v0.2.20 (#713)

Author: njzjz

.git_archival.txt

@@ -1,4 +1,3 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$

.github/workflows/benchmark.yml

@@ -1,11 +1,11 @@
-name: Python package
+name: Benchmark
 
 on:
   - push
   - pull_request
 
 jobs:
-  build:
+  benchmark:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
@@ -15,9 +15,9 @@ jobs:
         python-version: 3.12
     - run: curl -LsSf https://astral.sh/uv/install.sh | sh
     - name: Install dependencies
-      run: uv pip install --system .[amber,ase,pymatgen,benchmark] rdkit openbabel-wheel
+      run: uv pip install --system .[test,amber,ase,pymatgen,benchmark] rdkit openbabel-wheel
     - name: Run benchmarks
-      uses: CodSpeedHQ/action@v2
+      uses: CodSpeedHQ/action@v3
       with:
         token: ${{ secrets.CODSPEED_TOKEN }}
         run: pytest benchmark/ --codspeed

.github/workflows/test.yml

@@ -20,7 +20,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - run: curl -LsSf https://astral.sh/uv/install.sh | sh
     - name: Install dependencies
-      run: uv pip install --system .[amber,ase,pymatgen] coverage ./tests/plugin rdkit openbabel-wheel
+      run: uv pip install --system .[test,amber,ase,pymatgen] coverage ./tests/plugin rdkit openbabel-wheel
     - name: Test
       run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report
     - name: Run codecov

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.7
+    rev: v0.6.3
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -36,7 +36,7 @@ repos:
       args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.16.0
+    rev: 1.18.0
     hooks:
     -   id: blacken-docs
 ci:

README.md

@@ -49,7 +49,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "numpydoc",
-    "m2r2",
+    "myst_parser",
     "sphinxarg.ext",
     "jupyterlite_sphinx",
 ]

docs/conf.py

@@ -6,22 +6,23 @@
 Welcome to dpdata's documentation!
 ==================================
 
+dpdata is a Python package for manipulating atomistic data of software in computational science.
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
-   Overview <self>
+   installation
+   systems/index
    try_dpdata
    cli
    formats
    drivers
    minimizers
+   plugin
    api/api
    credits
 
-.. mdinclude:: ../README.md
-
-
 Indices and tables
 ==================
 

docs/index.rst

@@ -0,0 +1,13 @@
+# Installation
+
+DP-GEN only supports Python 3.7 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install DP-GEN:
+
+- Install via pip: `pip install dpdata`
+- Install via conda: `conda install -c conda-forge dpdata`
+- Install from source code: `git clone https://github.com/deepmodeling/dpdata && pip install ./dpdata`
+
+To test if the installation is successful, you may execute
+
+```bash
+dpdata --version
+```

docs/installation.md

@@ -0,0 +1,9 @@
+# Plugins
+
+One can follow a simple example under `plugin_example/` directory to add their own format by creating and installing plugins.
+It's critical to add the :class:`Format` class to `entry_points['dpdata.plugins']` in `pyproject.toml`:
+
+```toml
+[project.entry-points.'dpdata.plugins']
+random = "dpdata_random:RandomFormat"
+```

docs/plugin.md

@@ -0,0 +1,51 @@
+
+## BondOrderSystem
+A new class :class:`BondOrderSystem` which inherits from class :class:`System` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).
+```python
+import dpdata
+
+system_1 = dpdata.BondOrderSystem(
+    "tests/bond_order/CH3OH.mol", fmt="mol"
+)  # read from .mol file
+system_2 = dpdata.BondOrderSystem(
+    "tests/bond_order/methane.sdf", fmt="sdf"
+)  # read from .sdf file
+```
+In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
+`BondOrderSystem` also supports initialize from a :class:`rdkit.Chem.rdchem.Mol` object directly.
+```python
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import dpdata
+
+mol = Chem.MolFromSmiles("CC")
+mol = Chem.AddHs(mol)
+AllChem.EmbedMultipleConfs(mol, 10)
+system = dpdata.BondOrderSystem(rdkit_mol=mol)
+```
+
+### Bond Order Assignment
+The :class:`BondOrderSystem` implements a more robust sanitize procedure for rdkit Mol, as defined in :class:`dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
++ low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
++ medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
++ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
+According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
+ `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.
+
+```python
+import dpdata
+
+for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
+    syst = dpdata.BondOrderSystem(sdf_file, sanitize_level="high", verbose=False)
+```
+### Formal Charge Assignment
+BondOrderSystem implement a method to assign formal charge for each atom based on the 8-electron rule (see below). Note that it only supports common elements in bio-system: B,C,N,O,P,S,As
+```python
+import dpdata
+
+syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt="mol")
+print(syst.get_formal_charges())  # return the formal charge on each atom
+print(syst.get_charge())  # return the total charge of the system
+```
+
+If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.