Question

Hello I need your help on the following problem.
I am parsing the file that looks like this

@<TRIPOS>MOLECULE
NAME123
line3
line4
line5
line6
@<TRIPOS>MOLECULE
NAME434543
line3
line4
line5
@<TRIPOS>MOLECULE
NAME343566
line3
line4

I currenly have this code that is working ok…

mols = [] 
with open("test2.mol2", mode="r") as molfile: 
    for line in molfile: 
        if line.startswith("@<TRIPOS>MOLECULE"): 
            mols.append(line) 
        else: 
            mols[-1] += line
#
for i in range(len(mols)): 
    out_filename = "file%d.mol2" % i 
    with open(out_filename, mode="w") as out_file: out_file.write(mols[i]);

but whem I tried to save the files with name according to the second field of array, the one after @MOLECULE (NAME….) with code like this – it doesn’t work. Please, help me to fix the code. Thank’s!

for i in mols:
    out_filename = str(i.split()[1]) + ".mol2" % i
    with open(out_filename, mode="w") as out_file: out_file.write(mols[i]);

The error is

Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
TypeError: not all arguments converted during string formatting

Answer 1

I recommend using a more structured list:

for line in molfile:
    if line.startswith("@"):
        mols.append([])
        mols[-1].append(line) # Keep first line
    else:
        mols[-1].append(line)

then:

for i in mols:
    out_filename = i[0].strip() + ".mol2"
    with open(out_filename, mode="w") as out_file:
        out_file.write(''.join(i));