GlobalChem DNA

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

Import the Package

from global_chem_extensions import GlobalChemExtensions
bioinformatics = GlobalChemExtensions().bioinformatics()

Initialize a DNA Object

dna_molecule = bioinformatics.initialize_globalchem_dna(
        peptide_sequence='TGGGGAGGGTG',
)

Convert to SMILES

Code

dna_molecule.convert_to_smiles()

Output

Nc1nc2nc(C3CC(OP(=O)([O-])OCC4OC(Cc5c[nH]c(=O)[nH]c5=O)CC4OP(=O)([O-])OCC4OC(c5nc6nc(N)[nH]c(=O)c6[nH]5)CC4OP(=O)([O-])OCC4OC(Cc5c[nH]c(=O)[nH]c5=O)CC4OP(=O)([O-])OCC4OC(c5nc6nc(N)[nH]c(=O)c6[nH]5)CC4OP(=O)([O-])OCC4OC(Cc5c[nH]c(=O)[nH]c5=O)CC4OP(=O)([O-])OCC4OC(c5nc6nc(N)[nH]c(=O)c6[nH]5)CC4OP(=O)([O-])OCC4OC(Cc5c[nH]c(=O)[nH]c5=O)CC4OP(=O)([O-])OCC4OC(c5nc6ncnc(N)c6[nH]5)CC4OP(=O)([O-])OCC4OC(c5nc6ncnc(N)c6[nH]5)CC4OP(=O)([O-])OCC4OC(c5nc6ncnc(N)c6[nH]5)CC4OP(=O)([O-])OCC4OC(c5nc6ncnc(N)c6[nH]5)CC4OP(=O)([O-])[O-])C(COP(=O)([O-])OC4CCOC4CO)O3)[nH]c2c(=O)[nH]1

Convert to SMARTS

Code

dna_molecule.convert_to_smarts()

Output

[#7]-[#6]1:[#7]:[#6]2:[#7]:[#6](-[#6]3-[#6]-[#6](-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]-[#6]5:[#6]:[#7H]:[#6](=[#8]):[#7H]:[#6]:5=[#8])-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]5:[#7]:[#6]6:[#7]:[#6](-[#7]):[#7H]:[#6](=[#8]):[#6]:6:[#7H]:5)-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]-[#6]5:[#6]:[#7H]:[#6](=[#8]):[#7H]:[#6]:5=[#8])-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]5:[#7]:[#6]6:[#7]:[#6](-[#7]):[#7H]:[#6](=[#8]):[#6]:6:[#7H]:5)-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]-[#6]5:[#6]:[#7H]:[#6](=[#8]):[#7H]:[#6]:5=[#8])-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]5:[#7]:[#6]6:[#7]:[#6](-[#7]):[#7H]:[#6](=[#8]):[#6]:6:[#7H]:5)-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]-[#6]5:[#6]:[#7H]:[#6](=[#8]):[#7H]:[#6]:5=[#8])-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]5:[#7]:[#6]6:[#7]:[#6]:[#7]:[#6](-[#7]):[#6]:6:[#7H]:5)-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]5:[#7]:[#6]6:[#7]:[#6]:[#7]:[#6](-[#7]):[#6]:6:[#7H]:5)-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]5:[#7]:[#6]6:[#7]:[#6]:[#7]:[#6](-[#7]):[#6]:6:[#7H]:5)-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]-[#6]4-[#8]-[#6](-[#6]5:[#7]:[#6]6:[#7]:[#6]:[#7]:[#6](-[#7]):[#6]:6:[#7H]:5)-[#6]-[#6]-4-[#8]-[#15](=[#8])(-[#8-])-[#8-])-[#6](-[#6]-[#8]-[#15](=[#8])(-[#8-])-[#8]-[#6]4-[#6]-[#6]-[#8]-[#6]-4-[#6]-[#8])-[#8]-3):[#7H]:[#6]:2:[#6](=[#8]):[#7H]:1

Visualize the DNA Strand

Code

dna_molecule.visualize_strand()

Output

Visualize and Label the DNA Strand

Code

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

dna_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 DNA Image to a file

dna.save_to_image()