Merge branch 'develop' of github.com:RBVI/ChimeraX into develop

docs/presentations.html

@@ -71,6 +71,10 @@ <h2>ChimeraX Demonstrations, Talks and Posters</h2>
 <a href="https://www.rbvi.ucsf.edu/chimerax/data/dms-june2024/deep_mutational_scan.html">Visualizating deep mutational scan scores in ChimeraX</a>. June 10, 2024.
 </p>
 
+<p>
+<a href="https://www.rbvi.ucsf.edu/chimerax/data/membrane-jun2024/projection.html">Adding slices to see membrane complexes in tomograms</a>. May 2, 2024.
+</p>
+
 <p>
 <a href="https://www.rbvi.ucsf.edu/chimerax/data/diffplot-apr2024/diffplot.html">Clustering protein structures with UMAP</a>. April 24, 2024.
 </p>

src/bundles/build_structure/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-BuildStructure" version="2.13" package="chimerax.build_structure"
+<BundleInfo name="ChimeraX-BuildStructure" version="2.13.1" package="chimerax.build_structure"
   	    customInit="true" minSessionVersion="1" maxSessionVersion="1">
 
   <!-- Additional information about bundle source -->

src/bundles/build_structure/src/tool.py

@@ -48,7 +48,7 @@ def confirm_close(self):
                 msg_box.setWindowTitle("Confirm Close")
                 msg_box.setText(f"There are active {text}")
                 msg_box.setInformativeText(f"Closing Build Structure will deactivate these {text}"
-                    " md forget their orignal values.\nReally close?" )
+                    " and forget their original values.\nReally close?" )
                 msg_box.setStandardButtons(QMessageBox.No | QMessageBox.Yes)
                 msg_box.setDefaultButton(QMessageBox.Yes)
                 cb = QCheckBox("Don't ask in the future")

src/bundles/dicom/src/__init__.py

@@ -10,7 +10,7 @@
 # including partial copies, of the software or any revisions
 # or derivations thereof.
 # === UCSF ChimeraX Copyright ===
-__version__ = "1.2.5"
+__version__ = "1.2.6"
 from chimerax.core.toolshed import BundleAPI
 from chimerax.map import add_map_format
 from chimerax.core.tools import get_singleton

src/bundles/dicom/src/ui/metadata_tool.py

@@ -32,7 +32,7 @@
 from .widgets import DICOMTable
 
 dicom_template_url: str = (
-    "http://dicomlookup.com/lookup.asp?sw=Tnumber&q=%s"  # noqa they don't have https
+    "https://dicomlookup.com/dicomtags/%s"
 )
 
 try:

src/bundles/mutation_scores/src/ms_csv_file.py

@@ -22,7 +22,7 @@
 # copies, of the software or any revisions or derivations thereof.
 # === UCSF ChimeraX Copyright ===
 
-def open_mutation_scores_csv(session, path, chain = None, name = None):
+def open_mutation_scores_csv(session, path, chain = None, name = None, show_plot = True):
     mset = _read_mutation_scores_csv(path, name = name)
 
     from .ms_data import mutation_scores_manager
@@ -45,6 +45,11 @@ def open_mutation_scores_csv(session, path, chain = None, name = None):
         if mres > 0:
             message += f' Found scores for {mres} residues not present in atomic model.'
 
+    if show_plot and session.ui.is_gui and len(mset.score_names()) >= 2:
+        x_score_name, y_score_name = mset.score_names()[:2]
+        from .ms_scatter_plot import mutation_scores_scatter_plot
+        mutation_scores_scatter_plot(session, x_score_name, y_score_name, mset.name, replace = False)
+
     return mset, message
 
 def _read_mutation_scores_csv(path, name = None):

src/bundles/phenix_ui/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-PhenixUI" version="1.4"
+<BundleInfo name="ChimeraX-PhenixUI" version="1.4.1"
 	    package="chimerax.phenix_ui"
   	    minSessionVersion="1" maxSessionVersion="1">
 

src/bundles/phenix_ui/src/emplace_local.py

@@ -94,7 +94,7 @@ def running(self):
     'verbose': False
 }
 def phenix_local_fit(session, model, center=None, map_data=None, *, resolution=0.0, show_sharpened_map=False,
-        apply_symmetry=False, prefitted=None, block=None, phenix_location=None,
+        apply_symmetry=False, prefitted=None, show_tool=True, block=None, phenix_location=None,
         verbose=command_defaults['verbose'], option_arg=[], position_arg=[]):
 
     # Find the phenix.voyager.emplace_local executable
@@ -147,9 +147,9 @@ def phenix_local_fit(session, model, center=None, map_data=None, *, resolution=0
     # Run phenix.voyager.emplace_local
     # keep a reference to 'd' in the callback so that the temporary directory isn't removed before
     # the program runs
-    callback = lambda transform, sharpened_map, *args, session=session, maps=map_data, \
-        ssm=show_sharpened_map, app_sym=apply_symmetry, d_ref=d: _process_results(session,
-        transform, sharpened_map, model, maps, ssm, app_sym)
+    callback = lambda transforms, sharpened_map, llgs, ccs, *args, session=session, maps=map_data, \
+        ssm=show_sharpened_map, app_sym=apply_symmetry, show_tool=show_tool, d_ref=d: \
+        _process_results(session, transforms, sharpened_map, llgs, ccs, model, maps, ssm, app_sym, show_tool)
     FitJob(session, exe_path, option_arg, map_arg1, map_arg2, search_center,
         "model.pdb", prefitted_arg, position_arg, temp_dir, resolution, verbose, callback, block)
 
@@ -215,36 +215,44 @@ def view_box(session, model):
         return (face_intercepts[0] + face_intercepts[1]) / 2
     raise ViewBoxError("Center of view does not intersect %s bounding box" % model)
 
-def _process_results(session, transform, sharpened_map, orig_model, maps, show_sharpened_map,
-        apply_symmetry):
+def _process_results(session, transforms, llgs, ccs, sharpened_map, orig_model, maps, show_sharpened_map,
+        apply_symmetry, show_tool):
+    session.logger.status("Fitting job finished")
     if orig_model.deleted:
         raise UserError("Structure being fitting was deleted during fitting")
-    from chimerax.geometry import Place
-    orig_model.scene_position = Place(transform) * orig_model.scene_position
     sharpened_map.name = "sharpened local map"
     sharpened_map.display = show_sharpened_map
     session.models.add([sharpened_map])
-    session.logger.status("Fitting job finished")
+    from chimerax.core.commands import run, concise_model_spec, StringArg
     if apply_symmetry:
         sym_map = maps[0]
         if sym_map.deleted:
-            raise UserError("Map being fitted has been deleted; not applying symmetry")
-        from chimerax.core.commands import run, concise_model_spec, StringArg
-        run(session, "measure symmetry " + sym_map.atomspec)
-        if maps[0].data.symmetries:
+            session.logger.warning("Map being fitted has been deleted; not applying symmetry")
+            apply_symmetry = False
+        else:
+            run(session, "measure symmetry " + sym_map.atomspec)
+            if not sym_map.data.symmetries:
+                session.logger.warning(
+                    'Could not determine symmetry for %s<br><br>'
+                    'If you know the symmetry of the map, you can create symmetry copies of the structure'
+                    ' with the <a href="help:user/commands/sym.html">sym</a> command and then combine the'
+                    ' symmetry copies with the original structure with the <a'
+                    ' href="help:user/commands/combine.html">combine</a> command'
+                    % sym_map, is_html=True)
+                apply_symmetry = False
+    if show_tool and len(transforms) > 1 and session.ui.is_gui:
+        from .tool import EmplaceLocalResultsViewer
+        EmplaceLocalResultsViewer(session, orig_model, transforms, llgs, ccs,
+            sym_map if apply_symmetry else None)
+    else:
+        from chimerax.geometry import Place
+        orig_model.scene_position = Place(transforms[0]) * orig_model.scene_position
+        if apply_symmetry:
             prev_models = set(session.models[:])
             run(session, "sym " + orig_model.atomspec + " symmetry " + sym_map.atomspec + " copies true")
             added = [m for m in session.models if m not in prev_models]
             run(session, "combine " + concise_model_spec(session, [orig_model] + added) + " close true"
                 " modelId %d name %s" % (orig_model.id[0], StringArg.unparse(orig_model.name)))
-        else:
-            session.logger.warning(
-                'Could not determine symmetry for %s<br><br>'
-                'If you know the symmetry of the map, you can create symmetry copies of the structure'
-                ' with the <a href="help:user/commands/sym.html">sym</a> command and then combine the'
-                ' symmetry copies with the original structure with the <a'
-                ' href="help:user/commands/combine.html">combine</a> command'
-                % sym_map, is_html=True)
 
 #NOTE: We don't use a REST server; reference code retained in douse.py
 
@@ -313,7 +321,7 @@ def _run_fit_subprocess(session, exe_path, optional_args, map1_file_name, map2_f
         ', '.join(["%g" % v for v in info["mapCC"]])))
 
     from numpy import array
-    return array(info['RT'][0]), sharpened_maps[0]
+    return [array(rt) for rt in info['RT']], info["mapLLG"], info["mapCC"], sharpened_maps[0]
 
 def register_command(logger):
     from chimerax.core.commands import CmdDesc, register
@@ -336,6 +344,7 @@ def register_command(logger):
                    ('resolution', NonNegativeFloatArg),
                    ('show_sharpened_map', BoolArg),
                    ('apply_symmetry', BoolArg),
+                   ('show_tool', BoolArg),
         ],
         synopsis = 'Place structure in map'
     )

src/bundles/phenix_ui/src/tool.py

@@ -182,6 +182,113 @@ def launch_douse(self):
         run(self.session, cmd)
         self.delete()
 
+class EmplaceLocalResultsViewer(ToolInstance):
+    def __init__(self, session, *args):
+        # if 'args' is empty, we are being restored from a session and _finalize_init() will be called later
+        super().__init__(session, "Local EM Fitting Results")
+        if not args:
+            return
+        self._finalize_init(*args)
+
+    def _finalize_init(self, orig_model, transforms, llgs, ccs, sym_map, *, table_state=None):
+        self.orig_model = orig_model
+        self.orig_position = orig_model.position
+        self.transforms = transforms
+        self.llgs = llgs
+        self.ccs = ccs
+        self.sym_map = sym_map
+
+        from chimerax.core.models import REMOVE_MODELS
+        from chimerax.atomic import get_triggers
+        self.handlers = [
+            self.session.triggers.add_handler(REMOVE_MODELS, self._models_removed_cb),
+        ]
+        self._interpolate_handler = None
+
+        from chimerax.ui import MainToolWindow
+        self.tool_window = tw = MainToolWindow(self, close_destroys=False)
+        parent = tw.ui_area
+
+        from Qt.QtWidgets import QHBoxLayout, QButtonGroup, QVBoxLayout, QRadioButton, QCheckBox
+        from Qt.QtWidgets import QPushButton, QLabel, QToolButton, QGridLayout
+        layout = QVBoxLayout()
+        layout.setContentsMargins(2,2,2,2)
+        layout.setSpacing(0)
+        parent.setLayout(layout)
+
+        #TODO
+        self.table = self._build_table(table_state)
+        layout.addWidget(self.table, stretch=1)
+
+        self.tool_window.manage('side')
+
+    def delete(self):
+        for handler in self.handlers:
+            handler.remove()
+        if self._interpolate_handler:
+            self._interpolate_handler.remove()
+        self.orig_model = self.sym_map = None
+        super().delete()
+
+    def _build_table(self, table_state):
+        class TableDatum:
+            def __init__(self, num, transform, llg, cc):
+                self.num = num
+                self.transform = transform
+                self.llg = llg
+                self.cc = cc
+        from chimerax.ui.widgets import ItemTable
+        table = ItemTable()
+        result_col = table.add_column("Result", "num")
+        table.add_column("Correlation Coefficient", "cc", format="%g")
+        table.add_column("Log-Likelihood Gain", "llg", format="%g")
+        table.data = [TableDatum(*args)
+            for args in zip(range(1, len(self.transforms)+1), self.transforms, self.llgs, self.ccs)]
+        table.launch(select_mode=table.SelectionMode.SingleSelection, session_info=table_state)
+        table.sort_by(result_col, table.SORT_ASCENDING)
+        table.selection_changed.connect(self._new_selection)
+        table.selected = table.data[0:1]
+        return table
+
+    def _interpolate(self, destination):
+        if self._interpolate_handler:
+            self._interpolate_handler.remove()
+        # interpolation code largely cribbed from map_fit.search.move_models/move_step
+        def make_step(trig_name, trig_data, *, tool=self, destination=destination, frame_info=[10]):
+            m = tool.orig_model
+            b = m.bounds()
+            finish = False
+            if b:
+                num_frames = frame_info[0]
+                cscene = .5 * (b.xyz_min + b.xyz_max)
+                c = m.scene_position.inverse() * cscene # Center in model coordinates
+                m.position = m.position.interpolate(destination, c, 1.0/num_frames)
+                if num_frames > 1:
+                    frame_info[0] = num_frames - 1
+                else:
+                    finish = True
+            else:
+                m.position = destination
+                finish = True
+            if finish:
+                tool._interpolate_handler.remove()
+                tool._interpolate_handler = None
+        self._interpolate_handler = self.session.triggers.add_handler("new frame", make_step)
+
+    def _models_removed_cb(self, trig_name, trig_data):
+        if self.orig_model in trig_data:
+            self.delete()
+
+    def _new_selection(self, selected, unselected):
+        if not selected:
+            return
+        from chimerax.geometry import Place
+        destination = Place(selected[0].transform) * self.orig_position
+        if unselected:
+            self._interpolate(destination)
+        else:
+            self.orig_model.position = destination
+
 class LaunchEmplaceLocalTool(ToolInstance):
     help = "help:user/tools/localemfitting.html"
 

src/bundles/surface/src/updaters.py

@@ -35,7 +35,7 @@ def reset_state(self, session):
 #
 def _updater_active(u):
     if hasattr(u, 'surface'):
-        if u.surface is None or u.surface.deleted:
+        if u.surface is None or u.surface.deleted or not u.surface.SESSION_SAVE:
             return False
     if hasattr(u, 'closed') and u.closed():
         return False