor, use EntityHandle::EditXCS() and
+/// EntityHandle::EditICS(), respectively.
///
/// For an introduction to the concept of editors go \ref editors "here"
class DLLEXPORT_OST_MOL EditorBase {
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index 17c47cd81112c92ef308c598cf7c03202a1c6648..1de8bff483b9d256e0784fc68b054c31d30010e7 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -304,13 +304,13 @@ AtomHandleIter EntityHandle::AtomsEnd() const
impl::end(r.back()->GetAtomList()), ent, false);
}
-XCSEditor EntityHandle::RequestXCSEditor(EditMode mode) const
+XCSEditor EntityHandle::EditXCS(EditMode mode) const
{
this->CheckValidity();
return XCSEditor(*this, mode);
}
-ICSEditor EntityHandle::RequestICSEditor(EditMode mode) const
+ICSEditor EntityHandle::EditICS(EditMode mode) const
{
this->CheckValidity();
Impl()->EnableICS();
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 540425c70219e49396c29ce19ef54850712edd70..d67d9c754d20d22ddb67ec156315388fef76be6d 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -263,12 +263,12 @@ public:
/// \brief Get editor for external coordinate system to manipulate atom
/// positions
/// \sa editors
- XCSEditor RequestXCSEditor(EditMode mode=UNBUFFERED_EDIT) const;
+ XCSEditor EditXCS(EditMode mode=UNBUFFERED_EDIT) const;
/// \brief Get editor for the internal coordinate system to manipulate
/// torsions bond lengths and angles between bonds
/// \sa editors
- ICSEditor RequestICSEditor(EditMode mode=UNBUFFERED_EDIT) const;
+ ICSEditor EditICS(EditMode mode=UNBUFFERED_EDIT) const;
/// \brief get this handle
///
diff --git a/modules/mol/base/src/impl/atom_impl.hh b/modules/mol/base/src/impl/atom_impl.hh
index 90507b1029575ad86c811d68a07c7142a514d438..f13b729cba5c4ccfe00f98da5f340c05ef96dbf1 100644
--- a/modules/mol/base/src/impl/atom_impl.hh
+++ b/modules/mol/base/src/impl/atom_impl.hh
@@ -119,7 +119,7 @@ public:
prop_=impl::AtomProp::GetDefaultProps(element_);
}
}
-
+ bool HasDefaultProps() const { return prop_->is_default; }
void SetAnisou(const geom::Mat3& anisou)
{
if (prop_->is_default && prop_->anisou!=anisou) {
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 77948203633cb010a0a81da80dd582643f6cf327..64fed74185c0efa3759a64780c6634035232eeea 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -66,6 +66,7 @@ ResidueImplPtr ChainImpl::AppendResidue(const ResidueImplPtr& res)
dst_res->SetOneLetterCode(res->GetOneLetterCode());
dst_res->SetSecStructure(res->GetSecStructure());
dst_res->SetChemClass(res->GetChemClass());
+ dst_res->SetProtein(res->IsProtein());
return dst_res;
}
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index ef6ffd7291e2cf513c20d2047d4e9fe01478b996..1f2fe7faf12ffed48227845659186bc20e02c7f7 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -61,8 +61,19 @@ AtomImplPtr ResidueImpl::InsertAtom(const AtomImplPtr& atom)
AtomImplPtr dst_atom=this->InsertAtom(atom->GetName(),
atom->GetPos(),
atom->GetElement());
+
dst_atom->Assign(*atom.get());
dst_atom->SetState(atom->GetState());
+ dst_atom->SetBFactor(atom->GetBFactor());
+ dst_atom->SetOccupancy(atom->GetOccupancy());
+ dst_atom->SetHetAtom(atom->IsHetAtom());
+
+ if (!atom->HasDefaultProps()) {
+ dst_atom->SetRadius(atom->GetRadius());
+ dst_atom->SetCharge(atom->GetCharge());
+ dst_atom->SetMass(atom->GetMass());
+ dst_atom->SetAnisou(atom->GetAnisou());
+ }
return dst_atom;
}
diff --git a/modules/mol/base/src/residue_handle.hh b/modules/mol/base/src/residue_handle.hh
index 83890f3afb5741bf410bbc9e9fc126aac67e609a..3dc7e85def436e2327f6058c6cd5d7ca645c46fb 100644
--- a/modules/mol/base/src/residue_handle.hh
+++ b/modules/mol/base/src/residue_handle.hh
@@ -49,7 +49,7 @@ namespace ost { namespace mol {
/// EditorBase::InsertAtom() or EditorBase::InsertAltAtom()
///
/// \code
-/// XCSEditor edi=residue.GetEntity().RequestXCSEditor();
+/// XCSEditor edi=residue.GetEntity().EditXCS();
/// edi.InsertAtom(residue, "CA", geom.Vec3(1.0, 0.0, 0.0));
/// \endcode
class DLLEXPORT_OST_MOL ResidueHandle : public ResidueBase {
diff --git a/modules/mol/base/tests/dummy_ent.hh b/modules/mol/base/tests/dummy_ent.hh
index c4689027302ae8c21ab863058134c6e7e6f376d9..8e00291764489e2afc301f82dc88c4767e5a0413 100644
--- a/modules/mol/base/tests/dummy_ent.hh
+++ b/modules/mol/base/tests/dummy_ent.hh
@@ -28,7 +28,7 @@ namespace ost { namespace test {
struct DummyEnt {
DummyEnt() {
e=CreateEntity();
- XCSEditor editor=e.RequestXCSEditor();
+ XCSEditor editor=e.EditXCS();
c=editor.InsertChain("A");
r=editor.AppendResidue(c, "XXX");
aa=editor.InsertAtom(r, "A", geom::Vec3());
diff --git a/modules/mol/base/tests/test_atom_groups.cc b/modules/mol/base/tests/test_atom_groups.cc
index 01e3510ff365c0336fe5ce1532005884e4cbd6f7..b1ed9118e4a1ef910ab800c6ddf9f1db369cd27e 100644
--- a/modules/mol/base/tests/test_atom_groups.cc
+++ b/modules/mol/base/tests/test_atom_groups.cc
@@ -37,7 +37,7 @@ BOOST_AUTO_TEST_CASE(switch_pos)
geom::Vec3 y=geom::Vec3(0.0, 1.0, 0.0);
geom::Vec3 z=geom::Vec3(0.0, 0.0, 1.0);
// Should throw, since aa has no alt-location set.
- XCSEditor editor=ent.e.RequestXCSEditor();
+ XCSEditor editor=ent.e.EditXCS();
BOOST_CHECK_THROW(editor.AddAltAtomPos("B", ent.aa, y),
Error);
AtomHandle xx=editor.InsertAltAtom(ent.r, "ZZ", "A", y);
@@ -55,7 +55,7 @@ BOOST_AUTO_TEST_CASE(switch_pos)
BOOST_AUTO_TEST_CASE(delete_atom)
{
test::DummyEnt ent;
- XCSEditor editor=ent.e.RequestXCSEditor();
+ XCSEditor editor=ent.e.EditXCS();
AtomHandle xx=editor.InsertAltAtom(ent.r, "ZZ", "A", geom::Vec3());
AtomHandle zz=editor.InsertAltAtom(ent.r, "XX", "A", geom::Vec3());
@@ -75,7 +75,7 @@ BOOST_AUTO_TEST_CASE(atom_group_triv)
BOOST_CHECK(ent.r.HasAltAtomGroup("")==false);
std::vector<String> names=ent.r.GetAltAtomGroupNames();
BOOST_CHECK(names.empty());
- XCSEditor editor=ent.e.RequestXCSEditor();
+ XCSEditor editor=ent.e.EditXCS();
AtomHandle xx=editor.InsertAltAtom(ent.r, "A", "ZZ", geom::Vec3(0.0,1.0,0.0));
editor.AddAltAtomPos("B", xx, geom::Vec3(1.0, 0.0, 0.0));
BOOST_CHECK(ent.r.HasAltAtoms()==true);
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index e03c588a5b0a83ed7b959d02e99e8b386b0381f4..2e42ea77184ab789a659abff5857cef576950f76 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -46,7 +46,7 @@ void no_find_res(ChainHandle chain, const ResNum& n) {
void test_res_pos() {
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
e.AppendResidue(ch1, "A");
e.AppendResidue(ch1, "B");
@@ -76,7 +76,7 @@ BOOST_AUTO_TEST_SUITE( mol_base )
BOOST_AUTO_TEST_CASE(test_comparison)
{
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
ChainHandle ch2=e.InsertChain("B");
ChainHandle cc=ch1;
@@ -89,7 +89,7 @@ BOOST_AUTO_TEST_CASE(test_comparison)
BOOST_AUTO_TEST_CASE(res_pos)
{
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
e.AppendResidue(ch1, "A");
e.AppendResidue(ch1, "B");
@@ -118,7 +118,7 @@ BOOST_AUTO_TEST_CASE(res_pos)
BOOST_AUTO_TEST_CASE(res_pos_with_insertion_code)
{
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
e.AppendResidue(ch1, "A");
e.AppendResidue(ch1, "B");
@@ -148,7 +148,7 @@ BOOST_AUTO_TEST_CASE(res_pos_with_insertion_code)
BOOST_AUTO_TEST_CASE(prev_next)
{
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
e.AppendResidue(ch1, "A");
e.AppendResidue(ch1, "B");
diff --git a/modules/mol/base/tests/test_conn.cc b/modules/mol/base/tests/test_conn.cc
index b36e5f754e453cba393920adc8c0852b81059b84..0c81d6900611ee77b826af1faaa74d7808a3fa9a 100644
--- a/modules/mol/base/tests/test_conn.cc
+++ b/modules/mol/base/tests/test_conn.cc
@@ -31,7 +31,7 @@ BOOST_AUTO_TEST_SUITE( mol_base )
BOOST_AUTO_TEST_CASE(connect)
{
EntityHandle e=CreateEntity();
- XCSEditor editor=e.RequestXCSEditor();
+ XCSEditor editor=e.EditXCS();
ChainHandle c=editor.InsertChain("A");
ResidueHandle r=editor.AppendResidue(c, "GLY");
diff --git a/modules/mol/base/tests/test_coord_group.cc b/modules/mol/base/tests/test_coord_group.cc
index f2012b9983cd652d373cb68b813fea65cd460aa6..cce3eb4873336242739b2cae689e8d18073a742b 100644
--- a/modules/mol/base/tests/test_coord_group.cc
+++ b/modules/mol/base/tests/test_coord_group.cc
@@ -33,7 +33,7 @@ BOOST_AUTO_TEST_SUITE( io )
BOOST_AUTO_TEST_CASE(coord_group)
{
EntityHandle e=CreateEntity();
- XCSEditor editor=e.RequestXCSEditor();
+ XCSEditor editor=e.EditXCS();
ChainHandle c=editor.InsertChain("A");
ResidueHandle r=editor.AppendResidue(c, "XXX");
AtomHandle aa=editor.InsertAtom(r, "A", geom::Vec3(0,1,2));
diff --git a/modules/mol/base/tests/test_delete.cc b/modules/mol/base/tests/test_delete.cc
index c117f5d9ae50dfd0d26a41c665627b957d3dd751..56d78f0a016d1671292ad091a849ddd13403871b 100644
--- a/modules/mol/base/tests/test_delete.cc
+++ b/modules/mol/base/tests/test_delete.cc
@@ -42,7 +42,7 @@ public:
struct Fixture {
Fixture() {
e=CreateEntity();
- XCSEditor editor=e.RequestXCSEditor();
+ XCSEditor editor=e.EditXCS();
c=editor.InsertChain("A");
r=editor.AppendResidue(c, "XXX");
aa=editor.InsertAtom(r, "A", geom::Vec3());
@@ -71,7 +71,7 @@ BOOST_AUTO_TEST_SUITE( mol_base )
BOOST_AUTO_TEST_CASE(atom_delete)
{
Fixture f;
- XCSEditor e=f.e.RequestXCSEditor();
+ XCSEditor e=f.e.EditXCS();
e.DeleteAtom(f.ab);
E ev;
BOOST_CHECK_NO_THROW(f.e.Apply(ev));
diff --git a/modules/mol/base/tests/test_entity.cc b/modules/mol/base/tests/test_entity.cc
index 0504422946e34546f0c3dee532bb05de4fbd232a..93114774015661befd2dca50f2e94eacea521ab3 100644
--- a/modules/mol/base/tests/test_entity.cc
+++ b/modules/mol/base/tests/test_entity.cc
@@ -19,6 +19,8 @@
/*
* Authors: Marco Biasini, Juergen Haas
*/
+
+#include <ost/mol/chem_class.hh>
#include <ost/mol/mol.hh>
#include <cmath>
#define BOOST_TEST_DYN_LINK
@@ -42,10 +44,12 @@
using namespace ost;
using namespace ost::mol;
+
+
EntityHandle make_test_entity()
{
EntityHandle eh = CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle chain = e.InsertChain("A");
ResidueHandle res1 = e.AppendResidue(chain, "MET");
@@ -83,7 +87,7 @@ BOOST_AUTO_TEST_CASE(entity_creator)
eh.SetName("TestEntity");
BOOST_CHECK(eh.GetName()=="TestEntity");
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle chain = e.InsertChain("C");
BOOST_CHECK(chain.GetName()=="C");
@@ -118,7 +122,7 @@ BOOST_AUTO_TEST_CASE(entity_creator)
BOOST_AUTO_TEST_CASE(spatial_organizer)
{
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle chain = e.InsertChain("A");
ResidueHandle res = e.AppendResidue(chain, "X");
@@ -139,7 +143,7 @@ BOOST_AUTO_TEST_CASE(spatial_organizer)
BOOST_AUTO_TEST_CASE(transformation)
{
EntityHandle eh = CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle chain = e.InsertChain("A");
ResidueHandle res = e.AppendResidue(chain, "X");
@@ -240,7 +244,7 @@ BOOST_AUTO_TEST_CASE(transformation)
BOOST_CHECK(bond1.GetLength()==1.5);
BOOST_CHECK(bond2.GetLength()==2.0);
- ICSEditor i = eh.RequestICSEditor();
+ ICSEditor i = eh.EditICS();
i.SetBondLength(bond1,1.0);
i.SetBondLength(bond2,3.0);
@@ -325,4 +329,54 @@ BOOST_AUTO_TEST_CASE(copy)
BOOST_CHECK(r2.GetPhiTorsion());
}
+BOOST_AUTO_TEST_CASE(copy_residue_props)
+{
+ EntityHandle ent=mol::CreateEntity();
+ XCSEditor edi=ent.EditXCS();
+ ChainHandle ch=edi.InsertChain("A");
+ ResidueHandle res=edi.AppendResidue(ch, "DUMMY", mol::ResNum(666, '6'));
+ res.SetOneLetterCode('X');
+ res.SetIsProtein(true);
+ ChemClass cl(ChemClass::LPeptideLinking);
+ res.SetSecStructure(SecStructure(SecStructure::ALPHA_HELIX));
+ res.SetChemClass(cl);
+ EntityHandle copy=ent.Copy();
+ ResidueHandle res2=copy.GetResidueList()[0];
+ BOOST_CHECK_EQUAL(res2.GetName(), String("DUMMY"));
+ BOOST_CHECK_EQUAL(res2.GetOneLetterCode(), 'X');
+
+ BOOST_CHECK_EQUAL(res2.GetChemClass(), cl);
+ BOOST_CHECK_EQUAL(res.GetSecStructure(), SecStructure::ALPHA_HELIX);
+ BOOST_CHECK(res2.IsProtein()==true);
+ BOOST_CHECK_EQUAL(res2.GetNumber(), ResNum(666, '6'));
+}
+
+BOOST_AUTO_TEST_CASE(copy_atom_props)
+{
+ EntityHandle ent=mol::CreateEntity();
+ XCSEditor edi=ent.EditXCS();
+ ChainHandle ch=edi.InsertChain("A");
+ ResidueHandle res=edi.AppendResidue(ch, "DUMMY");
+ AtomHandle atom=edi.InsertAtom(res, "X", geom::Vec3(1,2,3), "C");
+ atom.SetMass(100.0);
+ atom.SetBFactor(200.0);
+ atom.SetOccupancy(300.0);
+ atom.SetHetAtom(true);
+ atom.SetRadius(500);
+ atom.SetCharge(800);
+ atom.SetAnisou(geom::Mat3(100,200,300));
+ EntityHandle copy=ent.Copy();
+ AtomHandle atom2=copy.GetAtomList()[0];
+ BOOST_CHECK_EQUAL(atom2.GetPos(), geom::Vec3(1,2,3));
+ BOOST_CHECK_EQUAL(atom2.GetName(), String("X"));
+ BOOST_CHECK_EQUAL(atom2.GetElement(), String("C"));
+ BOOST_CHECK_EQUAL(atom2.GetMass(), Real(100.0));
+ BOOST_CHECK_EQUAL(atom2.GetCharge(), Real(800.0));
+ BOOST_CHECK_EQUAL(atom2.GetBFactor(), Real(200.0));
+ BOOST_CHECK_EQUAL(atom2.IsHetAtom(), true);
+ BOOST_CHECK_EQUAL(atom2.GetAnisou(), geom::Mat3(100,200,300));
+ BOOST_CHECK_EQUAL(atom2.GetRadius(), Real(500.0));
+}
+
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/mol/base/tests/test_ics.cc b/modules/mol/base/tests/test_ics.cc
index 37955909398b208a556a3a9feaf4c7f1f8c48ba0..d577f8ca9dd60a720ea1f780b5f3922e311e4993 100644
--- a/modules/mol/base/tests/test_ics.cc
+++ b/modules/mol/base/tests/test_ics.cc
@@ -36,7 +36,7 @@ struct Structure {
Structure()
{
e=CreateEntity();
- ICSEditor editor=e.RequestICSEditor();
+ ICSEditor editor=e.EditICS();
c=editor.InsertChain("A");
r=editor.AppendResidue(c, "ANGELIN");
a1=editor.InsertAtom(r, "CC", geom::Vec3(-1.0, 0.0, 0.0));
@@ -76,7 +76,7 @@ BOOST_AUTO_TEST_SUITE( mol_base )
BOOST_AUTO_TEST_CASE(ics_angle_trivia)
{
Structure s;
- ICSEditor e=s.e.RequestICSEditor();
+ ICSEditor e=s.e.EditICS();
BOOST_CHECK(!e.SetAngle(s.a1, s.a3, s.a2, 0));
BOOST_CHECK(!e.SetAngle(s.a2, s.a3, s.a1, 0));
BOOST_CHECK(e.SetAngle(s.a1, s.a2, s.a3, 0));
@@ -94,7 +94,7 @@ BOOST_AUTO_TEST_CASE(ics_set_angle_sec)
{
Structure s;
// test for set angle of two secondary connectors
- ICSEditor e=s.e.RequestICSEditor();
+ ICSEditor e=s.e.EditICS();
geom::Plane p(s.a3.GetPos(), s.a2.GetPos(), s.a4.GetPos());
e.SetAngle(s.a3, s.a2, s.a4, M_PI/4);
e.UpdateXCS();
@@ -111,7 +111,7 @@ BOOST_AUTO_TEST_CASE(ics_set_angle_prim)
{
Structure s;
// test for set angle of two secondary connectors
- ICSEditor e=s.e.RequestICSEditor();
+ ICSEditor e=s.e.EditICS();
e.SetAngle(s.a1, s.a2, s.a4, M_PI/4);
e.UpdateXCS();
geom::Plane p(s.a1.GetPos(), s.a2.GetPos(), s.a4.GetPos());
diff --git a/modules/mol/base/tests/test_iterators.cc b/modules/mol/base/tests/test_iterators.cc
index 8dfc0dca0f1215b730a6e637cd98f36b0b2b59d0..0c2900571e9e4482f03dce839eb4c19b593649fe 100644
--- a/modules/mol/base/tests/test_iterators.cc
+++ b/modules/mol/base/tests/test_iterators.cc
@@ -140,7 +140,7 @@ BOOST_AUTO_TEST_SUITE( mol_base )
BOOST_AUTO_TEST_CASE(chain_handle_iterator)
{
EntityHandle ent=CreateEntity();
- XCSEditor editor=ent.RequestXCSEditor();
+ XCSEditor editor=ent.EditXCS();
ChainHandle ch1=editor.InsertChain("A");
ChainHandle ch2=editor.InsertChain("B");
ChainHandle ch3=editor.InsertChain("C");
@@ -161,7 +161,7 @@ BOOST_AUTO_TEST_CASE(chain_handle_iterator)
BOOST_AUTO_TEST_CASE(test_res_handle_iterator)
{
EntityHandle eh=CreateEntity();
- XCSEditor editor=eh.RequestXCSEditor();
+ XCSEditor editor=eh.EditXCS();
ChainHandle ch1=editor.InsertChain("A");
editor.AppendResidue(ch1, "A");
editor.AppendResidue(ch1, "B");
@@ -197,7 +197,7 @@ BOOST_AUTO_TEST_CASE(test_empty_iterators)
BOOST_CHECK(eh.ChainsBegin()==eh.ChainsEnd());
BOOST_CHECK(eh.ResiduesBegin()==eh.ResiduesEnd());
BOOST_CHECK(eh.AtomsBegin()==eh.AtomsEnd());
- XCSEditor editor=eh.RequestXCSEditor();
+ XCSEditor editor=eh.EditXCS();
ChainHandle ch1=editor.InsertChain("A");
BOOST_CHECK(ch1.ResiduesBegin()==ch1.ResiduesEnd());
BOOST_CHECK(ch1.AtomsBegin()==ch1.AtomsEnd());
@@ -205,7 +205,7 @@ BOOST_AUTO_TEST_CASE(test_empty_iterators)
BOOST_CHECK(r1.AtomsBegin()==r1.AtomsEnd());
eh=CreateEntity();
- editor=eh.RequestXCSEditor();
+ editor=eh.EditXCS();
ch1=editor.InsertChain("A");
r1=editor.AppendResidue(ch1, "A");
ResidueHandle r2=editor.AppendResidue(ch1, "B");
@@ -229,7 +229,7 @@ BOOST_AUTO_TEST_CASE(test_empty_iterators)
BOOST_AUTO_TEST_CASE(test_atom_handle_iterator)
{
EntityHandle eh=CreateEntity();
- XCSEditor editor=eh.RequestXCSEditor();
+ XCSEditor editor=eh.EditXCS();
ChainHandle ch1=editor.InsertChain("A");
ResidueHandle r1=editor.AppendResidue(ch1, "A");
ResidueHandle r2=editor.AppendResidue(ch1, "B");
diff --git a/modules/mol/base/tests/test_query.cc b/modules/mol/base/tests/test_query.cc
index c3f779a872aac92060c96572378458c090598b38..6e603a16adf42d60671bf2b916d4cfc29f0dbee1 100644
--- a/modules/mol/base/tests/test_query.cc
+++ b/modules/mol/base/tests/test_query.cc
@@ -31,7 +31,7 @@ using namespace ost::mol;
EntityHandle make_query_test_entity()
{
EntityHandle eh = CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle chain = e.InsertChain("A");
chain.SetFloatProp("testprop_c", 1.0);
ResidueHandle res = e.AppendResidue(chain, "MET");
diff --git a/modules/mol/base/tests/test_residue.cc b/modules/mol/base/tests/test_residue.cc
index 332d60edd6534837b9511314b4a3aecceadbffae..d6cc11f4a447e4d62a0a2f82f867f3173e18f8b3 100644
--- a/modules/mol/base/tests/test_residue.cc
+++ b/modules/mol/base/tests/test_residue.cc
@@ -34,7 +34,7 @@ BOOST_AUTO_TEST_SUITE( mol_base )
BOOST_AUTO_TEST_CASE(test_in_sequence)
{
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
ResidueHandle rA = e.AppendResidue(ch1, "A");
ResidueHandle rB = e.AppendResidue(ch1, "B");
@@ -48,7 +48,7 @@ BOOST_AUTO_TEST_CASE(test_in_sequence)
BOOST_AUTO_TEST_CASE(test_res_index)
{
EntityHandle eh=CreateEntity();
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
ResidueHandle rA = e.AppendResidue(ch1, "A");
ResidueHandle rB = e.AppendResidue(ch1, "B");
diff --git a/modules/mol/base/tests/test_view.cc b/modules/mol/base/tests/test_view.cc
index 26399e10e1c240182d87f59a453a605d69dd3902..3f60928d627552a50450a62a6b89cb0de31c7ae8 100644
--- a/modules/mol/base/tests/test_view.cc
+++ b/modules/mol/base/tests/test_view.cc
@@ -30,7 +30,7 @@ using namespace ost::mol;
struct Fixture {
Fixture() {
e=CreateEntity();
- XCSEditor editor=e.RequestXCSEditor();
+ XCSEditor editor=e.EditXCS();
c=editor.InsertChain("A");
r=editor.AppendResidue(c, "ANGELIN");
aa=editor.InsertAtom(r, "X1", geom::Vec3( 0.0, 0.0, 0.0));
diff --git a/modules/mol/base/tests/test_view_op.cc b/modules/mol/base/tests/test_view_op.cc
index f589bf2107638956d21663a4db196044c020c610..fb9d8ffda7b0fd210268a4ae3e5a6f3eb7074875 100644
--- a/modules/mol/base/tests/test_view_op.cc
+++ b/modules/mol/base/tests/test_view_op.cc
@@ -31,7 +31,7 @@ EntityHandle mk_test_ent()
{
EntityHandle ent=CreateEntity();
ent.SetName("TestEntity");
- XCSEditor edi=ent.RequestXCSEditor();
+ XCSEditor edi=ent.EditXCS();
ChainHandle chain_a=edi.InsertChain("A");
ResidueHandle res_a=edi.AppendResidue(chain_a, "A");
AtomHandle atom_a=edi.InsertAtom(res_a, "A", geom::Vec3());
@@ -334,7 +334,8 @@ BOOST_AUTO_TEST_CASE(test_intersection_b)
bonds));
}
-BOOST_AUTO_TEST_CASE(entity_from_view) {
+BOOST_AUTO_TEST_CASE(entity_from_view)
+{
EntityHandle ent=mk_test_ent();
EntityView v1=ent.Select("aname=B,C,F,G");
EntityHandle ent_fv=mol::CreateEntityFromView(v1, false);
@@ -347,5 +348,54 @@ BOOST_AUTO_TEST_CASE(entity_from_view) {
}
+BOOST_AUTO_TEST_CASE(ent_from_view_residue_props)
+{
+ EntityHandle ent=mol::CreateEntity();
+ XCSEditor edi=ent.EditXCS();
+ ChainHandle ch=edi.InsertChain("A");
+ ResidueHandle res=edi.AppendResidue(ch, "DUMMY", mol::ResNum(666, '6'));
+ res.SetOneLetterCode('X');
+ res.SetIsProtein(true);
+ ChemClass cl(ChemClass::LPeptideLinking);
+ res.SetSecStructure(SecStructure(SecStructure::ALPHA_HELIX));
+ res.SetChemClass(cl);
+ EntityHandle copy=mol::CreateEntityFromView(ent.Select(""), false);
+ ResidueHandle res2=copy.GetResidueList()[0];
+ BOOST_CHECK_EQUAL(res2.GetName(), String("DUMMY"));
+ BOOST_CHECK_EQUAL(res2.GetOneLetterCode(), 'X');
+
+ BOOST_CHECK_EQUAL(res2.GetChemClass(), cl);
+ BOOST_CHECK_EQUAL(res.GetSecStructure(), SecStructure::ALPHA_HELIX);
+ BOOST_CHECK(res2.IsProtein()==true);
+ BOOST_CHECK_EQUAL(res2.GetNumber(), ResNum(666, '6'));
+}
+
+BOOST_AUTO_TEST_CASE(ent_from_view_atom_props)
+{
+ EntityHandle ent=mol::CreateEntity();
+ XCSEditor edi=ent.EditXCS();
+ ChainHandle ch=edi.InsertChain("A");
+ ResidueHandle res=edi.AppendResidue(ch, "DUMMY");
+ AtomHandle atom=edi.InsertAtom(res, "X", geom::Vec3(1,2,3), "C");
+ atom.SetMass(100.0);
+ atom.SetBFactor(200.0);
+ atom.SetOccupancy(300.0);
+ atom.SetHetAtom(true);
+ atom.SetRadius(500);
+ atom.SetCharge(800);
+ atom.SetAnisou(geom::Mat3(100,200,300));
+ EntityHandle copy=mol::CreateEntityFromView(ent.Select(""), false);
+ AtomHandle atom2=copy.GetAtomList()[0];
+ BOOST_CHECK_EQUAL(atom2.GetPos(), geom::Vec3(1,2,3));
+ BOOST_CHECK_EQUAL(atom2.GetName(), String("X"));
+ BOOST_CHECK_EQUAL(atom2.GetElement(), String("C"));
+ BOOST_CHECK_EQUAL(atom2.GetMass(), Real(100.0));
+ BOOST_CHECK_EQUAL(atom2.GetCharge(), Real(800.0));
+ BOOST_CHECK_EQUAL(atom2.GetBFactor(), Real(200.0));
+ BOOST_CHECK_EQUAL(atom2.IsHetAtom(), true);
+ BOOST_CHECK_EQUAL(atom2.GetAnisou(), geom::Mat3(100,200,300));
+ BOOST_CHECK_EQUAL(atom2.GetRadius(), Real(500.0));
+}
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/seq/alg/pymod/renumber.py b/modules/seq/alg/pymod/renumber.py
index 39ea9fb489949845fb65681ac1cbb6f000f4e56e..f6d7d128f115dc499d2ded3ad2f265114227a9ad 100644
--- a/modules/seq/alg/pymod/renumber.py
+++ b/modules/seq/alg/pymod/renumber.py
@@ -25,7 +25,7 @@ def Renumber(seq_handle):
changed_residue_count=0
renumberingFlag = False
ent_n=mol.CreateEntity()
- ed=ent_n.RequestXCSEditor()
+ ed=ent_n.EditXCS()
c=ed.InsertChain(" ")
for pos in range(len(seq_handle)):
if seq_handle[pos]!='-':
diff --git a/modules/seq/base/tests/test_aligned_column.cc b/modules/seq/base/tests/test_aligned_column.cc
index f76573df3c883f7f91b076442dae9900e0c5a42e..757c8d8cb5496119324f0e666388b390b7ee2929 100644
--- a/modules/seq/base/tests/test_aligned_column.cc
+++ b/modules/seq/base/tests/test_aligned_column.cc
@@ -43,7 +43,7 @@ struct Fixture {
Fixture() {
eh = CreateEntity();
eh.SetName("TestEntity");
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
chain = e.InsertChain("A");
res1 = e.AppendResidue(chain, "ARG");
e.InsertAtom(res1, "CA",geom::Vec3(1,0,0));
diff --git a/modules/seq/base/tests/test_alignment.cc b/modules/seq/base/tests/test_alignment.cc
index 0491f7d35c124c846b5ddd48cee8965e77492025..516c966a487dc92979034befd7f89ec12a994f81 100644
--- a/modules/seq/base/tests/test_alignment.cc
+++ b/modules/seq/base/tests/test_alignment.cc
@@ -38,7 +38,7 @@ struct Fixture {
Fixture() {
eh = CreateEntity();
eh.SetName("TestEntity");
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
chain = e.InsertChain("A");
res1 = e.AppendResidue(chain, "ARG");
e.InsertAtom(res1, "CA",geom::Vec3(1,0,0));
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
index 26abba6896e53f32f19ef43cb4d44e5999bb6c2f..80f13e364c07e3ba9665f34e62a462af79ae79ec 100644
--- a/modules/seq/base/tests/test_seq.py
+++ b/modules/seq/base/tests/test_seq.py
@@ -6,7 +6,7 @@ from ost import seq
def fixture():
e=mol.CreateEntity()
- ede=e.RequestXCSEditor()
+ ede=e.EditXCS()
chain=ede.InsertChain('A')
for res in 'ABCDEFGH':
r=ede.AppendResidue(chain, res)
diff --git a/modules/seq/base/tests/test_sequence.cc b/modules/seq/base/tests/test_sequence.cc
index e787aafb7c3de95e8d93c2b55de8b3b9bba7c8f4..264a902ea81455dcdeb994893536d24c9c9f9455 100644
--- a/modules/seq/base/tests/test_sequence.cc
+++ b/modules/seq/base/tests/test_sequence.cc
@@ -34,7 +34,7 @@ struct Fixture {
Fixture() {
eh = CreateEntity();
eh.SetName("TestEntity");
- XCSEditor e=eh.RequestXCSEditor();
+ XCSEditor e=eh.EditXCS();
chain = e.InsertChain("A");
res1 = e.AppendResidue(chain, "ARG");
e.InsertAtom(res1, "CA",geom::Vec3(1,0,0));