Add int_ptr property to RefinableObj, Mol{Atom, Bond, DihedralAngle}, RigidGroup to be able to test the identity between python objects.

Crystal: add _display_list() function to generate a list of atoms and bonds for display. Update the 3D view accordingly, so bonds are not broken anymore. Fixes vincefn#2.
MonteCarlo: add basic widget to display the current LLK, run and trial number.
Allow to disable UpdateDisplay (useful if not in the main process when using multiprocessing).
RefinableObj.XMLInput() : allow input directly from an XML string, without requiring the initial tag.
Add an example notebook using multiprocessing to automatically test multiple spacegroups (while adapting to the multiplicity).

Author: vincefn

examples/cimetidine-structure-solution-powder.ipynb

@@ -90,5 +90,6 @@ void wrap_molatom()
         .add_property("Occupancy", &MolAtom::GetOccupancy,
                 &MolAtom::SetOccupancy)
         .def("__str__", &__str__)
+        .def("int_ptr", &MolAtom::int_ptr)
         ;
 }

examples/crystal_3d_widget.ipynb

@@ -103,5 +103,6 @@ void wrap_molbond()
             &MolBond::SetBondOrder)
         .def("__getitem__", &_GetAtom,
             return_internal_reference<>())
+        .def("int_ptr", &MolBond::int_ptr)
         ;
 }

examples/structure-solution-multiprocessing.ipynb

@@ -110,5 +110,6 @@ void wrap_molbondangle()
         // Iterate other the atoms involved
         .def("__iter__", range<return_value_policy<reference_existing_object> >
                            (&MolBondAngle::begin, &MolBondAngle::end))
+        .def("int_ptr", &MolBondAngle::int_ptr)
         ;
 }

src/extensions/molatom_ext.cpp

@@ -113,5 +113,6 @@ void wrap_moldihedralangle()
         // Iterate other the atoms involved
         .def("__iter__", range<return_value_policy<reference_existing_object> >
                            (&MolDihedralAngle::begin, &MolDihedralAngle::end))
+        .def("int_ptr", &MolDihedralAngle::int_ptr)
         ;
 }

src/extensions/molbond_ext.cpp

@@ -37,6 +37,7 @@
 #include <boost/python/copy_const_reference.hpp>
 
 #include <string>
+#include <sstream>
 #include <map>
 
 #include <ObjCryst/RefinableObj/RefinableObj.h>
@@ -404,6 +405,15 @@ void _XMLInput(
     in.sync();
 }
 
+void _XMLInputString(RefinableObj& r, const string& s)
+{
+  stringstream ss(s);
+  ss.imbue(std::locale::classic());
+  XMLCrystTag tag;
+  ss>>tag;
+  r.XMLInput(ss, tag);
+}
+
 } // anonymous namespace
 
 
@@ -555,6 +565,7 @@ void wrap_refinableobj()
         .def("XMLInput", &_XMLInput, (bp::arg("file"), bp::arg("tag")))
         .def("XMLInput", &RefinableObj::XMLInput,
             &RefinableObjWrap::default_XMLInput)
+        .def("XMLInput", &_XMLInputString, (bp::arg("xml")))
         .def("GetGeneGroup", &RefinableObj::GetGeneGroup,
             &RefinableObjWrap::default_GetGeneGroup)
         .def("UpdateDisplay", &RefinableObj::UpdateDisplay,
@@ -563,6 +574,7 @@ void wrap_refinableobj()
             &RefinableObjWrap::default_GetRestraintCost)
         .def("TagNewBestConfig", &RefinableObj::TagNewBestConfig,
             &RefinableObjWrap::default_TagNewBestConfig)
+        .def("int_ptr", &RefinableObj::int_ptr)
         // Additional methods for python only
         .def("__str__", &__str__<RefinableObj>)
         ;

src/extensions/molbondangle_ext.cpp

@@ -44,5 +44,6 @@ void wrap_rigidgroup()
     class_<RigidGroup, bases<MolAtomSet> >("RigidGroup")
         .def(init<const RigidGroup&>())
         .def("GetName", &RigidGroup::GetName)
+        .def("int_ptr", &RigidGroup::int_ptr)
         ;
 }

src/extensions/moldihedralangle_ext.cpp

@@ -20,6 +20,11 @@
 """
 __all__ = ["MonteCarlo", "AnnealingSchedule", "GlobalOptimType"]
 
+import warnings
+try:
+    import ipywidgets as widgets
+except ImportError:
+    widgets = None
 from pyobjcryst._pyobjcryst import MonteCarlo as MonteCarlo_orig, AnnealingSchedule, GlobalOptimType
 from .refinableobj import *
 
@@ -44,16 +49,55 @@ def RunParallelTempering(self, nb_step: int, final_cost=0, max_time=-1):
 
     def _fix_parameters_for_global_optim(self):
         # Fix parameters that should not be optimised in a MonterCarlo run
-        self.SetParIsFixed(refpartype_unitcell, True);
-        self.SetParIsFixed(refpartype_scattdata_scale, True);
-        self.SetParIsFixed(refpartype_scattdata_profile, True);
-        self.SetParIsFixed(refpartype_scattdata_corr, True);
-        self.SetParIsFixed(refpartype_scattdata_background, True);
-        self.SetParIsFixed(refpartype_scattdata_radiation, True);
+        self.SetParIsFixed(refpartype_unitcell, True)
+        self.SetParIsFixed(refpartype_scattdata_scale, True)
+        self.SetParIsFixed(refpartype_scattdata_profile, True)
+        self.SetParIsFixed(refpartype_scattdata_corr, True)
+        self.SetParIsFixed(refpartype_scattdata_background, True)
+        self.SetParIsFixed(refpartype_scattdata_radiation, True)
 
+    def widget(self):
+        """
+        Display a simple widget for this MonteCarloObj, which only updates the current
+        cost (log-likelihood). Requires ipywidgets
+        """
+        if widgets is None:
+            warnings.warn("You need to install ipywidgets to use MonteCarlo.widget()")
+            return
+        self._widget = widgets.Box()
+        # See https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Styling.html
+        self._widget_label = widgets.Label("", layout=widgets.Layout(max_width='25%', width='20em'))
+        self._widget_llk = widgets.Text("", disabled=True, layout=widgets.Layout(max_width='50%', width='30em'))
+        self._widget.children = [widgets.HBox([self._widget_label, self._widget_llk])]
+        self._widget_update()
+        return self._widget
 
     def UpdateDisplay(self):
+        try:
+            if self._display_update_disabled:
+                return
+        except:
+            pass
+        try:
+            if self._widget is not None:
+                self._widget_update()
+        except AttributeError:
+            # self._3d_widget does not exist
+            pass
+
+    def disable_display_update(self):
+        """ Disable display (useful for multiprocessing)"""
+        self._display_update_disabled = True
+
+    def enable_display_update(self):
+        """ Enable display"""
+        self._display_update_disabled = False
+
+    def _widget_update(self):
+        self._widget_label.value = "MonteCarlo:%s" % self.GetName()
+        self._widget_label.layout.width = '%dem' % len(self._widget_label.value)
         if self.IsOptimizing():
-            print("Run %2d  Trial %8d  LLK=%12.2f" % (self.run, self.trial, self.llk))
+            self._widget_llk.value = "LLK=%12.2f  Run %2d  Trial %8d" % (self.llk, self.run, self.trial)
         else:
-            print("MonteCarlo: current LLK=%12.2f" % self.llk)
+            self._widget_llk.value = "LLK=%12.2f                        " % self.llk
+        self._widget_llk.layout.width = '%dem' % len(self._widget_llk.value)

src/extensions/refinableobj_ext.cpp

@@ -19,6 +19,7 @@
 """
 
 import urllib
+from multiprocessing import current_process
 import numpy as np
 
 __all__ = ["PowderPattern", "CreatePowderPatternFromCIF",
@@ -54,12 +55,25 @@ def __init__(self):
         self.evts = []
 
     def UpdateDisplay(self):
+        try:
+            if self._display_update_disabled:
+                return
+        except:
+            pass
         if self._plot_fig is not None:
             import matplotlib.pyplot as plt
             if 'inline' not in plt.get_backend():
                 if plt.fignum_exists(self._plot_fig.number):
                     self.plot()
 
+    def disable_display_update(self):
+        """ Disable display (useful for multiprocessing)"""
+        self._display_update_disabled = True
+
+    def enable_display_update(self):
+        """ Enable display"""
+        self._display_update_disabled = False
+
     def plot(self, diff=None, hkl=None, figsize=(9, 4), fontsize_hkl=6, reset=False, **kwargs):
         """
         Show the powder pattern in a plot using matplotlib

src/extensions/rigidgroup_ext.cpp

@@ -154,14 +154,13 @@ def __init__(self, level1):
 
         return
 
-    def test_cif_display(self):
-        """Test the creation of a CIF just for display"""
+    def test_display_list(self):
+        """Test the creation of a atoms list for display using 3dmol"""
         c = makeCrystal(*makeScatterer())
-        s = c._display_cif()
-        s = c._display_cif(full_molecule=True)
-        s = c._display_cif(enantiomer=True)
-        s = c._display_cif(only_independent_atoms=True)
-
+        s = c._display_list()
+        s = c._display_list(full_molecule=True)
+        s = c._display_list(enantiomer=True)
+        s = c._display_list(only_independent_atoms=True)
 
 
 if __name__ == "__main__":