Crate sci_form 

sci-form — computational chemistry library for conformer generation, quantum methods, spectroscopy, molecular properties, and materials science.

Architecture

The crate is organized in layers from molecular construction up to derived properties:

• Parsing & topology — smiles, graph, smarts, smirks, rings, topology
• Geometry — distgeom, etkdg, conformer, alignment, forcefield, optimization
• Charges & surface — charges, charges_eeq, dipole, surface, esp, population
• Solvation — solvation, solvation_alpb
• Electronic structure — scf, eht, pm3, xtb, hf, dos
• Spectroscopy — spectroscopy, ir, nmr
• Neural potentials — ani
• ML & descriptors — ml, reactivity
• Materials — materials, periodic
• Transport & infra — transport, gpu, mesh

Coordinate convention

All coordinate arrays are flat [x0, y0, z0, x1, y1, z1, ...] in ångströms. Element arrays are atomic numbers (u8): 1 = H, 6 = C, 7 = N, 8 = O, etc.

Targets

The public surface is mirrored across four targets: Rust (this crate), Python (crates/python/), WASM/TypeScript (crates/wasm/), and CLI (crates/cli/). Changes to public types or functions must be propagated to all targets.

Modules

alignment

Molecular alignment and RMSD calculation.

ani

ANI (Accurate NeurAl networK engINe) machine-learning potentials.

canonical_smiles

Canonical SMILES generation using the Morgan algorithm.

charges

Partial-charge solvers for molecular systems.

charges_eeq

EEQ (Electronegativity Equilibration) Charges — Core Module

clustering

Butina (Taylor-Butina) clustering for conformer ensembles.

conformer

dipole

Molecular dipole moments from EHT results.

dispersion

DFT-D4 Dispersion Correction — Core Module

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

experimental_status

E4 – Experimental Module Validation & Retention Criteria

forcefield

Molecular force fields: UFF, MMFF94, ETKDG refinement, and minimization.

gpu

GPU-accelerated compute infrastructure for quantum chemistry and visualization.

graph

Molecular graph representation backed by petgraph.

hf

HF-3c: Minimal Hartree-Fock with composite corrections.

ir

IR Spectroscopy module: numerical Hessian, vibrational frequencies, and IR intensities.

materials

Crystallographic materials: unit cells, space groups, framework assembly, and periodic geometry optimization.

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

Generic numerical optimizers used internally by force fields and geometry refinement.

periodic

Periodic molecular graph support for 3D crystalline systems.

pm3

PM3 (Parameterized Model 3) semi-empirical method.

population

Population analysis: Mulliken, Löwdin, and Natural (NPA/NBO) partial charges.

reactivity

Frontier-orbital reactivity descriptors derived from EHT molecular orbitals.

rings

Smallest Set of Smallest Rings (SSSR) perception and ECFP fingerprints.

scf

Core SCF (Self-Consistent Field) engine.

smarts

SMARTS pattern parsing and substructure matching.

smiles

smirks

SMIRKS reaction transform support.

solvation

Implicit solvation modeling: ASP non-polar solvation and Generalized Born (GB).

solvation_alpb

ALPB (Analytical Linearized Poisson-Boltzmann) Solvation — Core Module

spectroscopy

Advanced Spectroscopy — Core Module

stereo

Stereochemistry perception: CIP priority, R/S, and E/Z assignment.

surface

Surface analysis: solvent-accessible surface area and related properties.

topology

transport

Batch transport layer for conformer results.

xtb

GFN0-xTB-inspired tight-binding method.

Structs

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.

GiaoNmrConfig

Configuration for the high-level GIAO NMR route.

GiaoNmrEntry

One isotope-specific shielding entry returned by the high-level GIAO API.

GiaoNmrResult

Result of a high-level SCF-backed GIAO NMR calculation.

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.

Enums

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.

Functions

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_ecfp_batch

Compute ECFP fingerprints for a batch of SMILES (parallelized with rayon when enabled).

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_giao_nmr

Compute isotope-specific GIAO NMR shieldings using the public SCF route.

compute_giao_nmr_configured

Compute isotope-specific GIAO NMR shieldings using the public SCF route and explicit settings.

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_nmr_spectrum_with_coords

Generate a complete NMR spectrum from SMILES and optional 3D coordinates. When coordinates are provided, vicinal ³J couplings use the Karplus equation.

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_pm3_gradient

Compute PM3 analytical energy gradients.

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_tpsa

Compute Topological Polar Surface Area (TPSA) in Ų.

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.

compute_xtb_gradient

Compute xTB analytical energy gradients.

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_ensemble

Predict molecular properties using ensemble ML models.

predict_ml_properties

Predict molecular properties using ML proxy models.

predict_nmr_couplings

Predict J-coupling constants for a molecule.

predict_nmr_shifts

Predict representative NMR chemical shifts from SMILES.

predict_nmr_shifts_for_nucleus

Predict chemical shifts for a specific NMR nucleus from SMILES.

search_conformers_with_uff

Search conformers by sampling multiple embeddings, optimizing torsions, and ranking with UFF.

to_canonical_smiles

Generate a canonical SMILES string from an input SMILES.

version

Library version string.