I am using the Spyder4.0.0b5 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
On Sunday, September 15, 2019 at 3:02:51 PM UTC-4, Carlos Córdoba wrote:
>
> Hi all,
>
> On the behalf of the Spyder Project Contributors
> <https://github.com/spyder-ide/spyder/graphs/contributors>, I’m pleased
> to announce the fifth beta of our next major version: Spyder *4.0*.
>
> We’ve been working on this version for almost three years now and as far
> as we know it’s working very well. There are still several bugs to squash
> but we encourage all people who like the bleeding edge to give it a try.
> This beta version is released 6 weeks after Spyder 4.0 beta4 and it
> includes more than 540 commits.
>
> Spyder 4.0 comes with several interesting and exciting new features. The
> most important ones are:
>
> -
>
> Main Window
> - Dark theme for the entire application.
> - A new Plots pane to browse all inline figures generated by the
> IPython console.
> - Rename the following panes:
> - Static code analysis to Code Analysis
> - File explorer to Files
> - Find in files to Find
> - History log to History
> - Project explorer to Project
> - Create a separate window when undocking all panes.
> - Show current conda environment (if any) in the status bar.
> -
>
> Editor
> - Code folding.
> - Indentation guides.
> - A class/method/function lookup panel. This can be shown in the
> menu Source > Show selector for classes and functions.
> - Autosave functionality to recover unsaved files after a crash.
> - Code completion and linting are provided by the Python Language
> Server.
> -
>
> IPython Console
> - Run files in an empty namespace.
> - Create dedicated consoles for Pylab, Sympy and Cython.
> - Run cells through a new function called runcell.
> - Run cells by name.
> -
>
> Debugger
> - runfile and runcell can be called when the debugger is active.
> - Debug cells by pressing Alt+Shift+Return.
> - Permanent history.
> - Syntax highlighting.
> -
>
> Variable Explorer
> - New viewer to inspect any Python object in a tree-like view.
> - Filter variables by name or type.
> - MultiIndex support in the Dataframe viewer.
> - Support for all Pandas indexes.
> - Support for sets.
> - Support for Numpy object arrays.
> -
>
> Files
> - Associate external applications to open specific file extensions.
> - Context menu action to open files externally.
> - Multi-select functionality with Ctrl/Shift + mouse click.
> - Copy/paste files and their absolute or relative paths.
> - Use special icons for different file types.
> -
>
> Outline
> - Show cells grouped in sections.
> - Add default name to all cells.
>
> For a more complete list of changes, please see our changelog
> <https://github.com/spyder-ide/spyder/wiki/Beta-version-changelog>
>
> You can easily install this beta if you use Anaconda by running:
>
> conda update qt pyqt
> conda install -c spyder-ide spyder=4.0.0b5
>
> Or you can use pip with this command:
>
> pip install --pre -U spyder
>
> Enjoy!
> Carlos
>
>
>
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