Name of the Program: TorsiFlex
Program Version : 2022.1
Program Version Date: Jul 12, 2022
Manual Version Date: Jul 12, 2022
TorsiFlex is an user-friendly program written in Python 3. It was designed to seek the conformers of a given molecule by using a combined low-level/high-level (LL/HL) methodology.
The following publications must be cited in any work presenting results obtained with TorsiFlex:
- D. Ferro-Costas and A. Fernández-Ramos (2020). “A Combined Systematic-Stochastic Algorithm for the Conformational Search in Flexible Acyclic Molecules”. Front. Chem., 8:16.
- D. Ferro-Costas, I. Mosquera-Lois and A. Fernández-Ramos (2021). “TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids”. J. Cheminformatics., 13:100.
TorsiFlex version 2022.1
MIT LICENSE
Copyright (c) 2022, David Ferro Costas (david.ferro@usc.es) and Antonio Fernandez Ramos (qf.ramos@usc.es)
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Contents of the folders distributed in this version:
- src/ : TorsiFlex source files
- docs/ : Manual of TorsiFlex
- tests/ : All the files related to the tests set
TorsiFlex is a program written in Python 3. Consequently, it does not need any kind of compilation, as it would be the case with C or Fortran programs. The user should install Python 3 in order to use TorsiFlex, as well as the following Python libraries:
- cmath
- fcntl
- glob
- math
- matplotlib
- multiprocessing
- numpy
- os
- random
- rdkit
- scipy
- sys
- time
WARNING: do not use Python 2 to execute TorsiFlex.
Before using TorsiFlex, the user has to define the path to the executable(s) of the software for the electronic structure calculation (ESSO). At the moment TorsiFlex supports Gaussian as ESSO.
In order to interact with the ESSO, TorsiFlex needs to know the location of some executable files. Such information is obtained from the following environment variables, which have to be defined and exported by the user in their .bashrc file:
For Gaussian, the environment variable is:
- GauExe, the path to the Gaussian executable and
Example of paths are:
export Gauexe="/home/programs/G09_64D/g09/g09"
You can run TorsiFlex by invoking the Python interpreter manually as follows:
python3 torsiflex.py
If you prefer to avoid invoking the Python interpreter, you have to follow these two simple steps:
Add as the first line in the torsiflex.py file the following:
#!PATH_FOR_PYTHON python
where PATH_FOR_PYTHON indicates the location of the Python interpreter.
Example:
#!/usr/bin/python3
In this example Python is located in /usr/bin/.
Make the main program torsiflex.py executable:
chmod u+x torsiflex.py
This allows you to run TorsiFlex just using:
torsiflex.py
Before run TorsiFlex, we recommend to read the help menu. It can be displayed either by typing
torsiflex.py --help
or
torsiflex.py -h
Directory tests/ contains the z-matrix files associated to the four worked examples (see manual).