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

docs/user/commands/color.html

@@ -608,6 +608,7 @@ <h3>Coloring Surfaces by Map Value</h3>
 [&nbsp;<a href="#palette"><b>palette</b></a>&nbsp;&nbsp;<i>palette</i>&nbsp;]
 [&nbsp;<b>range</b>&nbsp;&nbsp;<i>low</i>,<i>high</i>&nbsp;|&nbsp;full&nbsp;]
 [&nbsp;<a href="#transparency-bfactor"><b>transparency</b></a>&nbsp;&nbsp;<i>percent</i>&nbsp;]
+[&nbsp;<b>outsideColor</b>&nbsp&nbsp;<a href="colornames.html"><i>color-spec</i></a>&nbsp;]
 </blockquote>
 <p>
 The <b>sample</b>, <b>electrostatic</b>, and <b>gradient</b> coloring options
@@ -627,7 +628,12 @@ <h3>Coloring Surfaces by Map Value</h3>
 <td bgcolor=white width="10px" title="white"></td>
 <td bgcolor=blue width="10px" title="blue"></td>
 </tr></table> and the <a href="#range"><b>range</b></a> default depends on the 
-specific type of map coloring, explained below.
+specific type of map coloring, explained below;
+the <b>outsideColor</b> is used for surface vertices 
+that fall outside the volume data grid box
+(default <b>#808080</b> <table border cellpadding="4" cellspacing="0"
+style="display:inline-block"><tr>
+<td bgcolor="#808080" width="10px" title="#808080"></td></tr></table>).
 </p><p>
 When the coloring command is run interactively (in gui mode and not via a
 <a href="usageconventions.html#cxc-files">script</a>),
@@ -1311,5 +1317,5 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>:
 
 <hr>
 <address>UCSF Resource for Biocomputing, Visualization, and Informatics / 
-November 2024</address>
+January 2025</address>
 </body></html>

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:

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/seqalign/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-Alignments" version="2.17" package="chimerax.seqalign"
+<BundleInfo name="ChimeraX-Alignments" version="2.18" package="chimerax.seqalign"
   	    minSessionVersion="1" maxSessionVersion="1">
 
   <!-- Additional information about bundle source -->

src/bundles/seqalign/src/alignment.py

@@ -109,6 +109,7 @@ def __init__(self, session, seqs, ident, file_attrs, file_markups, auto_destroy,
         self.viewers = []
         self.viewers_by_subcommand = {}
         self.viewer_to_subcommand = {}
+        self._column_counts_cache = None
         self._observer_notification_suspended = 0
         self._ob_note_suspended_data = []
         self._modified_mmaps = []
@@ -490,6 +491,19 @@ def auto_associate(self, assoc):
     def being_destroyed(self):
         return self._in_destroy
 
+    def column_counts(self):
+        """Returns a dictionary keyed on column index, with values that are 2-tuples of numpy
+           arrays; the first member is the array of unique characters in that column, and the
+           second array is the corresponding counts for those characters.
+        """
+        if self._column_counts_cache is None:
+            import numpy
+            data = numpy.array([list(seq.characters) for seq in self._seqs])
+            cache = self._column_counts_cache = {}
+            for i in range(len(data[0])):
+                cache[i] = numpy.unique(data[:,i], return_counts=True)
+        return self._column_counts_cache.copy()
+
     def detach_viewer(self, viewer):
         """Called when a viewer is done with the alignment (see attach_viewer)"""
         self.viewers.remove(viewer)
@@ -666,6 +680,27 @@ def match(self, ref_chain, match_chains, *, iterate=-1, restriction=None):
                 return_vals.append((None, None, None, None, None))
         return return_vals
 
+    def most_common(self, col_index, *, non_gap=True):
+        """Returns most common character in the column given by 'col_index' and the count for that character.
+           For ties, one of the most common characters, chosen arbitrarily, will be returned.  If 'non_gap'
+           is True, gap characters will be ignored.
+        """
+        chars, counts = self.column_counts()[col_index]
+        if non_gap:
+            max_count = 0
+            for char, count in zip(chars, counts):
+                if not char.isalpha():
+                    continue
+                if count > max_count:
+                    max_count = count
+                    max_char = char
+            if max_count == 0:
+                return ' ', 0
+            return max_char, max_count
+        import numpy
+        max_index = numpy.argmax(counts)
+        return chars[max_index], counts[max_index]
+
     def notify(self, note_name, note_data):
         """Used by headers to issue notifications, but theoretically could be used by anyone"""
         self._notify_observers(note_name, note_data)
@@ -982,6 +1017,7 @@ def _rmsd_atomic_cb(self, trig_name, changes):
                 break
 
     def _seq_characters_changed_cb(self, trig_name, seq):
+        self._column_counts_cache = None
         if not getattr(self, '_realigning', False):
             self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)
 
@@ -1021,22 +1057,7 @@ def process_attr(attr_name, col_vals):
         if headers is None:
             headers = [hdr for hdr in self._headers if hdr.shown or hdr.eval_while_hidden]
             if len(self.seqs) > 1:
-                values = []
-                for i in range(len(self._seqs[0])):
-                    counts = {}
-                    for seq in self._seqs:
-                        c = seq[i]
-                        if not c.isalnum():
-                            continue
-                        counts[c] = counts.get(c, 0) + 1
-                    if not counts:
-                        values.append(0.0)
-                        continue
-                    max_count = None
-                    for c, count in counts.items():
-                        if max_count is None or count > max_count:
-                            max_count = count
-                    values.append(100.0 * max_count / len(self._seqs))
+                values = [100.0 * self.most_common(col)[1] for col in range(len(self._seqs[0]))]
                 process_attr(self.COL_IDENTITY_ATTR, values)
         from chimerax.atomic import Residue
         for header in headers: