File Management

This page documents file management scripts for organizing and converting computational chemistry files.

File Organization Script

The file_organizer.py script organizes computational chemistry output files based on an Excel spreadsheet. It creates folders, renames files, and moves them to their corresponding directories.

For this script, -t/--filetype is only a filename-suffix filter. It matches extensions such as .log or .out and does not inspect file contents or detect whether a file came from Gaussian, ORCA, or another program.

Usage

file_organizer.py [-d path/to/directory] [-f excel_file] [-t filetype]
                  [-n sheet_name] [-c columns] [-s skip_row(s)]
                  [-r organize_row(s)] [--keep-default-na|--no-keep-default-na]

Options

Option	Type	Description
`-d, --directory`	string	Directory containing files to organize (default: current directory)
`-f, --filename`	string	Excel file with metadata (required)
`-t, --filetype`	string	File extension to organize (default: log). This is suffix-based only; the script does not parse file content.
`-n, --name`	string	Excel sheet name (required)
`-c, --cols`	string	Column range for metadata (default: B:D)
`-s, --skip`	int	Rows to skip at start
`-r, --row`	int	Number of rows to process
`--keep-default-na/--no-keep-default-na`	bool	Include default NaN values when reading Excel

Example

Organize conformer files based on an Excel spreadsheet:

file_organizer.py -f test.xlsx -n co2 -c B:D -s 2 -r 45

This skips the first 2 rows and processes up to 45 rows. The script:

Creates target folders if they don’t exist
Copies files with new names to the target folders
Preserves original files

If you set -t out, the script will organize every .out file that matches the spreadsheet mapping, regardless of whether the file was created by Gaussian, ORCA, or another tool.

File Conversion Script

Prefer the built-in CLI for structure conversion:

chemsmart run convert -i molecule.pdb
chemsmart run convert -i molecule.pdb -o .mol2
chemsmart run convert -d /path/to/dir -t log --output-filetype xyz

See Convert CLI Options and Molecule Input Formats for convert options, supported formats, and the Open Babel write fallback for non-native output types.

The legacy file_converter.py script remains available for the same workflow.

For directory-based conversion, -t/--filetype selects files by extension, while -p/--program is only needed when CHEMSMART must know which program-specific parser to use.

Usage

file_converter.py [-d path/to/directory] [-t filetype] [-p program]
                  [-f filename] [-o output_type] [-i]

Options

Option	Type	Description
`-d, --directory`	string	Directory for batch conversion (mutually exclusive with -f)
`-t, --filetype`	string	Input file type: log, com, gjf, out, inp, xyz, sdf. This filters files by extension.
`-p, --program`	choice	Program that produced the files: `gaussian` or `orca`. Use this when conversion depends on program identity, such as `.out` files where Gaussian and ORCA share the same extension.
`-f, --filename`	string	Specific file(s) to convert (mutually exclusive with -d)
`-o, --output-filetype`	string	Output format: xyz or com (default: xyz)
`-i, --include-intermediate-structures`	bool	Include intermediate structures (default: disabled)

Examples

Single file conversion:

file_converter.py -f co2.log

Output co2.xyz:

3
co2.xyz    Empirical formula: CO2    Energy(Hartree): -188.444680
O        0.0000000000    0.0000000000    1.1630620000
O        0.0000000000    0.0000000000   -1.1630620000
C        0.0000000000    0.0000000000    0.0000000000

Batch conversion of .log file:

file_converter.py -d . -t log -o com -i

Converts all .log files in the current directory to .com files, including intermediate structures.

Batch conversion of .out files (program required):

# Gaussian .out files
file_converter.py -d . -t out -p gaussian -o xyz

# ORCA .out files
file_converter.py -d . -t out -p orca -o xyz