global-chem-extensions 0.1.1

No project description provided

Global-Chem-Extensions: Functinality for applications of GlobalChem for Cheminformaticians.

Global Chem is an open-source graph database and api for common and rare chemical lists using IUPAC as input and SMILES/SMARTS as output. As mostly needed by myself as I search through chemical infinity.

I have useful tools I use to analyze chemical data starting with functional groups.

Installation

GlobalChemExtensions is going to be distribute via PyPi and as the content store grows we can expand it to other pieces of software making it accessible to all regardless of what you use. Alternatively, you could have a glance at the source code and copy/paste it yourself.

pip install global-chem-extensions

Quick Start

Just with no dependencies, intialize the class and there you go! All the common and rare groups of the world at your disposal

Use the Sunbursting Extensions

dependencies: plotly, rdkit, kaleiodo, global-chem

from global_chem_extensions.global_chem_extensions import GlobalChemExtensions

test_set = [
    'c1[n+](cc2n(c1OCCc1cc(c(cc1)F)F)c(nn2)c1ccc(cc1)OC(F)F)[O-]',
    'c1nc(c2n(c1OCCc1cc(c(cc1)F)F)c(nn2)c1ccc(cc1)OC(F)F)Cl',
    'c1ncc2n(c1CCO)c(nn2)c1ccc(cc1)OC(F)F',
    'C1NCc2n(C1CCO)c(nn2)c1ccc(cc1)OC(F)F',
    'C1(CN(C1)c1cc(c(cc1)F)F)Oc1cncc2n1c(nn2)c1ccc(cc1)OC(F)F',
    'c1ncc2n(c1N1CCC(C1)c1ccccc1)c(nn2)c1ccc(cc1)OC(F)F',
]

GlobalChemExtensions().sunburst_chemical_list(test_set, save_file=False)

PCA Analysis

Conduct PCA Analysis with a SMILES list input.

dependencies: bokeh, rdkit

from global_chem.global_chem import GlobalChem
from global_chem_extensions.global_chem_extensions import GlobalChemExtensions

gc = GlobalChem()
gc = GlobalChem()
gc.build_global_chem_network(print_output=False, debugger=False)
smiles_list = list(gc.get_node_smiles('schedule_one').values())

mol_ids = GlobalChemExtensions().node_pca_analysis(
            smiles_list,
            morgan_radius = 1,
            bit_representation = 512,
            number_of_clusters = 5,
            number_of_components = 0.95,
            random_state = 0,
            file_name 'global_chem_pca.html',
            save_file=False,
            return_mol_ids=True,
)