Seems file name is:
17-3_apo-1acl.RMSD in the first case and
13-7_apo-1acl.RMSD in the second ?
You should probably only post once about an issue?
/bjorn
On Tuesday, September 24, 2019 at 1:57:58 PM UTC+1, Stephen P. Molnar wrote:
>
> I am using the Spyder3 IDE with Python 3.7.3 and have encountered, what to
> me at least, is a rather strange problem.
>
> The code, at this point is:
>
> #!/usr/bin/env python3
> # -*- coding: utf-8 -*-
> """
> Created on Sat Apr 8 15:17:07 2017
>
> @author: comp
>
> """
> #import numpy as np
> #import matplotlib.pyplot as plt
> import pandas as pd
>
> name = input("Enter Molecule ID: ")
>
> print(name)
>
> ligand_file = name+'_apo-1acl.RMSD'
>
> print('Ligand file = ',ligand_file)
>
> data = pd.read_table('ligand_file',skiprows = 7)
>
> print(data)
>
> The input file, in this example, 17-3_apo-1acl.RMSD is:
>
> RMSD TABLE
> __________
>
> _____________________________________________________________________
> | | | | | |
> Rank | Sub- | Run | Binding | Cluster | Reference | Grep
> | Rank | | Energy | RMSD | RMSD | Pattern
> _____|______|______|___________|_________|_________________|___________
> 1 1 8 -7.23 0.00 93.07 RANKING
> 1 2 9 -6.79 1.39 92.64 RANKING
> 2 1 16 -7.18 0.00 93.19 RANKING
> 3 1 2 -6.93 0.00 93.38 RANKING
> 3 2 17 -6.84 0.23 93.45 RANKING
> 4 1 15 -6.55 0.00 91.83 RANKING
> 4 2 7 -6.34 0.33 91.77 RANKING
> 5 1 5 -6.41 0.00 93.05 RANKING
> 6 1 3 -6.36 0.00 92.84 RANKING
> 6 2 10 -6.28 0.47 92.92 RANKING
> 6 3 6 -6.27 0.43 92.82 RANKING
> 6 4 18 -6.25 0.32 92.88 RANKING
> 6 5 13 -6.24 0.96 92.75 RANKING
> 6 6 1 -6.24 0.87 92.60 RANKING
> 6 7 14 -6.21 0.51 92.90 RANKING
> 6 8 11 -6.14 0.98 92.78 RANKING
> 6 9 20 -6.11 0.71 92.67 RANKING
> 6 10 19 -6.01 1.36 93.00 RANKING
> 7 1 12 -6.30 0.00 93.28 RANKING
> 8 1 4 -5.85 0.00 92.97 RANKING
> _______________________________________________________________________
>
> The output at this point is:
>
> Enter Molecule ID: 17-3
> 17-3
> Ligand file = 17-3_apo-1acl.RMSD
> Traceback (most recent call last):
>
> File "<ipython-input-3-48de0a8fd907>", line 1, in <module>
> runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.',
>
> wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable')
>
>
>
> File
> "/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py",
>
> line 827, in runfile
> execfile(filename, namespace)
>
> File
> "/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py",
>
> line 110, in execfile
> exec(compile(f.read(), filename, 'exec'), namespace)
>
> File
> "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.",
>
> line 23, in <module>
> data = pd.read_table('ligand_file',skiprows = 7)
>
> File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line
> 685, in parser_f
> return _read(filepath_or_buffer, kwds)
>
> File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line
> 457, in _read
> parser = TextFileReader(fp_or_buf, **kwds)
>
> File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line
> 895, in __init__
> self._make_engine(self.engine)
>
> File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line
> 1135, in _make_engine
> self._engine = CParserWrapper(self.f, **self.options)
>
> File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line
> 1917, in __init__
> self._reader = parsers.TextReader(src, **kwds)
>
> File "pandas/_libs/parsers.pyx", line 382, in
> pandas._libs.parsers.TextReader.__cinit__
>
> File "pandas/_libs/parsers.pyx", line 689, in
> pandas._libs.parsers.TextReader._setup_parser_source
>
> FileNotFoundError: [Errno 2] File b'ligand_file' does not exist:
> b'ligand_file'
>
>
> However, if I change the data = line to:
>
> data = pd.read_table('13-7_apo-1acl.RMSD',skiprows = 7)
>
> The output is:
>
> runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.',
>
> wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable')
>
>
>
> Enter Molecule ID: 13-7
> 13-7
> Ligand file = 13-7_apo-1acl.RMSD
> _____|______|______|___________|_________|_________________|___________
> 0 1 1 8 -7.23 0.00 9...
> 1 1 2 9 -6.79 1.39 9...
> 2 2 1 16 -7.18 0.00 9...
> 3 3 1 2 -6.93 0.00 9...
> 4 3 2 17 -6.84 0.23 9...
> 5 4 1 15 -6.55 0.00 9...
> 6 4 2 7 -6.34 0.33 9...
> 7 5 1 5 -6.41 0.00 9...
> 8 6 1 3 -6.36 0.00 9...
> 9 6 2 10 -6.28 0.47 9...
> 10 6 3 6 -6.27 0.43 9...
> 11 6 4 18 -6.25 0.32 9...
> 12 6 5 13 -6.24 0.96 9...
> 13 6 6 1 -6.24 0.87 9...
> 14 6 7 14 -6.21 0.51 9...
> 15 6 8 11 -6.14 0.98 9...
> 16 6 9 20 -6.11 0.71 9...
> 17 6 10 19 -6.01 1.36 9...
> 18 7 1 12 -6.30 0.00 9...
> 19 8 1 4 -5.85 0.00 9...
> 20 ______________________________________________...
>
> I have used the ligand_file = line in other Python script that has worked
> without any errors.
>
> Google has not been a solution in his case. Pointers towards wolutions to
> this problem will be much appreciated.
>
> Thanks in advance.
>
> --
> Stephen P. Molnar, Ph.D. Life is a fuzzy set
> http://www.Molecular-Modeling.net Multivariate and stochastic
> 614.312.7528 (c)
> Skype: smolnar1
>
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