I am embarrassed to be asking this question, but I have exhausted Google at this point .

I have a number of identically formatted text files from which I want to extract data, as an example (hopefully, putting these in as quotes will persevere the format):

=======================================================================
PSOVina version 2.0
Giotto H. K. Tai & Shirley W. I. Siu

Computational Biology and Bioinformatics Lab
University of Macau

Visit http://cbbio.cis.umac.mo for more information.

PSOVina was developed based on the framework of AutoDock Vina.

For more information about Vina, please visit http://vina.scripps.edu.

=======================================================================

Output will be 13-7_out.pdbqt
Reading input ... done.
Setting up the scoring function ... done.
Analyzing the binding site ... done.
Using random seed: 1828390527
Performing search ... done.

Refining results ... done.

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1    -8.862004149      0.000      0.000
   2    -8.403522829      2.992      6.553
   3    -8.401384636      2.707      5.220
   4    -7.886402037      4.907      6.862
   5    -7.845519031      3.233      5.915
   6    -7.837434227      3.954      5.641
   7    -7.834584887      3.188      7.294
   8    -7.694395765      3.746      7.553
   9    -7.691211177      3.536      5.745
  10    -7.670759445      3.698      7.587
  11    -7.661882758      4.882      7.044
  12    -7.636280303      2.347      3.284
  13    -7.635788052      3.511      6.250
  14    -7.611175249      2.427      3.449
  15    -7.586368357      2.142      2.864
  16    -7.531307666      2.976      4.980
  17    -7.520501084      3.085      5.775
  18    -7.512906514      4.220      7.672
  19    -7.307403528      3.240      4.354
  20    -7.256063348      3.694      7.252
Writing output ... done.
 At this point, my python script consists of only the following:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""

Created on Tue Sep 24 07:51:11 2019

"""
import numpy as np

data = []

data = np.genfromtxt("13-7.log", usecols=(1), dtype=None, skip_header=27, skip_footer=1, encoding=None)

print(data)

np.savetxt('13-7', [data], fmt='%15.9f', header='13-7')

The problem lies in tfe np.savetxt line, on execution I get:

runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/VINA20/SmallSet/DeltaGTable_V_s.py', wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/VINA20/SmallSet', current_namespace=True)
['-8.839713733' '-8.743377250' '-8.151051167' '-8.090452911'
 '-7.967494477' '-7.854890056' '-7.757417879' '-7.741557490'
 '-7.643885488' '-7.611595767' '-7.507605524' '-7.413920814'
 '-7.389408331' '-7.384446364' '-7.374206276' '-7.368808179'
 '-7.346641418' '-7.325037898' '-7.309614787' '-7.113209147']
Traceback (most recent call last):

File "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/VINA20/SmallSet/DeltaGTable_V_s.py", line 16, in <module>
    np.savetxt('13-7', [data], fmt='%16.9f', header='13-7')

  File "<__array_function__ internals>", line 6, in savetxt

File "/home/comp/Apps/Miniconda3/lib/python3.7/site-packages/numpy/lib/npyio.py", line 1438, in savetxt
    % (str(X.dtype), format))

TypeError: Mismatch between array dtype ('<U12') and format specifier ('%16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f')

The data is in the data file, but the only entry in '13-7', the saved file, is the label. Obviously, the error is in the format argument.

Help will be much appreciated.

Thanks in advance.

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

_______________________________________________
NumPy-Discussion mailing list
NumPy-Discussion@python.org
https://mail.python.org/mailman/listinfo/numpy-discussion

Reply via email to