feat(hphobic): detect hydrophobic contacts (#4)

* feat(hphobic): detect hydrophobic contacts

* docs(readme): finished hydrophobic contact

README.md

@@ -11,12 +11,13 @@ This is a port of the [Arpeggio](https://github.com/PDBeurope/arpeggio/) library
 - Identify protein-protein interactions
   - [x] Steric clashes
   - [x] VdW interactions
-  - [ ] Hydrophobic interactions
+  - [x] Hydrophobic interactions
   - [ ] Aromatic interactions
   - [ ] Cation-pi interactions
   - [x] Ionic interactions
   - [x] Hydrogen bonds
   - [x] Weak hydrogen bonds
+  - [ ] Disulfide bonds
   - [ ] Covalent bonds
 - [ ] Output results in various formats (e.g., JSON, CSV)
 - [ ] Bundle into a `PyO3` extension module

src/interactions/complex.rs

@@ -1,7 +1,7 @@
-use super::hbond::*;
-use super::ionic::*;
-use super::structs::{InteractingEntity, Interaction, ResultEntry};
-use super::vdw::*;
+use super::{
+    find_hydrogen_bond, find_hydrophobic_contact, find_ionic_bond, find_vdw_contact,
+    find_weak_hydrogen_bond, InteractingEntity, Interaction, ResultEntry,
+};
 use crate::utils::parse_groups;
 
 use pdbtbx::*;
@@ -136,6 +136,16 @@ impl Interactions for InteractionComplex {
                 });
                 atomic_contacts.extend(ionic_bonds);
 
+                // Hydrophobic contacts
+                let hydrophobic_contacts =
+                    find_hydrophobic_contact(&x.0, &x.1).map(|intxn| ResultEntry {
+                        interaction: intxn,
+                        ligand: hierarchy_to_entity(&x.0),
+                        receptor: hierarchy_to_entity(&x.1),
+                        distance: x.0.atom().distance(x.1.atom()),
+                    });
+                atomic_contacts.extend(hydrophobic_contacts);
+
                 Some(atomic_contacts)
             })
             .flatten()

src/interactions/hydrophobic.rs

@@ -0,0 +1,68 @@
+use super::structs::Interaction;
+
+use pdbtbx::*;
+
+const HYDROPHOBIC_CONTACT_DIST: f64 = 4.5;
+
+/// Search for hydrophobic contacts.
+///
+/// Check if the distance between two hydrophobics is within [`HYDROPHOBIC_CONTACT_DIST`].
+pub fn find_hydrophobic_contact(
+    entity1: &AtomConformerResidueChainModel,
+    entity2: &AtomConformerResidueChainModel,
+) -> Option<Interaction> {
+    let e1_atom = entity1.atom();
+    let e2_atom = entity2.atom();
+    match is_hydrophobic(entity1.residue().name().unwrap(), e1_atom.name())
+        & is_hydrophobic(entity2.residue().name().unwrap(), e2_atom.name())
+        & (e1_atom.distance(e2_atom) <= HYDROPHOBIC_CONTACT_DIST)
+    {
+        true => Some(Interaction::HydrophobicContact),
+        false => None,
+    }
+}
+
+/// Check if the entity has an atom that belongs to the hydrophobic category.
+fn is_hydrophobic(res_name: &str, atom_name: &str) -> bool {
+    // Carbon beta of all other than Glycine/Serine
+    if (atom_name == "CB") & (res_name != "SER") {
+        return true;
+    }
+    matches!(
+        (res_name, atom_name),
+        ("ARG", "CG") | ("GLN", "CG")
+            | ("GLU", "CG")
+            | ("ILE", "CG1")
+            | ("ILE", "CD1")
+            | ("ILE", "CG2")
+            | ("LEU", "CG")
+            | ("LEU", "CD1")
+            | ("LEU", "CD2")
+            | ("LYS", "CG")
+            | ("LYS", "CD")
+            | ("MET", "CG")
+            | ("MET", "SD") // sulfur in CYS has a hydrogen and is polarized
+            | ("MET", "CE")
+            | ("PHE", "CG")
+            | ("PHE", "CD1")
+            | ("PHE", "CD2")
+            | ("PHE", "CE1")
+            | ("PHE", "CE2")
+            | ("PHE", "CZ")
+            | ("PRO", "CG")
+            | ("THR", "CG2")
+            | ("TRP", "CG")
+            | ("TRP", "CD2")
+            | ("TRP", "CE3")
+            | ("TRP", "CZ3")
+            | ("TRP", "CH2")
+            | ("TRP", "CZ2")
+            | ("TYR", "CG")
+            | ("TYR", "CD1")
+            | ("TYR", "CD2")
+            | ("TYR", "CE1")
+            | ("TYR", "CE2")
+            | ("VAL", "CG1")
+            | ("VAL", "CG2")
+    )
+}

src/interactions/mod.rs

@@ -1,5 +1,12 @@
 pub mod complex;
 pub mod hbond;
+pub mod hydrophobic;
 pub mod ionic;
 pub mod structs;
 pub mod vdw;
+
+use hbond::{find_hydrogen_bond, find_weak_hydrogen_bond};
+use hydrophobic::find_hydrophobic_contact;
+use ionic::find_ionic_bond;
+use structs::*;
+use vdw::find_vdw_contact;