GlobalChem RNA

GlobalChem has the concept of a RNA into a 1-Dimensional format that can be used later on for rna-smiles to rna-ligand interaction of lexical strings. This way we can perhaps make casual inference between sets of ligands and sets of rna or proteins later on.

Import the Package

from global_chem_extensions import GlobalChemExtensions

bioinformatics = GlobalChemExtensions().bioinformatics()

Initialize a RNA Object

Code

rna_molecule = bioinformatics.initialize_globalchem_rna(
        peptide_sequence='UUUGGGGAGGGUG',
)

Convert to SMILES

Code

rna_molecule.convert_to_smiles()

Output

Convert to SMARTS

Code

rna_molecule.convert_to_smarts()

Output

Visualize the RNA Strand

Code

rna_molecule.visualize_strand()

Output

Visualize and Label the RNA Strand

Code

rna_molecule.label_feature(
    start=0,
    end=3,
    label='Start'
)

rna_molecule.label_feature(
    start=4,
    end=8,
    label='Middle'
)


dna_molecule.label_feature(
    start=4,
    end=8,
    label='Middle 2',
    color='Blue'
)

dna_molecule.label_feature(
    start=8,
    end=12,
    label='End',
    color='Green'
)

dna_molecule.visualize_strand()

Output

Save the RNA Image to a file

rna.save_to_image()