diff --git a/modules/gui/pymod/export_file_loader.cc b/modules/gui/pymod/export_file_loader.cc
index 3cd27c6edf6b6cc355edff91b1989a5bbe883b6b..5e006fb2cea35df25a72e46dfe6c2c3850a55216 100644
--- a/modules/gui/pymod/export_file_loader.cc
+++ b/modules/gui/pymod/export_file_loader.cc
@@ -31,16 +31,31 @@ using namespace ost::gui;
namespace {
-void load_object(const QString& file_name)
+void load_object_a(const QString& file_name)
{
FileLoader::LoadObject(file_name);
}
-void load_from_site(const QString& id, const QString& site)
+void load_object_b(const QString& file_name, const QString& selection)
+{
+ FileLoader::LoadObject(file_name, selection);
+}
+
+void load_from_site_a(const QString& id)
+{
+ FileLoader::LoadFrom(id);
+}
+
+void load_from_site_b(const QString& id, const QString& site)
{
FileLoader::LoadFrom(id,site);
}
+void load_from_site_c(const QString& id, const QString& site, const QString& selection)
+{
+ FileLoader::LoadFrom(id,site,selection);
+}
+
void add_remote_site_loader(LoaderManager* loader_manager, const QString& site, RemoteSiteLoader* site_loader){
loader_manager->AddRemoteSiteLoader(site,site_loader);
}
@@ -56,11 +71,12 @@ void export_FileLoader()
;
class_<FileLoader, boost::noncopyable>("FileLoader", no_init)
- .def("LoadObject", &FileLoader::LoadObject)
- .def("LoadObject", &load_object)
+ .def("LoadObject", &load_object_a)
+ .def("LoadObject", &load_object_b)
.staticmethod("LoadObject")
- .def("LoadFrom", &FileLoader::LoadFrom)
- .def("LoadFrom", &load_from_site)
+ .def("LoadFrom", &load_from_site_a)
+ .def("LoadFrom", &load_from_site_b)
+ .def("LoadFrom", &load_from_site_c)
.staticmethod("LoadFrom")
.def("GetSiteLoaderIdents", &FileLoader::GetSiteLoaderIdents)
.staticmethod("GetSiteLoaderIdents")
diff --git a/modules/gui/pymod/export_remote_site_loader.cc b/modules/gui/pymod/export_remote_site_loader.cc
index 257e8d3feeae4f42ef39be2238117c508eae0f68..3446fd6c09425f7b98fed48dcc41efc6e63ee79c 100644
--- a/modules/gui/pymod/export_remote_site_loader.cc
+++ b/modules/gui/pymod/export_remote_site_loader.cc
@@ -37,8 +37,8 @@ struct WrappedRemoteSiteLoader : public RemoteSiteLoader
RemoteSiteLoader(), self(p)
{ }
- virtual void LoadById(const QString& id){
- return call_method<void, std::string>(self, "LoadById", id.toStdString());
+ virtual void LoadById(const QString& id, const QString& selection=QString()){
+ return call_method<void, std::string>(self, "LoadById", id.toStdString(), selection.toStdString());
}
virtual QString GetRemoteSiteName(){
@@ -49,9 +49,9 @@ struct WrappedRemoteSiteLoader : public RemoteSiteLoader
return call_method<bool>(self, "IsImg");
}
- virtual QNetworkReply* ById(const QString& id){
+ virtual QNetworkReply* ById(const QString& id, const QString& selection=QString()){
//This hackish code will be changed soon(er or later)
- unsigned long addr=call_method<unsigned long, std::string>(self, "ByIdAddr", id.toStdString());
+ unsigned long addr=call_method<unsigned long, std::string>(self, "ByIdAddr", id.toStdString(), selection.toStdString());
QNetworkReply* network_reply= reinterpret_cast<QNetworkReply*>(addr);
if(network_reply){
return network_reply;
diff --git a/modules/gui/pymod/scene/file_loader.py b/modules/gui/pymod/scene/file_loader.py
index f39403c802a56d4228484d848b9d6899127d94df..105ec8910efb314ff93c0a7606a0c9618d509dea 100644
--- a/modules/gui/pymod/scene/file_loader.py
+++ b/modules/gui/pymod/scene/file_loader.py
@@ -33,25 +33,25 @@ class BaseRemoteLoader(gui.RemoteSiteLoader):
self.downloads_=dict()
QtCore.QObject.connect(self.networkmanager_, QtCore.SIGNAL("finished(QNetworkReply*)"), self.DownloadFinished)
- def LoadById(self, id):
- self.ById(id)
+ def LoadById(self, id, selection=""):
+ self.ById(id, selection)
- def ById(self, id):
+ def ById(self, id, selection=""):
file_name=self.GetFileName(id)
file = QtCore.QFile(file_name)
if(file.size()==0):
url = QtCore.QUrl(self.GetUrl(id))
request = QtNetwork.QNetworkRequest(url)
reply = self.networkmanager_.get(request)
- self.downloads_[reply]=id
+ self.downloads_[reply]=[id,selection]
return reply
else:
- gui.FileLoader.LoadObject(str(file_name))
+ gui.FileLoader.LoadObject(str(file_name),str(selection))
return None
#Hack for C++ (will be changed soon)
- def ByIdAddr(self,id):
- reply = self.ById(id)
+ def ByIdAddr(self,id,selection):
+ reply = self.ById(id,selection)
if reply is not None:
return sip.unwrapinstance(reply)
return 0
@@ -69,7 +69,7 @@ class BaseRemoteLoader(gui.RemoteSiteLoader):
pass
def DownloadFinished(self, reply):
- file_name=self.GetFileName(self.downloads_[reply])
+ file_name=self.GetFileName(self.downloads_[reply][0])
file = QtCore.QFile(file_name)
if(reply.error()!=QtNetwork.QNetworkReply.NoError or reply.bytesAvailable()==0):
self.HandleError(reply.errorString());
@@ -79,8 +79,9 @@ class BaseRemoteLoader(gui.RemoteSiteLoader):
if(file.open(QtCore.QIODevice.WriteOnly)):
file.write(reply.readAll());
file.close();
+ selection=self.downloads_[reply][1]
del(self.downloads_[reply])
- gui.FileLoader.LoadObject(str(file_name))
+ gui.FileLoader.LoadObject(str(file_name),str(selection))
class GenericLoader(BaseRemoteLoader):
EXT_NAME_ATTRIBUTE_NAME = "ExtName"
diff --git a/modules/gui/src/file_loader.cc b/modules/gui/src/file_loader.cc
index f768b0b4f93548589d5dc2e7c22fd5a08e87c98f..eab3697c59d2b9f757f17f8d06a8dd3e31ff44be 100644
--- a/modules/gui/src/file_loader.cc
+++ b/modules/gui/src/file_loader.cc
@@ -64,7 +64,7 @@ LoaderManagerPtr FileLoader::loader_manager_ = LoaderManagerPtr();
FileLoader::FileLoader(){}
-void FileLoader::LoadObject(const QString& filename)
+void FileLoader::LoadObject(const QString& filename, const QString& selection)
{
gfx::GfxObjP obj;
if(filename.endsWith(".py",Qt::CaseInsensitive)){
@@ -74,11 +74,11 @@ void FileLoader::LoadObject(const QString& filename)
filename.endsWith(".ent",Qt::CaseInsensitive)||
filename.endsWith(".pdb.gz",Qt::CaseInsensitive)||
filename.endsWith(".ent.gz",Qt::CaseInsensitive)){
- FileLoader::LoadPDB(filename);
+ FileLoader::LoadPDB(filename, selection);
}
else{
try{
- obj=FileLoader::TryLoadEntity(filename);
+ obj=FileLoader::TryLoadEntity(filename, io::EntityIOHandlerP(), selection);
#if OST_IMG_ENABLED
if (!obj) {
try{
@@ -136,18 +136,18 @@ gfx::GfxObjP FileLoader::NoHandlerFound(const QString& filename)
return gfx::GfxObjP();
}
-void FileLoader::LoadFrom(const QString& id, const QString& site)
+void FileLoader::LoadFrom(const QString& id, const QString& site, const QString& selection)
{
if(!loader_manager_)
loader_manager_ = LoaderManagerPtr(new LoaderManager());
RemoteSiteLoader* remote_site = loader_manager_->GetRemoteSiteLoader(site);
if(remote_site){
- remote_site->LoadById(id);
+ remote_site->LoadById(id,selection);
}
else{
remote_site = loader_manager_->GetCurrentSiteLoader();
if(remote_site){
- remote_site->LoadById(id);
+ remote_site->LoadById(id,selection);
}
}
}
@@ -201,7 +201,7 @@ void FileLoader::HandleError(Message m, ErrorType type, const QString& filename,
}
}
-gfx::GfxObjP FileLoader::TryLoadEntity(const QString& filename, io::EntityIOHandlerP handler) throw (io::IOException)
+gfx::GfxObjP FileLoader::TryLoadEntity(const QString& filename, io::EntityIOHandlerP handler, const QString& selection) throw (io::IOException)
{
if(!handler){
try{
@@ -213,7 +213,7 @@ gfx::GfxObjP FileLoader::TryLoadEntity(const QString& filename, io::EntityIOHand
}
if(handler){
if(dynamic_cast<io::EntityIOPDBHandler*>(handler.get())){
- FileLoader::LoadPDB(filename);
+ FileLoader::LoadPDB(filename, selection);
}
else{
QFileInfo file_info(filename);
@@ -224,7 +224,7 @@ gfx::GfxObjP FileLoader::TryLoadEntity(const QString& filename, io::EntityIOHand
conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
conop::Conopology::Instance().ConnectAll(builder,eh,0);
}
- gfx::GfxObjP obj(new gfx::Entity(file_info.baseName().toStdString(),eh));
+ gfx::GfxObjP obj(new gfx::Entity(file_info.baseName().toStdString(),eh,mol::Query(selection.toStdString())));
return obj;
}
}
@@ -305,7 +305,7 @@ void FileLoader::RunScript(const QString& filename)
//HackerMode Off
}
-void FileLoader::LoadPDB(const QString& filename)
+void FileLoader::LoadPDB(const QString& filename, const QString& selection)
{
io::PDBReader reader(filename.toStdString());
QList<mol::EntityHandle> entities;
@@ -319,7 +319,7 @@ void FileLoader::LoadPDB(const QString& filename)
QFileInfo file_info(filename);
if(entities.size()==1){
- gfx::EntityP gfx_ent(new gfx::Entity(file_info.baseName().toStdString(),entities.first()));
+ gfx::EntityP gfx_ent(new gfx::Entity(file_info.baseName().toStdString(),entities.first(),mol::Query(selection.toStdString())));
try{
gfx::Scene::Instance().Add(gfx_ent);
}
@@ -333,7 +333,7 @@ void FileLoader::LoadPDB(const QString& filename)
else{
try{
for(int i = 0 ; i<entities.size(); i++){
- gfx::EntityP gfx_ent(new gfx::Entity(QString(file_info.baseName()+" ("+QString::number(i)+")").toStdString(),entities[i]));
+ gfx::EntityP gfx_ent(new gfx::Entity(QString(file_info.baseName()+" ("+QString::number(i)+")").toStdString(),entities[i],mol::Query(selection.toStdString())));
gfx::Scene::Instance().Add(gfx_ent);
}
}
diff --git a/modules/gui/src/file_loader.hh b/modules/gui/src/file_loader.hh
index aefd67589e439363d84c8d9eeb63c291336f6de1..b102e17f69e0a62df75e1078c64dd79459b277a9 100644
--- a/modules/gui/src/file_loader.hh
+++ b/modules/gui/src/file_loader.hh
@@ -49,13 +49,13 @@ private:
};
FileLoader();
- static gfx::GfxObjP TryLoadEntity(const QString& filename, io::EntityIOHandlerP handler=io::EntityIOHandlerP()) throw (io::IOException);
+ static gfx::GfxObjP TryLoadEntity(const QString& filename, io::EntityIOHandlerP handler=io::EntityIOHandlerP(), const QString& selection=QString()) throw (io::IOException);
static gfx::GfxObjP TryLoadSurface(const QString& filename, io::SurfaceIOHandlerPtr handler=io::SurfaceIOHandlerPtr()) throw (io::IOException);
#if OST_IMG_ENABLED
static gfx::GfxObjP TryLoadMap(const QString& filename, io::MapIOHandlerPtr handler=io::MapIOHandlerPtr()) throw (io::IOException, io::IOFileAlreadyLoadedException);
#endif
static void RunScript(const QString& filename);
- static void LoadPDB(const QString& filename);
+ static void LoadPDB(const QString& filename, const QString& selection=QString());
static void AddToScene(const QString& filename, gfx::GfxObjP obj);
static void HandleError(Message m, ErrorType type, const QString& filename, gfx::GfxObjP obj=gfx::GfxObjP());
static gfx::GfxObjP NoHandlerFound(const QString& filename);
@@ -68,8 +68,8 @@ private:
#endif
public:
- static void LoadObject(const QString& filename);
- static void LoadFrom(const QString& id, const QString& site=QString());
+ static void LoadObject(const QString& filename, const QString& selection=QString());
+ static void LoadFrom(const QString& id, const QString& site=QString(), const QString& selection=QString());
static std::vector<String> GetSiteLoaderIdents();
static LoaderManagerPtr GetLoaderManager();
};
diff --git a/modules/gui/src/remote_site_loader.cc b/modules/gui/src/remote_site_loader.cc
index 8955715e0082d756433f2bf104226c4487d8d23e..26bd25cc50958655c5e58e791c9470b692fb7c90 100644
--- a/modules/gui/src/remote_site_loader.cc
+++ b/modules/gui/src/remote_site_loader.cc
@@ -21,8 +21,8 @@
namespace ost { namespace gui {
RemoteSiteLoader::RemoteSiteLoader(){}
- void RemoteSiteLoader::LoadById(const QString& id){this->ById(id);}
- QNetworkReply* RemoteSiteLoader::ById(const QString& id){return NULL;}
+ void RemoteSiteLoader::LoadById(const QString& id, const QString& selection){this->ById(id,selection);}
+ QNetworkReply* RemoteSiteLoader::ById(const QString& id, const QString& selection){return NULL;}
QString RemoteSiteLoader::GetRemoteSiteName(){return QString();}
bool RemoteSiteLoader::IsImg() const { return false; }
}}
diff --git a/modules/gui/src/remote_site_loader.hh b/modules/gui/src/remote_site_loader.hh
index cc4d7dc6cacfec548bbdbc5a704101f0cc34ffc4..648850fd5df57578311947545b487e2719ed389c 100644
--- a/modules/gui/src/remote_site_loader.hh
+++ b/modules/gui/src/remote_site_loader.hh
@@ -35,8 +35,8 @@ class DLLEXPORT_OST_GUI RemoteSiteLoader{
public:
RemoteSiteLoader();
- virtual QNetworkReply* ById(const QString& id);
- virtual void LoadById(const QString& id);
+ virtual QNetworkReply* ById(const QString& id, const QString& selection=QString());
+ virtual void LoadById(const QString& id, const QString& selection=QString());
virtual QString GetRemoteSiteName();
virtual bool IsImg() const;
virtual ~RemoteSiteLoader(){};
diff --git a/scripts/init.py b/scripts/init.py
index 5032dc4b1eabd43ce9e3f562d9ee730b8fd202f7..f3549c69a6898944f6cafdb2f175972594c13e12 100644
--- a/scripts/init.py
+++ b/scripts/init.py
@@ -1,9 +1,8 @@
import __main__
-from ost import gui
import sip
import sys
import optparse
-from ost import io, mol, seq, geom, conop
+from ost import io, mol, seq, geom, conop, gui
import ost
try:
from ost import img
@@ -61,93 +60,26 @@ def _InitFrontEnd():
_InitInspector()
def _load_files():
- input_files=[_SplitIDSel(arg) for arg in loading_list]
for pdb_id in options.pdb_ids:
pdb_id, sel=_SplitIDSel(pdb_id)
- GetModelFromPDB(pdb_id, '/tmp')
- input_files.append(('/tmp/pdb%s.ent' % pdb_id, sel))
- index=0
- c=geom.Vec3()
- graphical_objects=[]
- try:
- for f in input_files:
- is_pdb_file=False
- for ext in ['.pdb', '.ent', '.ent.gz', '.pdb.gz']:
- if f[0].endswith(ext):
- is_pdb_file=True
- break
- if is_pdb_file:
- es=io.LoadPDB(f[0], load_multi=True)
- for i, e in enumerate(es):
- index+=1
- s=None
- if len(options.query)>0:
- if len(f[1])>0:
- s=e.Select('(%s) and (%s)' % (options.query, f[1]))
- else:
- s=e.Select(options.query)
- elif len(f[1])>0:
- s=e.Select(f[1])
- else:
- s=e
- g=None
- name=os.path.basename(f[0])
- if name.find('.')>-1:
- name=name[:name.find('.')]
- if len(es)>1:
- name+=' (%d)' % i
- g=gfx.Entity(name, s)
- graphical_objects.append(g)
-
- gfx.Scene().Add(g)
- c+=s.geometric_center
- elif e=='.sdf':
- index+=1
- e=io.LoadSDF(f[0])
- name=os.path.basename(f[0])
- if name.find('.')>-1:
- name=name[:name.find('.')]
- g=gfx.Entity(name, e)
- graphical_objects.append(g)
- gfx.Scene().Add(g)
- c+=e.geometric_center
- else:
- if _img_present:
- m=io.LoadMap(f[0])
- if m.GetExtent().GetDepth()==1:
- images.append(m)
- v=gui.CreateDataViewer(m)
- viewers.append(v)
- app=gui.GostyApp.Instance()
- widget=gui.BPQtHandle(v.GetSipHandle())
- main_area=app.perspective.main_area
- main_area.AddWidget(f[0], widget)
- else:
- stat=ost.img.alg.Stat()
- m.Apply(stat)
- miso=gfx.MapIso(os.path.basename(f[0]), m,stat.GetMean())
- c+=miso.center
- graphical_objects.append(miso)
- scene.Add(miso)
- else:
- raise Exception("unknown file type:"+f[0])
- step_size=0.0
- if len(input_files)>1:
- step_size=1.0/(len(input_files)-1)
- for i, go in enumerate(graphical_objects):
- if hasattr(go, 'SetColor'):
- if _img_present:
- if type(go)==gfx.MapIso:
- go.SetColor(gradient.GetColorAt(step_size*i))
- else:
- go.SetColor(gradient.GetColorAt(step_size*i), 'aname=CA')
- else:
- go.SetColor(gradient.GetColorAt(step_size*i), 'aname=CA')
- scene.center=c/index
- except:
- QtGui.QApplication.instance().exit()
- raise
-import __main__
+ selection=_get_selection_query(sel)
+ gui.FileLoader.LoadFrom(pdb_id,"pdb.org",selection)
+
+ input_files=[_SplitIDSel(arg) for arg in loading_list]
+ for f in input_files:
+ selection=_get_selection_query(f[1])
+ gui.FileLoader.LoadObject(f[0],selection)
+
+def _get_selection_query(sel):
+ if len(options.query)>0:
+ if len(sel)>0:
+ return '(%s) and (%s)' % (options.query, sel)
+ else:
+ return options.query
+ elif len(sel)>0:
+ return sel
+ return ""
+
def _execute_script():
script=script_argv[0]
sys_argv_backup=sys.argv
@@ -168,37 +100,12 @@ def parse_script_option(option, opt, value, parser):
script_argv.append(arg)
del parser.rargs[0:len(parser.rargs)]
-def GetModelFromPDB(model_id, output_dir, file_pattern='pdb%s.ent'):
- conn=httplib.HTTPConnection('www.pdb.org')
- print 'getting file for model with id=%s...' % model_id.lower()
- conn.request('GET', '/pdb/files/%s.pdb' % model_id )
- response=conn.getresponse()
- print response.reason
- if response.status==200:
- data=response.read()
- f=open(os.path.join(output_dir, file_pattern % model_id), 'w+')
- f.write(data)
- f.close()
- conn.close()
- return True
- conn.close()
- return False
-
def _SplitIDSel(name):
pos=name.find('[')
if pos>-1:
return name[:pos], name[pos+1:-1]
return name, ''
-# the nicest gradient the world has ever seen
-gradient=gfx.Gradient()
-gradient.SetColorAt(0.00, gfx.RED)
-gradient.SetColorAt(0.25, gfx.GREY)
-gradient.SetColorAt(0.50, gfx.LIGHTCYAN)
-gradient.SetColorAt(0.75, gfx.YELLOW)
-gradient.SetColorAt(1.00, gfx.DARKMAGENTA)
-
-
loading_list=[]
script_argv=[]
images=[]
@@ -251,4 +158,3 @@ if len(loading_list)!=0 or len(options.pdb_ids)!=0:
if len(script_argv)!=0:
_execute_script()
-a=2