silentsketchextractcaprotein

#!/usr/bin/env python

import os
import sys
# if you pip installed this is wrong but you have silent_tools installed anyways
silent_tools_dir = os.path.dirname(os.path.realpath(__file__))
if silent_tools_dir not in sys.path:
    sys.path.append(silent_tools_dir)

import silent_tools
from silent_tools import eprint

# Don't throw an error when someone uses head
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE, SIG_DFL) 

if (len(sys.argv) == 1):
    eprint("")
    eprint('silentsketchextractcaprotein by bcov - a tool to allow you extract the CA atoms from a protein silent file')
    eprint("Usage:")
    eprint("        cat list_of_tags.list | silentslice myfile.silent > new.silent")
    eprint("                             or")
    eprint("        silentslice myfile.silent tag1 tag2 tag3 > new.silent")
    sys.exit(1)



silent_file = sys.argv[1]

silent_index = silent_tools.get_silent_index( silent_file )

with open(silent_file, errors='ignore') as sf:
    for tag in silent_index['tags']:

        if ( tag not in silent_index['index'] ):
            eprint("silentsketchextractcaprotein: Unable to find tag: %s"%tag)
            continue
        structure = silent_tools.get_silent_structure_file_open( sf, silent_index, tag )

        sequence = "".join(silent_tools.get_sequence_chunks(structure))
        try:
            cas = silent_tools.sketch_get_cas_protein_struct(structure)
        except:
            eprint("silentsketchextractcaprotein: %s corrupt"%(tag))

        lines = silent_tools.write_pdb_atoms( cas, sequence, ["CA"] )

        with open(tag + ".pdb", "w") as f:
            f.write("".join(lines))


        print(tag)