From f7bb6c0091851323c2f9755b25d04a51d88db93d Mon Sep 17 00:00:00 2001 From: Kazuya Ujihara Date: Tue, 2 Dec 2025 04:45:43 +0000 Subject: [PATCH] fix writeFormatPDB for Cl and Br atom --- src/pmx/ligand_alchemy.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/pmx/ligand_alchemy.py b/src/pmx/ligand_alchemy.py index eccdd44a..94c82de1 100644 --- a/src/pmx/ligand_alchemy.py +++ b/src/pmx/ligand_alchemy.py @@ -92,12 +92,12 @@ def writeFormatPDB(fname,m,title="",nr=1,bStrict=False): for atom in m.atoms: foo = cp.deepcopy(atom) # chlorine - if( 'CL' in atom.name or 'Cl' in atom.name or 'cl' in atom.name ): - foo.name = "CL"#+" " + if atom.name.upper().startswith("CL"): + foo.name = ("Cl" + atom.name[2:])[:atNameLen] print(foo,file=fp) # bromine - elif( 'BR' in atom.name or 'Br' in atom.name or 'br' in atom.name ): - foo.name = "BR"#+" " + elif atom.name.upper().startswith("BR"): + foo.name = ("Br" + atom.name[2:])[:atNameLen] print(foo,file=fp) elif( len(atom.name) > atNameLen): # too long atom name foo = cp.deepcopy(atom)