class PDBFile:
def __init__(self, code, in_pdb):
self.code = code
self.struct = PDBParser(PERMISSIVE=1,
QUIET=1).get_structure(self.code, in_pdb)
def residues_map(self, selected_chain=None, standard_aa=True):
rmap = {}
for chain in self.struct.get_chains():
if (not selected_chain) or (selected_chain == chain.id):
residues = [
x for x in chain.get_residues()
if is_aa(x, standard=standard_aa)
]
rmap[chain.id] = {i: x.id for i, x in enumerate(residues)}
return rmap
def seq(self, selected_chain=None, standard_aa=True):
records = []
for chain in self.struct.get_chains():
if (not selected_chain) or (selected_chain == chain.id):
residues = [
x for x in chain.get_residues()
if is_aa(x, standard=standard_aa)
]
if residues:
seq = "".join([seq1(x.resname) for x in residues])
start = str(residues[0].id[1])
end = str(residues[-1].id[1])
record = SeqRecord(id="_".join(
[self.code, chain.id, start, end]),
description="",
seq=Seq(seq))
records.append(record)
return records
def records_from_pdb(self, pdb, pdb_file_path, standard_aa=True, selected_chain=None):
records = []
struct = PDBParser(PERMISSIVE=1, QUIET=1).get_structure(pdb, pdb_file_path)[0]
for chain in struct.get_chains():
if (not selected_chain) or (selected_chain == chain.id):
residues = [x for x in chain.get_residues() if is_aa(x, standard=standard_aa)]
if residues:
seq = "".join([seq1(x.resname) for x in residues])
start = str(residues[0].id[1])
end = str(residues[-1].id[1])
record = SeqRecord(id="_".join([pdb, chain.id, start, end]), description="", seq=Seq(seq))
records.append(record)
return records
def FASTA_Gen(pdb_file, pdb_id, output_file):
m = PDBParser(PERMISSIVE=1).get_structure(pdb_id, pdb_file)
w = open(output_file, 'w')
for chain in m.get_chains():
residues = list(chain.get_residues())
chain_id = chain.get_id()
s = ''
peptides = PPBuilder().build_peptides(chain, aa_only=False)
for peptide in peptides:
s = s + peptide.get_sequence() + '\n\n'
w.write('>{0}_{1}|{2}-{3}\n'.format(pdb_id, chain_id,
residues[0].get_id()[1],
residues[-1].get_id()[1]))
w.write(str(s))
w.close()
# %%
import os
io = PDBIO()
end = "_ligand.pdb"
directory = "./ligands/"
for filename in os.listdir(directory):
if filename.endswith(end): # IF the file ends with the generic ending,
fileid = filename # duplicate the fileid for a shortened title
fileid = fileid.replace(end, '') # remove the end
pdb = PDBParser().get_structure(fileid, directory +
filename) # get the structure
ress = model.get_residues()
for chain in pdb.get_chains():
for res in chain.get_residues(
): # for each chain in the structure,
io.set_structure(residue) # set the structure to the chain
#io.save(pdb.get_id() + "_" + chain.get_id() + ".pdb") # save the chain to a new PDB file
io.save(fileid + "_" + chain.get_id() +
".pdb") # save the chain to a new PDB file
# %%
ligs = structure[:][:][:]
# %%
import os
io = PDBIO()
end = "_ligand.pdb"
