Petro, There isn't currently a way to query bonds from within the PyMOL API. However, you can travel a Pythonic data structure derived from PyMOL's internal state: for bond in cmd.get_model().bond: print bond.index ...where the index displayed corresponds to PyMOL's internal atom index... iterate all, print (resn, resi, name, index) -- DeLano Scientific LLC Subscriber Support Services mailto:[email protected] "Not yet a PyMOL Subscriber, but want to support the project? Email [email protected] to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD
_____ From: [email protected] [mailto:[email protected]] On Behalf Of Piter_ Sent: Wednesday, October 17, 2007 3:52 AM To: [email protected] Subject: [PyMOL] is there bond ? How to check? Hi all I want to write a script like this: if there is bond between atom1 and atom2 do something elif there is no bond between atom1 and atom2 do something else. But I don't know how to check the bond existence between atoms in Pymol. Thanks in advance for any idea how to do it. Petro
