fragment_combination_point¶

This module was developed to label atom indices while considering symmetry.

Warning

The numbering begins at 1 instead of 0.

Usage¶

>>> from rdkit import Chem
>>> from npfc import fragment_combination_point

Module fragment_combination_point¶

This modules contains the functions for annotating and parsing fragment combination point labels in fragments.

npfc.fragment_combination_point.clear_fcp_suffixes(fcp_str)[source]¶

Remove suffixes from each fcp within provided string.

>>> For instance:
>>> '1a,1b,2' becomes: '1,1,2'

Parameters: fcp – a list of Fragment Connection Points
Return type: List[str]
Returns: the simplified list

npfc.fragment_combination_point.clear_fcp_suffixes_in_edges(edges)[source]¶

Remove suffixes from each fcp within the attributes found in a list of edges

Parameters: edges (list) – a list of edges ([[u1, v1, d1], [u2, v2, d2]]), with u and v the nodes and d a dictionary of attributes
Return type: list
Returns: the updated edges

npfc.fragment_combination_point.count_symmetry_groups(val)[source]¶

Return the number of symmetry groups found in a fragment.

Parameters: val (Union[Mol, List[str]]) – either a fragment as Mol object or the fragment connection points as dict
Return type: int
Returns: the count of symmetry groups

npfc.fragment_combination_point.find_symmetry_groups(mol)[source]¶

Search for symmetry groups within a molecule. Symmetry groups are defined as atoms that can have equivalent positions in substructure matches.

This function has been copied from https://sourceforge.net/p/rdkit/mailman/message/27897393/

Parameters: mol (Mol) – the input molecule
Return type: Tuple[Tuple[int]]
Returns: a tuple of tuples of atom indices. Each tuple represents a symmetry group and inside are the atom indices.

npfc.fragment_combination_point.get_fcp_labels(mol)[source]¶

Search for symmetry groups within the input molecule and defines accordingly a label each atom. This label is composed of 2 parts:

a prefix: sequential number that gets incremented for each group

a suffix: sequential letter or string that gets incremented for each element in group

This means that equivalent atoms (within the same group) are given the same prefix but different suffixes.

>>> For instance:
>>> '1a', '1b', '2'  # 2 equivalent atoms in position 1
>>> '1', '2', '3', '4', '5', '6'  # a 6-atoms fragment with no symmetry group
>>> '1a', '1b', '1c', '1d', '1e', '1f'  # a benzene or cyclohexane

Note

labels prefixes begin at 1, not 0 like atom indices.

Parameters: mol (Mol) – the input molecule
Return type: dict
Returns: a dictionary with the correspondance between atom indices (keys) and atom labels (values)

npfc.fragment_combination_point.idx_to_label(n)[source]¶

Convert a number to a corresponding letter in the alphabet. In case the number is higher than the number of letters in the english alphabet, then a second character is appended.

>>> For instance:
>>>idx_to_label(0)
>>> 'a'
>>> idx_to_label(25)
>>> 'z'
>>> idx_to_label(26)
>>> 'aa'

This function was inspired after: https://stackoverflow.com/questions/2267362/how-to-convert-an-integer-to-a-string-in-any-base

Parameters: n (int) – the input number
Return type: str
Returns: the corresponding string