Merge pull request #34 from RMeli/develop

Publication and Minor Improvements

.github/FUNDING.yml

@@ -9,4 +9,4 @@ community_bridge: # Replace with a single Community Bridge project-name e.g., cl
 liberapay: # Replace with a single Liberapay username
 issuehunt: # Replace with a single IssueHunt username
 otechie: # Replace with a single Otechie username
-custom: ["https://www.buymeacoffee.com/rmeli"]
+custom: # ["https://www.buymeacoffee.com/rmeli"]

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,54 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [develop, master]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [develop]
+  schedule:
+    - cron: '0 0 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+      with:
+        # We must fetch at least the immediate parents so that if this is
+        # a pull request then we can checkout the head.
+        fetch-depth: 2
+
+    # If this run was triggered by a pull request event, then checkout
+    # the head of the pull request instead of the merge commit.
+    - run: git checkout HEAD^2
+      if: ${{ github.event_name == 'pull_request' }}
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      # Override language selection by uncommenting this and choosing your languages
+      # with:
+      #   languages: go, javascript, csharp, python, cpp, java
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

README.md

@@ -10,13 +10,31 @@
 [![Docs](https://img.shields.io/badge/docs-spyrmsd.readthedocs.io-blueviolet)](https://spyrmsd.readthedocs.io)
 [![Documentation Status](https://readthedocs.org/projects/spyrmsd/badge/?version=develop)](https://spyrmsd.readthedocs.io/en/develop/?badge=develop)
 
-[![DOI](https://zenodo.org/badge/214157073.svg)](https://zenodo.org/badge/latestdoi/214157073)
 [![License](https://img.shields.io/github/license/RMeli/pyrmsd?color=%2333BBFF)](https://opensource.org/licenses/MIT)
-[![PyPI](https://img.shields.io/badge/PyPI-v0.3.3%20-ff69b4)](https://pypi.org/project/spyrmsd/)
+[![PyPI](https://img.shields.io/badge/PyPI-v0.3.5%20-ff69b4)](https://pypi.org/project/spyrmsd/)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/spyrmsd.svg)](https://anaconda.org/conda-forge/spyrmsd)
 
+[![J. Cheminform.](https://img.shields.io/badge/J.%20Cheminform.-10.1186%2Fs13321--020--00455--2-blue)](https://doi.org/10.1186/s13321-020-00455-2)
+[![Zenodo](https://zenodo.org/badge/214157073.svg)](https://zenodo.org/badge/latestdoi/214157073)
+
 Python tool for symmetry-corrected RMSD calculations.
 
+---
+
+If you find `spyrmsd` useful, please consider citing the following paper:
+
+```
+@article{spyrmsd2020,
+  Author = {Meli, Rocco and Biggin, Philip C.},
+  Journal = {Journal of Cheminformatics},
+  Number = {1},
+  Pages = {49},
+  Title = {spyrmsd: symmetry-corrected RMSD calculations in Python},
+  Volume = {12},
+  Year = {2020}
+}
+```
+
 ## Installation
 
 `spyrmsd` is available on [PyPI](https://pypi.org/project/spyrmsd/) and [conda-forge](https://github.com/conda-forge/spyrmsd-feedstock) and can be easily installed from source. See [Dependencies](###Dependencies) for a description of all the dependencies.
@@ -56,7 +74,7 @@ The following packages are required to use `spyrmsd` as a module:
 * [scipy](https://www.scipy.org/)
 * [qcelemental](http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/)
 
-_Note_: `spyrmsd` uses [graph-tool](https://graph-tool.skewed.de/) by default but will  fall back  to [NetworkX](https://networkx.github.io/) if the former is not installed (e.g. on Windows).
+_Note_: `spyrmsd` uses [graph-tool](https://graph-tool.skewed.de/) by default but will fall back to [NetworkX](https://networkx.github.io/) if the former is not installed (e.g. on Windows). However, in order to support cross-platform installation [NetworkX](https://networkx.github.io/) is installed by default.
 
 #### Standalone Tool
 
@@ -65,7 +83,7 @@ Additionally, one of the following packages is required to use `spyrmsd` as a st
 * [Open Babel](http://openbabel.org/)
 * [RDKit](https://rdkit.org/)
 
-_Note_: [RDKit](https://rdkit.org/) has to be installed using `conda` ([Why the RDKit isn't available on PyPi](https://rdkit.blogspot.com/2019/11/why-rdkit-isnt-available-on-pypi.html)).
+_Note_: [RDKit](https://rdkit.org/) is not available on PyPI ([Why the RDKit isn't available on PyPi](https://rdkit.blogspot.com/2019/11/why-rdkit-isnt-available-on-pypi.html)). See [RDKit Installation](http://www.rdkit.org/docs/Install.html) for installation instructions.
 
 ## Usage
 
@@ -76,8 +94,7 @@ python -m spyrmsd.spyrmsd -h
 ```
 
 ```text
-usage: spyrmsd.py [-h] [-m] [-c] [--hydrogens] [-n]
-                  reference molecules [molecules ...]
+usage: spyrmsd.py [-h] [-m] [-c] [--hydrogens] [-n] reference molecules [molecules ...]
 
 Python RMSD tool.
 

pyproject.toml

@@ -8,7 +8,7 @@ dist-name = "spyrmsd"
 description-file = "README.md"
 author = "Rocco Meli"
 author-email = "[email protected]"
-home-page = "https://pyrmsd.readthedocs.io"
+home-page = "https://spyrmsd.readthedocs.io"
 classifiers = [
     "License :: OSI Approved :: MIT License", 
     "Programming Language :: Python :: 3",]

spyrmsd/__init__.py

@@ -2,8 +2,8 @@
 Python RMSD tool with symmetry correction.
 """
 
-from .due import due, Doi
 from ._version import get_versions
+from .due import Doi, due
 
 versions = get_versions()
 __version__ = versions["version"]
@@ -14,5 +14,11 @@
 due.cite(
     Doi("10.5281/zenodo.3631876"),  # lgtm[py/procedure-return-value-used]
     path="spyrmsd",
-    description="spyRMSD: Symmetry-Corrected RMSD in Python",
+    description="spyrmsd",
+)
+
+due.cite(
+    Doi("10.1186/s13321-020-00455-2"),  # lgtm[py/procedure-return-value-used]
+    path="spyrmsd",
+    description="spyrmsd",
 )

spyrmsd/graphs/gt.py

@@ -87,7 +87,10 @@ def match_graphs(G1, G2) -> List[Tuple[List[int], List[int]]]:
     # Check if graphs are actually isomorphic
     if len(maps) == 0:
         # TODO: Create a new exception
-        raise ValueError(f"Graphs {G1} and {G2} are not isomorphic.")
+        raise ValueError(
+            "Graphs are not isomorphic."
+            "\nMake sure graphs have the same connectivity."
+        )
 
     n = num_vertices(G1)
 

spyrmsd/graphs/nx.py

@@ -84,7 +84,10 @@ def match_atomicnum(node1, node2):
     # Check if graphs are actually isomorphic
     if not GM.is_isomorphic():
         # TODO: Create a new exception
-        raise ValueError(f"Graphs {G1} and {G2} are not isomorphic.")
+        raise ValueError(
+            "Graphs are not isomorphic."
+            "\nMake sure graphs have the same connectivity."
+        )
 
     return [
         (list(isomorphism.keys()), list(isomorphism.values()))

spyrmsd/hungarian.py

@@ -1,7 +1,7 @@
 import numpy as np
 import scipy
 
-from .due import due, Doi
+from .due import Doi, due
 
 due.cite(
     Doi("10.1021/ci400534h"),  # lgtm[py/procedure-return-value-used]

spyrmsd/qcp.py

@@ -3,7 +3,7 @@
 import numpy as np
 from scipy import optimize
 
-from .due import due, Doi
+from .due import Doi, due
 
 due.cite(
     Doi("10.1107/S0108767305015266"),  # lgtm[py/procedure-return-value-used]

tests/test_rmsd.py

@@ -219,34 +219,36 @@ def test_rmsd_hungarian_benzene_rotated(angle: float, tol: float) -> None:
     ) == pytest.approx(0, abs=tol)
 
 
+@pytest.mark.parametrize("d", [-0.5, 0.0, 0.5, 1.0, 1.5])
 @pytest.mark.parametrize(
     "angle, tol", [(60, 1e-4), (120, 1e-4), (180, 1e-4), (240, 1e-4), (300, 1e-4)]
 )
-def test_rmsd_hungarian_benzene_shifted_rotated(angle: float, tol: float) -> None:
+def test_rmsd_hungarian_benzene_shifted_rotated(
+    d: float, angle: float, tol: float
+) -> None:
 
     mol1 = copy.deepcopy(molecules.benzene)
     mol2 = copy.deepcopy(molecules.benzene)
 
-    mol2.translate([0, 0, 1])
+    mol2.translate([0, 0, d])
 
     assert rmsd.rmsd(
         mol1.coordinates, mol2.coordinates, mol1.atomicnums, mol2.atomicnums
-    ) == pytest.approx(1)
+    ) == pytest.approx(abs(d))
 
     assert rmsd.hrmsd(
         mol1.coordinates, mol2.coordinates, mol1.atomicnums, mol2.atomicnums
-    ) == pytest.approx(1)
+    ) == pytest.approx(abs(d))
 
     # Rotations different than 180 degrees introduce numerical errors (~1e-11)
     mol2.rotate(angle, [0, 0, 1], units="deg")
 
-    assert (
-        rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums, mol2.atomicnums)
-        > 1
-    )
+    assert rmsd.rmsd(
+        mol1.coordinates, mol2.coordinates, mol1.atomicnums, mol2.atomicnums
+    ) > abs(d)
     assert rmsd.hrmsd(
         mol1.coordinates, mol2.coordinates, mol1.atomicnums, mol2.atomicnums
-    ) == pytest.approx(1, abs=tol)
+    ) == pytest.approx(abs(d), abs=tol)
 
 
 @pytest.mark.parametrize("mol", molecules.allmolecules)