Most of the match tool (missing the "create region" option)

Author: e-pettersen

src/bundles/atomic/src/widgets.py

@@ -31,15 +31,15 @@ def __init__(self, session, **kw):
 
 class StructureMenuButton(ModelMenuButton):
     def __init__(self, session, **kw):
-        super().__init__(session, class_filter=Structure, **kw)
+        super().__init__(session, no_value_button_text="No structure chosen", class_filter=Structure, **kw)
 
 class AtomicStructureListWidget(ModelListWidget):
     def __init__(self, session, **kw):
         super().__init__(session, class_filter=AtomicStructure, **kw)
 
 class AtomicStructureMenuButton(ModelMenuButton):
     def __init__(self, session, **kw):
-        super().__init__(session, class_filter=AtomicStructure, **kw)
+        super().__init__(session, no_value_button_text="No structure chosen", class_filter=AtomicStructure, **kw)
 
 class ChainListWidget(ItemListWidget):
     def __init__(self, session, *, group_identical=False, **kw):
@@ -136,8 +136,8 @@ def _item_text_func(self, item):
         return specs
 
 class ChainMenuButton(ItemMenuButton):
-    def __init__(self, session, **kw):
-        super().__init__(**_process_chain_kw(session, **kw))
+    def __init__(self, session, no_value_button_text="No chain chosen", **kw):
+        super().__init__(no_value_button_text=no_value_button_text,  **_process_chain_kw(session, **kw))
 
 def _process_chain_kw(session, list_func=None, trigger_info=None, **kw):
     if list_func is None:
@@ -163,8 +163,8 @@ def __init__(self, session, **kw):
         super().__init__(**_process_residue_kw(session, **kw))
 
 class ResidueMenuButton(ItemMenuButton):
-    def __init__(self, session, **kw):
-        super().__init__(**_process_residue_kw(session, **kw))
+    def __init__(self, session, no_value_button_text="No residue chosen", **kw):
+        super().__init__(no_value_button_text=no_value_button_text, **_process_residue_kw(session, **kw))
 
 def _process_residue_kw(session, list_func=None, trigger_info=None, **kw):
     if list_func is None:

src/bundles/log/src/tool.py

@@ -244,6 +244,7 @@ def sizeHint(self):
                 from Qt.QtCore import QSize
                 return QSize(600, 300)
         self.error_dialog = BiggerErrorDialog(parent)
+        self.error_dialog.finished.connect(lambda *args: print("error dialog finished"))
         self._add_report_bug_button()
         layout = QGridLayout(parent)
         layout.setContentsMargins(0,0,0,0)

src/bundles/seq_view/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-SeqView" version="2.15"
+<BundleInfo name="ChimeraX-SeqView" version="2.16"
 	    package="chimerax.seq_view"
 	    supercedes="ChimeraX-SEQ-VIEW"
   	    minSessionVersion="1" maxSessionVersion="1">

src/bundles/seq_view/src/match.py

@@ -0,0 +1,147 @@
+# vim: set expandtab ts=4 sw=4:
+
+# === UCSF ChimeraX Copyright ===
+# Copyright 2022 Regents of the University of California. All rights reserved.
+# The ChimeraX application is provided pursuant to the ChimeraX license
+# agreement, which covers academic and commercial uses. For more details, see
+# <https://www.rbvi.ucsf.edu/chimerax/docs/licensing.html>
+#
+# This particular file is part of the ChimeraX library. You can also
+# redistribute and/or modify it under the terms of the GNU Lesser General
+# Public License version 2.1 as published by the Free Software Foundation.
+# For more details, see
+# <https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html>
+#
+# THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
+# EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. ADDITIONAL LIABILITY
+# LIMITATIONS ARE DESCRIBED IN THE GNU LESSER GENERAL PUBLIC LICENSE
+# VERSION 2.1
+#
+# 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 ===
+
+class MatchDialog:
+    def __init__(self, sv, tool_window):
+        self.sv = sv
+        self.tool_window = tool_window
+        tool_window.help = "help:user/tools/sequenceviewer.html#match"
+
+        from Qt.QtWidgets import QHBoxLayout, QVBoxLayout, QLabel, QGridLayout, QLineEdit, QCheckBox
+        from Qt.QtGui import QDoubleValidator
+        from Qt.QtCore import Qt
+        layout = QVBoxLayout()
+        #layout.setContentsMargins(0,0,0,0)
+        layout.setSpacing(0)
+
+        from chimerax.atomic.widgets import ChainMenuButton, ChainListWidget
+        chains_layout = QGridLayout()
+        chains_layout.setSpacing(3)
+        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)
+        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))
+        chains_layout.addWidget(self.match_chain_list, 1, 1)
+        self.ref_chain_menu.value_changed.connect(self.match_chain_list.refresh)
+        chains_layout.setRowStretch(1, 1)
+        layout.addLayout(chains_layout)
+
+        cv_layout = QHBoxLayout()
+        self.conserved_check_box = QCheckBox("Only match residues in columns with at least ")
+        cv_layout.addWidget(self.conserved_check_box)
+        self.conservation_value = cv = QLineEdit("80")
+        cv.setAlignment(Qt.AlignCenter)
+        cv.setMaximumWidth(4 * cv.fontMetrics().averageCharWidth())
+        cv.setValidator(QDoubleValidator(0.0, 100.0, -1))
+        cv_layout.addWidget(cv)
+        cv_layout.addWidget(QLabel("% identity"), alignment=Qt.AlignLeft, stretch=1)
+        layout.addLayout(cv_layout)
+
+        it_layout = QHBoxLayout()
+        self.iterate_check_box = QCheckBox("Iterate by pruning long atom pairs until no pair exceeds ")
+        it_layout.addWidget(self.iterate_check_box)
+        self.iteration_value = iv = QLineEdit("2.0")
+        iv.setAlignment(Qt.AlignCenter)
+        iv.setMaximumWidth(4 * iv.fontMetrics().averageCharWidth())
+        dv = QDoubleValidator()
+        dv.setBottom(0.0)
+        iv.setValidator(dv)
+        it_layout.addWidget(iv)
+        it_layout.addWidget(QLabel(" angstroms"), alignment=Qt.AlignLeft, stretch=1)
+        layout.addLayout(it_layout)
+
+        ur_layout = QHBoxLayout()
+        self.use_region_check_box = QCheckBox("Match active region only")
+        ur_layout.addWidget(self.use_region_check_box, alignment=Qt.AlignLeft, stretch=1)
+        layout.addLayout(ur_layout)
+
+        #cr_layout = QHBoxLayout()
+        #self.create_region_check_box = QCheckBox("Create region showing matched residues")
+        #cr_layout.addWidget(self.create_region_check_box, alignment=Qt.AlignLeft, stretch=1)
+        #layout.addLayout(cr_layout)
+
+        from Qt.QtWidgets import QDialogButtonBox as qbbox
+        bbox = qbbox(qbbox.Ok | qbbox.Apply | qbbox.Close | qbbox.Help)
+        bbox.accepted.connect(self.match)
+        bbox.button(qbbox.Apply).clicked.connect(lambda f = self.match: f(apply=True))
+        hide_self = lambda *args, tw=tool_window: setattr(tool_window, 'shown', False)
+        bbox.rejected.connect(hide_self)
+        from chimerax.core.commands import run
+        bbox.helpRequested.connect(lambda *, run=run, ses=self.sv.session, help=tool_window.help:
+            run(ses, "help " + help))
+        layout.addWidget(bbox)
+
+        tool_window.ui_area.setLayout(layout)
+
+    def match(self, *, apply=False):
+        from chimerax.core.errors import UserError
+        ref = self.ref_chain_menu.value
+        if ref is None:
+            raise UserError("No reference chain chosen")
+        used_chains = { ref.structure: ref }
+        matches = self.match_chain_list.value
+        if not matches:
+            raise UserError("No match chains chosen")
+        for match in matches:
+            if match.structure in used_chains:
+                self.tool_window.shown = True
+                raise UserError("Cannot match multiple chains from the same structure (%s and %s)"
+                    % (used_chains[match.structure], match))
+            used_chains[match.structure] = match
+
+        args = ""
+        if self.conserved_check_box.isChecked():
+            if not self.conservation_value.hasAcceptableInput():
+                raise UserError("Percent identity value must be between 0 and 100")
+            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()
+        else:
+            args += " iterate none"
+        if self.use_region_check_box.isChecked():
+            region = self.sv.active_region
+            if region is None:
+                raise UserError("No active region")
+            cols = []
+            for block in region.blocks:
+                line1, line2, pos1, pos2 = block
+                cols.extend(list(range(pos1+1,pos2+2)))
+            if not cols:
+                raise UserError("Active region is empty")
+            args += " columns %s" % ','.join(["%d" % col for col in cols])
+
+        if not apply:
+            self.tool_window.shown = False
+        from chimerax.core.commands import run, StringArg
+        results = run(self.sv.session, "seq match %s %s to %s%s"
+            % (StringArg.unparse(self.sv.alignment.ident), ref.atomspec,
+            ','.join([c.atomspec for c in matches]), args))
+
+        if self.create_region_check_box.isChecked():
+            pass #TODO

src/bundles/seq_view/src/tool.py

@@ -585,6 +585,11 @@ def fill_context_menu(self, menu, x, y):
                 action.triggered.connect(lambda act, *args, func=self.select_by_column_identity, val=value:
                     func(val))
                 cons_sel_menu.addAction(action)
+        match_action = QAction("Match...", structure_menu)
+        match_action.triggered.connect(self.show_match_dialog)
+        match_action.setEnabled(
+            len(set([chain.structure for chain in self.alignment.associations.keys()])) > 1)
+        structure_menu.addAction(match_action)
         xfer_action = QAction("Update Chain Sequence...", structure_menu)
         xfer_action.triggered.connect(self.show_transfer_seq_dialog)
         xfer_action.setEnabled(bool(self.alignment.associations))
@@ -808,6 +813,14 @@ def show_feature_browser(self, seq, *, state=None):
             self._feature_browsers[seq].tool_window.manage(None)
         self._feature_browsers[seq].tool_window.shown = True
 
+    def show_match_dialog(self):
+        if not hasattr(self, "match_dialog"):
+            from .match import MatchDialog
+            self.match_dialog = MatchDialog(self,
+                self.tool_window.create_child_window("Match", close_destroys=False))
+            self.match_dialog.tool_window.manage(None)
+        self.match_dialog.tool_window.shown = True
+
     def show_percent_identity_dialog(self):
         if not hasattr(self, "percent_identity_dialog"):
             from .identity import PercentIdentityDialog

src/bundles/seqalign/src/cmd.py

@@ -498,7 +498,7 @@ def seqalign_align(session, seq_source, *, program=CLUSTAL_OMEGA, replace=False)
 def register_seqalign_command(logger):
     # REMINDER: update manager._builtin_subcommands as additional subcommands are added
     from chimerax.core.commands import CmdDesc, register, create_alias, Or, EmptyArg, RestOfLine, ListOf, \
-        EnumOf, BoolArg, NoneArg, PositiveIntArg, PercentFloatArg
+        EnumOf, BoolArg, NoneArg, PositiveIntArg, PercentFloatArg, NonNegativeFloatArg
     from chimerax.atomic import UniqueChainsArg, SequencesArg, ChainArg
 
     apns = list(alignment_program_name_args.keys())
@@ -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, PositiveIntArg)),
+        keyword = [('to', ChainArg), ('iterate', Or(NoneArg, NonNegativeFloatArg)),
             ('conservation', PercentFloatArg),
             ('columns', ListOf(PositiveIntArg))],
         synopsis = "superimpose chains associated with sequence alignment"