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mctc-convert(1) Manual Page

Name

mctc-convert - Convert between supported geometry file formats

Synopsis

mctc-convert [options] input output

mctc-convert --help

mctc-convert --version

Description

The mctc-convert program reads molecular structure data from an input file and writes it to an output file, optionally converting between different geometry file formats. The format is automatically determined by the file extension, or can be explicitly specified using format hint options.

The program supports reading from standard input and writing to standard output by using - as the file argument. When using standard input/output, a format hint option should be provided.

Supported Formats

The following geometry formats are supported for both reading and writing:

Format hint Description File extensions

xyz

Xmol/xyz coordinate files

.xyz, .log

tmol, coord

Turbomole coord files (including periodic/riper)

.tmol, .coord

gen

DFTB+ genFormat (cluster, supercell, fractional)

.gen

vasp, poscar, contcar

VASP POSCAR/CONTCAR geometry files

.vasp, .poscar, .contcar

pdb

Protein Data Bank files (single structures only)

.pdb

mol

MDL Molfile connection table

.mol

sdf

MDL Structure Data Format

.sdf

ein

Gaussian external program input

.ein

qcjson, json

QCSchema JSON (qcschema_molecule or qcschema_input)

.qcjson, .json

cjson, json

Chemical JSON (Avogadro)

.cjson, .json

pmgjson, json

Pymatgen JSON (Molecule or Structure schema)

.pmgjson, .json

aims

FHI-aims geometry input

geometry.in

qchem

Q-Chem molecule block

.qchem
Note
 JSON format support requires mctc-lib to be compiled with the jonquil dependency.

Options

-i, --input format

Specify the format of the input file. Use this option when the input file has a non-standard extension or when reading from standard input. See Supported Formats for valid format hints.

-o, --output format

Specify the format of the output file. Use this option when the output file should have a non-standard extension or when writing to standard output. See Supported Formats for valid format hints.

--normalize

Normalize all element symbols to standard capitalized format (e.g., "CL" becomes "Cl", "h" becomes "H"). Useful when working with files that have non-standard element symbol casing.

--template file

Use the specified file as a template to transfer metadata to the output. This option transfers lattice parameters, periodicity information, comments, and format-specific annotations (such as PDB residue information or SDF bond data) from the template to the input structure. The input and template structures must have the same number of atoms.

If - is provided as the template file, the template structure is read from standard input before the input structure.

--template-format format

Specify the format of the template file. Only used when a template file is provided via --template.

--ignore-dot-files

Do not read molecular charge from .CHRG files or spin state from .UHF files in the input file’s directory. By default, these files are read if present.

--version

Print the program version and exit.

--help

Display a brief help message and exit.

Examples

Convert an xyz file to Turbomole coord format
mctc-convert molecule.xyz molecule.coord
Convert a VASP POSCAR to xyz format
mctc-convert POSCAR structure.xyz
Read from standard input and write to standard output
cat molecule.xyz | mctc-convert -i xyz -o mol - -
Convert format while preserving SDF bond information
mctc-convert optimized.xyz final.sdf --template original.sdf
Normalize element symbols during conversion
mctc-convert --normalize input.xyz output.xyz
Force input format for non-standard extension
mctc-convert -i xyz geometry.dat output.mol

Environment

.CHRG

If a file named .CHRG exists in the same directory as the input file, the molecular charge is read from it (unless --ignore-dot-files is specified).

.UHF

If a file named .UHF exists in the same directory as the input file, the number of unpaired electrons is read from it (unless --ignore-dot-files is specified).

Exit Status

0

Success.

non-zero

An error occurred during file reading, writing, or conversion. Error messages are written to standard error with source location information when available.

See Also

The mctc-lib API documentation: https://grimme-lab.github.io/mctc-lib

Authors

mctc-lib is developed by the Grimme group at the University of Bonn. See https://github.com/grimme-lab/mctc-lib/graphs/contributors for a list of all contributors.

Reporting Bugs

Report bugs and unclear error messages at: https://github.com/grimme-lab/mctc-lib/issues