Initial commit
This commit is contained in:
redclawsystems
@@ -0,0 +1,692 @@
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//! Sample data utilities for drug binding demo.
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//!
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//! Provides SMILES parsing and protein lookup functionality.
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use drugbinder_shared::{
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Atom, BindingPocket, Bond, BondType, Coordinate3D, Element, Hybridization, MolecularProperties,
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Molecule, ProteinTarget,
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};
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use crate::DrugBinderError;
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/// Convert SMILES string to Molecule.
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pub fn smiles_to_molecule(smiles: &str, name: Option<String>) -> Result<Molecule, DrugBinderError> {
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// Parse SMILES
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let (atoms, bonds) = parse_smiles(smiles)?;
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// Calculate molecular weight
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let mw: f32 = atoms.iter().map(|a| element_mass(&a.element)).sum();
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// Calculate properties
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let properties = calculate_properties(&atoms, &bonds);
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Ok(Molecule {
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id: format!("mol_{}", hash_smiles(smiles)),
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name,
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smiles: smiles.to_string(),
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molecular_weight: mw,
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num_atoms: atoms.len(),
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num_bonds: bonds.len(),
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atoms,
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bonds,
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coordinates_3d: None,
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properties,
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})
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}
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/// Get protein by ID.
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pub fn get_protein_by_id(protein_id: &str) -> Result<ProteinTarget, DrugBinderError> {
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// Look up in sample database
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let targets = get_protein_database();
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targets
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.into_iter()
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.find(|t| t.id == protein_id)
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.ok_or_else(|| {
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DrugBinderError::InvalidProtein(format!("Unknown protein ID: {protein_id}"))
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})
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}
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/// Convert sequence to protein.
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#[must_use]
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pub fn sequence_to_protein(sequence: &str, name: Option<String>) -> ProteinTarget {
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ProteinTarget {
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id: format!("seq_{}", hash_sequence(sequence)),
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name: name.unwrap_or_else(|| "Custom protein".to_string()),
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organism: "Unknown".to_string(),
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sequence: sequence.to_string(),
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pdb_id: None,
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pockets: vec![],
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}
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}
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/// Parse SMILES to atoms and bonds.
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fn parse_smiles(smiles: &str) -> Result<(Vec<Atom>, Vec<Bond>), DrugBinderError> {
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let mut atoms = Vec::new();
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let mut bonds = Vec::new();
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let mut ring_atoms: std::collections::HashMap<char, usize> = std::collections::HashMap::new();
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let mut branch_stack: Vec<usize> = Vec::new();
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let mut prev_atom: Option<usize> = None;
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let mut pending_bond_type = BondType::Single;
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let mut in_aromatic = false;
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let chars: Vec<char> = smiles.chars().collect();
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let mut i = 0;
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while i < chars.len() {
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let c = chars[i];
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match c {
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// Branch handling
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'(' => {
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if let Some(atom_idx) = prev_atom {
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branch_stack.push(atom_idx);
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}
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i += 1;
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continue;
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}
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')' => {
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prev_atom = branch_stack.pop();
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i += 1;
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continue;
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}
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// Bond types
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'-' => {
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pending_bond_type = BondType::Single;
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i += 1;
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continue;
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}
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'=' => {
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pending_bond_type = BondType::Double;
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i += 1;
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continue;
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}
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'#' => {
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pending_bond_type = BondType::Triple;
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i += 1;
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continue;
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}
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':' => {
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pending_bond_type = BondType::Aromatic;
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i += 1;
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continue;
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}
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// Ring closures
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'0'..='9' => {
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if let Some(atom_idx) = prev_atom {
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if let Some(&ring_start) = ring_atoms.get(&c) {
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// Close ring
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bonds.push(Bond {
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atom1: ring_start,
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atom2: atom_idx,
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bond_type: if in_aromatic {
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BondType::Aromatic
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} else {
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BondType::Single
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},
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is_conjugated: in_aromatic,
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is_in_ring: true,
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});
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ring_atoms.remove(&c);
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} else {
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// Start ring
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ring_atoms.insert(c, atom_idx);
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}
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}
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i += 1;
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continue;
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}
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// Skip stereochemistry and charges
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'/' | '\\' | '@' | '+' | '[' | ']' => {
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// Skip bracket contents
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if c == '[' {
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while i < chars.len() && chars[i] != ']' {
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i += 1;
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}
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}
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i += 1;
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continue;
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}
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_ => {}
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}
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// Try to parse element
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let (element, is_aromatic_elem, chars_consumed) = parse_element(&chars, i);
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if let Some(elem) = element {
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let atom_idx = atoms.len();
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// Determine aromaticity
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let is_aromatic_atom = is_aromatic_elem;
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if is_aromatic_atom {
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in_aromatic = true;
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}
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atoms.push(Atom {
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index: atom_idx,
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element: elem,
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formal_charge: 0,
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num_hydrogens: implicit_h_count(&elem, is_aromatic_atom),
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is_aromatic: is_aromatic_atom,
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hybridization: if is_aromatic_atom {
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Hybridization::Sp2
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} else {
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Hybridization::Sp3
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},
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});
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// Add bond to previous atom
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if let Some(prev_idx) = prev_atom {
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let bond_type = if is_aromatic_atom
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&& atoms.get(prev_idx).is_some_and(|a| a.is_aromatic)
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{
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BondType::Aromatic
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} else {
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pending_bond_type
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};
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bonds.push(Bond {
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atom1: prev_idx,
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atom2: atom_idx,
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bond_type,
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is_conjugated: bond_type == BondType::Aromatic || bond_type == BondType::Double,
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is_in_ring: false, // Updated later for ring bonds
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});
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}
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prev_atom = Some(atom_idx);
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pending_bond_type = BondType::Single;
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i += chars_consumed;
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} else {
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i += 1;
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}
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}
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if atoms.is_empty() {
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return Err(DrugBinderError::InvalidMolecule(format!(
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"Could not parse SMILES: {smiles}"
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)));
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}
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Ok((atoms, bonds))
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}
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/// Parse element from character stream.
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fn parse_element(chars: &[char], start: usize) -> (Option<Element>, bool, usize) {
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if start >= chars.len() {
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return (None, false, 0);
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}
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let c = chars[start];
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// Check for two-letter elements
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if start + 1 < chars.len() {
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let next = chars[start + 1];
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if next.is_lowercase() {
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let elem_str: String = vec![c, next].into_iter().collect();
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let elem = match elem_str.as_str() {
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"Cl" => Some(Element::Cl),
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"Br" => Some(Element::Br),
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"Na" => Some(Element::Na),
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"Mg" => Some(Element::Mg),
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"Ca" => Some(Element::Ca),
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"Fe" => Some(Element::Fe),
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"Zn" => Some(Element::Zn),
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"Cu" => Some(Element::Cu),
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_ => None,
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};
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if elem.is_some() {
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return (elem, false, 2);
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}
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}
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}
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// Single letter elements
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match c {
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'C' => (Some(Element::C), false, 1),
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'N' => (Some(Element::N), false, 1),
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'O' => (Some(Element::O), false, 1),
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'S' => (Some(Element::S), false, 1),
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'P' => (Some(Element::P), false, 1),
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'F' => (Some(Element::F), false, 1),
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'I' => (Some(Element::I), false, 1),
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'H' => (Some(Element::H), false, 1),
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// Aromatic atoms (lowercase)
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'c' => (Some(Element::C), true, 1),
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'n' => (Some(Element::N), true, 1),
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'o' => (Some(Element::O), true, 1),
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's' => (Some(Element::S), true, 1),
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_ => (None, false, 1),
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}
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}
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/// Calculate implicit hydrogen count.
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fn implicit_h_count(element: &Element, is_aromatic: bool) -> u8 {
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let valence: u8 = match element {
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Element::C => 4,
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Element::N => 3,
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Element::O => 2,
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Element::S => 2,
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Element::P => 3,
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Element::F | Element::Cl | Element::Br | Element::I => 1,
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_ => 0,
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};
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// Aromatic atoms typically have one less H
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if is_aromatic {
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valence.saturating_sub(1)
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} else {
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valence
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}
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}
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/// Calculate molecular properties.
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fn calculate_properties(atoms: &[Atom], bonds: &[Bond]) -> MolecularProperties {
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// Count HBD (NH, OH)
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let hbd: u8 = atoms
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.iter()
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.filter(|a| matches!(a.element, Element::N | Element::O) && a.num_hydrogens > 0)
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.count() as u8;
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// Count HBA (N, O)
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let hba: u8 = atoms
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.iter()
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.filter(|a| matches!(a.element, Element::N | Element::O))
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.count() as u8;
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// Calculate LogP (Wildman-Crippen method, simplified)
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let mut log_p = 0.0_f32;
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for atom in atoms {
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log_p += match atom.element {
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Element::C => {
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if atom.is_aromatic {
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0.29
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} else {
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0.50
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}
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}
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Element::N => {
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if atom.num_hydrogens > 0 {
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-1.03
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} else {
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-0.57
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}
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}
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Element::O => {
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if atom.num_hydrogens > 0 {
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-0.47
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} else {
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-0.11
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}
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}
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Element::S => 0.37,
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Element::F => 0.37,
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Element::Cl => 0.71,
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Element::Br => 0.86,
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Element::I => 1.15,
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Element::H => 0.12,
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_ => 0.0,
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};
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}
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// Count rotatable bonds
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let rotatable_bonds: u8 = bonds
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.iter()
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.filter(|b| b.bond_type == BondType::Single && !b.is_in_ring)
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.count() as u8;
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// Count rings (estimate from ring bonds)
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let ring_bond_count = bonds.iter().filter(|b| b.is_in_ring).count();
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let num_rings = (ring_bond_count / 5).max(1) as u8;
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// Count aromatic rings
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let aromatic_atoms = atoms.iter().filter(|a| a.is_aromatic).count();
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let num_aromatic_rings = (aromatic_atoms / 5) as u8;
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// Calculate TPSA
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let tpsa: f32 = atoms
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.iter()
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.map(|a| match a.element {
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Element::N => {
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if a.num_hydrogens > 0 {
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26.0
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} else {
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12.0
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}
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}
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Element::O => {
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if a.num_hydrogens > 0 {
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20.0
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} else {
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9.2
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}
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}
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Element::S => 25.0,
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_ => 0.0,
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})
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.sum();
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// Calculate MW
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let mw: f32 = atoms.iter().map(|a| element_mass(&a.element)).sum();
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// Check Lipinski
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let lipinski_pass = mw <= 500.0 && log_p <= 5.0 && hbd <= 5 && hba <= 10;
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// Calculate QED
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let qed = calculate_qed(mw, log_p, hbd, hba, tpsa, rotatable_bonds);
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MolecularProperties {
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log_p,
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hbd,
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hba,
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tpsa,
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rotatable_bonds,
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num_rings,
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num_aromatic_rings,
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lipinski_pass,
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qed,
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}
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}
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fn calculate_qed(mw: f32, log_p: f32, hbd: u8, hba: u8, tpsa: f32, rotatable_bonds: u8) -> f32 {
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let gaussian =
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|x: f32, mean: f32, std: f32| -> f32 { (-0.5 * ((x - mean) / std).powi(2)).exp() };
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let mw_score = gaussian(mw, 350.0, 100.0);
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let logp_score = gaussian(log_p, 2.5, 1.5);
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let hbd_score = gaussian(f32::from(hbd), 1.0, 2.0);
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let hba_score = gaussian(f32::from(hba), 4.0, 3.0);
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let tpsa_score = gaussian(tpsa, 70.0, 30.0);
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let rotb_score = gaussian(f32::from(rotatable_bonds), 3.0, 3.0);
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(mw_score * logp_score * hbd_score * hba_score * tpsa_score * rotb_score).powf(1.0 / 6.0)
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}
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fn element_mass(element: &Element) -> f32 {
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match element {
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Element::H => 1.008,
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Element::C => 12.011,
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Element::N => 14.007,
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Element::O => 15.999,
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Element::F => 18.998,
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Element::P => 30.974,
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Element::S => 32.065,
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Element::Cl => 35.453,
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Element::Br => 79.904,
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Element::I => 126.90,
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Element::Na => 22.990,
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Element::Mg => 24.305,
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Element::K => 39.098,
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Element::Ca => 40.078,
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Element::Fe => 55.845,
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Element::Zn => 65.38,
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Element::Cu => 63.546,
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Element::Other => 12.0,
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}
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}
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fn hash_smiles(smiles: &str) -> u32 {
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smiles
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.bytes()
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.fold(0u32, |acc, b| acc.wrapping_mul(31).wrapping_add(u32::from(b)))
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}
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fn hash_sequence(sequence: &str) -> u32 {
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sequence
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.bytes()
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.fold(0u32, |acc, b| acc.wrapping_mul(37).wrapping_add(u32::from(b)))
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}
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/// Get protein database.
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fn get_protein_database() -> Vec<ProteinTarget> {
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vec![
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// Carbonic anhydrase 2
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ProteinTarget {
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id: "P00918".to_string(),
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name: "Carbonic anhydrase 2".to_string(),
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organism: "Homo sapiens".to_string(),
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sequence: "MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK".to_string(),
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pdb_id: Some("1CA2".to_string()),
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pockets: vec![
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BindingPocket {
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id: 0,
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name: "Active site".to_string(),
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residues: vec![91, 92, 94, 96, 119, 143, 198, 199, 200],
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center: Coordinate3D { x: 12.5, y: 8.3, z: 15.2 },
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volume: 350.0,
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druggability: 0.85,
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},
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],
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},
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// EGFR
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ProteinTarget {
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id: "P00533".to_string(),
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name: "Epidermal growth factor receptor".to_string(),
|
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organism: "Homo sapiens".to_string(),
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sequence: "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPS".to_string(),
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pdb_id: Some("1M17".to_string()),
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pockets: vec![
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BindingPocket {
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id: 0,
|
||||
name: "ATP binding site".to_string(),
|
||||
residues: vec![718, 719, 721, 726, 745, 790, 791, 792, 793, 854, 855],
|
||||
center: Coordinate3D { x: 25.0, y: 18.5, z: 42.0 },
|
||||
volume: 480.0,
|
||||
druggability: 0.92,
|
||||
},
|
||||
],
|
||||
},
|
||||
// COX-2
|
||||
ProteinTarget {
|
||||
id: "P35354".to_string(),
|
||||
name: "Prostaglandin G/H synthase 2 (COX-2)".to_string(),
|
||||
organism: "Homo sapiens".to_string(),
|
||||
sequence: "MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADY".to_string(),
|
||||
pdb_id: Some("5KIR".to_string()),
|
||||
pockets: vec![
|
||||
BindingPocket {
|
||||
id: 0,
|
||||
name: "Cyclooxygenase active site".to_string(),
|
||||
residues: vec![83, 89, 90, 120, 355, 523, 530],
|
||||
center: Coordinate3D { x: 30.0, y: 25.0, z: 35.0 },
|
||||
volume: 420.0,
|
||||
druggability: 0.88,
|
||||
},
|
||||
],
|
||||
},
|
||||
// ACE2
|
||||
ProteinTarget {
|
||||
id: "Q9BYF1".to_string(),
|
||||
name: "Angiotensin-converting enzyme 2 (ACE2)".to_string(),
|
||||
organism: "Homo sapiens".to_string(),
|
||||
sequence: "MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDNSLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENPYASIDISKGENNPGFQNTDDVQTSF".to_string(),
|
||||
pdb_id: Some("6M0J".to_string()),
|
||||
pockets: vec![
|
||||
BindingPocket {
|
||||
id: 0,
|
||||
name: "Peptidase active site".to_string(),
|
||||
residues: vec![273, 345, 371, 374, 378, 384, 394, 402, 417],
|
||||
center: Coordinate3D { x: 40.0, y: 32.0, z: 28.0 },
|
||||
volume: 520.0,
|
||||
druggability: 0.82,
|
||||
},
|
||||
],
|
||||
},
|
||||
// HIV protease
|
||||
ProteinTarget {
|
||||
id: "P04585".to_string(),
|
||||
name: "HIV-1 protease".to_string(),
|
||||
organism: "Human immunodeficiency virus 1".to_string(),
|
||||
sequence: "PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF".to_string(),
|
||||
pdb_id: Some("1HVR".to_string()),
|
||||
pockets: vec![
|
||||
BindingPocket {
|
||||
id: 0,
|
||||
name: "Active site".to_string(),
|
||||
residues: vec![23, 25, 27, 28, 29, 30, 32, 47, 48, 49, 50, 76, 80, 81, 82, 84],
|
||||
center: Coordinate3D { x: 18.0, y: 12.0, z: 22.0 },
|
||||
volume: 380.0,
|
||||
druggability: 0.95,
|
||||
},
|
||||
],
|
||||
},
|
||||
]
|
||||
}
|
||||
|
||||
#[cfg(test)]
|
||||
mod tests {
|
||||
use super::*;
|
||||
|
||||
#[test]
|
||||
fn test_smiles_to_molecule() {
|
||||
let mol = smiles_to_molecule("CCO", Some("Ethanol".to_string()));
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
assert_eq!(molecule.name, Some("Ethanol".to_string()));
|
||||
assert!(molecule.atoms.len() >= 2); // At least C and O
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_smiles_benzene() {
|
||||
let mol = smiles_to_molecule("c1ccccc1", None);
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
assert!(molecule.atoms.iter().any(|a| a.is_aromatic));
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_smiles_aspirin() {
|
||||
let mol = smiles_to_molecule("CC(=O)OC1=CC=CC=C1C(=O)O", Some("Aspirin".to_string()));
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
assert!(molecule.molecular_weight > 150.0);
|
||||
assert!(molecule.molecular_weight < 200.0);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_get_protein_by_id() {
|
||||
let result = get_protein_by_id("P00918");
|
||||
assert!(result.is_ok());
|
||||
|
||||
let protein = result.unwrap();
|
||||
assert_eq!(protein.name, "Carbonic anhydrase 2");
|
||||
assert!(!protein.pockets.is_empty());
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_get_unknown_protein() {
|
||||
let result = get_protein_by_id("UNKNOWN123");
|
||||
assert!(result.is_err());
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_sequence_to_protein() {
|
||||
let protein = sequence_to_protein("MKLAVLKLAGLLAGLLAL", Some("Test protein".to_string()));
|
||||
assert_eq!(protein.name, "Test protein");
|
||||
assert_eq!(protein.sequence.len(), 18);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_parse_smiles_with_branches() {
|
||||
let mol = smiles_to_molecule("CC(C)C", None); // Isobutane
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
assert!(molecule.atoms.len() >= 4);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_parse_smiles_with_ring() {
|
||||
let mol = smiles_to_molecule("C1CCCCC1", None); // Cyclohexane
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
// Should have ring closure bond
|
||||
assert!(molecule.bonds.iter().any(|b| b.is_in_ring));
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_molecular_properties() {
|
||||
let mol = smiles_to_molecule("c1ccc(O)cc1", None).unwrap(); // Phenol
|
||||
assert!(mol.properties.hbd >= 1); // OH is HBD
|
||||
assert!(mol.properties.hba >= 1); // O is HBA
|
||||
assert!(mol.properties.num_aromatic_rings >= 1);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_lipinski_check() {
|
||||
// Small drug-like molecule
|
||||
let mol = smiles_to_molecule("CCO", None).unwrap();
|
||||
assert!(mol.properties.lipinski_pass);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_element_mass_lookup() {
|
||||
assert!((element_mass(&Element::C) - 12.011).abs() < 0.01);
|
||||
assert!((element_mass(&Element::O) - 15.999).abs() < 0.01);
|
||||
assert!((element_mass(&Element::N) - 14.007).abs() < 0.01);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_protein_database() {
|
||||
let proteins = get_protein_database();
|
||||
assert!(proteins.len() >= 5);
|
||||
|
||||
// Check for key proteins
|
||||
assert!(proteins.iter().any(|p| p.id == "P00918")); // CA2
|
||||
assert!(proteins.iter().any(|p| p.id == "P00533")); // EGFR
|
||||
assert!(proteins.iter().any(|p| p.id == "P04585")); // HIV protease
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_qed_calculation() {
|
||||
// Drug-like molecule (aspirin)
|
||||
let mol = smiles_to_molecule("CC(=O)OC1=CC=CC=C1C(=O)O", None).unwrap();
|
||||
assert!(mol.properties.qed > 0.3);
|
||||
assert!(mol.properties.qed < 1.0);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_halogen_parsing() {
|
||||
let mol = smiles_to_molecule("CCCl", None); // Chloroethane
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
assert!(molecule.atoms.iter().any(|a| a.element == Element::Cl));
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_double_bond() {
|
||||
let mol = smiles_to_molecule("C=C", None); // Ethene
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
assert!(
|
||||
molecule
|
||||
.bonds
|
||||
.iter()
|
||||
.any(|b| b.bond_type == BondType::Double)
|
||||
);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn test_triple_bond() {
|
||||
let mol = smiles_to_molecule("C#N", None); // HCN
|
||||
assert!(mol.is_ok());
|
||||
|
||||
let molecule = mol.unwrap();
|
||||
assert!(
|
||||
molecule
|
||||
.bonds
|
||||
.iter()
|
||||
.any(|b| b.bond_type == BondType::Triple)
|
||||
);
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user