Conformer¶

3D conformer generation from a molecular graph. Conformer takes an Atomistic (typically from a SMILES or CGsmiles parse, which carries no coordinates) and returns a structure with embedded 3D positions, using the native ETKDGv3 → torsion refinement → MMFF94 cleanup pipeline. Available via import molpy as mp (mp.Conformer).

Quick reference¶

Symbol	Summary	Preferred for
`Conformer`	Generate 3D coordinates for a graph	Turning a parsed graph into a 3D structure
`ConformerReport`	Per-run summary of the generation pipeline	Inspecting which stages ran / succeeded
`ConformerStageReport`	Single-stage record within a report	Debugging a specific embedding stage

Builder — Assembler consumes 3D units; embed a CGsmiles fragment with Conformer (this module) and its ports are kept. It is the only embedder MolPy ships.

Full API¶

Conformer ¶

Conformer(speed='medium', add_hydrogens=True, seed=None)

Bases: Conformer

3D conformer generator for molpy molecules.

Subclasses the native Conformer; the constructor parameters (speed, add_hydrogens, seed) are inherited unchanged. Only the empty-molecule guard in :meth:generate is added.

Examples:

>>> import molpy as mp
>>> mol = mp.io.read_smiles("CCO")
>>> mol_3d, report = Conformer(seed=42).generate(mol)
>>> mol_3d.n_atoms   # heavy atoms + added hydrogens
9

generate ¶

generate(mol)

Generate 3D coordinates, returning a fresh Atomistic.

mol is the native graph, so the inherited Rust generator embeds it directly and its result is returned as is. The core reads the canonical integer "formal_charge" key for valence filling ([N+] / [N-] hydrogen counts); the parsers emit that key, so a charged input must already carry it. The core clones the graph internally, so the input is not mutated.

Parameters:

Name	Type	Description	Default
`mol`	`Atomistic`	Input molecular graph. Element symbols and bond orders are required; coordinates may be missing.	required

Returns:

Type	Description
`Atomistic`	A tuple of the generated structure (an `Atomistic`) and the
`ConformerReport`	per-stage :class:`~molpy.ConformerReport`.

Raises:

Type	Description
`ValueError`	If `mol` has no atoms.

ConformerReport ¶

Aggregate report from a conformer generation run.

ConformerStageReport ¶

Per-stage report from the conformer generation pipeline.