Function reference • tidychem

Load molecules

Read and parse SMILES, SDF, MOL files or strings.

read_smiles(): Read molecules from a SMILES file.

read_sdf(): Read molecules from a SDF/MOL file.

parse_smiles(): Parse molecules from SMILES strings

parse_sdf(): Parse molecules from SDF/MOL text block.

print(<tidymol>): Print parsed molecules object.

Molecular fingerprints

Compute molecular fingerprints.

fp_morgan(): Compute Morgan fingerprints (circular fingerprints).

fp_maccs(): Compute MACCS keys as molecular fingerprints

fp_rdkit(): Compute RDKit fingerprints

fp_atompair(): Compute atom pairs fingerprints

fp_torsion(): Compute topological torsions fingerprints.

fp_pharm2d(): Compute 2D pharmacophore fingerprints.

fp_erg(): Compute extended reduced graphs fingerprints derived from the ErG fingerprint

fp_pattern(): Compute pattern fingerprints, a topological fingerprint optimized for substructure screening

print(<tidyfps>): Print molecular fingerprints object.

Molecular descriptors

Compute 2D/3D molecular descriptors.

desc_2d(): Compute all 2D molecular descriptors

desc_3d(): Compute all 3D molecular descriptors.

get_alldesc_2d(): Get all available 2D descriptor names

print(<tidydesc>): Print molecular descriptors object.

Fingerprint similarity

Compute molecular fingerprint similarities.

sim(): Calculate fingerprint similarity.

Utilities

Utility functions.

tidychem-package: tidychem: Tidy Chemical Data

tidychem_example(): Generate path to the example data.

rdkit_version(): Get RDKit version.

rdkit: Global reference to RDKit