Preparing charged participants#

Combining stored chemistry, charge-center recognition and whole-center selections.

Prepare charged participants from an explicit small-molecule state before a geometric analysis. These SMILES examples require the optional RDKit converter. The feature recognizer is independent of that backend and does not parameterize.

Added in version 1.0.0.

Loading explicit chemistry#

Zwitterionic glycine demonstrates why total molecular charge does not determine whether local charged centers exist. Its atom formal charges sum to zero.

import molsysmt as msm
import numpy as np
from molsysmt import pyunitwizard as puw

molsys = msm.convert('smiles:[NH3+]CC(=O)[O-]', to_form='molsysmt.Topology')
formal = msm.get(molsys, element='atom', formal_charge=True)
centers = msm.physchem.get_charge_centers(molsys)
charges = puw.get_value(centers['charges'], to_unit='e')
print('Net formal charge in e:', np.sum(formal))
print('Local center charges in e:', charges)

Net formal charge in e: 0
Local center charges in e: [ 1. -1.]

Preparing complete selections#

Use whole participant membership for chemical selections. Distance-reference atoms are a separate field: the carboxylate reference omits its central carbon, but that carbon belongs to the participant. Here we select the whole negative center on the original system, preserving its atom indices.

negative_center = int(np.flatnonzero(charges < 0)[0])
start, stop = centers['atom_offsets'][negative_center:negative_center + 2]
negative_atoms = centers['atom_indices'][start:stop]
selected = msm.physchem.get_charge_centers(molsys, selection=negative_atoms)
print('Participant atom indices:', selected['atom_indices'])
print('Distance-reference atom indices:', selected['geometry_atom_indices'])
print('Source:', selected['charge_source'], selected['rule_version'])

Participant atom indices: [2 3 4]
Distance-reference atom indices: [3 4]
Source: chemical_states.formal_charge formal_charge_centers@1

Checking a neutral control#

A neutral nitro group has positive and negative atom formal charges, which cancel within the directly connected charged group. It produces no center in this bounded definition. A geometric detector must retain this scientific distinction.

molsys = msm.convert('smiles:C[N+](=O)[O-]', to_form='molsysmt.Topology')
neutral = msm.physchem.get_charge_centers(molsys)
print('Neutral control centers:', len(neutral['charges']))
print('Empty membership offsets:', neutral['atom_offsets'])

Neutral control centers: 0
Empty membership offsets: [0]

The feature dictionary does not contain observed interactions or periodic geometry. The ionic detector is a subsequent delivery; do not attach these features directly to MolSys.interactions. The current motif rules do not provide complete classification of phosphates, sulfates or aromatic charged systems.