Merge branch 'devel' into ase_db

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,25 @@
+---
+name: Bug report
+about: Create a bug report to help us eliminate issues and improve dpdata. If this
+  doesn’t look right, [choose a different type](https://github.com/deepmodeling/dpdata/issues/new/choose).
+title: "[BUG] _Replace With Suitable Title_"
+labels: bug
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what the bug is.-->
+
+<!--Please provide necessary information including the version of software and installation way, input file, running commands, error log , etc., AS  DETAILED AS POSSIBLE to help locate and reproduce your problem. -->
+
+<!--If applicable, specify what platform you are running on. -->
+
+**Steps to Reproduce**
+
+<!--Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,21 @@
+---
+name: Feature request
+about: Suggest an idea for this project. If this doesn’t work right, [choose a different
+  type]( https://github.com/deepmodeling/dpdata/issues/new/choose).
+title: "[Feature Request] _Replace with Title_"
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a brief and concise description of the suggested feature or change-->
+
+**Detailed Description**
+
+<!--Please explain how you would like to see dpdata enhanced, what feature(s) you are looking for, what specific data format this will support or what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/generic-issue.md

@@ -0,0 +1,17 @@
+---
+name: Generic issue
+about: For issues that do not fit any of the other categories. If this doesn’t work
+  right, [choose a different type]( https://github.com/deepmodeling/dpdata/issues/new/choose).
+title: ''
+labels: wontfix
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what the question is.-->
+
+**Details**
+
+<!--Please explain the issue in detail here-->

.github/ISSUE_TEMPLATE/request-for-help.md

@@ -0,0 +1,21 @@
+---
+name: Request for Help
+about: Don't post help requests here, go to [discussions](https://github.com/deepmodeling/dpdata/discussions)
+  instead. If this doesn’t look right, choose a different type.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Before asking questions, you can
+
+search the previous issues or discussions
+check the [README](https://github.com/deepmodeling/dpdata/#readme).
+
+Please **do not** post requests for help (e.g. with installing or using dpdata) here. 
+Instead go to [discussions](https://github.com/deepmodeling/dpdata/discussions).
+
+This issue tracker is for tracking dpdata development related issues only.
+
+Thanks for your cooperation.

.github/workflows/test.yml

@@ -0,0 +1,30 @@
+name: Python package
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    # set up conda
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-activate-base: true
+        activate-environment: ""
+    # install rdkit and openbabel
+    - name: Install rdkit
+      run: conda create -c conda-forge -n my-rdkit-env python=${{ matrix.python-version }} rdkit openbabel;
+    - name: Install dependencies
+      run: source $CONDA/bin/activate my-rdkit-env && pip install .[amber] coverage codecov
+    - name: Test
+      run: source $CONDA/bin/activate my-rdkit-env && cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report
+    - name: Run codecov
+      run: source $CONDA/bin/activate my-rdkit-env && codecov

.gitignore

@@ -20,4 +20,5 @@ dist
 dpdata.egg-info
 _version.py
 !tests/cp2k/aimd/cp2k.log
+!tests/cp2k/restart_aimd/ch4.log
 __pycache__

README.md

@@ -78,7 +78,8 @@ The `System` or `LabeledSystem` can be constructed from the following file forma
 | PWmat   | movement    | True         | True    | LabeledSystem | 'pwmat/movement'     |
 | PWmat   | OUT.MLMD    | True         | True    | LabeledSystem | 'pwmat/out.mlmd'     |
 | Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
-| Gromacs | gro         | False        | False   | System        | 'gromacs/gro'        |
+| Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
+| Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
 
 
 The Class `dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
@@ -197,3 +198,68 @@ perturbed_system = dpdata.System('./POSCAR').perturb(pert_num=3,
     atom_pert_style='normal')
 print(perturbed_system.data)
 ```
+
+## replace
+By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged.
+```python
+s=dpdata.System('tests/poscars/POSCAR.P42nmc',fmt='vasp/poscar')
+s.replace('Hf', 'Zr', 8)
+s.to_vasp_poscar('POSCAR.P42nmc.replace')
+```
+
+# BondOrderSystem
+A new class `BondOrderSystem` which inherits from 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 `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 `BondOrderSystem` implements a more robust sanitize procedure for rdkit Mol, as defined in `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.
+
+# Plugins
+
+One can follow [a simple example](plugin_example/) to add their own format by creating and installing plugins. It's crirical to add the [Format](dpdata/format.py) class to `entry_points['dpdata.plugins']` in `setup.py`:
+```py
+    entry_points={
+        'dpdata.plugins': [
+            'random=dpdata_random:RandomFormat'
+        ]
+    },
+```

dpdata/__init__.py

@@ -9,3 +9,16 @@
     from ._version import version as __version__
 except ImportError:
     from .__about__ import __version__
+
+# BondOrder System has dependency on rdkit
+try:
+    # prevent conflict with dpdata.rdkit
+    import rdkit as _
+    USE_RDKIT = True
+except ModuleNotFoundError:
+    USE_RDKIT = False
+
+if USE_RDKIT:
+    from .bond_order_system import BondOrderSystem
+
+