Get name for file from python array

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

jpaugh · Accepted Answer · 2012-05-31 04:00:55Z

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));

edited May 31, 2012 at 4:00

answered May 31, 2012 at 3:47

jpaugh

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5 Comments

John Amraph Over a year ago

But this one output just the first array, and not the others.

John Amraph Over a year ago

And I also need @<TRIPOS>MOLECULE as first line of every file.

John Amraph Over a year ago

Sorry, still produce 1 file instead of all avaliable arrays in mols

John Amraph Over a year ago

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

jpaugh Over a year ago

Well, it worked for me: Idk what went wrong in the mind to mind transmission, but my, aren't these antennas crufty? I'm guessing you got it working, though.

BrenBarn · Accepted Answer · 2012-05-31 03:41:00Z

1

Your code includes ".mol2" % i which looks it's supposed to be string interpolation, but provides no placeholders to be interpolated. Assuming you know how to use string interpolation with the % sign, perhaps you meant something like ".mol%s" % i?

answered May 31, 2012 at 3:41

BrenBarn

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1 Comment

John Amraph Over a year ago

No, I am new to python. Every file should be ended with .mol2

cthrall · Accepted Answer · 2012-05-31 03:45:07Z

0

When you use "%" followed by a variable name in Python, it's going to look for a string formatting sequence in your string and attempt to format it. In your second code snippet, Python isn't finding a format specifier in your string.

answered May 31, 2012 at 3:45

cthrall

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