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clean_structure.py
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clean_structure.py
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# Developed by Natália Teruel
# Najmanovich Research Group
# Cite this work as Surfaces: A software to quantify and visualize interactions within and between proteins and ligands - Teruel, N. F. B., Borges, V. M., & Najmanovich, R. (2023)
#Imports
import argparse
def get_atoms(line): #take strings after the ' ' and before the ':'
list_atoms = []
L = line[5:-2].split(",")
for item in L:
if len(item) > 0:
item = item.strip()
id = item.index(":")
list_atoms.append(item[:id])
return (list_atoms)
def read_atom(line):
atnum = int(line[6:11])
attype = line[11:16].strip()
resnum = line[23:30].strip()
res = line[17:20].strip()
chain = line[21:22].strip()
return (atnum,attype,resnum,res,chain)
def check_line(line,res,atoms): #see if the atom of that line is described in the def file
atnum,attype,resnum,residue,chain = read_atom(line)
if residue in res:
id = res.index(residue)
if attype in atoms[id]:
return (True)
else:
print ("WARNING: ATOM " + attype + " NOT DEFINED FOR " + residue)
return (False)
else:
print ("WARNING: " + residue + " NOT DEFINED")
return (False)
def main():
parser= argparse.ArgumentParser(description="the arguments.", add_help=False)
parser.add_argument("-f","--pdb_file", action="store")
parser.add_argument("-def","--atomtypes_definition", action="store")
args=parser.parse_args()
res = []
atoms = []
def_file = open(args.atomtypes_definition, "r")
Lines = def_file.readlines()
for line in Lines:
res.append(line[:3])
atoms.append(get_atoms(line))
def_file.close()
#print (res)
#print (atoms)
pdb_file = open(args.pdb_file, "r")
clean_pdb_file = open("clean_" + args.pdb_file, "w")
Lines = pdb_file.readlines()
for line in Lines:
if line[:4] == 'ATOM' or line[:4] == 'HETA':
if check_line(line,res,atoms):
clean_pdb_file.write(line)
pdb_file.close()
clean_pdb_file.close()
return
main()