#ball82_data = bbtmio.read_ball_file(ball_fn+'82') bbtmio.write_displacement_file(bbtmio.get_ball_coords(ball_data), bbtmio.get_ball_coords(ball_pdb_data), dfn) print( '\tFile '+pdbcode+'.displacement written.\n' ) ################################################ # write extended ball and stick including supporting balls and sticks print( '\tPreparing extended ball and stick files for DSM analysis' ) extballfn = pdbfn[:-4]+'.balls.ext' extstickfn = pdbfn[:-4]+'.sticks.ext' if os.path.isfile(extballfn) and os.path.isfile(extstickfn) and not args['overwrite']: print( '\tFile '+pdbcode+'.balls.ext and '+pdbcode+'.sticks.ext exists. Nothing changed.\n' ) else: bbtmio.write_extended_files(ball_fn, stick_fn, extballfn, extstickfn) #bbtmio.write_extended_files(pdbfn[:-4]+'.balls', pdbfn[:-4]+'.sticks', extballfn, extstickfn) print( '\tFile '+pdbcode+'.balls.ext and '+pdbcode+'.sticks.ext written.\n' ) # # trim the ball outside TM # TODO # if args['trim']: # print( '\tTrimming non TM parts in the ball and stick files' ) # balltrim_fn = ball_fn + '.trim' # #ballpdbtrim_fn = ball_pdb_fn + '.trim' # sticktrim_fn = stick_fn + '.trim' # extballtrim_fn = extballfn + '.trim' # extsticktrim_fn = extstickfn + '.trim' # if os.path.isfile(balltrim_fn) and os.path.isfile(sticktrim_fn) and os.path.isfile(extballtrim_fn) and os.path.isfile(extballtrim_fn) and not args['overwrite']: # print( '\tTrimmed file of '+pdbcode+' exists. Nothing changed.\n' )
import os
import glob
import random
# ignore annoying warnings from biopython
import warnings
from Bio import BiopythonWarning
warnings.simplefilter('ignore', BiopythonWarning)
# add the script path
import sys
sys.path.append(os.path.abspath(os.path.dirname(__file__))+'/../../../pyscripts/')
import bbtmml
import bbtmio
import bbtmequs
from typeutils import *
datapath = '../../../dataubuntu/'
codes = [ '1BXW', '1FEP', '1I78', '1K24', '1KMO', '1NQE', '1P4T' ]
for coden in codes:
restingballfn = datapath+'testdata/'+coden+'.balls.ideallarge'
stickfn = datapath+coden+'.sticks'
extrestingballfn = datapath+'testdata/'+coden+'.balls.ideallarge.ext'
extstickfn = datapath+'testdata/'+coden+'.sticks.ideallarge.ext'
bbtmio.write_extended_files(restingballfn, stickfn, extrestingballfn, extstickfn)
import os
import glob
import random
# ignore annoying warnings from biopython
import warnings
from Bio import BiopythonWarning
warnings.simplefilter("ignore", BiopythonWarning)
# add the script path
import sys
sys.path.append(os.path.abspath(os.path.dirname(__file__)) + "/../../../pyscripts/")
import bbtmml
import bbtmio
import bbtmdsm
from typeutils import *
testset = ["1I78", "1T16", "1FEP", "1BXW", "2F1C", "1QJ8", "1NQE", "1UYN"]
for coden in testset:
ballfn = "../../../data/testdata/" + coden + ".balls.ideallarge"
stickfn = "../../../data/" + coden + ".sticks"
newballfn = "../../../data/testdata/" + coden + ".balls.ideallarge.ext"
newstickfn = "../../../data/testdata/" + coden + ".sticks.ideallarge.ext"
bbtmio.write_extended_files(ballfn, stickfn, newballfn, newstickfn)