export

Convert Pharmacon HDF5 artifacts into human-readable flat files for use in spreadsheets, R, pandas, or bioinformatics pipelines.

---

export pta

Export a Pharmacon Trajectory Analysis (.pta) file to CSV or TSV. All datasets inside the file are written as separate files into the specified output directory.

Arguments

Flag	Required	Description
-i / --input	Yes	Input .pta file
-f / --format	Yes	Output format: csv or tsv
-o / --output	Yes	Output directory where exported files will be written
--overwrite	No	Overwrite existing output files

Examples

Export RMSD results to CSV:

pharmacon export pta \
    -i rmsd.pta \
    -f csv \
    -o ./results/

Export interaction data to TSV:

pharmacon export pta \
    -i pl_interactions.pta \
    -f tsv \
    -o ./exports/

Export a merged artifact to CSV and overwrite existing output:

pharmacon export pta \
    -i pli_merged.pta \
    -f csv \
    -o ./results/ \
    --overwrite

Quick inspect then export workflow:

pharmacon dump   pta -i rmsd.pta
pharmacon export pta -i rmsd.pta -f csv -o ./results/

---

export psa

Export a Pharmacon Structure Analysis (.psa) file to CSV, TSV, or FASTA.

Arguments

Flag	Required	Description
-i / --input	Yes	Input .psa file
-f / --format	Yes	Output format: csv, tsv, or fasta
-o / --output	Yes	Output directory where exported files will be written
--overwrite	No	Overwrite existing output files

Examples

Export molecular properties to CSV:

pharmacon export psa \
    -i properties.psa \
    -f csv \
    -o ./results/

Export amino-acid sequence to FASTA (for downstream bioinformatics):

pharmacon export psa \
    -i sequence.psa \
    -f fasta \
    -o ./results/

Export to TSV and overwrite existing output:

pharmacon export psa \
    -i properties.psa \
    -f tsv \
    -o ./results/ \
    --overwrite