cheapocrest

for when you want conformers fast!

cheapocrest does automatic conformer generation directly from SMILES using OpenBabel, refines them using xtb & crest bypassing the computationally expensive parts of (specifically, the metadynamics section). cheapocrest is a much less powerful conformer generator than CREST, but it is significantly faster. It is appropriate for fairly stiff organic molecules (where conformer generation is easy) and optical excitation studies (where conformation effects are small).

To generate conformers, use

  cheapocrest [--ff FORCEFIELD] [--nconfs N] [--chrg C] [--theory
  --gfn2/--gfnff] -- INPUTSMILES

where FORCEFIELD is the openbabel forcefield used in the generation (defaults to UFF), N is the requested maximum number of conformers generated by openbabel (defaults to 10), C is the charge of your system and INPUTSMILES is either an input SMILES or a file containing an input SMILES. The level of theory used in the refinement steps is controlled by the --theory argument, which can either be --gfnff or --gfn2 (it is --gfnff by default).

Note that cheapocrest works with charged molecules, and the SMILES-detected global charge will be automatically stored into a .CHRG file for use with xtb. If you manually specified a charge with --chrg, the automatic charge detection process is skipped and the value is written to a .CHRG file instead.

This repo also contains an utility script split_conformers takes an xyz file containing multiple conformers as input and splits it into folders conf-0, conf-1, etc.

installation

To install, simply add the content of this directory to $PATH. You'll need relatively recent versions of xtb, OpenBabel and crest as well as a Perl 5 compatible interpreter. There are no other dependencies.

license

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.