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

Author: tomgoddard

docs/user/commands/cartoon.html

@@ -304,7 +304,7 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>:
 <a href="#hmode"><b>cylinder</b> mode</a>,
 a constant <b>radius</b> <i>r</i> can be specified, otherwise
 (<b>auto</b>, default) a radius will be determined separately for each helix
-according to the average distance of the &alpha;-carbons to the tube midline,
+according to the average distance of the &alpha;-carbons to the midline,
 capped at a maximum of 2.5 &Aring;.
 Where a displayed &alpha;-carbon is offset from the tube surface,
 a <a href="#tether">tether</a> will be drawn.

docs/user/commands/matchmaker.html

@@ -228,6 +228,19 @@ <h3>Options</h3>
 </td></tr></tbody></table>
   </blockquote>
 </blockquote>
+<blockquote>
+<a name="rmsd"><b>rmsd</b> &nbsp;true&nbsp;|&nbsp;<b>false</b></a>
+<br>
+With <a href="#show"><b>showAlignment</b></a> <b>false</b>, the
+<a href="../tools/sequenceviewer.html"><b>Sequence Viewer</b></a> window
+is not shown, and the
+<a href="../tools/sequenceviewer.html#headers">alignment-header attributes</a>
+<b>seq_rmsd</b> and <b>seq_conservation</b> are not automatically assigned.
+Specifying <b>rmsd true</b> forces calculating and assigning these attributes 
+even though the pairwise sequence alignment is not displayed.
+If <a href="#show"><b>showAlignment</b></a> is <b>true</b>, the <b>rmsd</b>
+option is unnecessary and ignored.
+</blockquote>
 <blockquote>
   <a name="cutoffDistance"><b>cutoffDistance</b> 
   &nbsp;<i>cutoff</i>&nbsp;|&nbsp;none</a>
@@ -459,6 +472,6 @@ <h3>Sequence-Alignment Scoring Options</h3>
 
 <hr>
 <address>UCSF Resource for Biocomputing, Visualization, and Informatics / 
-March 2025</address>
+April 2026</address>
 
-</body></html>
+</body></html>

src/bundles/atomic/atomic_cpp/molc.cpp

@@ -4156,6 +4156,47 @@ extern "C" EXPORT void structure_combine(void *combination, void *s, void *pos,
     }
 }
 
+extern "C" EXPORT void *structure_break_triangle_waters(void *mol)
+{
+    Structure *m = static_cast<Structure *>(mol);
+    try {
+        for (auto r: m->residues()) {
+            auto& atoms = r->atoms();
+            if (atoms.size() != 3)
+                continue;
+            Atom* o = nullptr;
+            Atom* h1 = nullptr;
+            Atom* h2 = nullptr;
+            for (auto a: atoms) {
+                if (a->element() == Element::O) {
+                    if (o == nullptr)
+                        o = a;
+                    else
+                        break;
+                } else if (a->element() == Element::H) {
+                    if (h1 == nullptr)
+                        h1 = a;
+                    else if (h2 == nullptr)
+                        h2 = a;
+                    else
+                        break;
+                } else
+                    break;
+            }
+            if (o != nullptr && h1 != nullptr && h2 != nullptr) {
+                for (auto& b: h1->bonds())
+                    if (b->other_atom(h1) == h2) {
+                        m->delete_bond(b);
+                        break;
+                    }
+            }
+        }
+    } catch (...) {
+        molc_error();
+    }
+    return nullptr;
+}
+
 extern "C" EXPORT void *structure_copy(void *mol)
 {
     Structure *m = static_cast<Structure *>(mol);

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="1.66"
+<BundleInfo name="ChimeraX-Atomic" version="1.67"
             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="1.66"
+<BundleInfo name="ChimeraX-Atomic" version="1.67"
             package="chimerax.atomic"
             purePython="false"
             customInit="true"

src/bundles/atomic/src/molobject.py

@@ -1737,6 +1737,11 @@ def bonded_groups(self, *, consider_missing_structure=True):
         import numpy
         return [Atoms(numpy.array(x, numpy.uintp)) for x in f(self._c_pointer, consider_missing_structure)]
 
+    def break_triangle_waters(self):
+        '''For waters with an H-H bond, break that bond'''
+        f = c_function('structure_break_triangle_waters', args = (ctypes.c_void_p,), ret = ctypes.c_void_p)
+        p = f(self._c_pointer)
+
     def chain_trace_atoms(self):
         '''
         Find pairs of atoms that should be connected in a chain trace.

src/bundles/atomic/src/structure.py

@@ -61,7 +61,7 @@ class Structure(Model, StructureData):
         'ribbon_tether_opacity', 'ribbon_tether_scale', 'worm_radii'])
 
     def __init__(self, session, *, name = "structure", c_pointer = None, restore_data = None,
-                 auto_style = True, log_info = True):
+                 auto_style = True, log_info = True, break_triangle_waters = True):
         from .molarray import Residues
         from numpy import array
         from .ribbon import XSectionManager
@@ -83,6 +83,7 @@ def __init__(self, session, *, name = "structure", c_pointer = None, restore_dat
         Model.__init__(self, name, session)
         self._auto_style = auto_style
         self._log_info = log_info
+        self._break_triangle_waters = break_triangle_waters
 
         # for now, restore attrs to default initial values even for sessions...
         self._atoms_drawing = None
@@ -202,6 +203,8 @@ def added_to_session(self, session):
         # but that is only certain to be correct if this is the first time the structure
         # has been added to the session, so always set it. [#18427]
         self._cpp_notify_position(self.scene_position)
+        if self._break_triangle_waters:
+            self.break_triangle_waters()
         if self._auto_style:
             self.apply_auto_styling(set_lighting = self._is_only_model())
         self._start_change_tracking(session.change_tracker)

src/bundles/match_maker/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-MatchMaker" version="2.2.2"
+<BundleInfo name="ChimeraX-MatchMaker" version="2.3"
 	    package="chimerax.match_maker"
   	    minSessionVersion="1" maxSessionVersion="1">
 

src/bundles/match_maker/src/match.py

@@ -194,7 +194,7 @@ def ss_let(r):
 
 def match(session, chain_pairing, match_items, matrix, alg, gap_open, gap_extend, *, cutoff_distance=None,
         show_alignment=defaults['show_alignment'], align=align, domain_residues=(None, None), bring=None,
-        verbose=defaults['verbose_logging'], always_raise_errors=False, report_matrix=False,
+        verbose=defaults['verbose_logging'], always_raise_errors=False, report_matrix=False, rmsd=False,
         log_parameters=defaults['log_parameters'],
         **align_kw):
     """Superimpose structures based on sequence alignment
@@ -554,7 +554,7 @@ def match(session, chain_pairing, match_items, matrix, alg, gap_open, gap_extend
                 s1.name, s1.structure.id_string, s2.name,
                 s2.structure.id_string, score), log=(verbose is not None))
             skip = set()
-            if show_alignment:
+            if show_alignment or rmsd:
                 for s in [s1,s2]:
                     if hasattr(s, '_dm_rebuild_info'):
                         residues = s.residues
@@ -578,7 +578,7 @@ def match(session, chain_pairing, match_items, matrix, alg, gap_open, gap_extend
                         s.bulk_set(residues, characters)
                 with show_context():
                     alignment = session.alignments.new_alignment([s1,s2], None, auto_associate=None,
-                        name="MatchMaker alignment")
+                        name="MatchMaker alignment", viewer=show_alignment)
                 alignment.auto_associate = True
                 for hdr in alignment.headers:
                     hdr.shown = hdr.ident == "rmsd"
@@ -690,7 +690,7 @@ def cmd_match(session, match_atoms, to=None, pairing=defaults["chain_pairing"],
         hgap=defaults["helix_open"], sgap=defaults["strand_open"], ogap=defaults["other_open"],
         cutoff_distance=defaults["iter_cutoff"], gap_extend=defaults["gap_extend"],
         show_alignment=defaults['show_alignment'], compute_s_s=defaults["compute_ss"],
-        keep_computed_s_s=defaults['overwrite_ss'], report_matrix=False,
+        keep_computed_s_s=defaults['overwrite_ss'], report_matrix=False, rmsd=False,
         log_parameters=defaults['log_parameters'],
         mat_h_h=default_ss_matrix[('H', 'H')],
         mat_s_s=default_ss_matrix[('S', 'S')],
@@ -775,7 +775,7 @@ def cmd_match(session, match_atoms, to=None, pairing=defaults["chain_pairing"],
     ss_matrix[('H', 'O')] = ss_matrix[('O', 'H')] = float(mat_h_o)
     ss_matrix[('S', 'O')] = ss_matrix[('O', 'S')] = float(mat_s_o)
     ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend,
-        ss_fraction=ss_fraction, ss_matrix=ss_matrix,
+        ss_fraction=ss_fraction, ss_matrix=ss_matrix, rmsd=rmsd,
         cutoff_distance=cutoff_distance, show_alignment=show_alignment, bring=bring,
         domain_residues=(ref_atoms.residues.unique(), match_atoms.residues.unique()),
         gap_open_helix=hgap, gap_open_strand=sgap, gap_open_other=ogap, report_matrix=report_matrix,
@@ -856,7 +856,7 @@ def register_command(logger):
             ('bring', TopModelsArg), ('show_alignment', BoolArg), ('compute_s_s', BoolArg),
             ('mat_h_h', FloatArg), ('mat_s_s', FloatArg), ('mat_o_o', FloatArg), ('mat_h_s', FloatArg),
             ('mat_h_o', FloatArg), ('mat_s_o', FloatArg), ('keep_computed_s_s', BoolArg),
-            ('report_matrix', BoolArg), ('log_parameters', BoolArg)],
+            ('report_matrix', BoolArg), ('rmsd', BoolArg), ('log_parameters', BoolArg)],
         synopsis = 'Align atomic structures using sequence alignment'
     )
     register('matchmaker', desc, cmd_match, logger=logger)

src/bundles/md_crds/src/__init__.py

@@ -56,6 +56,7 @@ def open_args(self):
                         from chimerax.core.commands import BoolArg, OpenFileNameArg, PositiveIntArg
                         return {
                             'auto_style': BoolArg,
+                            'break_triangle_waters': BoolArg,
                             'coords': OpenFileNameArg,
                             'end': PositiveIntArg,
                             'omit': omit_arg,
@@ -71,7 +72,7 @@ def open(self, session, data, file_name, **kw):
                     @property
                     def open_args(self):
                         from chimerax.core.commands import BoolArg
-                        return { 'auto_style': BoolArg }
+                        return { 'auto_style': BoolArg, 'break_triangle_waters': BoolArg }
             else:
                 class MDInfo(OpenerInfo):
                     def open(self, session, data, file_name, *, structure_model=None,