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HELMshaker

Compute mass and structure

cscoe-ddc-helmshaker

Compute mass and structure¶

HELMshaker can assemble the whole-molecule structure from the monomer records and report molecular weight, formula, SMILES and a molblock.

This needs RDKit, which is not part of the core install:

pip install "helmshaker[chem]"

It also needs a monomer library whose records carry smiles and rgroups. A dictionary without structures parses fine but cannot be assembled.

Weight and formula¶

from helmshaker import Molecule, MonomerLibrary

library = MonomerLibrary()
library.load_from_file("monomers.json")  # your dictionary, or one pulled from TMR

oligo = Molecule.from_helm(
    "RNA1{[moe](A)[sp].[moe](U)[sp].[moe](G)}$$$$V2.0", monomer_library=library
)

print(oligo.molecular_weight())    # 1124.996
print(oligo.molecular_formula())   # C38H54N12O20P2S2

The same works for peptides, including cyclic ones, where the disulfide is accounted for:

peptide = Molecule.from_helm(
    "PEPTIDE1{C.A.A.A.C}$PEPTIDE1,PEPTIDE1,1:R3-5:R3$$$V2.0", monomer_library=library
)

print(peptide.molecular_weight())   # 435.528
print(peptide.molecular_formula())  # C15H25N5O6S2

Structure output¶

smiles = oligo.to_smiles()
molblock = oligo.to_molblock()

print(smiles[:60])
print(len(molblock.splitlines()), "molblock lines")

Getting everything at once¶

Each of the calls above assembles the structure. When you want more than one value, call analyze_structure() once and read the fields off the result:

result = oligo.analyze_structure()

print(result.molecular_weight)
print(result.molecular_formula)
print(result.exact_mass)
result.smiles
result.molblock

From the command line¶

helmshaker mw 'RNA1{[moe](A)[sp].[moe](U)}$$$$V2.0' --dictionary oligos
helmshaker mw 'RNA1{[moe](A)[sp].[moe](U)}$$$$V2.0' --dictionary oligos --smiles