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

docs/presentations.html

@@ -39,6 +39,10 @@ <h2>ChimeraX Demonstrations, Talks and Posters</h2>
 <a href="https://rbvi.github.io/chimerax-recipes/">ChimeraX recipes</a>
 </p>
 
+<p>
+<a href="https://www.rbvi.ucsf.edu/chimerax/data/phenix-r24-jan2025/phenix_r24.html">ChimeraX graphical user interfaces for Phenix tools</a>. January 30, 2025.
+</p>
+
 <p>
 <a href="https://www.rbvi.ucsf.edu/chimerax/data/macromethods-jan2025/af3_drugs.html">AlphaFold 3 drug screening on the UCSF Wynton cluster</a>. January 13, 2025.
 </p>

src/bundles/Makefile

@@ -18,7 +18,7 @@ include $(TOP)/mk/config.make
 SYNC_DIR = $(wildcard $(TOP)/build/sync)
 
 REST_SUBDIRS = add_charge addh alignment_algs alignment_headers \
-	  alphafold altloc_explorer amber_info arrays atom_search \
+	  alphafold altloc_explorer amber_info aniso arrays atom_search \
 	  atomic atomic_lib axes_planes basic_actions bild \
 	  blastprotein bond_rot bug_reporter build_structure \
 	  bumps buttons cage_builder \

src/bundles/alignment_headers/pyproject.toml

@@ -9,7 +9,7 @@ authors= [{name = "UCSF RBVI", email="[email protected]"}]
 description = "Alignment header support"
 dependencies = [
 	"ChimeraX-Core ~=1.0"
-	, "ChimeraX-Alignments ~=2.17"
+	, "ChimeraX-Alignments ~=2.18"
 	, "ChimeraX-AlignmentMatrices ~=2.0"
 	, "ChimeraX-Geometry ~=1.0"
 ]

src/bundles/alignment_headers/src/__init__.py

@@ -21,7 +21,7 @@
 # This notice must be embedded in or attached to all copies, including partial
 # copies, of the software or any revisions or derivations thereof.
 # === UCSF ChimeraX Copyright ===
-__version__ = "3.5"
+__version__ = "3.6"
 
 import os
 

src/bundles/alignment_headers/src/conservation.py

@@ -171,24 +171,12 @@ def position_color(self, pos):
 
     def percent_identity(self, pos, for_histogram=False):
         """actually returns a fraction"""
-        occur = {}
-        for seq in self.alignment.seqs:
-            let = seq[pos]
-            try:
-                occur[let] += 1
-            except KeyError:
-                occur[let] = 1
-        best = 0
-        for let, num in occur.items():
-            if not let.isalpha():
-                continue
-            if num > best:
-                best = num
-        if best == 0:
+        char, count = self.alignment.most_common(pos)
+        if count == 0:
             return 0.0
         if for_histogram:
-            return (best - 1) / (len(self.alignment.seqs) - 1)
-        return best / len(self.alignment.seqs)
+            return (count - 1) / (len(self.alignment.seqs) - 1)
+        return count / len(self.alignment.seqs)
 
     def reevaluate(self, pos1=0, pos2=None, *, evaluation_func=None):
         if self.style == self.STYLE_AL2CO:
@@ -295,7 +283,7 @@ def _reeval_al2co(self, pos1, pos2):
             sseq.name = str(i)
             sseq.characters = sseq.characters.replace(' ', '.')
 
-        temp_alignment = session.alignments.new_alignment(sane_seqs, False, auto_associate=False, name="temp", create_headers=False, copy_seqs=False)
+        temp_alignment = session.alignments.new_alignment(sane_seqs, False, auto_associate=False, name="temp", create_headers=False)
         from tempfile import NamedTemporaryFile
         temp_stream = NamedTemporaryFile(mode='w', encoding='utf8', suffix=".aln", delete=False)
         temp_alignment.save(temp_stream, format_name="aln")

src/bundles/aniso/src/mgr.py

@@ -44,7 +44,7 @@ def __init__(self, session, structure, *, from_session=False):
         if not from_session:
             from chimerax.atomic import Atoms
             self.shown_atoms = Atoms()
-            self.atom_depictions = {}
+            self.atom_depictions = None
             self.drawing_params = {
                 'axis_color': None,
                 'axis_factor': None,
@@ -65,30 +65,28 @@ def destroy(self):
         for handler in self.handlers:
             handler.remove()
         if not self.structure.deleted:
-            self.structure.remove_drawings(self.atom_depictions.values())
+            self.structure.remove_drawing(self.atom_depictions)
         self.structure = self.session = None
         super().destroy()
 
     def hide(self, atoms):
         """Hide thermal ellipsoids for these atoms"""
         cur_shown = len(self.shown_atoms)
-        self.shown_atoms = self.shown_atoms.subtract(atoms)
-        if len(self.shown_atoms) == cur_shown:
-            return
-        for a in atoms:
-            self.atom_depictions[a].display = False
+        self.shown_atoms = self.shown_atoms.subtract(self._filter_aniso(atoms))
+        if len(self.shown_atoms) != cur_shown:
+            self._create_depictions()
 
     def show(self, atoms):
         """Show thermal ellipsoids for these atoms"""
         cur_shown = len(self.shown_atoms)
+        atoms = self._filter_aniso(atoms)
         self.shown_atoms = self.shown_atoms.merge(atoms)
         if len(self.shown_atoms) == cur_shown:
             return
-        displayed_atoms = atoms.filter(atoms.displays)
-        for a in displayed_atoms.filter(displayed_atoms.hides == 0):
-            self.atom_depictions[a].display = True
+        self._create_depictions(atoms)
 
     def style(self, **kw):
+        print("style keywords:", kw)
         need_rebuild = False
         for param, value in kw.items():
             if self.drawing_params.get(param) != value:
@@ -117,34 +115,31 @@ def _changes_cb(self, trigger_name, change_info):
         and set(changes.atom_reasons()).isdisjoint(self.atom_reasons)):
             self._create_depictions()
         elif changes.num_deleted_atoms() > 0:
-            dead_drawings = [d for a, d in self.atom_depictions.items() if a.deleted]
-            if dead_drawings:
-                structure.remove_drawings(dead_drawings)
-                self.atom_depictions = {a:d for a,d in self.atom_depictions.items() if not a.deleted}
-
-    def _create_depictions(self):
-        if self.atom_depictions:
-            self.structure.remove_drawings(self.atom_depictions.values())
-        self.atom_depictions.clear()
-
-        atoms = self.structure.atoms
-        atoms = atoms[atoms.has_aniso_u]
-        displayed_atoms = self.shown_atoms.filter(self.shown_atoms.displays)
-        explicitly_depicted = set(displayed_atoms.filter(displayed_atoms.hides == 0))
+            self._create_depictions()
+
+    def _create_depictions(self, added_atoms=None):
+        # added_atoms and self.shown_atoms already filtered for having aniso info
         from chimerax.atomic.shapedrawing import AtomicShapeDrawing
+        if not added_atoms:
+            if self.atom_depictions is not None:
+                self.structure.remove_drawing(self.atom_depictions)
+            self.atom_depictions = self.structure.new_drawing('thermal ellipsoid',
+                subclass=AtomicShapeDrawing)
+            added_atoms = self.shown_atoms
+
+        displayed_atoms = added_atoms.filter(added_atoms.displays)
+        explicitly_depicted = set(displayed_atoms.filter(displayed_atoms.hides == 0))
+
         from chimerax.atomic import Atoms
         from numpy.linalg import svd
         from numpy import dot, sqrt, negative, cross, array
         dp = self.drawing_params
         drawing_info = []
-        for a in atoms:
-            drawing = self.structure.new_drawing('thermal ellipsoid', subclass=AtomicShapeDrawing)
-            self.atom_depictions[a] = drawing
-            drawing.display = a in explicitly_depicted
+        for a in explicitly_depicted:
             ignore, lengths, axes = svd(a.aniso_u)
             lengths2 = sqrt(lengths)
             lengths2 *= dp['scale']
-            drawing_info.append((a, drawing, Atoms([a]), axes, lengths2))
+            drawing_info.append((Atoms([a]), axes, lengths2))
 
         smoothing = dp['smoothing']
 
@@ -154,7 +149,8 @@ def _create_depictions(self):
             transparency = dp['transparency']
             from chimerax.geometry.icosahedron import icosahedron_triangulation
             varray, tarray = icosahedron_triangulation(subdivision_levels=smoothing, sphere_factor=1.0)
-            for atom, drawing, atoms_arg, axes, lengths2 in drawing_info:
+            for atoms_arg, axes, lengths2 in drawing_info:
+                atom = atoms_arg[0]
                 ee = varray * lengths2
                 if dot(cross(axes[0], axes[1]), axes[2]) < 0:
                     axes = negative(axes)
@@ -168,13 +164,14 @@ def _create_depictions(self):
                 if transparency is not None:
                     # transparency is a percentage
                     color = color[:-1] + (round((100 - transparency) * 2.55),)
-                drawing.add_shape(ev, calc_normals(ev, tarray), tarray, color, atoms_arg)
+                self.atom_depictions.add_shape(ev, calc_normals(ev, tarray), tarray, color, atoms_arg)
 
         axis_factor = dp['axis_factor']
         if axis_factor is not None:
             color_param = dp['axis_color']
             thickness = dp['axis_thickness']
-            for atom, drawing, atoms_arg, axes, lengths2 in drawing_info:
+            for atoms_arg, axes, lengths2 in drawing_info:
+                atom = atoms_arg[0]
                 if color_param is None:
                     # match atom
                     color = atom.color
@@ -187,7 +184,7 @@ def _create_depictions(self):
                     ev = dot(ee, axes)
                     ev += atom.coord
                     tarray = cube_triangles
-                    drawing.add_shape(ev, calc_normals(ev, tarray), tarray, color, atoms_arg)
+                    self.atom_depictions.add_shape(ev, calc_normals(ev, tarray), tarray, color, atoms_arg)
 
         ellipse_factor = dp['ellipse_factor']
         if ellipse_factor is not None:
@@ -198,7 +195,8 @@ def _create_depictions(self):
                 nz, nc = cylinder_divisions(1.0, 1.0, 9 * (2**smoothing))
                 self._cylinder_cache[smoothing] = cylinder_geometry(1.0, 1.0, nz, nc, True)
             ellipse_vertices, ellipse_triangles = self._cylinder_cache[smoothing]
-            for atom, drawing, atoms_arg, axes, lengths2 in drawing_info:
+            for atoms_arg, axes, lengths2 in drawing_info:
+                atom = atoms_arg[0]
                 if color_param is None:
                     # match atom
                     color = atom.color
@@ -214,7 +212,10 @@ def _create_depictions(self):
                     ev = dot(ee, axes)
                     ev += atom.coord
                     tarray = ellipse_triangles
-                    drawing.add_shape(ev, calc_normals(ev, tarray), tarray, color, atoms_arg)
+                    self.atom_depictions.add_shape(ev, calc_normals(ev, tarray), tarray, color, atoms_arg)
+
+    def _filter_aniso(self, atoms):
+        return atoms[atoms.has_aniso_u]
 
     def _models_closed_cb(self, trigger_name, closed_models):
         if self.structure in closed_models:
@@ -228,6 +229,7 @@ def reset_state(self, session):
     def restore_snapshot(cls, session, data):
         inst = cls(session, data['structure'], from_session=True)
         inst.atom_depictions = data['atom_depictions']
+        inst.structure.add_drawing(inst.atom_depictions)
         inst.drawing_params = data['drawing_params']
         inst.shown_atoms = data['shown_atoms']
         def delayed_registration(*args, inst=inst):

src/bundles/atomic/bundle_info.xml

@@ -1,5 +1,5 @@
 <!-- Edit bundle_info.xml.in, not bundle_info.xml; then run make_selectors.py  -->
-<BundleInfo name="ChimeraX-Atomic" version="1.60"
+<BundleInfo name="ChimeraX-Atomic" version="1.60.2"
             package="chimerax.atomic"
             purePython="false"
             customInit="true"

src/bundles/atomic/bundle_info.xml.in

@@ -1,5 +1,5 @@
 <!-- Edit bundle_info.xml.in, not bundle_info.xml; then run make_selectors.py  -->
-<BundleInfo name="ChimeraX-Atomic" version="1.60"
+<BundleInfo name="ChimeraX-Atomic" version="1.60.2"
             package="chimerax.atomic"
             purePython="false"
             customInit="true"

src/bundles/atomic/src/molobject.py

@@ -859,6 +859,8 @@ def deleted(self):
     def __copy__(self, copy_seq=None):
         if copy_seq is None:
             copy_seq = Sequence(name=self.name, characters=self.characters)
+            if hasattr(self, 'description'):
+                copy_seq.description = self.description
         else:
             copy_seq.characters = self.characters
         from copy import copy
@@ -1139,6 +1141,8 @@ def bulk_set(self, residues, characters, *, fire_triggers=True):
             self._fire_trigger('residues changed', self)
 
     def __copy__(self):
+        if self.structure is None:
+            return super().__copy__()
         f = c_function('sseq_copy', args = (ctypes.c_void_p,), ret = ctypes.c_void_p)
         copy_sseq = StructureSeq(f(self._c_pointer))
         Sequence.__copy__(self, copy_seq = copy_sseq)

src/bundles/atomic/src/presets.py

@@ -56,4 +56,5 @@ def _execute(session, name):
         residues.ribbon_displays = False
         residues.ring_displays = False
         s.worm_ribbon = False
+        s.ribbon_mode_helix = s.RIBBON_MODE_DEFAULT
         s.apply_auto_styling(**kw)

src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/AtomTypes.cpp

@@ -865,7 +865,7 @@ t0 = t1;
                                     continue;
                                 if (sqlen > p4n2c)
                                     continue;
-                                if (bondee->idatm_type() == "Cac")
+                                if (bondee->idatm_type() == "Cac" || bondee->idatm_type() == "C")
                                     continue;
                                 if (bondee->idatm_type() == "C2") {
                                     bool grand_O2 = false;
@@ -1048,7 +1048,7 @@ std::cerr << "pass 3 took " << (t1 - t0) / (float)CLOCKS_PER_SEC << " seconds\n"
 t0 = t1;
 #endif
 
-    // "pass 4": re-examine all atoms with non-zero 'redo' values and
+    // "pass 4": re-examine most atoms with non-zero 'redo' values and
     //   retype them if necessary
     for (auto a: untyped_atoms) {
 
@@ -1081,7 +1081,7 @@ t0 = t1;
                         a->set_computed_idatm_type("Npl");
                     break;
                 }
-            } else {
+            } else if (redo[a] == 3) {
                 if ((sqlen <= p4c2c && bondee_element == Element::C)
                 || (sqlen <= p4c2n && bondee_element == Element::N)) {
                     a->set_computed_idatm_type("C2");

src/bundles/atomic_lib/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-AtomicLibrary" version="14.1.11"
+<BundleInfo name="ChimeraX-AtomicLibrary" version="14.1.13"
             package="chimerax.atomic_lib"
             purePython="false"
             installedDataDir="data"

src/bundles/clashes/src/clashes.py

@@ -128,7 +128,7 @@ def find_clashes(session, test_atoms,
                     if r:
                         chain_pos[r] = i
     from chimerax.atom_search import AtomSearchTree
-    tree = AtomSearchTree(search_atoms, scene_coords=inter_model)
+    tree = AtomSearchTree(search_atoms, scene_coords=use_scene_coords)
     clashes = {}
     from chimerax.geometry import distance
     intra_mol_map = {}

src/bundles/dicom/src/dicom_hierarchy.py

@@ -890,14 +890,21 @@ def pixel_spacing(self):
         return x_scale, y_scale, z_scale
 
     def rotation(self):
-        affine = self.affine
-        x_scale, y_scale, z_scale = self.pixel_spacing()
-        rotation_matrix = [
-            [affine[0][0] / x_scale, affine[0][1] / y_scale, affine[0][2] / z_scale],
-            [affine[1][0] / x_scale, affine[1][1] / y_scale, affine[1][2] / z_scale],
-            [affine[2][0] / x_scale, affine[2][1] / y_scale, affine[2][2] / z_scale],
-        ]
-        return rotation_matrix
+        #affine = self.affine
+        #x_scale, y_scale, z_scale = self.pixel_spacing()
+        #rotation_matrix = [
+        #    [affine[0][0] / x_scale, affine[0][1] / y_scale, affine[0][2] / z_scale],
+        #    [affine[1][0] / x_scale, affine[1][1] / y_scale, affine[1][2] / z_scale],
+        #    [affine[2][0] / x_scale, affine[2][1] / y_scale, affine[2][2] / z_scale],
+        #]
+        # We're ignoring the rotation given by the DICOM files until someone complains about it.
+        # Doing this simplifies other areas of the codebase significantly.
+        # 1) The plane viewers use orthographic cameras pointed down the X, Y, and Z axes, and
+        #    ignoring the rotations of the files means we don't have to calculate new axes to
+        #    point the cameras down when files aren't axis aligned.
+        # 2) We don't have to modify the raycasting shader to do such calculations either.
+        return [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+        #return rotation_matrix
 
     def origin(self):
         affine = self.affine

src/bundles/graphics/src/opengl.py

@@ -3199,7 +3199,13 @@ def reload_texture(self, data, now = False):
         '''
         # PyOpenGL 3.1.5 leaks memory if data not contiguous, PyOpenGL github issue #47.
         d = data if data.flags['C_CONTIGUOUS'] else data.copy()
-        self.data = d
+        # OpenGL doesn't support float64 textures so if for some reason that's the data type
+        # we end up with truncate it to float32
+        from numpy import float64, float32 
+        if d.dtype == float64:
+            self.data = d.astype(float32)
+        else:
+            self.data = d
         if now:
             self.fill_opengl_texture()
 

src/bundles/map/src/image3d.py

@@ -640,6 +640,9 @@ def _auto_projection_mode(self):
                 pm = ("2d-x", "2d-y", "2d-z")[list(s).index(smin)]
             else:
                 pm = "3d"
+        if pm == 'rays':
+            self._rendering_options.colormap_on_gpu = True
+            self._rendering_options.full_region_on_gpu = True
         return pm
 
     # ---------------------------------------------------------------------------

src/bundles/match_maker/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-MatchMaker" version="2.1.6"
+<BundleInfo name="ChimeraX-MatchMaker" version="2.1.7"
 	    package="chimerax.match_maker"
   	    minSessionVersion="1" maxSessionVersion="1">