def create_imprints_from_file(self, file, type, max_level=5, oriented=True):
list = []
list_impt = []
a = []
FILE = open(".." + os.sep + "config" + os.sep + file, "r")
iter(FILE)
for line in FILE:
pdbReader = PDBReader(line[:4], os.path.join("..", "repo"))
protein = pdbReader.get_protein_from_PDB()
splitted_line = line.split(" ")
name = str(splitted_line[0].strip("\n\t"))
chain_num = (len(splitted_line) - 1) / 2
atom_list = AtomList()
if chain_num >= 1:
start = 0
end = 0
i = 1
while chain_num > 0:
start = int(splitted_line[i].strip(("\n\t")))
i += 1
end = int(splitted_line[i].strip(("\n\t")))
i += 1
atom_list.add_atom_list(protein.get_typed_atom_list(type).filter(start, end))
chain_num -= 1
else:
atom_list.add_atom_list(protein.get_typed_atom_list(type))
list.append(atom_list)
list[-1].set_name(name)
FILE.close()
for atom_list in list:
impt = atom_list.get_imprint(max_level, oriented)
list_impt.append(impt)
name_file = atom_list.get_name() + "." + type + "im"
impt.write_on_file(name_file)
return list
repo = os.path.join("..", "repo")
imprints = os.path.join("..", "imprints")
if __name__ == "__main__":
prot1 = '1xwc' #the first protein
prot2 = '3trx' #the second protein
prot3 = '2vb1' #the third protein
prot4 = '1alc' #the fourth protein
prot5 = '1bb0' #the fifth protein
prot6 = '2drp' #the sixth protein
#prot1 single chain
pdbReader = PDBReader(prot1, repo)
protein1 = pdbReader.get_protein_from_PDB()
p1cA = protein1.get_chain('A').orient()
bb1 = protein1.get_backbone().orient()
batcher_p1cA = Batcher(p1cA, GREEN)
batcher_bb1 = Batcher(bb1, GREEN)
#prot2 single chain
pdbReader = PDBReader(prot2, repo)
protein2 = pdbReader.get_protein_from_PDB()
p2cA = protein2.get_chain('A').orient()
bb2 = protein2.get_backbone().orient()
batcher_p2cA = Batcher(p2cA, RED)
batcher_bb2 = Batcher(bb2, RED)
#prot3 single chain