Dihedral Fragments v1.0

Author: Bertrand Caron

Requirements

The root dihedral_fragments directory must be in your PYTHONPATH shell variable. Failure to do so will result in an ImportError being raised:

$ PYTHONPATH="" python3 -c 'from dihedral_fragments.dihedral_fragment import Dihedral_Fragment'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named 'dihedral_fragments'

Use cases

Create new fragment

Fragment is defined by 5 variables: left_substituents, left_atom, right_atom, right_substituents and cycles. For the example fragment (['A1','A2','A3'], 'B', 'C', ['D1', 'D2'], []), dihedral_angles should be a tuple of two lists of angles:

([d(A1, B, C, DX), d(A2, B, C, DX), d(A3, B, C, DX)], [d(D1, C, B, AX), d(D2, C, B, AX)])

where AX denotes one atom in {'A1', 'A2', 'A3'}, DX one atom in {'D1', 'D2'} and d() is the dihedral angle function (in either radians or degrees, units do not alter the relative ordering). If no dihedral_angles are provided, the fragment is canonised (substituents ordered by descending atomic number, then descending number of bonded partners). If they are provided, the stereochemistry is encoded into the fragment (order of the susbstituents).

>>> from dihedral_fragments.dihedral_fragment import Dihedral_Fragment
>>> left_substituents, left_atom, right_atom, right_substituents, cycles = (['C', 'N', 'H'], 'N', 'C', ['H', 'H', 'H'], [])
>>> str(Dihedral_Fragment(atom_list=(left_substituents, left_atom, right_atom, right_substituents, cycles)))
'N,C,H|N|C|H,H,H'
>>> str(Dihedral_Fragment(atom_list=(left_substituents, left_atom, right_atom, right_substituents, cycles), dihedral_angles=([0., 120., -120.], [-120, 0., 120])))
'N,H,C|N|C|H,H,H'
>>> str(Dihedral_Fragment(atom_list=(left_substituents, left_atom, right_atom, right_substituents, cycles), dihedral_angles=([0., -120., 120.], [-120, 0., 120])))
'N,C,H|N|C|H,H,H'

Canonise a fragment

Note how the stereochemistry of the fragment is conserved.

>>> from dihedral_fragments.dihedral_fragment import Dihedral_Fragment
>>> fragment = 'C,N,O|C|N|H,H,H'
>>> str(Dihedral_Fragment(fragment))
'H,H,H|N|C|C,N,O'

Citation / Attribution

To cite this work, please use the following Zenodo DOI.