def deleteChain():# Delete a complete chain from a pdb and save the new structure in pdbname_free.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
seq=''
nb_chain=input('How many chain do you want to delete : ')
for i in range(nb_chain):
rm_chain=raw_input('What chain you want to delete : ')
for model in structure:
for chain in model:
if(chain.id==rm_chain):
model.detach_child(chain.id)
pept = raw_input('Do you want to get a pdb with the sequence in its name : ')
if(pept == 'y'):
ppb=PPBuilder()
for pp in ppb.build_peptides(structure):
seq = seq + pp.get_sequence()
seq=seq.lower()
seq=str(seq)
w = PDBIO()
w.set_structure(structure)
w.save(seq+'_bound.pdb')
else:
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_without'+rm_chain+'.pdb')
def deleteChain():# Delete a complete chain from a pdb and save the new structure in pdbname_free.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
seq=''
nb_chain=input('How many chain do you want to delete : ')
for i in range(nb_chain):
rm_chain=raw_input('What chain you want to delete : ')
for model in structure:
for chain in model:
if(chain.id==rm_chain):
model.detach_child(chain.id)
pept = raw_input('Do you want to get a pdb with the sequence in its name : ')
if(pept == 'y'):
ppb=PPBuilder()
for pp in ppb.build_peptides(structure):
seq = seq + pp.get_sequence()
seq=seq.lower()
seq=str(seq)
w = PDBIO()
w.set_structure(structure)
w.save(seq+'_bound.pdb')
else:
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_without'+rm_chain+'.pdb')
def get_info(filename): ''' Return header. Function adapted from Biopython Package.\n get_info(filename)\n Filename needs to be a PDB file format (*.ent or *.pdb) ''' p = PDBParser(QUIET=True) s = p.get_header()
def get_info(filename):
'''
Return header. Function adapted from Biopython Package.\n
get_info(filename)\n
Filename needs to be a PDB file format (*.ent or *.pdb)
'''
p = PDBParser(QUIET=True)
s = p.get_header()
def removeDoubleAtoms():# Remove all double atoms defined in a pdb and save the new structure in pdbname_noDouble.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
structure.remove_disordered_atoms()
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_noDouble.pdb')
def removeDoubleAtoms():# Remove all double atoms defined in a pdb and save the new structure in pdbname_noDouble.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
structure.remove_disordered_atoms()
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_noDouble.pdb')
def renameChain():
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
what_chain=raw_input('What is the chain you want to rename : ')
what_chain2=raw_input('What is the new name of this chain : ')
for model in structure:
for chain in model:
if chain.id == what_chain:
chain.id = what_chain2
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_rename.pdb')
def removeHetero():# Remove all heteroatoms from a pdb and save the new structure in pdbname_noHetero.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
for model in structure:
for chain in model:
for residue in chain:
id = residue.id
if id[0] != ' ':
chain.detach_child(residue.id)
if len(chain) == 0:
model.detach_child(chain.id)
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_noHetero.pdb')
def renameChain():
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
what_chain=raw_input('What is the chain you want to rename : ')
what_chain2=raw_input('What is the new name of this chain : ')
for model in structure:
for chain in model:
if chain.id == what_chain:
chain.id = what_chain2
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_rename.pdb')
def removeHetero():# Remove all heteroatoms from a pdb and save the new structure in pdbname_noHetero.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
for model in structure:
for chain in model:
for residue in chain:
id = residue.id
if id[0] != ' ':
chain.detach_child(residue.id)
if len(chain) == 0:
model.detach_child(chain.id)
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_noHetero.pdb')
def deleteResidue():# Delete a residue from a pdb and save the new structure in pdbname_noResidue.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
rm_residue=raw_input('What residue you want to delete : ')
for model in structure:
for chain in model:
for residue in chain:
print residue.id
if(residue.id[1]==rm_residue):
print 'HELLO'
chain.detach_child(residue.id)
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_noResidue.pdb')
def deleteResidue():# Delete a residue from a pdb and save the new structure in pdbname_noResidue.pdb
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
rm_residue=raw_input('What residue you want to delete : ')
for model in structure:
for chain in model:
for residue in chain:
print residue.id
if(residue.id[1]==rm_residue):
print 'HELLO'
chain.detach_child(residue.id)
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_noResidue.pdb')
def getSequence(): # Get the sequence of a specific chain
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
seq=''
what_chain=raw_input('For what chain do you want the sequence : ')
for model in structure:
for chain in model:
if chain.id != what_chain:
model.detach_child(chain.id)
ppb=PPBuilder()
for pp in ppb.build_peptides(structure):
seq = seq + pp.get_sequence()
seq=seq.lower()
print seq
def getSequence(): # Get the sequence of a specific chain
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
seq=''
what_chain=raw_input('For what chain do you want the sequence : ')
for model in structure:
for chain in model:
if chain.id != what_chain:
model.detach_child(chain.id)
ppb=PPBuilder()
for pp in ppb.build_peptides(structure):
seq = seq + pp.get_sequence()
seq=seq.upper()
print seq
def assembleChain(): # Allow to assemble 2 chains together
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
what_chain=raw_input('What is the 1st chain you want to assemble : ')
what_chain2=raw_input('What is the 2nd chain you want to assemble : ')
for model in structure:
for chain in model:
if chain.id == what_chain:
parent=chain;
elif chain.id == what_chain2:
for residue in chain:
residue.get_parent().id=what_chain
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_assemble.pdb')
def assembleChain(): # Allow to assemble 2 chains together
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
what_chain=raw_input('What is the 1st chain you want to assemble : ')
what_chain2=raw_input('What is the 2nd chain you want to assemble : ')
for model in structure:
for chain in model:
if chain.id == what_chain:
parent=chain;
elif chain.id == what_chain2:
for residue in chain:
residue.get_parent().id=what_chain
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_assemble.pdb')
def renumberChain(): # Allow to renumber from what you want a specific chain
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
what_chain=raw_input('What is the chain you want to renumber : ')
number=input('What is the first number of the chain : ')
for model in structure:
for chain in model:
if chain.id == what_chain:
for residue in chain:
if residue.id[0] == ' ':
residue.id=(' ', number, ' ')
number=number+1
else:
chain.detach_child(residue.id)
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_ren.pdb')
def renumberChain(): # Allow to renumber from what you want a specific chain
parser = PDBParser()
nameStruct=pdb_name.partition('.')[0]
structure = parser.get_structure(nameStruct, pdb_name)
header = parser.get_header()
trailer = parser.get_trailer()
what_chain=raw_input('What is the chain you want to renumber : ')
number=input('What is the first number of the chain : ')
for model in structure:
for chain in model:
if chain.id == what_chain:
for residue in chain:
if residue.id[0] == ' ':
residue.id=(' ', number, ' ')
number=number+1
else:
chain.detach_child(residue.id)
w = PDBIO()
w.set_structure(structure)
w.save(nameStruct+'_ren.pdb')
def shannon_entropy_list_msa(alignment_file):
shannon_entropy_list = []
for col_no in xrange(len(list(alignment_file[0]))):
list_input = list(alignment_file[:, col_no])
shannon_entropy_list.append(shannon_entropy(list_input))
return shannon_entropy_list
#START ACTUAL PROGRAM
############################################
#find match
############################################
#read in .pdb sequence
parser = PDBParser()
structure = parser.get_structure('', '1OTH.pdb')
header = parser.get_header()
trailer = parser.get_trailer()
pdbSequence = ''
for residue in structure[0]['A'].get_residues():
if (residue.get_id()[0]==' '):
residueName = three_to_one(residue.get_resname())
pdbSequence += residueName
#check each fasta sequence for match to pdb sequence
bestMatch = ''
bestScore = 0
handle = open("uniprot-ornithine+transcarbamylase-2.fasta", "rU")
for record in SeqIO.parse(handle, "fasta") :
foundMatch = False
if foundMatch == False:
tempFile = open("temp.fasta", "w")
deleteContent(tempFile)