def __init__(self,path,mode="score"):
"""Parse a PSSM file from BLAST into a usable datastructure"""
self.pssmmap = {}
self.native_sequence = {}
pssmfile = fileutil.universal_open(path,'r')
pssmfile.readline()
pssmfile.readline()
header = pssmfile.readline()
header = header.split()
header = header[0:21]
for line in pssmfile:
#print line
line = line.split()
#self.native_sequence.append(
if len(line) == 0:
break
res_num = int(line[0])
res_id = line[1]
self.native_sequence[res_num] = res_id
line_map = {}
if mode == "score":
data = line[2:23]
if mode == "percent":
data = line[22:42]
#print data
for resname,score in zip(header,data):
line_map[resname] = int(score)
self.pssmmap[res_num] = line_map
pssmfile.close()
def __init__(self,filename):
"""load a param file into a data structure"""
self.atoms = {}
self.bonds = []
self.icoors = {}
infile = fileutil.universal_open(filename,'r')
for line in infile:
if len(line)==0:
continue
line = line.split()
tag = line[0]
if tag =="NAME":
self.name = line[1]
elif tag =="IO_STRING":
self.io_string = line[1]
elif tag == "TYPE":
self.type = line[1]
elif tag == "AA":
self.aa = line[1]
elif tag == "ATOM":
current_atom = Atom(line[1],line[2],line[3],line[4])
self.atoms[line[1]]= current_atom
elif tag == "BOND":
current_bond = Bond(line[1],line[2])
self.bonds.append(current_bond)
self.atoms[line[1]].add_bond(current_bond)
self.atoms[line[2]].add_bond(current_bond)
elif tag == "NBR_ATOM":
self.nbr_atom = line[1]
elif tag == "NBR_RADIUS":
self.nbr_radius = line[1]
elif tag == "ICOOR_INTERNAL":
current_icoor = icoor(line[1],line[2],line[3],line[4],line[5],line[6],line[7])
self.icoors[line[1]]=current_icoor
infile.close()
def load_pdb(path):
"""return a biopython structure object given a pdb file path"""
parser = PDBParser(PERMISSIVE=1)
pdb_file = fileutil.universal_open(path, 'rU')
structure = parser.get_structure(path[0:4], pdb_file)
pdb_file.close()
return structure
def __init__(self, path, mode="score"):
"""Parse a PSSM file from BLAST into a usable datastructure"""
self.pssmmap = {}
self.native_sequence = {}
pssmfile = fileutil.universal_open(path, 'r')
pssmfile.readline()
pssmfile.readline()
header = pssmfile.readline()
header = header.split()
header = header[0:21]
for line in pssmfile:
#print line
line = line.split()
#self.native_sequence.append(
if len(line) == 0:
break
res_num = int(line[0])
res_id = line[1]
self.native_sequence[res_num] = res_id
line_map = {}
if mode == "score":
data = line[2:23]
if mode == "percent":
data = line[22:42]
#print data
for resname, score in zip(header, data):
line_map[resname] = int(score)
self.pssmmap[res_num] = line_map
pssmfile.close()
def load_pdb(path): """return a biopython structure object given a pdb file path""" parser = PDBParser(PERMISSIVE=1) pdb_file = fileutil.universal_open(path,'rU') structure = parser.get_structure(path[0:4],pdb_file) pdb_file.close() return structure
def make_table(name_score_rmsd, out_name):
table = fileutil.universal_open(out_name, 'w')
table.write("file\tscore\tRMSD\n")
for point in name_score_rmsd:
table.write(
str(point[0]) + "\t" + str(point[2]) + "\t" + str(point[1]) + "\n")
table.close()
def read_bcl_file(self,path):
print "This function doesn't work yet"
sys.exit()
out_file = fileutil.universal_open(path,'r')
list_header ="bcl::storage::List<bcl::storage::VectorND2<bcl::math::Vector<double>>>"
vector_header = "bcl::storage::VectorND2<bcl::math::Vector<double>>"
double_header = "bcl::math::Vector<double>"
list_scope = False
vector_scope = False
double_scope = False
def write_file(self,filename):
out_file = fileutil.universal_open(filename,'w')
#write reference energies
out_file.write("METHOD_WEIGHTS\tref")
for key in aa_codes_in_order:
out_file.write("\t"+str(self.ref_energies[key]))
out_file.write("\n")
#write the other weights
for key in self.weights:
out_file.write(key+"\t"+str(self.weights[key])+"\n")
out_file.close()
def write_file(self, filename):
out_file = fileutil.universal_open(filename, 'w')
#write reference energies
out_file.write("METHOD_WEIGHTS\tref")
for key in aa_codes_in_order:
out_file.write("\t" + str(self.ref_energies[key]))
out_file.write("\n")
#write the other weights
for key in self.weights:
out_file.write(key + "\t" + str(self.weights[key]) + "\n")
out_file.close()
def read_file(self, filename):
self.ref_energies = {}
self.weights = {}
in_file = fileutil.universal_open(filename, 'rU')
for line in in_file:
line = line.split()
if line[0] == "METHOD_WEIGHTS":
#Reference energies are ordered by 1 letter name
for aa, value in zip(aa_codes_in_order, line[2:len(line)]):
self.ref_energies[aa] = float(value)
else:
self.weights[line[0]] = float(line[1])
in_file.close()
def read_file(self,filename):
self.ref_energies = {}
self.weights = {}
in_file = fileutil.universal_open(filename,'rU')
for line in in_file:
line = line.split()
if line[0] == "METHOD_WEIGHTS":
#Reference energies are ordered by 1 letter name
for aa, value in zip(aa_codes_in_order,line[2:len(line)]):
self.ref_energies[aa] = float(value)
else:
self.weights[line[0]] = float(line[1])
in_file.close()
def __init__(self, path):
infile = fileutil.universal_open(path, 'r')
table = False
appended_data = False
header = []
self.weights = {}
self.records = {}
for line in infile:
if len(line) == 0:
continue
line = line.split()
if line[0] == "#BEGIN_POSE_ENERGIES_TABLE":
table = True
elif line[0] == "#END_POSE_ENERGIES_TABLE":
appended_data = True
elif table and line[0] == "label":
header = line[1:len(line)]
elif table and line[0] == "weights":
weightline = line[1:len(line)]
for term, weight in zip(header, weightline):
if (weight != "NA"):
weight = float(weight)
self.weights[term] = weight
else:
self.weights[term] = 1.0
elif table and not appended_data:
name = line[0]
if name != "pose":
resid = int(name.split("_").pop())
else:
resid = 0
scores = line[1:len(line)]
scoredict = {}
for term, score in zip(header, scores):
score = float(score)
scoredict[term] = score
self.records[resid] = ScoreRecord(name, resid, scoredict)
elif table and appended_data:
if len(line) < 2:
continue
#all these apply to the whole pose, so we'll extract the scoredict for the pose
#this *must* come after the pose table, so we can get the whole set
term = line[0]
value = line[1]
try:
self.records[0].scores[term] = float(value)
except ValueError:
self.records[0].scores[term] = value
infile.close()
def __init__(self,path):
infile = fileutil.universal_open(path,'r')
table = False
appended_data = False
header=[]
self.weights = {}
self.records = {}
for line in infile:
if len(line) == 0:
continue
line = line.split()
if line[0] == "#BEGIN_POSE_ENERGIES_TABLE":
table = True
elif line[0] == "#END_POSE_ENERGIES_TABLE":
appended_data = True
elif table and line[0] == "label":
header = line[1:len(line)]
elif table and line[0] =="weights":
weightline = line[1:len(line)]
for term, weight in zip(header,weightline):
if(weight != "NA"):
weight = float(weight)
self.weights[term] = weight
else:
self.weights[term] = 1.0
elif table and not appended_data:
name = line[0]
if name != "pose":
resid = int(name.split("_").pop())
else:
resid = 0
scores = line[1:len(line)]
scoredict = {}
for term, score in zip(header,scores):
score = float(score)
scoredict[term] = score
self.records[resid] = ScoreRecord(name,resid,scoredict)
elif table and appended_data:
if len(line) < 2:
continue
#all these apply to the whole pose, so we'll extract the scoredict for the pose
#this *must* come after the pose table, so we can get the whole set
term = line[0]
value = line[1]
try:
self.records[0].scores[term] = float(value)
except ValueError:
self.records[0].scores[term] = value
infile.close()
def read(self,filename,append=False):
"""read a rosetta 3 loop file into the loop manager.
if append=True, add the contents of the loop file to the existing loops"""
if not append:
self.looplist = []
loop_file = fileutil.universal_open(filename,"rU")
for line in loop_file:
fields = line.split()
if line[0] == '#':
continue #this is a comment
if len(fields) <1 :
continue #this is a blank line
if fields[0] != "LOOP":
continue #this is something that is not a loop line
loop = RosettaLoop()
loop.set_loop_from_string(line)
self.looplist.append(loop)
loop_file.close()
def read(self, filename, append=False):
"""read a rosetta 3 loop file into the loop manager.
if append=True, add the contents of the loop file to the existing loops"""
if not append:
self.looplist = []
loop_file = fileutil.universal_open(filename, "rU")
for line in loop_file:
fields = line.split()
if line[0] == '#':
continue #this is a comment
if len(fields) < 1:
continue #this is a blank line
if fields[0] != "LOOP":
continue #this is something that is not a loop line
loop = RosettaLoop()
loop.set_loop_from_string(line)
self.looplist.append(loop)
loop_file.close()
def get_table(path):
"""return the score table from the bottom of a PDB as a list of lines"""
raw_table = []
infile = fileutil.universal_open(path,'r')
table = False
for line in infile:
line_split = line.split()
if len(line_split) <1:
break
if line_split[0] == "#BEGIN_POSE_ENERGIES_TABLE":
table =True
raw_table.append(line)
#elif table and line_split[0] == "#END_POSE_ENERGIES_TABLE":
# raw_table.append(line)
# break
elif table:
raw_table.append(line)
infile.close()
return raw_table
def get_table(path):
"""return the score table from the bottom of a PDB as a list of lines"""
raw_table = []
infile = fileutil.universal_open(path, 'r')
table = False
for line in infile:
line_split = line.split()
if len(line_split) < 1:
break
if line_split[0] == "#BEGIN_POSE_ENERGIES_TABLE":
table = True
raw_table.append(line)
#elif table and line_split[0] == "#END_POSE_ENERGIES_TABLE":
# raw_table.append(line)
# break
elif table:
raw_table.append(line)
infile.close()
return raw_table
def write_bcl_file(self,path):
out_file = fileutil.universal_open(path,'w')
list_header ="bcl::storage::List<bcl::storage::VectorND2<bcl::math::Vector<double>>>"
vector_header = "bcl::storage::VectorND2<bcl::math::Vector<double>>"
double_header = "bcl::math::Vector<double>"
out_file.write(list_header+"\n")
out_file.write(str(len(self.records))+"\n")
for first_col, second_col in self.records:
out_file.write(vector_header+"\n")
out_file.write(double_header+"\n")
out_file.write(str(1)+"\n")
out_file.write(str(first_col)+"\n")
out_file.write(double_header+"\n")
out_file.write(str(1)+"\n")
out_file.write(str(second_col)+"\n")
out_file.close()
def add_file(self, path, ignore_ref=True):
infile = fileutil.universal_open(path, 'r')
header = []
for line in infile:
if len(line) == 0:
continue
line = line.split()
if line[0] == "SCORES": #this is an atom tree diff file
tag = line[1]
if ignore_ref and tag[0:5] == "%REF%":
continue
record = PoseScoreRecord(tag)
record.set_file(path)
scorefields = line[2:len(line)]
try:
for pair in score_pairs(scorefields):
record.add_score(*pair)
self.records[tag] = record
except ValueError:
print "theres some problem with this score line, possible corruption, skipping line"
continue
#elif
elif line[0] == "SCORE:": #this is a normal silent file
if line[1] == "score" and len(
header) == 0: #this is the header
header = line[1:len(
line)] #stick the scoreterms in the header
else: #this is a score line
tag = line[-1] #the last item is the tag
record = PoseScoreRecord(tag)
record.set_file(path)
for term, score in zip(header, line[1:len(line) - 1]):
try:
record.add_score(term, float(score))
except ValueError:
record.add_score(term, score)
self.records[tag] = record
infile.close()
def add_file(self,path,ignore_ref=True):
infile = fileutil.universal_open(path,'r')
header=[]
for line in infile:
if len(line)== 0:
continue
line = line.split()
if line[0] == "SCORES": #this is an atom tree diff file
tag = line[1]
if ignore_ref and tag[0:5] =="%REF%":
continue
record = PoseScoreRecord(tag)
record.set_file(path)
scorefields = line[2:len(line)]
try:
for pair in score_pairs(scorefields):
record.add_score(*pair)
self.records[tag] = record
except ValueError:
print "theres some problem with this score line, possible corruption, skipping line"
continue
#elif
elif line[0] == "SCORE:": #this is a normal silent file
if line[1] == "score" and len(header) == 0: #this is the header
header = line[1:len(line)] #stick the scoreterms in the header
else: #this is a score line
tag = line[-1] #the last item is the tag
record = PoseScoreRecord(tag)
record.set_file(path)
for term,score in zip(header,line[1:len(line)-1]):
try:
record.add_score(term,float(score))
except ValueError:
record.add_score(term,score)
self.records[tag] = record
infile.close()
def __init__(self, filename):
"""load a param file into a data structure"""
self.atoms = {}
self.bonds = []
self.icoors = {}
infile = fileutil.universal_open(filename, 'r')
for line in infile:
if len(line) == 0:
continue
line = line.split()
tag = line[0]
if tag == "NAME":
self.name = line[1]
elif tag == "IO_STRING":
self.io_string = line[1]
elif tag == "TYPE":
self.type = line[1]
elif tag == "AA":
self.aa = line[1]
elif tag == "ATOM":
current_atom = Atom(line[1], line[2], line[3], line[4])
self.atoms[line[1]] = current_atom
elif tag == "BOND":
current_bond = Bond(line[1], line[2])
self.bonds.append(current_bond)
self.atoms[line[1]].add_bond(current_bond)
self.atoms[line[2]].add_bond(current_bond)
elif tag == "NBR_ATOM":
self.nbr_atom = line[1]
elif tag == "NBR_RADIUS":
self.nbr_radius = line[1]
elif tag == "ICOOR_INTERNAL":
current_icoor = icoor(line[1], line[2], line[3], line[4],
line[5], line[6], line[7])
self.icoors[line[1]] = current_icoor
infile.close()
scores.add_file(args[0])
structure_count = len(scores)
percent = float(options.percent)/100.0
structs_to_print =int(percent*structure_count)
sorted_scores = scores.sorted_score_generator(options.term)
count = 0
while count < structs_to_print:
(tag,score) = sorted_scores.next()
print tag,score
count += 1
elif options.mode =="pdb" or options.mode=="PDB":
file_scores = []
pathfile = fileutil.universal_open(args[0],"r")
for path in pathfile:
path = path.rstrip()
scores = rosettaScore.ScoreTable(path)
total_score = scores.get_score(0,options.term)
file_scores.append( (path,total_score) )
file_scores = sorted(file_scores,key=lambda x: x[1])
structure_count = len(file_scores)
percent = float(options.percent)/100.0
structs_to_print = int(percent*structure_count)
count = 0
for i in range(structs_to_print):
(tag,score) = file_scores[i]
print tag,score
else:
data = [] #list of tuples in form (tag,x_score,y_score)
if options.silent != "":
scores = rosettaScore.SilentScoreTable()
scores.add_file(options.silent)
x_axis_scores = scores.score_generator(options.x_axis)
y_axis_scores = scores.score_generator(options.y_axis)
for x_point, y_point in zip(x_axis_scores, y_axis_scores):
x_tag = x_point[0]
y_tag = y_point[0]
if x_tag != y_tag:
sys.exit("tags aren't equal, something is very wrong")
data.append((x_tag, x_point[1], y_point[1]))
elif options.silent_list != "":
silent_list = fileutil.universal_open(options.silent_list, "rU")
for path in silent_list:
scores = rosettaScore.SilentScoreTable()
scores.add_file(path.rstrip())
x_axis_scores = scores.score_generator(options.x_axis)
y_axis_scores = scores.score_generator(options.y_axis)
for x_point, y_point in zip(x_axis_scores, y_axis_scores):
x_tag = x_point[0]
y_tag = y_point[0]
if x_tag != y_tag:
sys.exit("tags aren't equal, something is very wrong")
data.append((x_tag, x_point[1], y_point[1]))
if options.pdb_list != "":
pdb_list = fileutil.universal_open(options.pdb_list, "rU")
for pdb in pdb_list:
def make_table(name_score_rmsd,out_name):
table = fileutil.universal_open(out_name,'w')
table.write("file\tscore\tRMSD\n")
for point in name_score_rmsd:
table.write(str(point[0])+"\t"+str(point[2])+"\t"+str(point[1])+"\n")
table.close()
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]
residue.id=(hetero,residue_id,insert)
else:
residue.id=(' ',residue_id,' ')
residue_id +=1
io=PDBIO()
io.set_structure(struct)
outfile = fileutil.universal_open(args[1],'w')
io.save(outfile)
if(options.table):
raw_table = rosettaScore.get_table(args[0])
#outfile = fileutil.universal_open(args[1],'a')
outfile.writelines(raw_table)
outfile.close()
def write(self, filename):
"""write the contents of the loop manager to a Rosetta3 loop file"""
loop_file = fileutil.universal_open(filename, "w")
for loop in self.looplist:
loop_file.write(loop.to_string() + "\n")
loop_file.close()
def write(self,filename):
"""write the contents of the loop manager to a Rosetta3 loop file"""
loop_file = fileutil.universal_open(filename,"w")
for loop in self.looplist:
loop_file.write(loop.to_string()+"\n")
loop_file.close()
for x in list:
yield x
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:
#!/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()
data = [] #list of tuples in form (tag,x_score,y_score)
if options.silent != "":
scores = rosettaScore.SilentScoreTable()
scores.add_file(options.silent)
x_axis_scores = scores.score_generator(options.x_axis)
y_axis_scores = scores.score_generator(options.y_axis)
for x_point, y_point in zip(x_axis_scores,y_axis_scores):
x_tag= x_point[0]
y_tag = y_point[0]
if x_tag != y_tag:
sys.exit("tags aren't equal, something is very wrong")
data.append( (x_tag,x_point[1],y_point[1]) )
elif options.silent_list != "":
silent_list = fileutil.universal_open(options.silent_list,"rU")
for path in silent_list:
scores = rosettaScore.SilentScoreTable()
scores.add_file(path.rstrip())
x_axis_scores = scores.score_generator(options.x_axis)
y_axis_scores = scores.score_generator(options.y_axis)
for x_point, y_point in zip(x_axis_scores,y_axis_scores):
x_tag= x_point[0]
y_tag = y_point[0]
if x_tag != y_tag:
sys.exit("tags aren't equal, something is very wrong")
data.append( (x_tag,x_point[1],y_point[1]) )
if options.pdb_list != "":
pdb_list = fileutil.universal_open(options.pdb_list,"rU")
for pdb in pdb_list:
def __init__(self,path):
self.sasamap = sasa_map()
sasafile = fileutil.universal_open(path,'r')
self.__parse__(sasafile)
sasafile.close()
current_item = ClusterItem(tag,cluster_id,struct_index)
if options.silent != "":
current_item.set_score(pose_scores.get_score(tag,"score"))
elif options.pdbs != "":
current_item.set_score(pose_scores.get_score(tag,0,"total"))
try:
clusters[cluster_id].append(current_item)
except KeyError:
clusters[cluster_id] = [current_item]
print "Clusters:",num_clusters
print "Structures:",num_structures
#output the cluster summary to a file
output_file = fileutil.universal_open(args[0],'w')
output_file.write("tag\tfile_name\tscore\tsize\n")
for key in clusters:
cluster_list = clusters[key]
cluster_list = sorted(cluster_list,key=lambda item: item.score)
output_file.write(cluster_list[0].tag+"\tc."+str(key)+"."+str(cluster_list[0].struct_index)+".pdb\t"+str(cluster_list[0].score)+"\t"+str(len(cluster_list))+"\n")
output_file.close()
#output the histogram to a file
bin_line = "bin"
count_line = "count"
for bin,count in histogram:
bin_line +="\t"+bin
count_line +="\t"+count
bin_line += "\n"
#!/usr/bin/env python2.5
from optparse import OptionParser
import sys
from rosettautil.util import fileutil
from rosettautil.bcl import file_formats
usage = "%prog [options] tabbed_input.txt bcl_output.txt"
parser = OptionParser(usage)
(options, args) = parser.parse_args()
in_file = fileutil.universal_open(args[0], "r")
vector_data = file_formats.list_of_2D_vectors()
for line in in_file:
line = line.split()
if len(line) == 0:
continue
vector_data.add_record(line[0], line[1])
in_file.close()
vector_data.write_bcl_file(args[1])
current_item = ClusterItem(tag, cluster_id, struct_index)
if options.silent != "":
current_item.set_score(pose_scores.get_score(tag, "score"))
elif options.pdbs != "":
current_item.set_score(pose_scores.get_score(tag, 0, "total"))
try:
clusters[cluster_id].append(current_item)
except KeyError:
clusters[cluster_id] = [current_item]
print "Clusters:", num_clusters
print "Structures:", num_structures
#output the cluster summary to a file
output_file = fileutil.universal_open(args[0], 'w')
output_file.write("tag\tfile_name\tscore\tsize\n")
for key in clusters:
cluster_list = clusters[key]
cluster_list = sorted(cluster_list, key=lambda item: item.score)
output_file.write(cluster_list[0].tag + "\tc." + str(key) + "." +
str(cluster_list[0].struct_index) + ".pdb\t" +
str(cluster_list[0].score) + "\t" +
str(len(cluster_list)) + "\n")
output_file.close()
#output the histogram to a file
bin_line = "bin"
count_line = "count"
for bin, count in histogram: