silentsketchparamsfrompdbs

#!/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
import stat
import math
import shutil
import io
from Bio.PDB import MMCIFParser, PDBIO

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



pdb_buffers = []
if ( stat.S_ISFIFO(os.stat("/dev/stdin").st_mode) ):
    pdb_buffers += sys.stdin.readlines()
pdb_buffers += sys.argv[1:]

if (len(pdb_buffers) == 0):
    eprint("")
    eprint('silentsketchparamsfrompdbs by bcov - generates really sketchy params files for pdbs WITHOUT rosetta')
    eprint("Usage:")
    eprint("        cat list_of_pdbs.list | silentsketchparamsfrompdbs")
    eprint("                             or")
    eprint("        silentsketchparamsfrompdbs 1.pdb 2.pdb 3.pdb ")
    sys.exit(1)


pdbs = []
for line in pdb_buffers:
    line = line.strip()
    if (len(line) == 0):
        continue
    sp = line.split(" ")
    for pdb in sp:
        pdbs.append(pdb)



pre_tags = [os.path.basename(pdbs) for pdbs in pdbs]

if (len(pdbs) != len(set(pdbs))):
    eprint("silentsketchparamsfrompdbs: Warning: %i duplicate paths specified"%(len(pdbs) - len(set(pdbs))))




written_params = {}
to_print = []

first = True
for pdb in pdbs:

    try:
        pdb_lines = open(pdb).readlines()
    except:
        eprint("silentsketchparamsfrompdbs: Error! pdb couldn't be opened", pdb)
        continue

    if pdb.endswith('.cif'):
        parser = MMCIFParser(QUIET=True)
        structure = parser.get_structure(pdb, io.StringIO(''.join(pdb_lines)))
        for residue in structure.get_residues():
            if len(residue.resname) > 3:
                residue.resname = residue.resname[:3]
        pdb_io = PDBIO()
        pdb_io.set_structure(structure)
        pdb_buffer = io.StringIO()
        pdb_io.save(pdb_buffer)
        pdb_lines = pdb_buffer.getvalue().splitlines(keepends=True)



    use_pdb_lines = use_pdb_lines = [line for line in pdb_lines if line.startswith(('CONECT', 'TER', 'HETATM'))]

    raw_params_dict = silent_tools.generate_params_for_pdb(use_pdb_lines)

    for name3, raw_params in raw_params_dict.items():
        if name3 in written_params:
            eprint(f'{name3}.params already written')
            continue

        with open(name3 + '.params', 'w') as f:
            f.write(raw_params)
        to_print.append(f'-extra_res_fa {name3}.params')

print(' '.join(to_print))