The code reads Cartesian representation of the molecule. It then makes heuristic analysis of molecular bonding to extract resonantly stabilized electronic configurations, internal rotation structure, beta-scission bonds, rotational symmetry number, and z-matrix representation of the molecule.
The following commands will build the executable and place it in your bin.
mkdir build
cd build
cmake ..
make
sudo make install
cd ..
You can then try it out on an xyz file like this:
x2z examples/ch4.xyz
If you wish to use the Python bindings, do
export PYTHONPATH=$PYTHONPATH:/usr/local/lib
and you should be able to do things like the following.
>>> import x2ztools
>>> x2ztools.is_linear(('H', 'H'), [(0., 0., 0.), (0., 0., 1.)])
True
This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences under DOE Contract Number DE-AC02-06CH11357 as well as the Exascale Computing Project (ECP), Project Number: 17-SC-20-SC. The ECP is a collaborative effort of two DOE organizations, the Office of Science and the National Nuclear Security Administration, responsible for the planning and preparation of a capable exascale ecosystem including software, applications, hardware, advanced system engineering, and early test bed platforms to support the nation's exascale computing imperative.
Copyright (c) 2018 Yuri Georgievski ([email protected]), Stephen J. Klippenstein ([email protected]), and Argonne National Laboratory.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.