schrodinger.application.pathfinder.filtering module¶
PathFinder functions for filtering and for computing descriptors, including similarity metrics.
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schrodinger.application.pathfinder.filtering.
NumChiralCenters
(mol)[source]¶ Wrapper for Chem.FindMolChiralCenters, so we can include it in DESCRIPTORS_DICT and pretend it’s an RDKit descriptor.
- Return type
int
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schrodinger.application.pathfinder.filtering.
TPSAIncludeSandP
(mol)[source]¶ The TPSA including S and P.
- Return type
float
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schrodinger.application.pathfinder.filtering.
MVCorrMW
(mol)[source]¶ The Molecular weight corrected for McGowan Volume, so it can be added to the DESCRIPTORS_DICT and pretend it is an RDKit descriptor.
- Return type
float
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schrodinger.application.pathfinder.filtering.
LongestConsecutiveRBCount
(mol)[source]¶ The maximum number of consecutive rotatable bonds in the molecule.
- Return type
int
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schrodinger.application.pathfinder.filtering.
MeanConsecutiveRBCount
(mol)[source]¶ The mean value of consecutive rotatable bonds in the molecule.
- Return type
int
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schrodinger.application.pathfinder.filtering.
LargestRingAtomCount
(mol)[source]¶ The size of the largest ring in mol.
- Return type
int
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schrodinger.application.pathfinder.filtering.
AlogP
(mol)[source]¶ The AlogP for the molecule as computed by canvas.
The canvas calculation is based on J. Phys. Chem A 1998, 102, 3762-3772. Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules. Using Fragmental Methods: An Analysis of ALOGP and CLOGP Methods. A. K. Ghose et al.
- Return type
float
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schrodinger.application.pathfinder.filtering.
NumSAtoms
(mol)[source]¶ The number of S atoms in the molecule.
- Return type
int
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schrodinger.application.pathfinder.filtering.
NumAlkyne
(mol)[source]¶ The number of alkynes in the molecule.
- Return type
int
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schrodinger.application.pathfinder.filtering.
FractionAromatic
(mol)[source]¶ The fraction of heavy atoms in the molecule that are aromatic atoms.
- Return type
float
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schrodinger.application.pathfinder.filtering.
logS
(mol)[source]¶ Calculate ESOL based on descriptors in the Delaney paper, coefficient refit for RDKit.
- Return type
float
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schrodinger.application.pathfinder.filtering.
NumNonSpiroCR4
(mol)[source]¶ The number of non spiro quaternary carbons attached to C, N, O or S.
- Return type
int
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schrodinger.application.pathfinder.filtering.
NumFiveFiveRings
(mol)[source]¶ The number of edge fused 5 atom ring pairs.
- Returns
int
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class
schrodinger.application.pathfinder.filtering.
JSONFilterAdapter
(filename)[source]¶ Bases:
object
An adapter to make a schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter look like a schrodinger.structutils.filter.Filter.
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class
schrodinger.application.pathfinder.filtering.
ComparableMol
(mol, prop, reverse=False)[source]¶ Bases:
object
A simple wrapper for a Mol object, adding the __lt__ operator so the mols can be put in a heap or sorted. Any double property may be used as the key.
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schrodinger.application.pathfinder.filtering.
keep_top_n
(products, nkeep, nsample, prop, reverse=False)[source]¶ A generator that yields only the best
nkeep
molecules out of the firstnsample
molecules inproducts
, compared byprop
. By default, the highest values ofprop
are kept; whenreverse
is true, the lowest values are kept instead.NOTE: this function holds all
nkeep
molecules in memory at once.- Parameters
products (iterator of rdkit.Chem.Mol) – molecules to filter
nkeep (int) – maximum number of molecules to yield
nsample (int) – maximum number of molecules to consume from
products
prop (str) – key property name
reverse (bool) – if true, keep the lowest instead of the highest values
- Returns
filtered/sorted products
- Return type
generator of rdkit.Chem.Mol
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schrodinger.application.pathfinder.filtering.
get_filter
(filename, smarts_filter=False)[source]¶ Factory function to generate a Filter-like object from a filename. Supports JSON and propfilter-like property filters files as well as canvasSearch-like SMARTS filter files.
- Parameters
filename (str) – filename
smarts_filter (bool) – is this a SMARTS filter file?
- Returns
filter object
- Return type
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schrodinger.application.pathfinder.filtering.
get_fingerprint
(mol)[source]¶ A cached version of RDKit’s FingerprintMol, so if it’s called again with a recently used molecule, we’ll save the recalculation of the fingerprint.
- Parameters
mol (rdkit.Chem.rdchem.Mol) – molecule
- Returns
fingerprint
- Return type
rdkit.DataStructs.cDataStructs.ExplicitBitVect
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schrodinger.application.pathfinder.filtering.
compute_similarity
(mol1, mol2)[source]¶ Compute the Tanimoto similarity between the RDKit fingerprints of two molecules.
- Parameters
mol1 (rdkit.Chem.rdchem.Mol) – molecule
mol2 (rdkit.Chem.rdchem.Mol) – molecule
- Returns
similarity
- Return type
float
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schrodinger.application.pathfinder.filtering.
add_descriptors
(mol, descriptor_names, refs)[source]¶ Compute the requested RDKit descriptors and store them as properties of the Mol object.
- Parameters
refs (sequence of Mol) – list of reference molecules (only used if similarity descriptors are requested)
- Returns
input mol (modified in place)
- Return type
Mol
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schrodinger.application.pathfinder.filtering.
add_descriptors_gen
(mols, descriptors, refs=None)[source]¶ Given a generator of Mol, return a generator of Mol with descriptors added. The original Mol objects are modified.
- Parameters
descriptors (sequence of str) – names of the descriptors to add
refs (sequence of Mol) – list of reference molecules (only used if similarity descriptors are requested)