fix: update use of openbabel (#39)

* fix: update use of openbabel

* Update push.yml

* Update tox.ini

* Update tox.ini

.github/workflows/push.yml

@@ -6,9 +6,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
-    - name: Tox
-      uses: njzjz/actions/tox-conda@master
+    - uses: actions/setup-python@v1
+      with:
+        python-version: '3.7'
+        architecture: 'x64'
+    - run: pip install tox-conda
+    - run: git clone --depth 1 https://github.com/circulosmeos/gdown.pl
+      working-directory: /home/runner/work
+    - run: ./gdown.pl/gdown.pl $GAUSSIANURL "g16.tgz">/dev/null 2>&1
+      env:
+        GAUSSIANURL: ${{ secrets.GAUSSIANURL }}
+      working-directory: /home/runner/work
+    - run: tar -xzvf g16.tgz
+      working-directory: /home/runner/work
+    - run: tox
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-        GAUSSIANURL: ${{ secrets.GAUSSIANURL }}
+        g16root: /home/runner/work

aimdfragmentation/frag.py

@@ -90,12 +90,12 @@ def _readpdb(self):
         conv.SetInAndOutFormats('xyz', 'pdb')
         mol = openbabel.OBMol()
         conv.ReadFile(mol, self.xyzfilename)
-        pdbstring = conv.WriteString(mol)
         bond = [[] for x in range(self._natom)]
-        for line in pdbstring.split('\n'):
-            if line.startswith("CONECT"):
-                s = line.split()
-                bond[int(s[1])-1] += [int(x)-1 for x in s[2:]]
+        for b in openbabel.OBMolBondIter(mol):
+            s1 = b.GetBeginAtom().GetId()
+            s2 = b.GetEndAtom().GetId()
+            bond[s1].append(s2)
+            bond[s2].append(s1)
         # connect molecules
         self._mols = connectmolecule(bond)
 

docs/README.md

@@ -1,23 +1,18 @@
 # Automated Fragmentation AIMD Calculation
 
+[![DOI:10.26434/chemrxiv.11462160](https://zenodo.org/badge/DOI/10.1039/C9CP05091D.svg)](https://doi.org/10.26434/chemrxiv.11462160)
 [![python version](https://img.shields.io/pypi/pyversions/aimdfragmentation.svg?logo=python&logoColor=white)](https://pypi.org/project/aimdfragmentation)
 [![PyPI](https://img.shields.io/pypi/v/aimdfragmentation.svg)](https://pypi.org/project/aimdfragmentation)
-[![Build Status](https://travis-ci.com/njzjz/aimdfragmentation.svg?branch=master)](https://travis-ci.com/njzjz/aimdfragmentation)
-[![Coverage Status](https://coveralls.io/repos/github/njzjz/aimdfragmentation/badge.svg?branch=master)](https://coveralls.io/github/njzjz/aimdfragmentation?branch=master)
 [![codecov](https://codecov.io/gh/njzjz/aimdfragmentation/branch/master/graph/badge.svg)](https://codecov.io/gh/njzjz/aimdfragmentation)
 
 A automated fragmentation method for Ab Initio Molecular Dynamics (AIMD).
 
+Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation, DOI: 10.26434/chemrxiv.11462160
+
 **Author**: Jinzhe Zeng
 
 **Email**: [email protected]
 
-## Requirements
-* [OpenBabel](https://github.com/openbabel/openbabel)
-* [numpy](https://github.com/numpy/numpy)
-* [ASE](https://gitlab.com/ase/ase)
-* [GaussianRunner](https://github.com/njzjz/GaussianRunner)
-
 ## Installation
 
 ### Using pip

tox.ini

@@ -3,19 +3,19 @@ envlist = py37
 
 [testenv]
 extras = test
-passenv = GAUSS_* CI TRAVIS TRAVIS_* CODECOV_* *_TOKEN
+passenv = GAUSS_* CI TRAVIS TRAVIS_* CODECOV_* *_TOKEN g16root
 deps =
     coveralls
     codecov>=1.4.0
     codacy-coverage
 conda_deps=
     openbabel
-    c-compiler
-    cxx-compiler
 conda_channels=
     conda-forge
+whitelist_externals =
+    bash
 commands =
-    pytest --pyargs aimdfragmentation --cov {envsitepackagesdir}/aimdfragmentation -s
+    bash -c "source $g16root/g16/bsd/g16.profile; pytest --pyargs aimdfragmentation --cov {envsitepackagesdir}/aimdfragmentation -s"
     - coveralls
     - codecov
     - python-codacy-coverage -r coverage.xml