Seems file name is:
17-3_apo-1acl.RMSD in the first case and
13-7_apo-1acl.RMSD in the second ?
On Tuesday, September 24, 2019 at 1:58:19 PM UTC+1, Stephen P. Molnar wrote:
>
> 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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