Strings

String forms in MolSysMT allow users to pass textual representations—ranging from PDB text buffers and chemical SMILES strings to database accession IDs and amino acid sequences—directly into API functions.

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String Form	Example Format / Content	Target Interpretation
string:pdb_text	Multi-line PDB formatted string	Parsed directly as a complete PDB structure in memory.
string:pdb_id	"1TUP", "4INS"	Fetches structure dynamically from the RCSB Protein Data Bank.
string:uniprot_id	"P04637"	Fetches protein sequence and metadata from UniProt.
string:alphafold_id	"AF-P04637-F1"	Fetches predicted 3D structure from the AlphaFold DB.
string:smiles	"CC(=O)OC1=CC=CC=C1C(=O)O"	Parsed into small molecule topology and conformers via RDKit/OpenFF.
string:amino_acids_1	"ACDEFGHIKLMNPQRSTVWY"	1-letter amino acid sequence parsed into peptide topology.
string:amino_acids_3	"ALA-CYS-ASP-GLU-PHE"	3-letter amino acid sequence parsed into peptide topology.