Entrypoint

ViennaPTM can be used via an entrypoint from the command line, a configuration file, or custom scripts.

COMMAND LINE

# 1. Activate the conda environment
conda activate viennaptm

# 2. Use the entrypoint (CLI) to run ViennaPTM
viennaptm --input tests/data/1vii.pdb \
          --modify "A:50=V3H" \
          --output testoutput.pdb

Help

The help parameter shows the available options in detail.

viennaptm --help

Help message:

Options:
  --config
      [Union, default=None]
      Path to a YAML or JSON configuration file (optional).
  --input
      [Union, default=None]
      Input structure, either CIF or PDB.
  --modify
      [Union, default=None]
      Modifications in the form of "A:50=V3H", which means "chain:residue=target".
  --output
      [Union, default=output.pdb]
      Output structure, either CIF or PDB.
  --gromacs.minimize
      [bool, default=False]
      Energy minimize the modified structure.
  --logger
      [Optional, default=console]
      Set logger to either console (default) or provide a file name.
  --ptm_list
      [Optional, default=None]
      List all PTMs if set to either "console" or a file path.
  --debug
      [Optional, default=False]
      If set to true, enable verbose debugging logging.

Also, you can list all available post-translational modifications with their metadata using ptm_list:

viennaptm --input tests/data/1vii.pdb --ptm_list

CONFIG FILE

# Example configuration file
input: ./tests/data/1vii.pdb
modify:
  - "A:50=V3H"
output: output.pdb
logger: console
debug: false

To run ViennaPTM using a configuration file:

viennaptm --config tests/data/example_config.yaml

PARAMETERS

Parameter	Description	Explanation	Example
`--input`	Input path or PDB identifier	If the input is a string ending with `.pdb` or `.cif`, it is treated as a local file path and converted to a `pathlib.Path`. Otherwise, the input is interpreted as a PDB database identifier and must be exactly four characters long.	`./tests/data/1vii.cif` or `1vii`
`--modify`	List of modifications	A modification is specified as a string consisting of a `chain_identifier`, a `residue_number`, and a `target_abbreviation`, for example: `"A:50=V3H"`. Multiple modifications can be provided as a list of strings.	`"A:50=V3H"` or `"A:50=V3H" "A:55=V3H"`
`--output`	Output path or filename	The output filename must end with `.pdb` or `.cif`. String paths are converted to `pathlib.Path`.	`output.pdb`
`--logger`	Logging destination	If set to `"console"`, log messages are printed to standard output. Otherwise, the value is interpreted as a file path and logging output is written to a file.	`console` or `log.txt`
`--debug`	Debug mode	Enables verbose debug logging when set to `true`.	`false` or `true`

BASH SCRIPT

Example Bash script:

#!/usr/bin/env bash

# Exit immediately if a command fails
set -e

# 1. Initialize conda (required outside an interactive shell)
# Adjust this path if your conda installation is located elsewhere
source "$(conda info --base)/etc/profile.d/conda.sh"

# 2. Activate the conda environment
conda activate viennaptm

# 3. Run ViennaPTM
viennaptm --input tests/data/1vii.pdb \
          --modify "A:50=V3H" \
          --output testoutput.pdb

Save the script as, for example:

run_viennaptm.sh

Make it executable:

chmod +x run_viennaptm.sh

Run it:

./run_viennaptm.sh

SLURM SCRIPT

Example SLURM submission script:

#!/usr/bin/env bash
#SBATCH --job-name=viennaptm
#SBATCH --output=viennaptm_%j.out
#SBATCH --error=viennaptm_%j.err
#SBATCH --time=01:00:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G

# Fail fast on errors and undefined variables
set -euo pipefail

echo "Job started on $(hostname) at $(date)"

# ---- Conda setup ----
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate viennaptm

# ---- Run ViennaPTM ----
viennaptm --input tests/data/1vii.pdb \
          --modify "A:50=V3H" \
          --output testoutput.pdb

echo "Job finished at $(date)"

NOTE: Alternatively, you can skip the conda initialization and directly provide the full path to the ViennaPTM entrypoint:

/path/to/your/installation/bin/viennaptm \
    --input tests/data/1vii.pdb \
    --modify "A:50=V3H" \
    --output testoutput.pdb

Submit the SLURM script to the cluster using:

sbatch run_viennaptm.slurm