Add 3D Crystal widget using py3Dmol. CreateCrystalFromCIF will now by default return a single Crystal as a python object which enables using the python methods

Author: vincefn

AUTHORS.txt

@@ -3,6 +3,7 @@ Authors:
 Christopher L. Farrow
 Pavol Juhas
 Simon J.L. Billinge
+Vincent Favre-Nicolin
 
 Contributors:
 

examples/cimetidine-structure-solution-powder.ipynb

@@ -166,6 +166,29 @@ std::string _CIF(const Crystal &c, double mindist)
     return s.str();
 }
 
+void _ImportCrystalFromCIF(Crystal &cryst, bp::object input,
+                           const bool oneScatteringPowerPerElement=false,
+                           const bool connectAtoms=false)
+{
+    // Reading a cif file creates some output via fpObjCrystInformUser.
+    // Mute the output and restore it on return or exception.
+    // Also mute any hardcoded output to cout.
+    MuteObjCrystUserInfo muzzle;
+    CaptureStdOut gag;
+
+    boost_adaptbx::python::streambuf sbuf(input);
+    boost_adaptbx::python::streambuf::istream in(sbuf);
+    ObjCryst::CIF cif(in);
+
+    const bool verbose = false;
+    const bool checkSymAsXYZ = true;
+    ObjCryst::CreateCrystalFromCIF(cif, verbose, checkSymAsXYZ, oneScatteringPowerPerElement,
+                                   connectAtoms, &cryst);
+
+    gag.release();
+    muzzle.release();
+}
+
 
 // wrap the virtual functions that need it
 class CrystalWrap : public Crystal, public wrapper<Crystal>
@@ -212,6 +235,16 @@ class CrystalWrap : public Crystal, public wrapper<Crystal>
         return default_GetScatteringComponentList();
     }
 
+    void default_UpdateDisplay() const
+    { this->Crystal::UpdateDisplay();}
+
+    virtual void UpdateDisplay() const
+    {
+        override f = this->get_override("UpdateDisplay");
+        if (f)  f();
+        else  default_UpdateDisplay();
+    }
+
 };
 
 // Easier than exposing all the CIF classes
@@ -350,6 +383,11 @@ void wrap_crystal()
              (bp::arg("min_relat_dist")=0.4, bp::arg("max_relat_dist")=1.3,
               bp::arg("warnuser_fail")=false))
         .def("GetFormula", &Crystal::GetFormula)
+        .def("ImportCrystalFromCIF", &_ImportCrystalFromCIF, (bp::arg("input"),
+            bp::arg("oneScatteringPowerPerElement")=false,
+            bp::arg("connectAtoms")=false))
+        .def("UpdateDisplay", &Crystal::UpdateDisplay,
+            &CrystalWrap::default_UpdateDisplay)
         ;
 
 

src/extensions/crystal_ext.cpp

@@ -122,9 +122,9 @@ void wrap_spacegroup()
         .def("GetTranslationVectors", &GetTranslationVectors)
         .def("GetSymmetryOperations", &GetSymmetryOperations)
         .def("GetAllSymmetrics", &SpaceGroup::GetAllSymmetrics,
-                (bp::arg("h"),
-                 bp::arg("k"),
-                 bp::arg("l"),
+                (bp::arg("x"),
+                 bp::arg("y"),
+                 bp::arg("z"),
                  bp::arg("noCenter")=false,
                  bp::arg("noTransl")=false,
                  bp::arg("noIdentical")=false))