Thanks for the reply. The first file was a mistake.
The problem was due to quotes around the file name. The problem has been solved. On Wed, Sep 25, 2019 at 3:48 AM Björn Johansson <[email protected]> wrote: > 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 >>> >> >> >>> >>> >> -- > You received this message because you are subscribed to a topic in the > Google Groups "spyder" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spyderlib/wEpgkXPF7bg/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spyderlib/b6e13272-746a-4a9a-8923-d24a355d33c7%40googlegroups.com > <https://groups.google.com/d/msgid/spyderlib/b6e13272-746a-4a9a-8923-d24a355d33c7%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Multivariate and stochastic http://www.Molecular-Modeling.net 614.312.7528 (c) Skype: smolnar1 -- You received this message because you are subscribed to the Google Groups "spyder" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spyderlib/CAOAitP8P_%2B25ra1JQkmydxYhJYnW8R13W_xZND2o2L8Pw_2gbA%40mail.gmail.com.
