Modules§
- alignment
- Molecular alignment and RMSD calculation.
- charges
- Partial-charge solvers for molecular systems.
- conformer
- dipole
- Molecular dipole moments from EHT results.
- distgeom
- dos
- Density of States (DOS) and Projected DOS (PDOS).
- dynamics
- eht
- Extended Hückel Theory (EHT) module.
- esp
- Electrostatic potential maps and .cube file I/O.
- etkdg
- forcefield
- graph
- materials
- ml
- Lightweight ML property proxies.
- optimization
- pm3
- PM3 (Parameterized Model 3) semi-empirical method.
- population
- Population analysis: Mulliken and Löwdin partial charges from EHT results.
- reactivity
- Frontier-orbital reactivity descriptors derived from EHT molecular orbitals.
- smarts
- SMARTS pattern parsing and substructure matching.
- smiles
- surface
- Surface analysis: solvent-accessible surface area and related properties.
- topology
- transport
- xtb
- GFN0-xTB-inspired tight-binding method.
Structs§
- Aromaticity
Analysis - Aromaticity analysis summary from graph-level bond annotations.
- Conformer
Cluster Summary - One RMSD-based cluster summary in a conformer-search ensemble.
- Conformer
Config - Configuration for conformer generation.
- Conformer
Ensemble Member - One conformer entry in a ranked conformer-search ensemble.
- Conformer
Result - Result of a 3D conformer generation for a single molecule.
- Conformer
Search Result - Result of a conformer-search workflow with UFF ranking and RMSD filtering.
- Graph
Feature Analysis - Combined structural graph feature analysis for UI/API consumers.
- Method
Capability - Capability status for one operation on a given element set.
- Method
Comparison Entry - One method row in the multi-method comparison workflow.
- Method
Comparison Result - Structured comparison result for multiple methods on the same geometry/system.
- Method
Metadata - Structured metadata for one method on a specific element set.
- Property
Method Plan - Recommended method plan for one requested property domain.
- Stereocenter
Analysis - Graph-level stereocenter analysis.
- System
Capabilities - Capability summary for core operations on a given element set.
- System
Method Plan - Full method-planning summary for a molecule element set.
Enums§
- Electronic
Workflow Result - Result of an electronic workflow with optional UFF fallback.
- Method
Comparison Payload - Compact per-method payload for multi-method comparison.
- Method
Comparison Status - Execution status for one method inside a multi-method comparison run.
- Property
Request - Property domain used when choosing a recommended computational method.
- Scientific
Method - Explicit computational method exposed by top-level planning APIs.
Functions§
- analyze_
graph_ features - Analyze aromaticity and graph-level stereocenters from a SMILES string.
- assemble_
framework - Assemble a framework crystal structure from node/linker SBUs on a topology.
- compare_
methods - Compare multiple supported methods on the same geometry/system.
- compute_
bond_ orders - Compute Wiberg-like and Mayer-like bond orders from EHT.
- compute_
charges - Compute Gasteiger-Marsili partial charges from a SMILES string.
- compute_
dipole - Compute molecular dipole moment (Debye) from atomic elements and positions.
- compute_
dos - Compute DOS/PDOS from EHT orbital energies.
- compute_
eht_ or_ uff_ fallback - Compute electronic properties with automatic fallback to UFF energy.
- compute_
empirical_ pka - Estimate acidic/basic pKa sites from graph environments and Gasteiger-charge heuristics.
- compute_
esp - Compute ESP grid from atomic elements, positions and Mulliken charges.
- compute_
frontier_ descriptors - Compute atom-resolved HOMO/LUMO frontier descriptors from EHT.
- compute_
fukui_ descriptors - Compute Fukui-function workflows and condensed per-atom descriptors from EHT.
- compute_
md_ trajectory - Run short exploratory molecular dynamics with Velocity Verlet (NVE-like).
- compute_
md_ trajectory_ nvt - Run short exploratory molecular dynamics with Velocity Verlet + Berendsen NVT thermostat.
- compute_
ml_ descriptors - Compute molecular descriptors for ML property prediction.
- compute_
mmff94_ energy - Compute MMFF94 force field energy for a molecule.
- compute_
pm3 - Run a PM3 semi-empirical calculation.
- compute_
population - Compute Mulliken & Löwdin population analysis from atomic elements and positions.
- compute_
reactivity_ ranking - Build empirical reactivity rankings using condensed Fukui descriptors and Mulliken charges.
- compute_
rmsd - Compute RMSD between two coordinate sets after Kabsch alignment.
- compute_
sasa - Compute solvent-accessible surface area from SMILES + 3D coordinates.
- compute_
simplified_ neb_ path - Build a simplified NEB path between two geometries.
- compute_
topology - Compute structured topology analysis for transition-metal coordination environments.
- compute_
uff_ energy - Compute UFF force field energy for a molecule.
- compute_
uff_ energy_ with_ aromatic_ heuristics - Compute UFF energy and apply an aromaticity-informed heuristic correction.
- compute_
uv_ vis_ spectrum - Build an exploratory UV-Vis-like spectrum from low-cost EHT transitions.
- compute_
xtb - Run an xTB tight-binding calculation.
- create_
unit_ cell - Create a periodic unit cell from lattice parameters (a, b, c in Å; α, β, γ in degrees).
- embed
- Generate a 3D conformer from a SMILES string.
- embed_
batch - Batch-embed multiple SMILES in parallel.
- get_
eht_ support - Report EHT capability metadata for a given element list.
- get_
system_ capabilities - Report operation capability metadata for a given element list.
- get_
system_ method_ plan - Build a structured method plan with recommendations, fallback paths, and confidence scores.
- parse
- Parse a SMILES string and return molecular structure (no 3D generation).
- predict_
ml_ properties - Predict molecular properties using ML proxy models.
- search_
conformers_ with_ uff - Search conformers by sampling multiple embeddings, optimizing torsions, and ranking with UFF.
- version
- Library version string.