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

src/bundles/alphafold/src/alphafold21_predict_colab.ipynb

@@ -266,8 +266,8 @@
         "# We have to use \"--no-warn-conflicts\" because colab already has a lot preinstalled with requirements different to ours\n",
         "pip install --no-warn-conflicts \"colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2\"\n",
         "# high risk high gain\n",
-        "pip uninstall jaxlib -y\n",
-        "pip install \"jax[cuda11_cudnn805]==0.3.24\" jaxlib==0.3.24+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n",
+        "pip uninstall jax jaxlib -y\n",
+        "pip install \"jax[cuda]==0.3.25\" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n",
         "touch COLABFOLD_READY\n",
         "'''\n",
         "    run_shell_commands(cmds, 'install_colabfold.sh', install_log)\n",

src/bundles/alphafold/src/alphafold_test_colab.ipynb

@@ -266,8 +266,8 @@
         "# We have to use \"--no-warn-conflicts\" because colab already has a lot preinstalled with requirements different to ours\n",
         "pip install --no-warn-conflicts \"colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2\"\n",
         "# high risk high gain\n",
-        "pip uninstall jaxlib -y\n",
-        "pip install \"jax[cuda11_cudnn805]==0.3.24\" jaxlib==0.3.24+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n",
+        "pip uninstall jax jaxlib -y\n",
+        "pip install \"jax[cuda]==0.3.25\" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n",
         "touch COLABFOLD_READY\n",
         "'''\n",
         "    run_shell_commands(cmds, 'install_colabfold.sh', install_log)\n",

src/bundles/alphafold/src/colabfold_predict.ipynb

@@ -266,8 +266,8 @@
         "# We have to use \"--no-warn-conflicts\" because colab already has a lot preinstalled with requirements different to ours\n",
         "pip install --no-warn-conflicts \"colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2\"\n",
         "# high risk high gain\n",
-        "pip uninstall jaxlib -y\n",
-        "pip install \"jax[cuda11_cudnn805]==0.3.24\" jaxlib==0.3.24+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n",
+        "pip uninstall jax jaxlib -y\n",
+        "pip install \"jax[cuda]==0.3.25\" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n",
         "touch COLABFOLD_READY\n",
         "'''\n",
         "    run_shell_commands(cmds, 'install_colabfold.sh', install_log)\n",

src/bundles/alphafold/src/colabfold_predict.py

@@ -239,8 +239,8 @@ def install(use_amber = False, use_templates = False, install_log = 'install_log
 # We have to use "--no-warn-conflicts" because colab already has a lot preinstalled with requirements different to ours
 pip install --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2"
 # high risk high gain
-pip uninstall jaxlib -y
-pip install "jax[cuda11_cudnn805]==0.3.24" jaxlib==0.3.24+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+pip uninstall jax jaxlib -y
+pip install "jax[cuda]==0.3.25" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 touch COLABFOLD_READY
 '''
     run_shell_commands(cmds, 'install_colabfold.sh', install_log)

src/bundles/atom_search/bundle_info.xml

@@ -26,7 +26,7 @@
 
   <Dependencies>
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
   </Dependencies>
 
   <Classifiers>

src/bundles/atomic/bundle_info.xml

@@ -62,7 +62,7 @@
   <!-- Edit bundle_info.xml.in, not bundle_info.xml; then run make_selectors.py  -->
   <Dependencies>
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
     <Dependency name="ChimeraX-ConnectStructure" version="~=2.0"/>
     <Dependency name="ChimeraX-Geometry" build="true" version="~=1.0"/>
     <Dependency name="ChimeraX-Graphics" build="true" version="~=1.0"/>

src/bundles/atomic/bundle_info.xml.in

@@ -62,7 +62,7 @@
   <!-- Edit bundle_info.xml.in, not bundle_info.xml; then run make_selectors.py  -->
   <Dependencies>
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
     <Dependency name="ChimeraX-ConnectStructure" version="~=2.0"/>
     <Dependency name="ChimeraX-Geometry" build="true" version="~=1.0"/>
     <Dependency name="ChimeraX-Graphics" build="true" version="~=1.0"/>

src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/AtomicStructure.cpp

@@ -294,15 +294,17 @@ AtomicStructure::normalize_ss_ids()
 }
 
 void
-AtomicStructure::make_chains() const
+AtomicStructure::_make_chains() const
 {
-    if (_chains != nullptr) {
-        for (auto c: *_chains)
-            delete c;
-        delete _chains;
+    std::set<ChainID> pre_existing;
+    if (_chains == nullptr) {
+        _chains = new Chains();
+    } else {
+        for (auto chain: *_chains)
+            pre_existing.insert(chain->chain_id());
     }
+    _chains_made = true; // prevent resursion
 
-    _chains = new Chains();
     auto polys = polymers();
 
     // In an ideal world there would be a one-to-one correspondence between
@@ -321,6 +323,8 @@ AtomicStructure::make_chains() const
     for (auto key_polys: id_to_polys) {
         auto id_type = key_polys.first;
         auto chain_id = id_type.first;
+        if (pre_existing.find(chain_id) != pre_existing.end())
+            continue;
         auto pt_type = id_type.second;
         auto& chain_polys = key_polys.second;
         std::vector<Residue*> res_list;

src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/AtomicStructure.h

@@ -33,19 +33,19 @@ namespace atomstruct {
 
 class ATOMSTRUCT_IMEX AtomicStructure: public Structure {
     friend class Atom; // for IDATM stuff and structure categories
-    friend class Bond; // for checking if make_chains() has been run yet, struct categories
+    friend class Bond; // struct categories
     friend class Residue; // for _polymers_computed
     friend class StructureSeq; // for remove_chain()
 private:
     void  _compute_atom_types();
     void  _compute_structure_cats() const;
+    void  _make_chains() const;
 public:
     AtomicStructure(PyObject* logger = nullptr) : Structure(logger) {}
 
     void  compute_secondary_structure(float energy_cutoff = -0.5, int min_helix_length = 3,
         int min_strand_length = 3, bool = false, CompSSInfo* = nullptr);
     AtomicStructure*  copy() const;
-    void  make_chains() const;
     void  normalize_ss_ids();
     std::vector<std::pair<Chain::Residues,PolymerType>>  polymers(
         PolymerMissingStructure missing_structure_treatment = PMS_ALWAYS_CONNECTS,

src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Structure.cpp

@@ -883,10 +883,10 @@ Structure::_delete_atoms(const std::set<Atom*>& atoms, bool verify)
 void
 Structure::_form_chain_check(Atom* a1, Atom* a2, Bond* b)
 {
-    // If initial construction is over (i.e. Python instance exists) and make_chains()
-    // has been called (i.e. _chains is not null), then need to check if new bond
+    // If initial construction is over (i.e. Python instance exists) and _make_chains()
+    // has been called (i.e. _chain_made is true), then need to check if new bond
     // or missing-structure pseudobond creates a chain or coalesces chain fragments
-    if (_chains == nullptr)
+    if (!_chains_made)
         return;
     auto inst = py_instance(false);
     Py_DECREF(inst);
@@ -1134,16 +1134,11 @@ Structure::find_residue(const ChainID& chain_id, int num, char insert, ResName&
 }
 
 void
-Structure::make_chains() const
+Structure::_make_chains() const
 {
-    // since Graphs don't have sequences, they don't have chains
-    if (_chains != nullptr) {
-        for (auto c: *_chains)
-            delete c;
-        delete _chains;
-    }
-
+    // since non-atomic Structures don't have sequences, they don't have chains
     _chains = new Chains();
+    _chains_made = true;
 }
 
 Atom *

src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Structure.h

@@ -146,6 +146,7 @@ class ATOMSTRUCT_IMEX Structure: public GraphicsChanges,
     float  _ball_scale = 0.25;
     Bonds  _bonds;
     mutable Chains*  _chains;
+    mutable bool  _chains_made = false;
     ChangeTracker*  _change_tracker;
     CoordSets  _coord_sets;
     bool  _display = true;
@@ -202,6 +203,7 @@ class ATOMSTRUCT_IMEX Structure: public GraphicsChanges,
             std::set<Atom*>& left_missing_structure_atoms,
             std::set<Atom*>& right_missing_structure_atoms,
             const std::set<Atom*>* deleted_atoms = nullptr) const;
+    virtual void  _make_chains() const;
     Bond*  _new_bond(Atom* a1, Atom* a2, bool bond_only);
     Chain*  _new_chain(const ChainID& chain_id, PolymerType pt = PT_NONE) const {
         auto chain = new Chain(chain_id, const_cast<Structure*>(this), pt);
@@ -243,7 +245,7 @@ class ATOMSTRUCT_IMEX Structure: public GraphicsChanges,
     void  bonded_groups(std::vector<std::vector<Atom*>>* groups,
         bool consider_missing_structure) const;
     const Bonds&  bonds() const { return _bonds; }
-    const Chains&  chains() const { if (_chains == nullptr) make_chains(); return *_chains; }
+    const Chains&  chains() const { if (!_chains_made) _make_chains(); return *_chains; }
     void  change_chain_ids(const std::vector<StructureSeq*>, const std::vector<ChainID>,
         bool /*non-polymeric*/=true);
     ChangeTracker*  change_tracker() { return _change_tracker; }
@@ -276,7 +278,6 @@ class ATOMSTRUCT_IMEX Structure: public GraphicsChanges,
     bool  is_traj;
     PyObject*  logger() const { return _logger; }
     bool  lower_case_chains;
-    virtual void  make_chains() const;
     std::map<std::string, std::vector<std::string>> metadata;
     Atom*  new_atom(const char* name, const Element& e);
     Bond*  new_bond(Atom* a1, Atom* a2) { return _new_bond(a1, a2, false); }

src/bundles/atomic_lib/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-AtomicLibrary" version="11.0"
+<BundleInfo name="ChimeraX-AtomicLibrary" version="12.0"
             package="chimerax.atomic_lib"
             purePython="false"
             installedDataDir="data"

src/bundles/chem_group/bundle_info.xml.in

@@ -26,7 +26,7 @@
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
     <Dependency name="ChimeraX-Arrays" build="true" version="~=1.0"/>
     <Dependency name="ChimeraX-Atomic" version="~=1.0"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
   </Dependencies>
 
   <Classifiers>

src/bundles/connect_structure/bundle_info.xml

@@ -22,7 +22,7 @@
 
   <Dependencies>
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
   </Dependencies>
 
   <Classifiers>

src/bundles/core/src/__main__.py

@@ -806,8 +806,8 @@ def init(argv, event_loop=True):
         import runpy
         import warnings
         exit = SystemExit(os.EX_OK)
-        from chimerax.core.python_utils import chimerax_user_base
-        with warnings.catch_warnings(), chimerax_user_base():
+        from chimerax.core.python_utils import chimerax_environment
+        with warnings.catch_warnings(), chimerax_environment():
             warnings.filterwarnings("ignore", category=BytesWarning)
             global_dict = {
                 'session': sess

src/bundles/core/src/python_utils.py

@@ -32,21 +32,57 @@ def chimerax_python_executable():
 
 
 @contextmanager
-def chimerax_user_base():
-    """Make pip install packages to ChimeraX's customary PYTHONUSERBASE.
+def chimerax_environment():
+    """Setup environment for Python to match ChimeraX setup
 
-    Without this context manager, Python will install packages in the traditional
-    user directory at, on macOS, ~/Library/Python/(version)/lib/python/site-packages
-    instead of our location at ~/Library/Application Support/ChimeraX/(cx_version)
+    In particular, set PYTHONUSERBASE so pip will install/uninstall packages
+    in the ChimeraX "user" location.  Also remove from environment any
+    variables that would alter ChimeraX's behaviour.
     """
     from chimerax import app_dirs
-    old_pythonuserbase = os.environ.get('PYTHONUSERBASE', None)
-    os.environ['PYTHONUSERBASE'] = app_dirs.user_data_dir
+    PROTECT = {
+        'PYTHONDONTWRITEBYTECODE': None,
+        # 'PYTHONDEBUG': None,
+        # 'PYTHONINSPECT': None,
+        # 'PYTHONOPTIMIZE': None,
+        'PYTHONNOUSERSITE': None,
+        # 'PYTHONUNBUFFERED': None,
+        # 'PYTHONVERBOSE': None,
+        # 'PYTHONWARNINGS': None,
+        'PYTHONSTARTUP': None,
+        'PYTHONPATH': None,
+        'PYTHONHOME': None,
+        'PYTHONPLATLIBDIR': None,
+        'PYTHONCASEOK': None,
+        'PYTHONUTF8': None,
+        'PYTHONIOENCODING': None,
+        'PYTHONFAULTHANDLER': None,
+        # 'PYTHONHASHSEED': None,
+        'PYTHONINTMAXSTRDIGITS': None,
+        # 'PYTHONMALLOC': None,
+        'PYTHONCOERCECLOCALE': None,
+        # 'PYTHONBREAKPOINT': None,
+        # 'PYTHONDEVMODE': None,
+        'PYTHONPYCACHEPREFIX': None,
+        'PYTHONWARNDEFAULTENCODING': None,
+        'PYTHONUSERBASE': app_dirs.user_data_dir,
+    }
+    old_environ = {}
+    for var, new_value in PROTECT.items():
+        old_value = os.environ.get(var, None)
+        if old_value is None and new_value is None:
+            continue
+        old_environ[var] = old_value
+        if new_value is None:
+            del os.environ[var]
+        else:
+            os.environ[var] = new_value
     yield
-    if old_pythonuserbase is None:
-        del os.environ['PYTHONUSERBASE']
-    else:
-        os.environ['PYTHONUSERBASE'] = old_pythonuserbase
+    for var, value in old_environ.items():
+        if value is None:
+            del os.environ[var]
+        else:
+            os.environ[var] = value
 
 
 def is_link(path):
@@ -83,10 +119,9 @@ def run_pip(command):
     # the user site directory is the ChimeraX application location.
     import subprocess
     prog = chimerax_python_executable()
-    pip_cmd = [prog] + subprocess._args_from_interpreter_flags() + ["-m", "pip"]
+    pip_cmd = [prog] + ["-m", "pip"]
     # pip_cmd = [sys.executable, "-m", "pip"]
-    from chimerax.core.python_utils import chimerax_user_base
-    with chimerax_user_base():
+    with chimerax_environment():
         cp = subprocess.run(pip_cmd + command, capture_output=True)
     return cp
 

src/bundles/core/src/scripting.py

@@ -223,8 +223,6 @@ def probably_chimera1_session(evalue):
     return False
 
 chimera1_session_message = """\
-ChimeraX cannot open a regular Chimera session.  An exporter from Chimera
-to ChimeraX is being worked on but only handles molecules and molecular surfaces
-(not volumes) at this time.  If that is sufficient, use the latest Chimera
-daily build and its File->Export Scene menu item, and change the resulting
-dialog's "File Type" to ChimeraX."""
+ChimeraX cannot open a regular Chimera session.  An exporter from Chimera to
+ChimeraX is available in the latest Chimera release.  Use its File->Export Scene
+menu item, and change the resulting dialog's "File Type" to ChimeraX."""

src/bundles/dssp/bundle_info.xml

@@ -25,7 +25,7 @@
   <Dependencies>
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
     <Dependency name="ChimeraX-Arrays" build="true" version="~=1.0"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
   </Dependencies>
 
   <Classifiers>

src/bundles/mmcif/bundle_info.xml

@@ -53,7 +53,7 @@
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
     <Dependency name="ChimeraX-Arrays" build="true" version="~=1.0"/>
     <Dependency name="ChimeraX-Atomic" version="~=1.34"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
     <Dependency name="ChimeraX-PDB" version="~=2.0"/>
     <Dependency name="ChimeraX-PDBLibrary" build="true" version="~=1.0"/>
     <Dependency name="ChimeraX-DataFormats" version="~=1.0"/>

src/bundles/mmtf/bundle_info.xml

@@ -32,7 +32,7 @@
     <Dependency name="ChimeraX-Core" version="~=1.0"/>
     <Dependency name="ChimeraX-Arrays" build="true" version="~=1.0"/>
     <Dependency name="ChimeraX-Atomic" version="~=1.0"/>
-    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=11.0"/>
+    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=12.0"/>
     <Dependency name="ChimeraX-PDB" version="~=2.0"/>
     <Dependency name="ChimeraX-PDBLibrary" build="true" version="~=1.0"/>
     <Dependency name="ChimeraX-DataFormats" version="~=1.0"/>