Getting CIP stereochemistry#

Analyzing absolute chemical configurations without changing your system.

Use msm.physchem.get_cip_stereochemistry() to analyze a supported chemical source: a native system, an RDKit molecule or a single SDF record. The selected state must supply chemical element symbols, complete connectivity, explicit formal charges and supported bond orders. Atom types mean element symbols; force-field atom types cannot replace them.

API documentation

molsysmt.physchem.get_cip_stereochemistry()

Scientific method and provider#

The method is hanson_2018, implementing the CIP algorithm described by Hanson et al. (2018). The explicit optional provider is engine='rdkit', using its accurate rdCIPLabeler, rather than its older approximate label assignment. Missing RDKit raises a dependency error. There is no silent fallback.

import molsysmt as msm
from rdkit import Chem

molsys = Chem.MolFromSmiles('N[C@@H](C)C(=O)O')
report = msm.physchem.get_cip_stereochemistry(molsys, selection=[1])
assert report['atom_indices'].tolist() == [1]
assert report['atom_stereochemistry'].tolist() == ['S']

The full graph is analyzed before selection. Returned indices belong to the source atom and bond axes; selecting one center does not truncate the branches needed to rank its substituents. Selection is deduplicated and sorted. Bonds are returned only when both endpoints belong to the selection. Empty arrays retain explicit shapes and dtypes. No assigned label is represented by None; it does not establish that an unspecified center is achiral.

Reference atoms and geometry#

Atom labels include R/S and pseudoasymmetric r/s. Double-bond labels use absolute E/Z. bond_stereo_atom_indices names two source reference atoms; bond_reference_stereochemistry describes cis/trans relative to those atoms. The reference atoms are not promised to be the highest-priority substituents. Do not substitute the relative label for E/Z.

The default interprets declared stereo. SDF interpretation also follows the source’s supported 2D wedge or 3D CTAB representation. To infer stereo from native coordinates, opt in with from_coordinates=True and select exactly one structure using structure_indices=[index]. The computation uses a copy, converts lengths explicitly to angstroms through PyUnitWizard and does not change stored chemical assignments. It does not reconstruct periodic molecules; provide compatible compact coordinates first. Degenerate geometry may leave centers unassigned. Multiple selected structures are an error.

Provenance and supported scope#

The detached dictionary retains method, provider, evidence, original software versions and bibliographic records. When Ackredit is available, successful analysis contributes to the application’s current session, including evaluated empty selections. Reading the dictionary does not register another calculation. The result and its bibliography remain available without Ackredit. Failed optional tracking preserves completed labels under strict warning filters. If its catalog diagnostic cannot be imported, created or emitted, a fallback log retains the signal code, operation and both failures. Inspect the diagnostic before claiming successful session tracking. Scientific errors and unrelated warnings still propagate.

The experimental contract covers tetrahedral atom and double-bond descriptors. Query, enhanced stereo, non-tetrahedral descriptors and parity-only encodings without a supported wedge or 3D interpretation are rejected. The function does not return a general CIP priority table or enumerate stereoisomers.