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

src/bundles/Makefile

@@ -26,7 +26,7 @@ REST_SUBDIRS = add_charge addh alignment_algs alignment_headers \
 	  clashes cmd_line color_actions \
 	  color_globe color_key connect_structure core_formats \
 	  coulombic crosslinks crystal crystal_contacts data_formats \
-	  dicom diffplot dist_monitor dock_prep dssp \
+	  deep_mutational_scan dicom diffplot dist_monitor dock_prep dssp \
 	  emdb_sff esmfold file_history function_key \
 	  geometry gltf graphics \
 	  hbonds help_viewer hkcage ihm image_formats imod \

src/bundles/Makefile.bundle

@@ -36,27 +36,24 @@ OS=Windows
 endif
 endif
 ifeq ($(OS),Windows)
-APP_PYTHON_EXE = $(CHIMERAX_APP)/bin/python.exe
+APP_PYTHON_EXE = $(wildcard $(CHIMERAX_APP)/bin/python.exe)
 CX_BIN = $(CHIMERAX_APP)/bin/ChimeraX-console.exe
 PYMOD_EXT = pyd
 endif
 ifeq ($(OS),Darwin)
-APP_PYTHON_EXE = $(CHIMERAX_APP)/Contents/bin/python3.11
+APP_PYTHON_EXE = $(wildcard $(CHIMERAX_APP)/Contents/bin/python3.11)
 CX_BIN = $(CHIMERAX_APP)/Contents/bin/ChimeraX
 PYMOD_EXT = so
 endif
 ifeq ($(OS),Linux)
-APP_PYTHON_EXE = $(CHIMERAX_APP)/bin/python3.11
+APP_PYTHON_EXE = $(wildcard $(CHIMERAX_APP)/bin/python3.11)
 CX_BIN = $(CHIMERAX_APP)/bin/chimerax
 PYMOD_EXT = so
 endif
 PYTHON ?= $(APP_PYTHON_EXE) -I
 RUN = PYTHONNOUSERSITE=1 $(PYTHON) -m chimerax.core --nogui --exit
 RUN_SAFE = $(RUN) --safemode
 RUN_CMD = $(RUN_SAFE) --cmd
-ifeq (,$(wildcard $(APP_PYTHON_EXE)))
-$(error missing ChimeraX application's python)
-endif
 
 ifdef INSTALL_TO_VENV
 WHEEL = $(wildcard dist/*.whl)
@@ -67,14 +64,26 @@ PYSRCS = $(wildcard src/*.py)
 .SECONDEXPANSION:
 
 wheel: $$(PYSRCS)
-	$(RUN_CMD) "devel build . exit true $(DEBUG_ARG) $(BUILD_ARGS)"
+	if [ -z "$(APP_PYTHON_EXE)" ]; then \
+		echo "missing ChimeraX application's python"; exit 1; \
+	else \
+		$(RUN_CMD) "devel build . exit true $(DEBUG_ARG) $(BUILD_ARGS)"; \
+	fi
 
 # The space means install and app-install are the same
 install app-install: $$(PYSRCS)
-	$(RUN_CMD) "devel install . user false exit true $(DEBUG_ARG) $(INSTALL_ARGS)"
+	if [ -z "$(APP_PYTHON_EXE)" ]; then \
+		echo "missing ChimeraX application's python"; exit 1; \
+	else \
+		$(RUN_CMD) "devel install . user false exit true $(DEBUG_ARG) $(INSTALL_ARGS)"; \
+	fi
 
 install-editable: clean
-	$(RUN_CMD) "devel install . user false editable true exit true $(DEBUG_ARG) $(INSTALL_ARGS)"
+	if [ -z "$(APP_PYTHON_EXE)" ]; then \
+		echo "missing ChimeraX application's python"; exit 1; \
+	else \
+		$(RUN_CMD) "devel install . user false editable true exit true $(DEBUG_ARG) $(INSTALL_ARGS)"; \
+	fi
 
 venv-install:
 ifndef VIRTUAL_ENV
@@ -116,7 +125,7 @@ debug:
 	$(CX_BIN) --debug
 
 clean:
-	if [ -x $(CX_BIN) -a -e bundle_info.xml ]; then \
+	if [ -x "$(APP_PYTHON_EXE)" -a -e bundle_info.xml ]; then \
 		$(RUN_CMD) "devel clean . exit true" ; \
 	else \
 		rm -rf $(CLEAN) ; \

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="1.58.1"
+<BundleInfo name="ChimeraX-Atomic" version="1.58.2"
             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="1.58.1"
+<BundleInfo name="ChimeraX-Atomic" version="1.58.2"
             package="chimerax.atomic"
             purePython="false"
             customInit="true"

src/bundles/atomic/src/molobject.py

@@ -1212,11 +1212,12 @@ def residue_after(self, r):
 
     @staticmethod
     def restore_snapshot(session, data):
+        if data['structure'] is None:
+            return Sequence.restore_snapshot(session, data['Sequence'])
         sseq = StructureSeq(chain_id=data['chain_id'], structure=data['structure'])
         Sequence.set_state_from_snapshot(sseq, session, data['Sequence'])
         sseq.description = data['description']
         sseq.bulk_set(data['residues'], sseq.characters, fire_triggers=False)
-        sseq.description = data.get('description', None)
         sseq.set_custom_attrs(data)
         return sseq
 

src/bundles/atomic_lib/atomic_cpp/pyinstance_cpp/PythonInstance.instantiate.h

@@ -88,10 +88,12 @@ PythonInstance<C>::~PythonInstance() {
     if (i == _pyinstance_object_map.end())
         return;
     PyObject* py_inst = (*i).second;
-    AcquireGIL gil; // Py_DECREF can cause code to run
-    PyObject_DelAttrString(py_inst, "_c_pointer");
-    PyObject_DelAttrString(py_inst, "_c_pointer_ref");
-    Py_DECREF(py_inst);
+    if (!PyObject_GC_IsFinalized(py_inst)) {
+        AcquireGIL gil; // Py_DECREF can cause code to run
+        PyObject_DelAttrString(py_inst, "_c_pointer");
+        PyObject_DelAttrString(py_inst, "_c_pointer_ref");
+        Py_DECREF(py_inst);
+    }
     _pyinstance_object_map.erase(i);
 }
 

src/bundles/atomic_lib/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-AtomicLibrary" version="14.1"
+<BundleInfo name="ChimeraX-AtomicLibrary" version="14.1.1"
             package="chimerax.atomic_lib"
             purePython="false"
             installedDataDir="data"

src/bundles/bug_reporter/src/bug_reporter_gui.py

@@ -747,7 +747,7 @@ def _linux_info():
 {newline.join(displays)}
 Manufacturer: {vendor}
 Model: {product}
-OS: {' '.join(distro.linux_distribution())}
+OS: {distro.name()} {distro.version()}
 Architecture: {' '.join(platform.architecture())}
 Virtual Machine: {virtual_machine}
 CPU: {count} {model_name}

src/bundles/deep_mutational_scan/Makefile

@@ -0,0 +1 @@
+include ../Makefile.bundle

src/bundles/deep_mutational_scan/bundle_info.xml

@@ -0,0 +1,41 @@
+<BundleInfo name="ChimeraX-DeepMutationalScan" version="1.0"
+	    package="chimerax.deep_mutational_scan"
+  	    minSessionVersion="1" maxSessionVersion="1">
+
+  <Author>UCSF RBVI</Author>
+  <Email>[email protected]</Email>
+  <URL>https://www.rbvi.ucsf.edu/chimerax/</URL>
+
+  <Synopsis>Visualize deep mutational scanning data</Synopsis>
+  <Description>Visualize deep mutational scanning data.</Description>
+
+  <Categories>
+    <Category name="Molecular structure"/>
+  </Categories>
+
+  <Dependencies>
+    <Dependency name="ChimeraX-Core" version="~=1.0"/>
+    <Dependency name="ChimeraX-DataFormats" version="~=1.0"/>
+    <Dependency name="ChimeraX-UI" version="~=1.0"/>
+  </Dependencies>
+
+  <Providers manager="data formats">
+    <Provider name="Deep mutational scan" synopsis="Deep mutational scan csv file" nicknames="dms" category="Molecular structure" suffixes=".csv" />
+  </Providers>
+
+  <Providers manager="open command">
+    <Provider name="Deep mutational scan" want_path="true" />
+  </Providers>
+
+  <Classifiers>
+    <PythonClassifier>Development Status :: 2 - Pre-Alpha</PythonClassifier>
+    <PythonClassifier>License :: Free for non-commercial use</PythonClassifier>
+    <ChimeraXClassifier>Command :: dms label :: Molecular structure :: Label residues with deep mutational scan values</ChimeraXClassifier>
+    <ChimeraXClassifier>Command :: dms attribute :: Molecular structure :: Assign a residue attribute computed from deep mutational scan values</ChimeraXClassifier>
+    <ChimeraXClassifier>Command :: dms scatterplot :: Molecular structure :: Show a scatter plot for two phenotypes from deep mutational scan data</ChimeraXClassifier>
+    <ChimeraXClassifier>Command :: dms statistics :: Molecular structure :: Report mean and standard deviation of deep mutational scan scores</ChimeraXClassifier>
+    <ChimeraXClassifier>Command :: dms histogram :: Molecular structure :: Show histogram of deep mutational scan scores</ChimeraXClassifier>
+    <ChimeraXClassifier>Command :: dms umap :: Molecular structure :: Show umap plot of residue deep mutational scan scores</ChimeraXClassifier>
+  </Classifiers>
+
+</BundleInfo>

src/bundles/deep_mutational_scan/src/__init__.py

@@ -0,0 +1,63 @@
+# 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
+# <http://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 ===
+
+from chimerax.core.toolshed import BundleAPI
+
+class _DeepMutationalScanAPI(BundleAPI):
+
+    @staticmethod
+    def register_command(command_name, logger):
+        # 'register_command' is called by the toolshed on start up
+        from . import dms_label
+        dms_label.register_command(logger)
+        from . import dms_attribute
+        dms_attribute.register_command(logger)
+        from . import dms_scatter_plot
+        dms_scatter_plot.register_command(logger)
+        from . import dms_stats
+        dms_stats.register_command(logger)
+        from . import dms_histogram
+        dms_histogram.register_command(logger)
+        from . import dms_umap
+        dms_umap.register_command(logger)
+
+    @staticmethod
+    def run_provider(session, name, mgr):
+        if mgr == session.open_command:
+            if name == 'Deep mutational scan':
+                from chimerax.open_command import OpenerInfo
+                class DeepMutationalScanInfo(OpenerInfo):
+                    def open(self, session, path, file_name, **kw):
+                        from .dms_data import open_deep_mutational_scan_csv
+                        dms_data, message = open_deep_mutational_scan_csv(session, path, **kw)
+                        return [], message
+
+                    @property
+                    def open_args(self):
+                        from chimerax.atomic import ChainArg
+                        return {'Chain': ChainArg}
+
+                return DeepMutationalScanInfo()
+
+bundle_api = _DeepMutationalScanAPI()

src/bundles/deep_mutational_scan/src/dms_attribute.py

@@ -0,0 +1,50 @@
+# Assign a residue attribute from deep mutational scan scores.
+def dms_attribute(session, chain, column_name, subtract_fit = None,
+                  name = None, type = 'sum_absolute', above = None, below = None):
+    from .dms_data import dms_data
+    data = dms_data(chain)
+    if data is None:
+        from chimerax.core.errors import UserError
+        raise UserError(f'No deep mutation scan data associated with chain {chain}')
+    scores = data.column_values(column_name, subtract_fit = subtract_fit)
+
+    attr_name = _attribute_name(column_name, type, above, below) if name is None else name
+    from chimerax.atomic import Residue
+    Residue.register_attr(session, attr_name, "Deep Mutational Scan", attr_type=float)
+
+    residues = chain.existing_residues
+    count = 0
+    for res in residues:
+        value = scores.residue_value(res.number, value_type=type, above=above, below=below)
+        if value is not None:
+            setattr(res, attr_name, value)
+            count += 1
+
+    message = f'Set attribute {attr_name} for {count} residues of chain {chain}'
+    session.logger.info(message)
+
+def _attribute_name(column_name, type, above, below):
+    attr_name = f'{column_name}_{type}'
+    if above is not None:
+        attr_name += f'_ge_{"%.3g"%above}'
+    if below is not None:
+        attr_name += f'_le_{"%.3g"%below}'
+    return attr_name
+
+def register_command(logger):
+    from chimerax.core.commands import CmdDesc, register, StringArg, EnumOf, FloatArg
+    from chimerax.atomic import ChainArg
+    from .dms_data import ColumnValues
+    desc = CmdDesc(
+        required = [('chain', ChainArg)],
+        keyword = [('column_name', StringArg),
+                   ('subtract_fit', StringArg),
+                   ('name', StringArg),
+                   ('type', EnumOf(ColumnValues.residue_value_types)),
+                   ('above', FloatArg),
+                   ('below', FloatArg),
+                   ],
+        required_arguments = ['column_name'],
+        synopsis = 'Assign a residue attribute using deep mutation scan scores'
+    )
+    register('dms attribute', desc, dms_attribute, logger=logger)