drugforge.data.backend.openeye

Functions

bytes64_to_oedu(bytes)

Convert bytes to an OpenEye DesignUnit

clear_SD_data(mol)

Clear all SD data on an OpenEye OEMol

combine_protein_ligand(prot, lig[, ...])

Combine a protein OEMol and ligand OEMol into one, handling residue/atom numbering, and HetAtom status.

get_SD_data(mol)

Get all SD data on an OpenEye OEMol, OEGraphMol, or OEConfBase object.

load_openeye_cif(cif_fn[, alt_loc])

Load an OpenEye OEGraphMol object from a CIF file.

load_openeye_cif1(cif1_fn)

Loads a biological assembly file into an OEGraphMol object.

load_openeye_design_unit(du_fn)

Load an OpenEye design unit from a file

load_openeye_mol2(mol2_fn)

Load an OpenEye MOL2 file and return it as an OpenEye OEMol object.

load_openeye_pdb(pdb_fn[, alt_loc])

Load an OpenEye OEGraphMol from a PDB file.

load_openeye_sdf(sdf_fn)

Load an OpenEye SDF file and return it as an OpenEye OEMol object.

load_openeye_sdfs(sdf_fn)

Load a list of OpenEye OEGraphMol objects from an SDF file.

load_openeye_smi(smi_fn)

Load an OpenEye SMILES file containing a set of molecules and return them as OpenEye OEGraphMol objects.

oe_smiles_roundtrip(smiles)

Canonical SMILES string of an OpenEye OEMol

oedu_to_bytes64(oedu)

Convert an OpenEye DesignUnit to bytes

oemol_to_inchi(mol[, fixed_hydrogens])

InChI string of an OpenEye OEMol

oemol_to_inchikey(mol[, fixed_hydrogens])

InChI key string of an OpenEye OEMol

oemol_to_pdb_string(mol)

Dumps an OpenEye OEMol to a PDB string

oemol_to_sdf_string(mol)

Dumps an OpenEye OEMol to an SDF string

oemol_to_smiles(mol[, isomeric])

Canonical SMILES string of an OpenEye OEMol

openeye_copy_pdb_data(source, destination, tag)

Copy over the PDB data from one object to another.

openeye_perceive_residues(prot[, preserve_all])

Re-perceive the residues of a protein molecule using OpenEye's OEPerceiveResidues function, which is necessary when changes are made to the protein to ensure correct atom ordering and CONECT record creation.

pdb_string_to_oemol(pdb_str)

Loads a PDB string into an OpenEye OEGraphMol

print_SD_data(mol)

save_openeye_design_unit(du, du_fn)

Write an OpenEye design unit to a file

save_openeye_pdb(mol, pdb_fn)

Write an OpenEye OEGraphMol object to a PDB file.

save_openeye_sdf(mol, sdf_fn)

Write an OpenEye OEGraphMol object to an SDF file.

save_openeye_sdfs(mols, sdf_fn)

Write a list of OpenEye OEGraphMol objects to a single SDF file.

save_receptor_grid(du_fn, out_fn)

Load in a design unit from a file and write out the receptor grid as a .ccp4 grid file.

sdf_string_to_oemol(sdf_str)

Loads an SDF string into an openeye molecule.

set_SD_data(mol, data)

Set the SD data on an OpenEye OEMol, overwriting any existing data with the same tag If a str or a single-length list is passed as the values of the dictionary, the data will be set to all conformers.

smiles_to_oemol(smiles)

Loads a smiles string into an openeye molecule

split_openeye_design_unit(du[, lig, lig_title])

split_openeye_mol(complex_mol[, ...])

Split an OpenEye-loaded molecule into protein, ligand, etc.

trim_small_chains(input_mol[, cutoff_len])

Remove short chains from a protein molecule object.