AlkEthOH (rings) snapshots and energies

.gitattributes

@@ -0,0 +1,2 @@
+*.ipynb linguist-documentation
+*.html linguist-documentation

.gitignore

@@ -134,3 +134,10 @@ dmypy.json
 
 # Parm@Frosst download
 parm_at_Frosst.tgz
+
+# PyCharm
+.idea
+
+
+.DS_Store
+espaloma/data/alkethoh/snapshots_and_energies

devtools/conda-envs/espaloma.yaml

@@ -14,7 +14,7 @@ dependencies:
   - numpy
   - matplotlib
   - scipy
-  - openforcefield
+  #- openforcefield # TODO: revert this when 0.7.0 is released
   - openmmforcefields
   # Testing
   - pytest
@@ -27,3 +27,5 @@ dependencies:
   - pip:
       - torch
       - dgl
+      # TODO: revert this when 0.7.0 is released (needed for https://github.com/openforcefield/openforcefield/pull/517 )
+      - git+https://github.com/openforcefield/openforcefield.git@97d31e6f5f789f8d2c0db8f0f22a3e8078184e1b

devtools/scripts/create_conda_env.py

@@ -1,11 +1,12 @@
 import argparse
+import glob
 import os
 import re
-import glob
 import shutil
 import subprocess as sp
-from tempfile import TemporaryDirectory
 from contextlib import contextmanager
+from tempfile import TemporaryDirectory
+
 # YAML imports
 try:
     import yaml  # PyYAML

docs/conf.py

@@ -15,11 +15,11 @@
 # Incase the project was not installed
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath('..'))
 
 import espaloma
 
-
 # -- Project information -----------------------------------------------------
 
 project = 'espaloma'

espaloma/__init__.py

@@ -3,24 +3,32 @@
 Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm
 """
 
-# Add imports here
-import espaloma
-from espaloma.graphs.graph import Graph
-from espaloma.graphs.molecule_graph import MoleculeGraph
-from espaloma.graphs.homogeneous_graph import HomogeneousGraph
-from espaloma.graphs.heterogeneous_graph import HeterogeneousGraph
-
 import espaloma.data
-import espaloma.nn
+from . import metrics, units
+import espaloma.app
 import espaloma.graphs
 import espaloma.mm
-
+import espaloma.nn
+from espaloma.app.experiment import *
+from espaloma.graphs.graph import Graph
+from espaloma.metrics import GraphMetric
 from espaloma.mm.geometry import *
 
+# Add imports here
+# import espaloma
+
 
 # Handle versioneer
 from ._version import get_versions
 
+#
+# from openforcefield.utils.toolkits import ToolkitRegistry, OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper
+# toolkit_registry = ToolkitRegistry()
+# toolkit_precedence = [ RDKitToolkitWrapper ] # , OpenEyeToolkitWrapper, AmberToolsToolkitWrapper]
+# [ toolkit_registry.register_toolkit(toolkit) for toolkit in toolkit_precedence if toolkit.is_available() ]
+#
+
+
 versions = get_versions()
 __version__ = versions["version"]
 __git_revision__ = versions["full-revisionid"]

espaloma/_version.py

@@ -68,7 +68,9 @@ def decorate(f):
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+def run_command(
+    commands, args, cwd=None, verbose=False, hide_stderr=False, env=None
+):
     """Call the given command(s)."""
     assert isinstance(commands, list)
     p = None
@@ -241,7 +243,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    out, rc = run_command(
+        GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True
+    )
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -293,7 +297,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            pieces["error"] = (
+                "unable to parse git-describe output: '%s'" % describe_out
+            )
             return pieces
 
         # tag
@@ -318,7 +324,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
+        count_out, rc = run_command(
+            GITS, ["rev-list", "HEAD", "--count"], cwd=root
+        )
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
@@ -515,7 +523,9 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
+        return git_versions_from_keywords(
+            get_keywords(), cfg.tag_prefix, verbose
+        )
     except NotThisMethod:
         pass
 

espaloma/app/__init__.py

@@ -0,0 +1 @@
+from . import experiment, report