rebond: support vmd scheme with param bond_scale_factor

Author: ybyygu

src/lib.rs

@@ -739,8 +739,8 @@ impl PyMolecule {
         Ok(n)
     }
 
-    #[pyo3(signature = (ignore_pbc=false, bond_tolerance=None, cov_radius_scale_factor=None, bonding_scheme=None))]
-    #[pyo3(text_signature = "(ignore_pbc=False, bond_tolerance=None, radius_scale_factor=None, bonding_scheme=None)")]
+    #[pyo3(signature = (ignore_pbc=false, bond_tolerance=None, bond_scale_factor=None, bonding_scheme=None))]
+    #[pyo3(text_signature = "(ignore_pbc=False, bond_tolerance=None, bond_scale_factor=None, bonding_scheme=None)")]
     /// Recalculates all bonds in molecule based on interatomic
     /// distances and covalent radii. For periodic system, the bonds
     /// are determined in miniumu image convention.
@@ -749,27 +749,23 @@ impl PyMolecule {
     /// * ignore_pbc: force to ignore periodicity when search nearest
     ///   neighbors. The default is False.
     /// * bonding_scheme: the bonding scheme for rebond. Avaialbe scheme
-    ///   includes jmol and multiwfn.
+    ///   includes jmol, multiwfn and vmd.
     /// * bond_tolerance: the bonding tolerance used in jmol scheme. The
     ///   default value is 0.45.
-    /// * cov_radius_scale_factor: set the scale factor for covalent
-    ///   radius for perception of bond in multiwfn scheme. The
-    ///   default value is 1.15.
+    /// * bond_scale_factor: set the scale factor for covalent or vdw radius
+    ///   for bond perception, only relevant in multiwfn or vmd scheme. The
+    ///   default value is 1.15 for multiwfn and 0.6 for vmd.
     pub fn rebond(
         &mut self,
         ignore_pbc: bool,
         bond_tolerance: Option<f64>,
-        cov_radius_scale_factor: Option<f64>,
+        bond_scale_factor: Option<f64>,
         bonding_scheme: Option<String>,
     ) {
         let mut options = Molecule::rebond_options();
         options.ignore_pbc = ignore_pbc;
-        if let Some(v) = bond_tolerance {
-            options.bond_tolerance = v;
-        }
-        if let Some(v) = cov_radius_scale_factor {
-            options.cov_radius_scale_factor = v;
-        }
+        options.bond_tolerance = bond_tolerance;
+        options.bond_scale_factor = bond_scale_factor;
         if let Some(s) = bonding_scheme {
             options.set_bonding_scheme(&s);
         }