v1.0.0-rc.179 (#90)

* Rugnux: Stills processing needs only the unit cell and space group beyond what the file records - detector distance, beam centre, tilt, panel placement, saturation level, gain and polarisation plane are found from the images - and is up to twice as fast.
* Rugnux: Stills can be indexed without a GPU, with a CPU implementation of the fast-feedback indexer (macOS, computers without a GPU).
* Rugnux: Rotation and stills data are integrated in the detector's own units with one gain model, improving data from CCD detectors.
* Web frontend: The Rugnux live page shows the placed model with its electron density and anomalous difference map in a Mol* viewer.

Reviewed-on: #90
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

writer/WriteModel.cpp

@@ -5,6 +5,7 @@
 
 #include <algorithm>
 #include <fstream>
+#include <sstream>
 
 #include <gemmi/to_mmcif.hpp>  // make_mmcif_document
 #include <gemmi/to_cif.hpp>    // write_cif_to_stream
@@ -27,20 +28,10 @@ bool coordinates_obey(const gemmi::SpaceGroup &coordinates_group, const gemmi::S
                          label_ops.begin(), label_ops.end());
 }
 
-}  // namespace
-
-void WritePlacedModel(const gemmi::Structure &placed,
-                      const UnitCell &cell,
-                      const gemmi::SpaceGroup &space_group,
-                      const std::string &output_prefix,
-                      Logger &logger) {
-    const std::string cif_path = output_prefix + "_model.cif";
-    // PDB as well as mmCIF, because the fragment-screening tools this file exists for take a PDB:
-    // PanDDA's per-dataset input is <name>.pdb beside <name>.mtz, and dimple produces the same pair.
-    // Same coordinates, same frame, both formats - a PDB cannot hold every cell, so it is written
-    // when it can be and skipped, with a line saying so, when it cannot.
-    const std::string pdb_path = output_prefix + "_model.pdb";
-
+// `placed` in `cell`, labelled with `space_group` wherever its coordinates obey it (see WritePlacedModel).
+// takes_model_group: the model's own group was kept instead.
+gemmi::Structure LabelledModel(const gemmi::Structure &placed, const UnitCell &cell,
+                               const gemmi::SpaceGroup &space_group, bool &takes_model_group) {
     gemmi::Structure st = placed;
     // The cell is the data's, taken from the same value the reflection files are written from: the
     // coordinates were re-fractionalized into it and genuinely sit there.
@@ -55,11 +46,30 @@ void WritePlacedModel(const gemmi::Structure &placed,
     // structure it refines is not the model, and it says so nowhere. A pair whose two files disagree
     // is worth a warning; a coordinate file that is quietly wrong on its own is not worth writing.
     const gemmi::SpaceGroup *model_group = st.find_spacegroup();
-    const bool takes_model_group = model_group != nullptr && !coordinates_obey(*model_group, space_group);
-    const gemmi::SpaceGroup &label = takes_model_group ? *model_group : space_group;
+    takes_model_group = model_group != nullptr && !coordinates_obey(*model_group, space_group);
     st.cell = cell;
-    st.spacegroup_hm = label.xhm();
+    st.spacegroup_hm = (takes_model_group ? *model_group : space_group).xhm();
     st.setup_cell_images();
+    return st;
+}
+
+}  // namespace
+
+void WritePlacedModel(const gemmi::Structure &placed,
+                      const UnitCell &cell,
+                      const gemmi::SpaceGroup &space_group,
+                      const std::string &output_prefix,
+                      Logger &logger) {
+    const std::string cif_path = output_prefix + "_model.cif";
+    // PDB as well as mmCIF, because the fragment-screening tools this file exists for take a PDB:
+    // PanDDA's per-dataset input is <name>.pdb beside <name>.mtz, and dimple produces the same pair.
+    // Same coordinates, same frame, both formats - a PDB cannot hold every cell, so it is written
+    // when it can be and skipped, with a line saying so, when it cannot.
+    const std::string pdb_path = output_prefix + "_model.pdb";
+
+    bool takes_model_group = false;
+    gemmi::Structure st = LabelledModel(placed, cell, space_group, takes_model_group);
+    const gemmi::SpaceGroup &label = takes_model_group ? *st.find_spacegroup() : space_group;
     // Fills in entity types and label_asym_id for a model read from a PDB, which carries neither.
     // Both are no-ops where the input already had them, i.e. for an mmCIF input.
     // setup_entities and make_mmcif_document can both throw, and this runs BEFORE the reflection files
@@ -100,3 +110,13 @@ void WritePlacedModel(const gemmi::Structure &placed,
                        label.short_name(), space_group.short_name(), space_group.short_name());
     }
 }
+
+std::string PlacedModelMmcif(const gemmi::Structure &placed, const UnitCell &cell,
+                             const gemmi::SpaceGroup &space_group) {
+    bool takes_model_group = false;
+    gemmi::Structure st = LabelledModel(placed, cell, space_group, takes_model_group);
+    gemmi::setup_entities(st);
+    std::ostringstream os;
+    gemmi::cif::write_cif_to_stream(os, gemmi::make_mmcif_document(st));
+    return os.str();
+}