ChemScripts

scripts for input and output in computational chemical calculation

setup

1. download by git clone or wget

git clone https://github.com/matsuicclab/ChemScripts
or
wget https://github.com/matsuicclab/ChemScripts/archive/master.tar.gz
tar xpvf master.tar.gz

2. set environment variables (append to ~/.bashrc)

source <DIR>/bashrc # replace the text <DIR> to this directory according to your environment

to use

bash

# generate smiles and structure
$ name='ethanol'
$ name2smiles "$name" | smiles2xyz -O test.xyz

# calc energy with Gaussian
$ xyz2gjf -O test_0.gjf --link0 '%chk=test_0.chk' --route '# opt b3lyp/6-31G(d)' --charge 0 test.xyz
$ g16 test_0.gjf
$ g16log2value --SCF-energy test_0.log
-155.033799257

# calc energy of cation with Gaussian
$ xyz2gjf -O test_1.gjf --link0 '%chk=test_1.chk' --route '# opt b3lyp/6-31G(d)' --charge 1 test.xyz
$ g16 test_1.gjf
$ g16log2value --SCF-energy test_1.log
-154.664421473

# calc DeltaE in kcal/mol
$ (g16log2value --SCF-energy test_1.log ; g16log2value --SCF-energy test_0.log) | energy2energy --from a.u. --to kcal/mol --format '%.10f' | tr '\n' ' ' | awk '{print $1-$2}'
231.788

python

from pyg16.fchk import FCHK
fchk = FCHK('test.fchk')
fchk.calcElectronDensity([0, 0, 0])

from pyg16.cube import visualizeCubeSlice
visualizeCubeSlice(cubeFile='test.cub', outFile='test_slice.pdf')

Are you in trouble?

Error1

ChemScripts/bash/abstract/data2data: line 15: exec: {ChemScript_data2data_stdout_fd}: not found

This is probably because the version of bash you are using is old. Check your bash version with /bin/bash --version. bash4.1 or higher is recommended.

TODO

• g16log2value

  • eliminate title section
  • geometry
  • theory

• g16log2xyz (wrapper of g16log2value --opt-geometry)

• g16log2csv

• csvsmiles2xyz

• name2xyz (For complexes that are difficult to express in SMILES notation)

• glog2prep (extend of mkresp)

• xyz2prep

• mksolv

• bkill-all -> bkill 0

• jdel-all

• sdf2mol

• pdb2pdbs

• xyz2gms

• mkmdin

• mdcrd2crd (ambpdb)

• xyz2xyz (consideration on isotope)

• file2seqfiles

• files2file

• void2file

• error handling for pdbid2pdb, name2sdf

• Cube class (generate cube with node data of original cube)

• convert CRLF to LF before processing