parser.add_option("--native",dest="native",help="native structure")
parser.add_option("--CA",dest="ca",help="calculate CA rmsd",default=False,action="store_true")
parser.add_option("--res",dest="residues",help="list of residues to use",default="")
parser.add_option("--table",dest="table",help="output a tab delimited table",default="")
parser.add_option("--chain",dest="chain",help="calculate RMSD of only 1 chain",default="")
parser.add_option("--term",dest="term",help="score term to use")
(options,args)=parser.parse_args()
if len(args) <1:
parser.error("specify at least 1 protein to compare to native")
print "calculating RMSD between ", len(args), " decoys and the native structure ", options.native
if options.ca:
print "calculating CA RMSD"
else:
print "calculating all-atom RMSD"
native = util.load_pdb(options.native)
score_rmsd = []
name_score_rmsd =[]
for decoy_file in args:
tag = decoy_file.split("/").pop().split(".")[0]
decoy = util.load_pdb(decoy_file.rstrip())
score_table = rosettaScore.ScoreTable(decoy_file)
rms = pdbStat.calculate_rms(native,decoy,options.ca,options.residues,"",options.chain)
score = score_table.get_score(0,options.term) #0 is the pose energy
score_rmsd.append( (rms,score) )
name_score_rmsd.append( (decoy_file,rms,score) )
make_table(name_score_rmsd,options.table)
usage = "%prog [options] alignment_file.aln template.pdb output.pdb"
parser=OptionParser(usage)
parser.add_option("--template",dest="template",help="name of the template sequence", default="template")
parser.add_option("--target", dest ="target",help="name of the target sequence",default="target")
parser.add_option("--chain",dest="chain",help="chain to thread pdb around",default="A")
parser.add_option("--align_format",dest="align_format",help="alignment file format, choose from clustal, emboss, fasta, fasta-m10,ig,nexus,phylip,stockholm. See http://biopython.org/wiki/AlignIO for details",default="clustal")
(options,args)= parser.parse_args()
if len(args) != 3:
parser.error("you must specify an alignment file, template pdb, and output pdb")
#read in our input files
alignment_file = fileutil.universal_open(args[0],'rU')
alignment_data = AlignIO.read(alignment_file,options.align_format)
alignment_file.close()
template_struct = util.load_pdb(args[1])
#if len(alignment_data) != 2:
# sys.exit("alignment file must have exactly 2 sequences!")
#find all the gaps, get numeric IDs from the string tags in the alignment file
try:
template_gaps = alignment.find_gaps(alignment_data,options.template)
except LookupError:
sys.exit("could not find "+options.template+" in alignment file")
try:
target_gaps = alignment.find_gaps(alignment_data,options.target)
except LookupError:
sys.exit("could not find "+options.target+" in alignment file")
try:
template_id = alignment.get_id_from_tag(alignment_data,options.template)
#!/usr/bin/env python2.5
import array
import Bio.PDB
from optparse import OptionParser
from rosettautil.protein import util
from rosettautil.rosetta import loops
from rosettautil.util import fileutil
usage = "%prog [options] loopfile.txt input.pdb output.pdb"
parser = OptionParser(usage)
(options, args) = parser.parse_args()
loop_manager = loops.RosettaLoopManager()
loop_manager.read(args[0])
input_struct = util.load_pdb(args[1])
zero_triplet = array.array('f', [0.0, 0.0, 0.0])
for atom in input_struct.get_atoms():
resnum = atom.get_parent().get_id()[1]
if loop_manager.is_res_in_loop(resnum):
atom.set_coord(zero_triplet)
atom.set_occupancy(-1.0)
pdb_io = Bio.PDB.PDBIO()
pdb_io.set_structure(input_struct)
outfile = fileutil.universal_open(args[2], 'w')
pdb_io.save(outfile)
outfile.close()
default=False,
action="store_true")
parser.add_option("--norestart",
dest="norestart",
help="don't start renumbering at each chain, default=False",
default=False,
action="store_true")
parser.add_option(
"--keep-table",
dest="table",
help="Preserve the rosetta score table at the bottom of the pdb",
action="store_true",
default=False)
(options, args) = parser.parse_args()
struct = util.load_pdb(args[0])
try:
residue_id = int(options.start)
except ValueError:
sys.exit("residue number specified with -n must be an integer")
chain_id = ""
for residue in struct.get_residues():
chain = residue.get_parent()
if (chain_id != chain.get_id() and not options.norestart):
chain_id = chain.get_id()
residue_id = int(options.start)
#print chain.get_id()
if (options.preserve):
hetero = residue.id[0]
insert = residue.id[2]
usage = "%prog [options] native.pdb designed.pdb"
parser = OptionParser(usage)
parser.add_option(
"--best",
dest="best",
help="print out the top n mutations in terms of total energy, default = 10",
default=10)
parser.add_option(
"--worst",
dest="worst",
help=
"print out the bottom n mutations in terms of total energy, default = 10",
default=10)
(options, args) = parser.parse_args()
native_struct = util.load_pdb(args[0])
designed_struct = util.load_pdb(args[1])
native_residues = native_struct.get_residues()
designed_residues = designed_struct.get_residues()
native_scores = rosettaScore.ScoreTable(args[0])
designed_scores = rosettaScore.ScoreTable(args[1])
native_sequence = ""
designed_sequence = ""
concensus = ""
conserved_count = 0.0
total_count = 0.0
class mutation:
def __init__(self,resno,nat,des,delta,nat_score,des_score):
self.native=nat
self.designed=des
self.delta=delta
self.native_score=nat_score
self.designed_score = des_score
self.resno = resno
usage = "%prog [options] native.pdb designed.pdb"
parser = OptionParser(usage)
parser.add_option("--best",dest="best",help="print out the top n mutations in terms of total energy, default = 10",default=10)
parser.add_option("--worst",dest="worst",help="print out the bottom n mutations in terms of total energy, default = 10",default=10)
(options,args) = parser.parse_args()
native_struct = util.load_pdb(args[0])
designed_struct = util.load_pdb(args[1])
native_residues = native_struct.get_residues()
designed_residues = designed_struct.get_residues()
native_scores = rosettaScore.ScoreTable(args[0])
designed_scores = rosettaScore.ScoreTable(args[1])
native_sequence = ""
designed_sequence = ""
concensus = ""
conserved_count = 0.0
dest="chain",
help="calculate RMSD of only 1 chain",
default="")
parser.add_option("--term", dest="term", help="score term to use")
(options, args) = parser.parse_args()
if len(args) < 1:
parser.error("specify at least 1 protein to compare to native")
print "calculating RMSD between ", len(
args), " decoys and the native structure ", options.native
if options.ca:
print "calculating CA RMSD"
else:
print "calculating all-atom RMSD"
native = util.load_pdb(options.native)
score_rmsd = []
name_score_rmsd = []
for decoy_file in args:
tag = decoy_file.split("/").pop().split(".")[0]
decoy = util.load_pdb(decoy_file.rstrip())
score_table = rosettaScore.ScoreTable(decoy_file)
rms = pdbStat.calculate_rms(native, decoy, options.ca, options.residues,
"", options.chain)
score = score_table.get_score(0, options.term) #0 is the pose energy
score_rmsd.append((rms, score))
name_score_rmsd.append((decoy_file, rms, score))
make_table(name_score_rmsd, options.table)
from rosettautil.rosetta import rosettaScore
from rosettautil.protein import util
from rosettautil.util import fileutil
from Bio.PDB import *
from optparse import OptionParser
usage = "%prog input.pdb output.pdb"
parser= OptionParser(usage)
parser.add_option("-n",dest="start",help="residue number to start with, default is 1",default=1)
parser.add_option("--preserve",dest="preserve",help="preserve insertion code and heteroflags",default=False, action="store_true")
parser.add_option("--norestart",dest="norestart",help="don't start renumbering at each chain, default=False",default=False, action="store_true")
parser.add_option("--keep-table",dest="table",help="Preserve the rosetta score table at the bottom of the pdb",action="store_true",default=False)
(options, args) = parser.parse_args()
struct = util.load_pdb(args[0])
try:
residue_id = int(options.start)
except ValueError:
sys.exit("residue number specified with -n must be an integer")
chain_id = ""
for residue in struct.get_residues():
chain = residue.get_parent()
if(chain_id != chain.get_id() and not options.norestart):
chain_id = chain.get_id()
residue_id=int(options.start)
#print chain.get_id()
if(options.preserve):
hetero = residue.id[0]
insert = residue.id[2]
