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Source - alignment
- Molecular alignment and RMSD calculation.
- ani
- ANI (Accurate NeurAl networK engINe) machine-learning potentials.
- charges
- Partial-charge solvers for molecular systems.
- clustering
- Butina (Taylor-Butina) clustering for conformer ensembles.
- 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
- hf
- HF-3c: Minimal Hartree-Fock with composite corrections.
- ir
- IR Spectroscopy module: numerical Hessian, vibrational frequencies, and IR intensities.
- materials
- mesh
- Generic orbital mesh generation for all electronic-structure methods.
- ml
- Lightweight ML property proxies.
- nmr
- NMR Spectroscopy module: chemical shift prediction and spectrum generation.
- 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.
- rings
- Smallest Set of Smallest Rings (SSSR) perception and ECFP fingerprints.
- smarts
- SMARTS pattern parsing and substructure matching.
- smiles
- solvation
- Implicit solvation modeling: ASP non-polar solvation and Generalized Born (GB).
- stereo
- Stereochemistry perception: CIP priority, R/S, and E/Z assignment.
- surface
- Surface analysis: solvent-accessible surface area and related properties.
- topology
- transport
- xtb
- GFN0-xTB-inspired tight-binding method.
- AromaticityAnalysis
- Aromaticity analysis summary from graph-level bond annotations.
- ConformerClusterSummary
- One RMSD-based cluster summary in a conformer-search ensemble.
- ConformerConfig
- Configuration for conformer generation.
- ConformerEnsembleMember
- One conformer entry in a ranked conformer-search ensemble.
- ConformerResult
- Result of a 3D conformer generation for a single molecule.
- ConformerSearchResult
- Result of a conformer-search workflow with UFF ranking and RMSD filtering.
- GraphFeatureAnalysis
- Combined structural graph feature analysis for UI/API consumers.
- MethodCapability
- Capability status for one operation on a given element set.
- MethodComparisonEntry
- One method row in the multi-method comparison workflow.
- MethodComparisonResult
- Structured comparison result for multiple methods on the same geometry/system.
- MethodMetadata
- Structured metadata for one method on a specific element set.
- PropertyMethodPlan
- Recommended method plan for one requested property domain.
- StereocenterAnalysis
- Graph-level stereocenter analysis.
- SystemCapabilities
- Capability summary for core operations on a given element set.
- SystemMethodPlan
- Full method-planning summary for a molecule element set.
- ElectronicWorkflowResult
- Result of an electronic workflow with optional UFF fallback.
- MethodComparisonPayload
- Compact per-method payload for multi-method comparison.
- MethodComparisonStatus
- Execution status for one method inside a multi-method comparison run.
- PropertyRequest
- Property domain used when choosing a recommended computational method.
- ScientificMethod
- Explicit computational method exposed by top-level planning APIs.
- analyze_graph_features
- Analyze aromaticity and graph-level stereocenters from a SMILES string.
- analyze_stereo
- Analyze stereochemistry: detect chiral centers (R/S) and E/Z double bonds.
- assemble_framework
- Assemble a framework crystal structure from node/linker SBUs on a topology.
- butina_cluster
- Cluster conformers using Butina (Taylor-Butina) algorithm based on RMSD.
- compare_methods
- Compare multiple supported methods on the same geometry/system.
- compute_ani
- Compute ANI neural-network potential energy (and optionally forces).
- compute_ani_with_models
- Compute ANI neural-network potential energy with custom config and pre-loaded models.
- 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_charges_configured
- Compute Gasteiger-Marsili charges with configurable parameters.
- compute_dipole
- Compute molecular dipole moment (Debye) from atomic elements and positions.
- compute_dos
- Compute DOS/PDOS from EHT orbital energies.
- compute_ecfp
- Compute Extended-Connectivity Fingerprint (ECFP/Morgan).
- 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_ensemble_j_couplings
- Predict J-couplings averaged over a conformer ensemble using Boltzmann weighting.
- compute_esp
- Compute ESP grid from atomic elements, positions and Mulliken charges.
- compute_esp_grid
- Compute ESP grid and return full result with values, origin, spacing and dimensions.
- 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_gb_solvation
- Compute Generalized Born electrostatic + non-polar solvation energy.
- compute_hf3c
- Run a complete HF-3c calculation (Hartree-Fock with D3, gCP, SRB corrections).
- compute_hose_codes
- Generate HOSE codes for all atoms in a molecule.
- compute_ir_spectrum
- Generate a Lorentzian-broadened IR spectrum from vibrational analysis.
- compute_ir_spectrum_broadened
- Compute IR spectrum with configurable broadening type.
- 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_nmr_spectrum
- Generate a complete NMR spectrum from SMILES.
- compute_nonpolar_solvation
- Compute non-polar solvation energy from SASA and atomic solvation parameters.
- compute_orbital_mesh
- Compute orbital isosurface mesh for visualization.
- 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_rmsd_matrix
- Compute all-pairs RMSD matrix for a set of conformers.
- compute_sasa
- Compute solvent-accessible surface area from SMILES + 3D coordinates.
- compute_simplified_neb_path
- Build a simplified NEB path between two geometries.
- compute_sssr
- Compute the Smallest Set of Smallest Rings (SSSR).
- compute_stda_uvvis
- Compute an sTDA UV-Vis spectrum with proper oscillator strengths.
- compute_tanimoto
- Compute Tanimoto similarity between two ECFP fingerprints.
- 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_vibrational_analysis
- Perform vibrational analysis via numerical Hessian.
- compute_vibrational_analysis_uff
- Perform vibrational analysis using UFF analytical Hessian.
- 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.
- embed_diverse
- Generate multiple conformers for a SMILES and filter by Butina RMSD clustering.
- 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.
- predict_nmr_couplings
- Predict J-coupling constants for a molecule.
- predict_nmr_shifts
- Predict NMR chemical shifts (¹H and ¹³C) from SMILES.
- search_conformers_with_uff
- Search conformers by sampling multiple embeddings, optimizing torsions, and ranking with UFF.
- version
- Library version string.