[Tutor] Extract element of dtype object

[Stephen P. Molnar]

On 12/06/2020 11:28 AM, Mats Wichmann wrote:
> On 12/6/20 6:37 AM, Stephen P. Molnar wrote:
>> I have a large number of files from which I wish to extract a number.
>
> Your succession of examples is not leaving me, at least, with any 
> clarity of what you're actually looking for.  You need to define for 
> yourself a description in words, then you can probably begin to code 
> it up. Youi include "and the code snippet" but there is no code 
> snippet...
>
> see below
>
>>
>> This is an example or a portion of the file:
>>
>> mode |   affinity | dist from best mode
>>       | (kcal/mol) | rmsd l.b.| rmsd u.b.
>> -----+------------+----------+----------
>>     1    -8.538750714      0.000      0.000
>>     2    -8.487003690      3.712      7.079
>>     3    -8.420436250      3.018      6.604
>>     4    -7.992952187      3.711      7.282
>>     5    -7.933139639      2.128      6.739
>>     6    -7.889517329      2.667      6.537
>>     7    -7.720785374     20.143     23.808
>>     8    -7.629772565     21.218     25.083
>>     9    -7.560349273      2.136      7.865
>> Writing output ... done.
>>
>> and the code snippet:
>>
>> Refining results ... done.
>>
>> 0 mode | affinity | dist from best mode
>>
>> 1 | (kcal/mol) | rmsd l.b.| rmsd u.b.
>>
>> 2 -----+------------+----------+----------
>>
>> 3 1 -8.538750714 0.000 0.000
>>
>> 4 2 -8.487003690 3.712 7.079
>>
>> the output:
>>
>> Refining results ... done. 1 -8.538750714 0.000 0.000
>>
>>
>>                     Refining results ... done.
>> 0     mode |   affinity | dist from best mode
>> 1         | (kcal/mol) | rmsd l.b.| rmsd u.b.
>> 2    -----+------------+----------+----------
>> 3     1           0.000      0.000
>> 4     2    -8.487003690      3.712      7.079
>> Refining results ... done.       1    -8.538750714      0.000 0.000
>> Name: 3, dtype: object
>>
>> The number that I want to extract is -8.538750714.
>
> If you're collecting lines from running an external script, you can 
> run that script with subprocess.run and then look through the 
> resulting output until you find a line that matches some recognizable 
> pattern. That pattern seems to be "Refining results ... done." but it 
> appears so many times in the above it's hard to sort out what's what. 
> If that's the case you can then trim that line either with plain 
> string handling routines or with a regular expression (regexes get a 
> bad reputation, they're good for handling text with recognizable 
> patterns, but may be overkill for this case)
>
> Will wait for some clarification before digging further...
>
>
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Oh oh. Here is the code:

import pandas as pd

df = pd.read_table('test.log')
df = df.dropna(axis=1)
print(df.head())

x = (df.iloc[3])
print(x)

from the origional post

This is an example or a portion of the file:

mode |   affinity | dist from best mode
       | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
     1    -8.538750714      0.000      0.000
          ^^^^^^^^^
           | |  |  | |  | | | |
          this is the number I want to extract.

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1