Rdkit scaffold

rdkit-sys/src/bridge/ro_mol.rs

@@ -18,6 +18,7 @@ pub mod ffi {
         include!("wrapper/include/ro_mol.h");
 
         pub type ROMol;
+
         pub type ExplicitBitVect = crate::fingerprint_ffi::ExplicitBitVect;
         pub type SmilesParserParams;
         pub type Atom;

rdkit-sys/src/bridge/scaffold_network.rs

@@ -1,43 +1,94 @@
+use cxx::{ExternType, SharedPtr};
+
 #[cxx::bridge(namespace = "RDKit")]
 pub mod ffi {
+
     unsafe extern "C++" {
         include!("wrapper/include/scaffold_network.h");
 
-        pub type ScaffoldNetworkParams;
-        //
-        // pub fn default_scaffold_network_params() -> SharedPtr<ScaffoldNetworkParams>;
+        pub type ROMol = crate::ro_mol_ffi::ROMol;
+        pub type ScaffoldNetworkParamsLocal;
 
-        pub fn default_scaffold_network_params() -> SharedPtr<ScaffoldNetworkParams>;
+        pub fn default_scaffold_network_params() -> SharedPtr<ScaffoldNetworkParamsLocal>;
 
         pub fn new_scaffold_network_params(
             bond_breaker_smarts: &Vec<String>,
-        ) -> SharedPtr<ScaffoldNetworkParams>;
+        ) -> SharedPtr<ScaffoldNetworkParamsLocal>;
 
         pub fn set_include_generic_scaffolds(
-            params: &mut SharedPtr<ScaffoldNetworkParams>,
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
             input: bool,
         );
-        pub fn include_generic_bond_scaffolds(
-            params: &mut SharedPtr<ScaffoldNetworkParams>,
+        pub fn set_include_generic_bond_scaffolds(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
             input: bool,
         );
-        pub fn include_scaffolds_without_attachments(
-            params: &mut SharedPtr<ScaffoldNetworkParams>,
+        pub fn set_include_scaffolds_without_attachments(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
             input: bool,
         );
-        pub fn include_scaffolds_with_attachments(
-            params: &mut SharedPtr<ScaffoldNetworkParams>,
+        pub fn set_include_scaffolds_with_attachments(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
             input: bool,
         );
-        pub fn keep_only_first_fragment(params: &mut SharedPtr<ScaffoldNetworkParams>, input: bool);
-        pub fn prune_before_fragmenting(params: &mut SharedPtr<ScaffoldNetworkParams>, input: bool);
-        pub fn flatten_isotopes(params: &mut SharedPtr<ScaffoldNetworkParams>, input: bool);
-        pub fn flatten_chirality(params: &mut SharedPtr<ScaffoldNetworkParams>, input: bool);
-        pub fn flatten_keep_largest(params: &mut SharedPtr<ScaffoldNetworkParams>, input: bool);
-        pub fn collect_mol_counts(params: &mut SharedPtr<ScaffoldNetworkParams>, input: bool);
+        pub fn set_keep_only_first_fragment(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
+            input: bool,
+        );
+        pub fn set_prune_before_fragmenting(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
+            input: bool,
+        );
+        pub fn set_flatten_isotopes(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
+            input: bool,
+        );
+        pub fn set_flatten_chirality(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
+            input: bool,
+        );
+        pub fn set_flatten_keep_largest(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
+            input: bool,
+        );
+        pub fn set_collect_mol_counts(
+            params: &mut SharedPtr<ScaffoldNetworkParamsLocal>,
+            input: bool,
+        );
+
+        pub fn get_include_generic_scaffolds(
+            params: &SharedPtr<ScaffoldNetworkParamsLocal>,
+        ) -> bool;
+        pub fn get_include_generic_bond_scaffolds(
+            params: &SharedPtr<ScaffoldNetworkParamsLocal>,
+        ) -> bool;
+        pub fn get_include_scaffolds_without_attachments(
+            params: &SharedPtr<ScaffoldNetworkParamsLocal>,
+        ) -> bool;
+        pub fn get_include_scaffolds_with_attachments(
+            params: &SharedPtr<ScaffoldNetworkParamsLocal>,
+        ) -> bool;
+        pub fn get_keep_only_first_fragment(params: &SharedPtr<ScaffoldNetworkParamsLocal>)
+            -> bool;
+        pub fn get_prune_before_fragmenting(params: &SharedPtr<ScaffoldNetworkParamsLocal>)
+            -> bool;
+        pub fn get_flatten_isotopes(params: &SharedPtr<ScaffoldNetworkParamsLocal>) -> bool;
+        pub fn get_flatten_chirality(params: &SharedPtr<ScaffoldNetworkParamsLocal>) -> bool;
+        pub fn get_flatten_keep_largest(params: &SharedPtr<ScaffoldNetworkParamsLocal>) -> bool;
+        pub fn get_collect_mol_counts(params: &SharedPtr<ScaffoldNetworkParamsLocal>) -> bool;
 
         pub type ScaffoldNetworkClass;
         pub fn default_scaffold_network() -> SharedPtr<ScaffoldNetworkClass>;
 
+        pub fn create_scaffold_network(
+            mol: &SharedPtr<ROMol>,
+            scaffold_network_params: &SharedPtr<ScaffoldNetworkParamsLocal>,
+        ) -> SharedPtr<ScaffoldNetworkClass>;
+
+        pub fn update_scaffold_network(
+            mol: &SharedPtr<ROMol>,
+            scaffold_network: &mut SharedPtr<ScaffoldNetworkClass>,
+            scaffold_network_params: &SharedPtr<ScaffoldNetworkParamsLocal>,
+        );
     }
 }

rdkit-sys/tests/test_atoms.rs

@@ -1,7 +1,7 @@
 #[test]
 fn test_atoms() {
     cxx::let_cxx_string!(smiles = "c1ccccc1CCCCCCCC");
-    let romol = rdkit_sys::ro_mol_ffi::smiles_to_mol(&smiles).unwrap();
+    let mut romol = rdkit_sys::ro_mol_ffi::smiles_to_mol(&smiles).unwrap();
 
     let num_atoms = rdkit_sys::ro_mol_ffi::get_num_atoms(&romol, true);
 

rdkit-sys/tests/test_scaffold_network.rs

@@ -1,3 +1,4 @@
+use cxx::let_cxx_string;
 use rdkit_sys::scaffold_network_ffi::*;
 
 #[test]
@@ -6,15 +7,30 @@ fn test_scaffold_network() {
     let mut params = new_scaffold_network_params(&vec![]);
 
     set_include_generic_scaffolds(&mut params, true);
-    include_generic_bond_scaffolds(&mut params, true);
-    include_scaffolds_without_attachments(&mut params, true);
-    include_scaffolds_with_attachments(&mut params, true);
-    keep_only_first_fragment(&mut params, true);
-    prune_before_fragmenting(&mut params, true);
-    flatten_isotopes(&mut params, true);
-    flatten_chirality(&mut params, true);
-    flatten_keep_largest(&mut params, true);
-    collect_mol_counts(&mut params, true);
+    set_include_generic_bond_scaffolds(&mut params, true);
+    set_include_scaffolds_without_attachments(&mut params, true);
+    set_include_scaffolds_with_attachments(&mut params, true);
+    set_keep_only_first_fragment(&mut params, true);
+    set_prune_before_fragmenting(&mut params, true);
+    set_flatten_isotopes(&mut params, true);
+    set_flatten_chirality(&mut params, true);
+    set_flatten_keep_largest(&mut params, true);
+    set_collect_mol_counts(&mut params, true);
 
-    let _scaffold_network = default_scaffold_network();
+    get_include_generic_scaffolds(&params);
+    get_include_generic_bond_scaffolds(&params);
+    get_include_scaffolds_without_attachments(&params);
+    get_include_scaffolds_with_attachments(&params);
+    get_keep_only_first_fragment(&params);
+    get_prune_before_fragmenting(&params);
+    get_flatten_isotopes(&params);
+    get_flatten_chirality(&params);
+    get_flatten_keep_largest(&params);
+    get_collect_mol_counts(&params);
+
+    let mut scaffold_network = default_scaffold_network();
+    let_cxx_string!(smiles = "CCC");
+    let mol = rdkit_sys::ro_mol_ffi::smiles_to_mol(&smiles).unwrap();
+
+    update_scaffold_network(&mol, &mut scaffold_network, &params);
 }

rdkit-sys/wrapper/include/ro_mol.h

@@ -9,6 +9,8 @@
 #include <GraphMol/MolStandardize/Tautomer.h>
 
 namespace RDKit {
+    using ROMolSharedPtr = std::shared_ptr<ROMol>;
+
     std::shared_ptr<ROMol> copy_mol(const std::shared_ptr<ROMol> &mol);
     std::shared_ptr<ROMol> smiles_to_mol(const std::string &smiles);
     rust::String mol_to_smiles(const std::shared_ptr<ROMol> &mol);

rdkit-sys/wrapper/include/scaffold_network.h

@@ -5,23 +5,46 @@
 #include <GraphMol/ScaffoldNetwork/ScaffoldNetwork.h>
 
 namespace RDKit {
-  using ScaffoldNetworkParams = ScaffoldNetwork::ScaffoldNetworkParams;
-
-  std::shared_ptr<ScaffoldNetworkParams> default_scaffold_network_params();
-  std::shared_ptr<ScaffoldNetworkParams> new_scaffold_network_params(const rust::Vec<rust::String> &bondBreakersSmarts);
-
-  void set_include_generic_scaffolds(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void include_generic_bond_scaffolds(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void include_scaffolds_without_attachments(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void include_scaffolds_with_attachments(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void keep_only_first_fragment(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void prune_before_fragmenting(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void flatten_isotopes(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void flatten_chirality(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void flatten_keep_largest(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
-  void collect_mol_counts(std::shared_ptr<ScaffoldNetworkParams> &params, bool input);
+  using ScaffoldNetworkParamsLocal = ScaffoldNetwork::ScaffoldNetworkParams;
+
+  std::shared_ptr<ScaffoldNetworkParamsLocal> default_scaffold_network_params();
+  std::shared_ptr<ScaffoldNetworkParamsLocal> new_scaffold_network_params(const rust::Vec<rust::String> &bondBreakersSmarts);
+
+  void set_include_generic_scaffolds(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_include_generic_bond_scaffolds(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_include_scaffolds_without_attachments(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_include_scaffolds_with_attachments(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_keep_only_first_fragment(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_prune_before_fragmenting(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_flatten_isotopes(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_flatten_chirality(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_flatten_keep_largest(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+  void set_collect_mol_counts(std::shared_ptr<ScaffoldNetworkParamsLocal> &params, bool input);
+
+  bool get_include_generic_scaffolds(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_include_generic_bond_scaffolds(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_include_scaffolds_without_attachments(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_include_scaffolds_with_attachments(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_keep_only_first_fragment(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_prune_before_fragmenting(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_flatten_isotopes(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_flatten_chirality(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_flatten_keep_largest(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
+  bool get_collect_mol_counts(const std::shared_ptr<ScaffoldNetworkParamsLocal> &params);
 
   using ScaffoldNetworkClass = ScaffoldNetwork::ScaffoldNetwork;
 
   std::shared_ptr<ScaffoldNetworkClass> default_scaffold_network();
+
+  std::shared_ptr<ScaffoldNetworkClass> create_scaffold_network(const std::shared_ptr<ROMol> &mol, const std::shared_ptr<ScaffoldNetworkParamsLocal> &scaffold_network_params) {
+    throw std::invalid_argument("sup");
+  }
+
+  void update_scaffold_network(const std::shared_ptr<ROMol> &mol, std::shared_ptr<ScaffoldNetworkClass> &scaffold_network, const std::shared_ptr<ScaffoldNetworkParamsLocal> &scaffold_network_params);
+
+//        pub fn update_scaffold_network(
+//            mol: &SharedPtr<ROMol>,
+//            scaffold_network: &mut SharedPtr<ScaffoldNetworkClass>,
+//            scaffold_network_params: &SharedPtr<ScaffoldNetworkParamsLocal>,
+//        );
 }

rdkit-sys/wrapper/src/scaffold_network.cc

@@ -25,39 +25,39 @@ namespace RDKit {
     params->includeGenericScaffolds = input;
   }
 
-  void include_generic_bond_scaffolds(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_include_generic_bond_scaffolds(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->includeGenericBondScaffolds = input;
   }
 
-  void include_scaffolds_without_attachments(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_include_scaffolds_without_attachments(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->includeScaffoldsWithoutAttachments = input;
   }
 
-  void include_scaffolds_with_attachments(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_include_scaffolds_with_attachments(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->includeScaffoldsWithAttachments = input;
   }
 
-  void keep_only_first_fragment(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_keep_only_first_fragment(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->keepOnlyFirstFragment = input;
   }
 
-  void prune_before_fragmenting(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_prune_before_fragmenting(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->pruneBeforeFragmenting = input;
   }
 
-  void flatten_isotopes(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_flatten_isotopes(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->flattenIsotopes = input;
   }
 
-  void flatten_chirality(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_flatten_chirality(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->flattenChirality = input;
   }
 
-  void flatten_keep_largest(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_flatten_keep_largest(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->flattenKeepLargest = input;
   }
 
-  void collect_mol_counts(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
+  void set_collect_mol_counts(std::shared_ptr<ScaffoldNetworkParams> &params, bool input) {
     params->collectMolCounts = input;
   }
 
@@ -68,4 +68,41 @@ namespace RDKit {
     return std::shared_ptr<ScaffoldNetworkClass>(scaffold_network);
   }
 
+  bool get_include_generic_scaffolds(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->includeGenericScaffolds;
+  }
+  bool get_include_generic_bond_scaffolds(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->includeGenericBondScaffolds;
+  }
+  bool get_include_scaffolds_without_attachments(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->includeScaffoldsWithoutAttachments;
+  }
+  bool get_include_scaffolds_with_attachments(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->includeScaffoldsWithAttachments;
+  }
+  bool get_keep_only_first_fragment(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->keepOnlyFirstFragment;
+  }
+  bool get_prune_before_fragmenting(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->pruneBeforeFragmenting;
+  }
+  bool get_flatten_isotopes(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->flattenIsotopes;
+  }
+  bool get_flatten_chirality(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->flattenChirality;
+  }
+  bool get_flatten_keep_largest(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->flattenKeepLargest;
+  }
+  bool get_collect_mol_counts(const std::shared_ptr<ScaffoldNetworkParams> &params) {
+    return params->collectMolCounts;
+  }
+
+  void update_scaffold_network(const std::shared_ptr<ROMol> &mol, std::shared_ptr<ScaffoldNetworkClass> &scaffold_network, const std::shared_ptr<ScaffoldNetworkParams> &scaffold_network_params) {
+    std::vector<ROMol> mols;
+    mols.push_back(*mol);
+    ScaffoldNetwork::updateScaffoldNetwork(&mols, *scaffold_network, *scaffold_network_params);
+  }
+
 }

src/lib.rs

@@ -16,6 +16,9 @@ pub use mol_standardize::*;
 mod periodic_table;
 pub use periodic_table::*;
 
+mod scaffold_network;
+pub use scaffold_network::*;
+
 mod substruct_match;
 pub use substruct_match::*;
 

src/scaffold_network/mod.rs

@@ -0,0 +1,5 @@
+mod scaffold_network;
+pub use scaffold_network::*;
+
+mod scaffold_network_params;
+pub use scaffold_network_params::*;

src/scaffold_network/scaffold_network.rs

@@ -0,0 +1,19 @@
+use cxx::SharedPtr;
+
+pub struct ScaffoldNetwork {
+    ptr: SharedPtr<rdkit_sys::scaffold_network_ffi::ScaffoldNetworkClass>,
+}
+
+impl Default for ScaffoldNetwork {
+    fn default() -> Self {
+        Self {
+            ptr: rdkit_sys::scaffold_network_ffi::default_scaffold_network(),
+        }
+    }
+}
+
+impl ScaffoldNetwork {
+    pub fn new() -> Self {
+        Self::default()
+    }
+}