Exemple #1
0
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()
Exemple #4
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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')
Exemple #6
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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')
Exemple #7
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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')
Exemple #8
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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')
Exemple #10
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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')
Exemple #11
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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')
Exemple #12
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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')
Exemple #13
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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
Exemple #14
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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
Exemple #15
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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')
Exemple #16
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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')
Exemple #17
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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')
Exemple #18
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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')
Exemple #19
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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)