Querying Functional Groups¶

Query a Specific Pattern in Fragments¶

group_decomposition.fg_query.query_pattern(frag_frame: DataFrame, patt: str) → int[source]¶

Determine number of functional groups matching pattern in fragment table

Parameters:

frag_frame – fragment frame from output of group_decomposition.fragfunctions.identify_connected_fragments group_decomposition.fragfunctions.count_uniques, or group_decomposition.fragfunctions.count_groups_in_set
patt – SMARTs string to match functional group. See group_decomposition.fg_query.fg_dict for SMARTS of common groups

Returns:

Number of matches of the functional group queried in the table

Example Usage:

>>> frag_frame
Smiles  Molecule        count
*C=CC=C <mol object>    3
*C=C    <mol object>    1
>>> query_pattern(frag_frame,'[$([CX3]=[CX3])]')
7

Note

If the column has a count of the number of times a fragment occurs (count column), multiply the number of matches in a group by the count of times it occurs

Query Many Functional Groups in Fragments¶

group_decomposition.fg_query.count_fgs(frag_frame: DataFrame, patt_dict: dict) → DataFrame[source]¶

Given functional group dictionary with patterns to match, return counts of each in fragment_frame

Parameters:

frag_frame – fragment frame from output of group_decomposition.fragfunctions.identify_connected_fragments group_decomposition.fragfunctions.count_uniques, or group_decomposition.fragfunctions.count_groups_in_set
patt_dict – has keys of functional group names and values being a SMARTs string to match

Returns:

Frame with one column containing names of functional group and another with count

Example Usage:

>>> frag_frame
Smiles  Molecule        count
*C=CC=C <mol object>    3
*C=O    <mol object>    1
>>> patt_dict
{
'aldehyde': '[CX3H1](=O)[#6]',
'vinylic carbon': '[$([CX3]=[CX3])]'
}
>>> count_fgs(frag_frame,patt_dict)
group           count
aldehye         1
vinylic carbon  6

Note

If the column has a count of the number of times a fragment occurs (count column), multiply the number of matches in a group by the count of times it occurs