structure

Analyze a single topology or structure file without requiring a trajectory. Results are written to a .psa (Pharmacon Structure Analysis) HDF5 artifact.

Supported formats: .mol2, .smi (properties); .pdb, .gro, .crd (sequence). .sdf is accepted by the parser but the reader is not yet implemented — use .mol2 or .smi.

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properties

Compute structural and chemical descriptors for small molecules using RDKit.

Computed properties:

• Molecular weight, LogP, TPSA (topological polar surface area)

• Rotatable bond count, ring count, aromaticity

• Stereocenter count, net charge

• Element composition, molecular volume, fragment counts

Computed fingerprints:

• Morgan / ECFP

• Topological torsion

• Atom pair

• MACCS keys

Arguments

Flag	Required	Description
-i / --input	Yes	Input small-molecule file (.mol2 or .smi; .sdf not yet supported)
-o / --output	No	Output .psa file (default: properties.psa)
--overwrite	No	Overwrite existing output file
-l / --log	No	Log file (default: properties.log)
-fl / --file-logging-level	No	File log verbosity (default: DEBUG)
-tl / --terminal-logging-level	No	Terminal log verbosity (default: INFO)

Examples

Compute properties for a single MOL2 ligand:

pharmacon structure properties \
    -i ligand.mol2 \
    -o ligand_props.psa

Process a SMILES file with multiple molecules:

pharmacon structure properties \
    -i ligands.smi \
    -o ligand_props.psa

Then export to CSV:

pharmacon export psa -i ligand_props.psa -f csv -o ./results/

Overwrite an existing output:

pharmacon structure properties \
    -i ligands.smi \
    -o ligand_props.psa \
    --overwrite

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sequence

Extract the amino-acid sequence from a protein topology, organized by chain. Outputs single-letter and three-letter representations with residue ID mappings. Supports FASTA export via pharmacon export psa.

Arguments

Flag	Required	Description
-p / --topology	Yes	Input topology file (.pdb, .gro, .crd)
-o / --output	No	Output .psa file (default: sequence.psa)
--overwrite	No	Overwrite existing output file
-l / --log	No	Log file (default: sequence.log)
-fl / --file-logging-level	No	File log verbosity (default: DEBUG)
-tl / --terminal-logging-level	No	Terminal log verbosity (default: INFO)

Examples

Extract sequence from a PDB file:

pharmacon structure sequence \
    -p protein.pdb \
    -o sequence.psa

Extract from a GROMACS structure:

pharmacon structure sequence \
    -p protein.gro \
    -o sequence.psa

Export the sequence to FASTA for downstream bioinformatics:

pharmacon structure sequence -p protein.pdb -o sequence.psa
pharmacon export psa -i sequence.psa -f fasta -o ./results/