filter

Ir_SP_filter(mol)

Special geometry rule designed to filter the correct conformers of Ir squareplanar complexes. So far, the ligands tested are those in DOI: https://doi.org/10.1039/D0SC00445F

RMSD_and_E_filter(outmols, selectedcids_initial, cenergy, args, calc_type)

This filter selects the first compound that it finds with energy an energy difference lower than the threshold with a higher than the threshold rms with respect to the nearest (in energy) accepted compound.

cluster_conformers(self, mols, program, csearch_file, name)

Performs a Butina clustering based on the RMS differences of the conformers

conformer_filters(self, sorted_all_cids, cenergy, outmols)

Sequence of three filters based on energy and RMSD

ewin_filter(sorted_all_cids, cenergy, energy_window)

Given a sorted list of Compound Ids and a sorted list of their energies it discards all compound Ids that have an energy higher than the args.ewin_csearch with respect to the lowest one.

Parameters

sorted_all_cidslist

[description]

cenergylist

[description]

energy_windowfloat

Minimum energy difference with respect to the lowest compound discard a compound.

Returns

list

list of cids accepted

filters(mol, log, molwt_cutoff)

Applies some basic filters (molwt, salts[currently off], weird atom symbols) that only require SMILES data from a compound and returns if the molecule passes the filters or not.

geom_filter(self, mol, geom)

Returns whether a mol object passes all the geometric rules.

Parameters

selfargparse.args

Self object with the AQME arguments used

molrdkit.Chem.Mol

Molecule to be tested.

Returns

bool

If True, it means that it is in accordance with the rules

matching_fun(self, mol, type_match, geom, passing)

Checks matches and analyzed if they pass the geometry rules

pre_E_filter(sortedcids, cenergy, threshold)

This filter selects the first compound that it finds with energy an energy difference higher or equal to the threshold with respect to the previously admitted compounds. (Thought as filter for rdkit)

Parameters

sortedcidslist or pd.Dataframe?

List of compound Ids.

cenergylist or pd.Dataframe?

list of compound energies

thresholdfloat

Minimum energy difference to consider two compounds as different. (kcal/mol)

Returns

list

list of accepted compound Ids