From bc229cda0bc87b242086cf323bf91c4d61400b48 Mon Sep 17 00:00:00 2001
From: Wenping Guo <ybyygu@gmail.com>
Date: Tue, 13 Jun 2023 08:54:47 +0800
Subject: [PATCH] rebond with options

---
 src/cli.rs | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/cli.rs b/src/cli.rs
index 32f6d16..20a451a 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -300,11 +300,10 @@ impl Commander {
             // }
             GoshCmd::Rebond { bond_tolerance } => {
                 self.check()?;
-                if let Some(r) = bond_tolerance {
-                    std::env::set_var("GCHEMOL_REBOND_BOND_TOLERANCE", format!("{}", r));
-                }
+                let mut options = Molecule::rebond_options();
+                options.bond_tolerance = *bond_tolerance;
                 for mol in self.molecules.iter_mut() {
-                    mol.rebond();
+                    mol.rebond_with_options(&options);
                     println!("Created {} bonds", mol.nbonds());
                 }
             }