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haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
384 stars 113 forks source link

input PDB file #73

Closed fedeserral closed 4 years ago

fedeserral commented 4 years ago

Hi! I am new using this tool. I just wanna know if a list of PDB IDs can be used as input file or I should use just one at time.

Thanks!!

joaomcteixeira commented 4 years ago

Hi @fedeserral

It depends, some tools accept several pdb files such as pdb_merge. Other accept only one such as pdb_chain.

You can view each tool help with pdb_chain -h for example.

Assuming you are on Linux (or bash), you can do the following to use a tool on several PDBs, say you want to change the chain ids of every PDB file in a folder to new_* files, navigate to that folder, then (I am assuming here you know a bit of bash):

for PDB in *.pdb; do pdb_chain -A $PDB > new_$PDB; done

If you are on Windows @JoaoRodrigues can help you :wink:

JoaoRodrigues commented 4 years ago

Hi @fedeserral

As @joaomcteixeira said, most tools work on one PDB file at a time, except for a few exceptions. You can use a for-loop in BASH for example do get multiple files processed. If you are on windows, I recommend you get the Windows Subsystem for Linux (WSL) installed, or alternatively download and install cmder (full version). You'll get a proper BASH shell with full interoperability with your Windows file system.