Merge pull request #1065 from choderalab/modeller-cleanup

Clean up Modeller Feature, Cut 0.23.3

.travis.yml

@@ -20,7 +20,7 @@ install:
   - source devtools/travis-ci/install.sh
   - export PYTHONUNBUFFERED=true
   # Add org channel
-  - conda config --add channels omnia --add channels conda-forge --add channels salilab
+  - conda config --add channels omnia --add channels conda-forge
   # Add omnia dev channels
   - if [ $DEVOMNIA ]; then conda config --add channels omnia/label/dev; fi
   # Update everything
@@ -34,10 +34,8 @@ script:
   - conda create --quiet --yes -n test python=$python
   # Activate the test environment
   - source activate test
-  # Install extras for OpenEye and testing
-  - conda install --yes --quiet pip nose nose-timer coverage
-  # Install extras for Modeller
-  - conda install --yes modeller
+  # Install extras for OpenEye, Modeller and testing
+  - conda install --yes --quiet pip nose nose-timer coverage modeller
   # Install OpenEye toolkit
   - pip install $OPENEYE_CHANNEL openeye-toolkits && python -c "import openeye; print(openeye.__version__)"
   # Build the recipe

Yank/pipeline.py

@@ -945,6 +945,7 @@ def add_missing_atoms(value):
     # Write the final structure
     PDBFile.writeFile(fixer.topology, fixer.positions, open(output_file_path, 'w'))
 
+
 def apply_modeller(input_file_path, output_file_path, directives):
     """
     Apply Salilab Modeller to make changes to the specified molecule.
@@ -969,14 +970,13 @@ def apply_modeller(input_file_path, output_file_path, directives):
         Dict containing directives for modeller.
     """
 
-    try:
-        import modeller
-    except ImportError:
+    if not utils.is_modeller_installed():
         raise ImportError('Modeller and license must be installed to use this feature.')
+    import modeller
 
     directives = copy.deepcopy(directives)
 
-    # Silence unecessart output to the log files
+    # Silence unnecessary output to the log files
     modeller.log.none()
 
     # Create modeller environment and point it to the PDB file
@@ -994,7 +994,6 @@ def apply_modeller(input_file_path, output_file_path, directives):
     model_original_numbering = modeller.model(env, file=atom_file_name)
     alignment.append_model(model, atom_files=atom_file_name, align_codes=atom_file_name)
 
-
     def apply_mutations_modeller(value):
         # Extract chain id
         chain_id = None
@@ -1033,6 +1032,7 @@ def apply_mutations_modeller(value):
     model.res_num_from(model_original_numbering, alignment)
     model.write(file=output_file_path)
 
+
 def read_csv_lines(file_path, lines):
     """Return a list of CSV records.
 

Yank/tests/test_experiment.py

@@ -1309,6 +1309,8 @@ def test_pdbfixer_mutations():
                     break
         assert has_mut_residue
 
+
+@unittest.skipIf(not utils.is_modeller_installed(), "This test requires Salilab Modeller")
 def test_modeller_mutations():
     """Test that modeller can apply mutations correctly."""
     mol_id = 'Abl'
@@ -1334,8 +1336,8 @@ def test_modeller_mutations():
 
         # Now we set the strip_protons options and repeat
         exp_builder._db.molecules[mol_id]['modeller'] = {
-            'apply_mutations' : {
-                'chain_id' : 'A',
+            'apply_mutations': {
+                'chain_id': 'A',
                 'mutations': 'T85I',
             }
         }

Yank/utils.py

@@ -1210,6 +1210,27 @@ def _compute_net_charge(residue):
         return tot_charge
 
 
+def is_modeller_installed():
+    """
+    Check if a Salilab Modeller tool is installed and Licensed.
+
+    If Modeller is not installed and licensed, returns False.
+
+    Returns
+    -------
+    installed : bool
+        True if all tools in ``oetools`` are installed and licensed, False otherwise.
+    """
+    try:
+        import modeller
+    except:
+        # This has to be broad because we cant trap the ModellerError invalid license
+        # since the act of even trying to import Modeller triggers it,
+        # and its NOT an import error which is raised.
+        return False
+    return True
+
+
 # -----------------
 # OpenEye functions
 # -----------------

docs/whatsnew.rst

@@ -7,10 +7,11 @@ This section features and improvements of note in each release.
 The full release history can be viewed `at the GitHub yank releases page <https://github.com/choderalab/yank/releases>`_.
 
 0.23.3 Adds support for single mutations using Modeller
-------------------------------------
-- - Adds an optional ``modeller` directive to the ``molecules`` section of the YAML file
+-------------------------------------------------------
+- Adds an optional ``modeller` directive to the ``molecules`` section of the YAML file
   through `Modeller <https://salilab.org/modeller/>`_, a tool for comparative modeling of protein structures.
 - The following options are accessible through the ``modeller`` directive. `(docs) <http://getyank.org/latest/yamlpages/molecules.html#modeller>`__
+
   - ``apply_mutations``: Specify protein single mutations (e.g., T315I). `(docs) <http://getyank.org/latest/yamlpages/molecules.html#modeller_mutations>`_
 
 

docs/yamlpages/molecules.rst

@@ -258,6 +258,9 @@ PDBFixer is applied after ``strip_protons`` if both are requested.
 Specifies whether modeller should be used to model in mutations.
 Can only be used on proteins, on files with ``.pdb`` file extensions.
 
+This feature requires the Modeller from the Sali Lab, which can be fetched from
+Omnia's Conda channel. You will need to provide your own license however.
+
 Mutations
 ^^^^^^^^^
 

setup.py

@@ -12,8 +12,8 @@
 
 ########################
 VERSION = "0.23.3"  # Primary base version of the build
-DEVBUILD = 0  # Dev build status, Either None or Integer
-ISRELEASED = False  # Are we releasing this as a full cut?
+DEVBUILD = None  # Dev build status, Either None or Integer
+ISRELEASED = True  # Are we releasing this as a full cut?
 __version__ = VERSION
 ########################
 CLASSIFIERS = """\