aimsim-core - npm Package Compare versions

Comparing version 2.1.4rc1 to 2.1.3

aimsim_core.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: aimsim_core
-Version: 2.1.4rc1
+Version: 2.1.3
 Summary: Core AIMSim molecular featurization and comparison utilities.
@@ -124,7 +124,7 @@ Home-page: https://github.com/VlachosGroup/AIMSim
   Step 3: Choose an arbitrary similarity measure.
-  Step 4: Select each molecule’s nearest and furthest neighbors in the set using the similarity measure.
-  Step 5: Measure the correlation between a molecule’s QoI and its nearest neighbor’s QoI.
-  Step 6: Measure the correlation between a molecule’s QoI and its further neighbor’s QoI.
+  Step 4: Select each molecule’s nearest and furthest neighbors in the set using the similarity measure.
+  Step 5: Measure the correlation between a molecule’s QoI and its nearest neighbor’s QoI.
+  Step 6: Measure the correlation between a molecule’s QoI and its further neighbor’s QoI.
   Step 7: Define a score which maximizes the value in Step 5 and minimizes the value in Step 6.
-  Step 8: Iterate Steps 1 – 7 to select the featurization scheme and similarity measure to maximize the result of Step 7. 
+  Step 8: Iterate Steps 1 – 7 to select the featurization scheme and similarity measure to maximize the result of Step 7. 
 2. See Property Variation with Similarity: Visualize the correlation in the QoI between nearest neighbor molecules (most similar pairs in the molecule set) and between the furthest neighbor molecules (most dissimilar pairs in the molecule set). This is used to verify that the chosen measure is appropriate for the task.
@@ -207,3 +207,3 @@
 ## Works Cited
-[1] Collins, K. and Glorius, F., A robustness screen for the rapid assessment of chemical reactions. Nature Chem 5, 597–601 (2013). https://doi.org/10.1038/nchem.1669
+[1] Collins, K. and Glorius, F., A robustness screen for the rapid assessment of chemical reactions. Nature Chem 5, 597–601 (2013). https://doi.org/10.1038/nchem.1669
 
@@ -210,0 +210,0 @@ [2] Chen, Y., Murray, P.R.D., Davies, A.T., and Willis M.C., J. Am. Chem. Soc. 140 (28), 8781-8787 (2018). https://doi.org/10.1021/jacs.8b04532

aimsim_core.egg-info/SOURCES.txt

@@ -10,5 +10,2 @@ AIMSim-GUI.png
 setup.py
-aimsim/__init__.py
-aimsim/__main__.py
-aimsim/exceptions.py
 aimsim/chemical_datastructures/__init__.py
@@ -41,3 +38,2 @@ aimsim/chemical_datastructures/molecule.py
 interfaces/UI/libraries/README.md
-tests/__init__.py
 tests/sulfonamide-substrate-scope-PDF.png
@@ -44,0 +40,0 @@ tests/sulfonamide-substrate-scope.png

aimsim/chemical_datastructures/__init__.py

 from .molecule import Molecule
 from .molecule_set import MoleculeSet

aimsim/chemical_datastructures/molecule_set.py

@@ -0,0 +0,0 @@ """Abstraction of a data set comprising multiple Molecule objects."""

aimsim/chemical_datastructures/molecule.py

@@ -0,0 +0,0 @@ """Abstraction of RDKit molecule with relevant property manipulation methods."""

aimsim/ops/__init__.py

 from .descriptor import Descriptor
 from .clustering import Cluster
 from .similarity_measures import SimilarityMeasure

aimsim/ops/clustering.py

@@ -0,0 +0,0 @@ """Operation for clustering molecules"""

aimsim/utils/ccbmlib_fingerprints.py

@@ -0,0 +0,0 @@ #   Copyright 2020 Martin Vogt, Antonio de la Vega de Leon

aimsim/utils/plotting_scripts.py

@@ -0,0 +0,0 @@ """Plotting functions"""

config.yaml

@@ -0,0 +0,0 @@ # see AIMSim-demo.ipynb for a comprehensive list of all possible configuration options

implemented_metrics.md

@@ -0,0 +0,0 @@ # Supported Similarity Metrics

interfaces/UI/AIMSim_ui_main.py

@@ -0,0 +0,0 @@ """User Interface and associated methods to access the key functionalities of

interfaces/UI/libraries/README.md

 This directory contains external GUI libraries used by AIMSim, which are both made available under the MIT license.
 
 They are included here rather than installed from a package manager for ease of packaging on our end.

LICENSE

@@ -0,0 +0,0 @@ MIT License

PKG-INFO

 Metadata-Version: 2.1
 Name: aimsim_core
-Version: 2.1.4rc1
+Version: 2.1.3
 Summary: Core AIMSim molecular featurization and comparison utilities.
@@ -124,7 +124,7 @@ Home-page: https://github.com/VlachosGroup/AIMSim
   Step 3: Choose an arbitrary similarity measure.
-  Step 4: Select each molecule’s nearest and furthest neighbors in the set using the similarity measure.
-  Step 5: Measure the correlation between a molecule’s QoI and its nearest neighbor’s QoI.
-  Step 6: Measure the correlation between a molecule’s QoI and its further neighbor’s QoI.
+  Step 4: Select each molecule’s nearest and furthest neighbors in the set using the similarity measure.
+  Step 5: Measure the correlation between a molecule’s QoI and its nearest neighbor’s QoI.
+  Step 6: Measure the correlation between a molecule’s QoI and its further neighbor’s QoI.
   Step 7: Define a score which maximizes the value in Step 5 and minimizes the value in Step 6.
-  Step 8: Iterate Steps 1 – 7 to select the featurization scheme and similarity measure to maximize the result of Step 7. 
+  Step 8: Iterate Steps 1 – 7 to select the featurization scheme and similarity measure to maximize the result of Step 7. 
 2. See Property Variation with Similarity: Visualize the correlation in the QoI between nearest neighbor molecules (most similar pairs in the molecule set) and between the furthest neighbor molecules (most dissimilar pairs in the molecule set). This is used to verify that the chosen measure is appropriate for the task.
@@ -207,3 +207,3 @@
 ## Works Cited
-[1] Collins, K. and Glorius, F., A robustness screen for the rapid assessment of chemical reactions. Nature Chem 5, 597–601 (2013). https://doi.org/10.1038/nchem.1669
+[1] Collins, K. and Glorius, F., A robustness screen for the rapid assessment of chemical reactions. Nature Chem 5, 597–601 (2013). https://doi.org/10.1038/nchem.1669
 
@@ -210,0 +210,0 @@ [2] Chen, Y., Murray, P.R.D., Davies, A.T., and Willis M.C., J. Am. Chem. Soc. 140 (28), 8781-8787 (2018). https://doi.org/10.1021/jacs.8b04532

README.md

@@ -0,0 +0,0 @@ <h1 align="center">AIMSim README</h1>

requirements_core.txt

@@ -0,0 +0,0 @@ psutil

requirements.txt

@@ -0,0 +0,0 @@ scipy

setup.cfg

@@ -0,0 +0,0 @@ [egg_info]

setup.py

@@ -33,3 +33,3 @@ import os.path
     reqs = read("requirements.txt").split("\n")
-    packages = find_packages(exclude=["docs", "tests", "examples"])
+    packages = find_packages(exclude=["docs", "tests"])
     entry_points = {
@@ -45,3 +45,17 @@ "console_scripts": [
     packages = find_packages(
-        exclude=["docs", "tests", "examples", "interfaces", "aimsim.tasks"],
+        # include=[
+        #     "aimsim.chemical_datastructures",
+        #     "aimsim.ops",
+        #     "aimsim.utils.ccbmlib_fingerprints",
+        #     "aimsim.exceptions",
+        #     "aimsim",
+        # ],
+        exclude=[
+            "docs",
+            "tests",
+            "examples",
+            "interfaces",
+            "aimsim.tasks",
+            "aimsim",
+        ],
     )
@@ -48,0 +62,0 @@ entry_points = {}

tests/data/README.md

@@ -0,0 +0,0 @@ The data in this directory is pulled from [moses](https://github.com/molecularsets/moses) and is available under the MIT License.

tests/test_CompareTargetMolecule.py

@@ -0,0 +0,0 @@ """ Test the task CompareTargetMolecule  """

tests/test_Descriptor.py

@@ -0,0 +0,0 @@ """Tests for the Descriptor class"""

tests/test_LoadingErrorException.py

@@ -0,0 +0,0 @@ """ Test the LoadingError Exception """

tests/test_MeasureSearch.py

@@ -0,0 +0,0 @@ """Test the MeasureSearch class."""

tests/test_Molecule.py

@@ -0,0 +0,0 @@ """ Test the methods of the Molecule class """

tests/test_MoleculeSet.py

@@ -0,0 +0,0 @@ """Test the MoleculeSet class."""

tests/test_SimilarityMeasure.py

@@ -0,0 +0,0 @@ """Test the SimilarityMEasure class"""

tests/test_SimilarityMeasureValueErrors.py

@@ -0,0 +0,0 @@ """ Test the ValueError exceptions in SimilarityMeasure """

tests/test_TaskManager.py

@@ -0,0 +0,0 @@ """Test the TaskManager class."""

tests/test_ToolTip.py

@@ -0,0 +0,0 @@ """ Test the ToolTip package (and all UI packages) """

aimsim/__init__.py

-from . import ops
-from . import chemical_datastructures
-from . import utils
-
-try:
-    from . import tasks
-except ImportError:
-    pass  # aimsim_core does not include this
-
-__version__ = "2.1.4rc1"

aimsim/__main__.py

-"""Command line and GUI access point."""
-import sys
-
-
-def start_AIMSim():
-    """Opens the GUI if no commands are given, otherwise passes through config
-    to the configuration reader.
-    """
-    if len(sys.argv) > 1:
-        from interfaces import config_reader
-
-        sys.exit(config_reader.main())
-    else:
-        from interfaces.UI import AIMSim_ui_main
-
-        sys.exit(AIMSim_ui_main.main())
-
-
-if __name__ == "__main__":
-    start_AIMSim()

aimsim/exceptions.py

-class NotInitializedError(AttributeError):
-    """Used when a class is called without proper initialization."""
-
-    def __init__(self, message=None):
-        self.message = message
-        super().__init__(message)
-
-
-class MordredCalculatorError(RuntimeError):
-    """Used in descriptor.py when the Mordred property calculator fails."""
-
-    def __init__(self, message=None):
-        self.message = message
-        super().__init__(message)
-
-
-class MordredNotInstalledWarning(RuntimeWarning):
-    """Used in descriptor.py when the Mordred property calculator is not present."""
-
-    def __init__(self, message=None):
-        self.message = message
-        super().__init__(message)
-
-
-class InvalidConfigurationError(IOError):
-    """Used when a configuration parameter is invalid."""
-
-    def __init__(self, message=None):
-        self.message = message
-        super().__init__(message)
-
-
-class LoadingError(ValueError):
-    """Used when an object cannot be loaded"""
-
-    def __init__(self, message=None):
-        self.message = message
-        super().__init__(message)

tests/__init__.py

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Worsened metrics

Total package byte prevSize

1284175

-1.06%

Number of package files

52

-7.14%

Lines of code

10467

-0.31%