从表格数据中提取列

Question

My task is to pull a column out of table and write down its length len () . But my code is emitting it into a column, which is why len () counts each element of the column separately, and not their total

water = water.readlines()
for col in water:
    el = list(col.split()[2])

water.txt:

     HETATM    1  H   HOH A   1      27.265  36.739  58.126
     HETATM    2  H   HOH A   1      27.109  35.124  57.944                          
     HETATM    3  O   HOH A   1      27.486  35.958  57.542
...
     HETATM 9999  O   HOH A3333      30.490  83.899  10.929

Desired intermediary output:

H
H
O
H
H
O

Answer 1

You are not correctly extracting the colum. The correct way is with a list comprehension:

with open(...) as water:
    el = [line.split()[2] for line in water]

With your sample data, I get ['H', 'H', 'O'] for el, which is the third column.

Answer 2

For the future you'll likely use other means to import data in tabular form. But this is an important exercise, because the following will apply to most issues you will face. The most important initial concept is to use plenty of print statements to understand what each step does.

file = "HETATM    1  H   HOH A   1      27.265  36.739  58.126\nHETATM    2  H   HOH A   1      27.109  35.124  57.944\nHETATM    3  O   HOH A   1      27.486  35.958  57.542\n"
        
lines=file.split('\n')
print(lines)

output is a list of strings:

['HETATM    1  H   HOH A   1      27.265  36.739  58.126',
 'HETATM    2  H   HOH A   1      27.109  35.124  57.944',
 'HETATM    3  O   HOH A   1      27.486  35.958  57.542',
 '']

Each line is now still a string, so you need to turn it into a list for example:

a=lines[2].split()
print(a)

output is a list of strings, each string one column value for this particular line/row:

['HETATM', '3', 'O', 'HOH', 'A', '1', '27.486', '35.958', '57.542']

To do that for every line and keep the 3rd column (index 2):

col2=[]  # make an empty list to hold the column

for l in lines:
    if len(l)>1:      # leaves empty lines, also at end of file 
        cols=l.split()
        col2.append(cols[2])


print(col2)    

output is a list representing your 2nd column

['H', 'H', 'O']

Because Python is used with many packages that do a lot in a single line, and also because of duck-typing, it is more important than in other languages to always know what the result of your last line is, both in type and in meaning.

In the future you will likely use numpy or pandas to read in tabular data in a single line. But to understand that single line can sometimes be hard. It is also hard to memorize. Doing it yourself in low level code as shown above will help you stay connected to your code. It will also help you to read how other people implemented higher level functions.