xyzedit command line arguments

[eneas77]

Hi,

I´d like to concatenate a large list of protein+ligand xyz files and it is not intuitive from the Tinker manual how to run in a single line of code from command line with xyzedit.

Any hints of how to use option 22 together with 2.xyz and 2.key files invoking xyzedit with appropiate arguments?

Something like xyzedit first.xyz 22 second.xyz

Thanks a lot

E77

[pren]

Xyzedit is interactive. You can hit enter and it will ask you for inputs.

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________________________________ From: eneas77 ***@***.***> Sent: Thursday, May 26, 2022 3:10 AM To: TinkerTools/tinker Cc: Subscribed Subject: [TinkerTools/tinker] xyzedit command line arguments (Issue #109) Hi, I´d like to concatenate a large list of protein+ligand xyz files and it is not intuitive from the Tinker manual how to run in a single line of code from command line with xyzedit. Any hints of how to use option 22 together with 2.xyz and 2.key files invoking xyzedit with appropiate arguments? Something like xyzedit first.xyz 22 second.xyz Thanks a lot E77 — Reply to this email directly, view it on GitHub<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FTinkerTools%2Ftinker%2Fissues%2F109&data=05%7C01%7C%7Cf5dd0b8d8a4d4e949eba08da3eef3477%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C637891494357249630%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XsgxjZxyS9Cq7m9Sll8MfXne8mCX3plaUTxadWmNVRY%3D&reserved=0>, or unsubscribe<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABNC6XXJLRTYYJVPGFZFOBDVL4WXLANCNFSM5XADYJXA&data=05%7C01%7C%7Cf5dd0b8d8a4d4e949eba08da3eef3477%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C637891494357249630%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0Kll2J2uUYB6jQOAcQFr3gq3D2DpavVspZWXkbFdMWk%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[zjing7]

Hello, Tinker takes standard input, so you can make use of pipe. For example, echo -e "22\nsecond.xyz\n22\nthird.xyz\n\n" | xyzedit first.xyz

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On Thu, May 26, 2022 at 3:10 AM eneas77 ***@***.***> wrote: Hi, I´d like to concatenate a large list of protein+ligand xyz files and it is not intuitive from the Tinker manual how to run in a single line of code from command line with xyzedit. Any hints of how to use option 22 together with 2.xyz and 2.key files invoking xyzedit with appropiate arguments? Something like xyzedit first.xyz 22 second.xyz Thanks a lot E77 — Reply to this email directly, view it on GitHub <#109>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABW6OEZ523OI6CFLMLB4SI3VL4WXLANCNFSM5XADYJXA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Zhifeng (Francis) Jing

[jayponder]

I think what you may be asking (?) is simply how to get the XYZEDIT program to exit after you run:

 xyzedit first.xyz 22 second.xyz

If you just enter that command in a terminal, then the program will be waiting for you to enter the next XYZEDIT option that you want to apply. A way to get it to exit when running from the command line is to enter "0" for the next option. This allows the program to drop through and quit. So you should use something like:

 xyzedit first.xyz 22 second.xyz 0

Then the program will exit correctly, and the merged and renumbered coordinates will be written to the file "first.xyz_2".

[eneas77]

Thanks a lot, it worked!!

E77