Crate chematic_3d 

chematic-3d — 3D coordinate generation and file formats for chematic.

Provides:

• generate_coords: rule-based 3D coordinate builder.
• parse_pdb_atoms, pdb_to_molecule, write_pdb: PDB file support.
• parse_xyz, write_xyz: XYZ file support.
• build_constraints, satisfy_constraints: distance geometry constraint satisfaction.
• generate_and_minimize_constrained: full pipeline with constraint projection.

Re-exports

pub use align::AlignResult;

pub use align::align_coords;

pub use align::apply_alignment;

pub use align::rmsd_no_align;

pub use conformer::ConformerEnsemble;

pub use conformer::ConformerError;

pub use constraints::AngleConstraint;

pub use constraints::BondConstraint;

pub use constraints::ConstraintSet;

pub use constraints::build_constraints;

pub use constraints::satisfy_constraints;

pub use determine_bonds::DetermineError;

pub use determine_bonds::MAX_ATOMS as DETERMINE_BONDS_MAX_ATOMS;

pub use determine_bonds::determine_bonds;

pub use coords::Coords3D;

pub use coords::Point3;

pub use descriptors_3d::autocorr_3d;

pub use descriptors_3d::getaway_descriptors;

pub use descriptors_3d::rdf_descriptors;

pub use descriptors_3d::whim_descriptors;

pub use descriptors_3d::whim_getaway_combined;

pub use dg::generate_coords;

pub use etkdg::generate_coords_etkdg;

pub use md::MDConfig;

pub use md::MDFrame;

pub use md::MDTrajectory;

pub use md::Thermostat;

pub use md::run_md;

pub use minimize::ForceField;

pub use minimize::MinimizeConfig;

pub use minimize::minimize;

pub use minimize::minimize_dreiding;

pub use minimize::minimize_dreiding_with_config;

pub use minimize::minimize_mmff94;

pub use minimize::minimize_uff;

pub use minimize::minimize_with_config;

pub use mol_transforms::center_on_origin;

pub use mol_transforms::compute_centroid;

pub use mol_transforms::get_bond_angle;

pub use mol_transforms::get_bond_angle_deg;

pub use mol_transforms::get_bond_length;

pub use mol_transforms::get_dihedral;

pub use mol_transforms::get_dihedral_deg;

pub use mol_transforms::set_dihedral;

pub use mol_transforms::transform_conformer;

pub use pdb::PdbAtom;

pub use pdb::parse_pdb_atoms;

pub use pdb::pdb_to_molecule;

pub use pdb::write_pdb;

pub use pharmacophore_fp_3d::pharmacophore_fp_3d;

pub use pharmacophore_fp_3d::tanimoto_pharmacophore_3d;

pub use sasa::PerElementSasa;

pub use sasa::SasaDescriptor;

pub use sasa::calc_mol_sasa;

pub use sasa::calc_mol_sasa_with_probe;

pub use sasa::sasa;

pub use sasa::sasa_descriptor;

pub use sasa::sasa_descriptor_from_dg;

pub use sasa::sasa_from_dg;

pub use sasa::sasa_per_atom;

pub use sasa::sasa_per_atom_from_dg;

pub use sasa::sasa_per_element;

pub use sasa::sasa_per_element_from_dg;

pub use sasa::shrake_rupley_sasa;

pub use shape_descriptors::asphericity;

pub use shape_descriptors::eccentricity;

pub use shape_descriptors::npr1;

pub use shape_descriptors::npr2;

pub use shape_descriptors::plane_of_best_fit;

pub use shape_descriptors::pmi;

pub use shape_descriptors::pmi1;

pub use shape_descriptors::pmi2;

pub use shape_descriptors::pmi3;

pub use shape_descriptors::radius_of_gyration;

pub use spectrophores::SpectrophoresConfig;

pub use spectrophores::SpectrophoresNorm;

pub use spectrophores::spectrophores;

pub use spectrophores::tanimoto_spectrophores;

pub use stereo3d::StereoAssignment3D;

pub use stereo3d::assign_stereo_from_3d;

pub use usr::shape_screen;

pub use usr::usr_descriptors;

pub use usr::usr_from_dg;

pub use usr::usr_similarity;

pub use xyz::XyzError;

pub use xyz::parse_xyz;

pub use xyz::write_xyz;

Modules

align

Standalone 3D coordinate alignment using the Kabsch algorithm.

conformer

Conformer ensemble: a molecule with multiple sets of 3D coordinates.

constraints

Distance geometry constraint satisfaction via projection.

coords

3D coordinate types for molecular structures.

descriptors_3d

3D molecular descriptors for ML pipelines.

determine_bonds

Bond order inference from 3D coordinates.

dg

Rule-based 3D coordinate generation.

dg_fft

Distance geometry with eigenvalue decomposition for 3D coordinate generation.

etkdg

ETKDG (Experimental Torsion Knowledge Distance Geometry) v3 conformer generation.

etkdg_knowledge

ETKDG Torsion Knowledge Base — experimental torsion angle preferences from CSD.

md

Molecular dynamics simulation using Velocity Verlet integration.

minimize

Simplified force-field geometry minimization for molecular structures.

mol_transforms

o3a

Open3DAlign (O3A)-style atom correspondence search for 3D molecular alignment.

pdb

PDB file format parser and writer.

pharmacophore_fp_3d

3D pharmacophore fingerprints using Euclidean distances.

sasa

Solvent-Accessible Surface Area (SASA) calculation using Shrake-Rupley algorithm.

shape_descriptors

Shape descriptors computed from 3D coordinates.

spectrophores

Spectrophores — 3D molecular fingerprints.

stereo3d

v0.1.93: Stereochemistry assignment from 3D coordinates with full CIP prioritization.

usr

Ultrafast Shape Recognition (USR) 3D similarity descriptors.

xyz

XYZ file format parser and writer.

Structs

ConformerConfig

Configuration for conformer ensemble generation.

Enums

ConformerForceField

Force field used for geometry minimization during conformer ensemble generation.

Functions

generate_and_minimize_constrained

Generate 3D coordinates with constraint satisfaction and energy minimization.

generate_and_minimize_dreiding

Generate 3D coordinates and minimize geometry in one step. Uses distance geometry for initial placement + DREIDING force field.

generate_and_minimize_uff

Generate 3D coordinates and minimize using UFF force field.

generate_conformer_ensemble

Generate multiple conformers with different initial geometries. Uses distance geometry for initial placement, then minimizes with DREIDING. Returns a ConformerEnsemble with all conformers.

generate_conformer_ensemble_mmff94

Generate multiple conformers minimized with MMFF94 (Halgren 1996).

generate_conformer_ensemble_with_config

Generate multiple conformers with force-field minimization and Kabsch-RMSD pruning.