General Tools

PubGrep

PubGrep is a command line tool that can automatically get random conformer structure data from the PubChem database, if it is available. This tool is very useful to quickly get a 3D structure of a compound. It comes either as a bash script or a Python implementation, both found on GitHub. The bashscipt can directly be used after making it executable, e.g.,:

chmod u+x PubGrep

The Python implementation can be installed with pip into the current environment:

pip install -e .

A complete list of functions is shown by executing

PubGrep --help

You can get a 3D structure by using, for example, the compound name or the PubGrep ID:

PubGrep <Name>
PubGrep <ID> --input cid

The result is per default an .sdf file named after the CID. If there is no 3D structure on PubChem, a 2D to 3D converter is used to generate a random conformer which must not be the energetically favored one.

Warning: The 2D to 3D structure conversition requires a working installation of xtb that is accessible by the script, e.g., by adding xtb to your path variable (see the xtb chapter).

Structure converter

The MCTC library provides access to many commonly required routines for structure handling and also has a stand-alone for structure converstion, namely the mctc-convert. The library is available on github and can be compiled with meson, cmake, or fpm with standard fortran compiler. A precompiled mctc-convert binary is also available on github. After extracting the mctc-convert-0.3.1.tar.xz archive, you can find the binary in the extracted bin directory. You can copy it to a path of your liking. Alternatively, you can install the mctc-lib via Homebrew:

brew tap grimme-lab/qc
brew install crest

The mctc-convert only requires an input coordinate file and writes the respective output file:

mctc-convert <input file> <output file>

Determining the file format of the input and output file is done automatically according to the respective file extension. For example, .xyz is recognized as Xmol file, while .coord defines the Turbomole format. Supported formats are:

Format	File extension
Xmol/xyz files	xyz, log
Turbomole’s coord, riper’s periodic coord	tmol, coord
DFTB+ genFormat geometry inputs	gen
VASP’s POSCAR/CONTCAR input files	vasp, poscar, contcar
Protein Database files (single files)	pdb
Connection table files (molfile, SDF)	mol, sdf
Gaussian’s external program input	ein
JSON input with qcschema structure	json
Chemical JSON input	cjson
FHI-AIMS’ input files	geometry.in
Q-Chem molecule block inputs	qchem

Further information are shown by using the –help command (mctc-convert --help).

RMSD tool

The MCTC RMSD tool can be used for calculating the root mean square deviation (RMSD) of two structures. This is useful qunatifying structural differences, e.g., to identify similar structures. It is available on github including precompiled binaries. After extracting the mctc-rmsd-0.1.1.tar.xz archive, the mctc-binary can be found in the extracted bin directory and can be copied to a place of your liking. It is called with

mctc-rmsd struc1.xyz struc2.xyz

Additional filters can be applied to, e.g., excluding hydrogen atoms by using the flag –filter heavy. Further information can be found with the –help flag (mctc-rmsd --help).