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

prereqs/PyQt/Makefile.wheel.qt6

@@ -13,7 +13,7 @@ BASE_VERSION = 6.8
 QT_MINOR_VERSION = 2
 PYQT_MINOR_VERSION = 1
 ifeq ($(OS),Linux)
-PYQT_REVISION = 1
+PYQT_REVISION =
 else
 PYQT_REVISION =
 endif

src/bundles/seq_view/src/match.py

@@ -41,7 +41,7 @@ def __init__(self, sv, tool_window):
         chains_layout.addWidget(QLabel("Reference chain"), 0, 0, alignment=Qt.AlignCenter)
         chains_layout.addWidget(QLabel("Match chain(s)"), 0, 1, alignment=Qt.AlignCenter)
         self.ref_chain_menu = ChainMenuButton(sv.session, list_func=sv.alignment.associations.keys)
-        chains_layout.addWidget(self.ref_chain_menu, 1, 0, alignment=Qt.AlignCenter)
+        chains_layout.addWidget(self.ref_chain_menu, 1, 0, alignment=Qt.AlignHCenter|Qt.AlignTop)
         self.match_chain_list = ChainListWidget(sv.session, autoselect=ChainListWidget.AUTOSELECT_FIRST,
             list_func=sv.alignment.associations.keys, filter_func=lambda c, menu=self.ref_chain_menu:
             c.structure is not getattr(menu.value, 'structure', None))
@@ -63,6 +63,7 @@ def __init__(self, sv, tool_window):
 
         it_layout = QHBoxLayout()
         self.iterate_check_box = QCheckBox("Iterate by pruning long atom pairs until no pair exceeds ")
+        self.iterate_check_box.setChecked(True)
         it_layout.addWidget(self.iterate_check_box)
         self.iteration_value = iv = QLineEdit("2.0")
         iv.setAlignment(Qt.AlignCenter)
@@ -120,10 +121,10 @@ def match(self, *, apply=False):
             args += " conservation " + self.conservation_value.text()
         if self.iterate_check_box.isChecked():
             if not self.iteration_value.hasAcceptableInput():
-                raise UserError("Iteration cutoff value must be 0 or more")
-            args += " iterate " + self.iteration_value.text()
+                raise UserError("Distance cutoff value must be 0 or more")
+            args += " cutoffDistance " + self.iteration_value.text()
         else:
-            args += " iterate none"
+            args += " cutoffDistance none"
         if self.use_region_check_box.isChecked():
             region = self.sv.active_region
             if region is None:

src/bundles/seqalign/src/cmd.py

@@ -374,7 +374,7 @@ def seqalign_identity(session, src1, src2=None, *, denominator=IdentityDenominat
     return identity
 
 def seqalign_match(session, alignment, match_chains, to=None, *,
-        iterate=-1, conservation=None, columns=None):
+        cutoff_distance=-1, conservation=None, columns=None):
     if alignment is None:
         alignment = get_alignment_by_id(session, None)
     if columns is None:
@@ -386,7 +386,7 @@ def seqalign_match(session, alignment, match_chains, to=None, *,
             if col > length:
                 raise UserError("match column (%d) greater than alignment length (%d)" % (col, length))
             indices.append(col-1)
-    return alignment.match(to, match_chains, iterate=iterate, conservation=conservation, restriction=indices)
+    return alignment.match(to, match_chains, iterate=cutoff_distance, conservation=conservation, restriction=indices)
 
 def seqalign_refresh_attrs(session, alignment):
     alignment._set_residue_attributes()
@@ -552,7 +552,7 @@ def register_seqalign_command(logger):
     desc = CmdDesc(
         required = [('alignment', Or(AlignmentArg, EmptyArg)), ('match_chains', UniqueChainsArg)],
         required_arguments = ['to'],
-        keyword = [('to', ChainArg), ('iterate', Or(NoneArg, NonNegativeFloatArg)),
+        keyword = [('to', ChainArg), ('cutoff_distance', Or(NoneArg, NonNegativeFloatArg)),
             ('conservation', PercentFloatArg),
             ('columns', ListOf(PositiveIntArg))],
         synopsis = "superimpose chains associated with sequence alignment"