rdkit_sys/bridge/
ro_mol.rs

1#[cxx::bridge(namespace = "RDKit")]
2pub mod ffi {
3    #[repr(i32)]
4    #[derive(Debug, PartialEq)]
5    pub enum HybridizationType {
6        UNSPECIFIED,
7        S,
8        SP,
9        SP2,
10        SP3,
11        SP2D,
12        SP3D,
13        SP3D2,
14        OTHER,
15    }
16
17    unsafe extern "C++" {
18        include!("wrapper/include/ro_mol.h");
19
20        pub type ROMol;
21        pub type ExplicitBitVect = crate::fingerprint_ffi::ExplicitBitVect;
22        pub type SmilesParserParams;
23        pub type Atom;
24        pub type HybridizationType;
25
26        pub type MolSanitizeException;
27        pub type MolSanitizeExceptionUniquePtr; //  = UniquePtr<MolSanitizeException>;
28
29        pub fn copy_mol(mol: &SharedPtr<ROMol>) -> SharedPtr<ROMol>;
30
31        pub fn smiles_to_mol(smi: &CxxString) -> Result<SharedPtr<ROMol>>;
32
33        pub fn smiles_to_mol_with_params(
34            smi: &CxxString,
35            params: &SharedPtr<SmilesParserParams>,
36        ) -> Result<SharedPtr<ROMol>>;
37        pub fn new_smiles_parser_params() -> SharedPtr<SmilesParserParams>;
38        pub fn smiles_parser_params_set_sanitize(
39            ptr: &SharedPtr<SmilesParserParams>,
40            sanitize: bool,
41        );
42        pub fn smiles_parser_params_get_sanitize(ptr: &SharedPtr<SmilesParserParams>) -> bool;
43
44        pub fn mol_to_smiles(mol: &SharedPtr<ROMol>) -> String;
45
46        pub fn mol_to_molblock(mol: &SharedPtr<ROMol>) -> String;
47
48        pub fn detect_chemistry_problems(
49            mol: &SharedPtr<ROMol>,
50        ) -> UniquePtr<CxxVector<MolSanitizeExceptionUniquePtr>>;
51
52        pub fn mol_sanitize_exception_type(
53            mol_sanitize_exception: &MolSanitizeExceptionUniquePtr,
54        ) -> String;
55
56        pub fn atom_sanitize_exception_get_atom_idx(
57            mol_sanitize_exception: &MolSanitizeExceptionUniquePtr,
58        ) -> u32;
59
60        pub fn get_num_atoms(mol: &SharedPtr<ROMol>, onlyExplicit: bool) -> u32;
61        pub fn get_atom_with_idx(mol: &mut SharedPtr<ROMol>, idx: u32) -> Pin<&mut Atom>;
62        pub fn get_symbol(atom: Pin<&Atom>) -> String;
63        pub fn get_is_aromatic(atom: Pin<&Atom>) -> bool;
64        pub fn get_atomic_num(atom: Pin<&Atom>) -> i32;
65        pub fn get_formal_charge(atom: Pin<&Atom>) -> i32;
66        pub fn get_total_num_hs(atom: Pin<&Atom>) -> u32;
67        pub fn get_total_valence(atom: Pin<&Atom>) -> u32;
68        pub fn set_formal_charge(atom: Pin<&mut Atom>, what: i32);
69        pub fn set_num_explicit_hs(atom: Pin<&mut Atom>, what: i32);
70        pub fn atom_update_property_cache(atom: Pin<&mut Atom>, strict: bool) -> Result<()>;
71        pub fn atom_set_hybridization(atom: Pin<&mut Atom>, what: HybridizationType);
72        pub fn atom_get_hybridization(atom: Pin<&Atom>) -> HybridizationType;
73
74        pub fn ro_mol_update_property_cache(atom: &mut SharedPtr<ROMol>, strict: bool);
75
76        pub fn set_int_prop(atom: Pin<&mut Atom>, key: &CxxString, value: i32);
77        pub fn get_int_prop(atom: Pin<&Atom>, key: &CxxString) -> Result<i32>;
78        pub fn set_float_prop(atom: Pin<&mut Atom>, key: &CxxString, value: f64);
79        pub fn get_float_prop(atom: Pin<&Atom>, key: &CxxString) -> Result<f64>;
80        pub fn set_bool_prop(atom: Pin<&mut Atom>, key: &CxxString, value: bool);
81        pub fn get_bool_prop(atom: Pin<&Atom>, key: &CxxString) -> Result<bool>;
82        pub fn set_prop(atom: Pin<&mut Atom>, key: &CxxString, value: &CxxString);
83        pub fn get_prop(atom: Pin<&Atom>, key: &CxxString) -> Result<String>;
84        pub fn get_num_radical_electrons(atom: Pin<&Atom>) -> u32;
85
86        //Returns the degree of the atom in the molecule.
87        pub fn get_degree(atom: Pin<&Atom>) -> u32;
88    }
89}
rdkit_sys/bridge/ro_mol.rs

rdkit_sys/bridge/
ro_mol.rs
