Error message pop-up while invoking PyRx from Destop icon

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Error message pop-up while invoking PyRx from Destop icon

Postby aneeshcna » Thu Jan 30, 2014 11:17 am

Dear Users,

I have just installed PyRx in my Ubuntu system. As a trail run, when I invoke PyRx from the the Destop icon, a wxPython stdout/stderr window pop-up with following error -

********************************************************************************************
Exception IOError: (13, 'Permission denied', '/home/aneesh/.enthought/traits/traits_ui.dir') in <bound method DbfilenameShelf.__del__ of {'enthought.traits.ui.table_filter.MenuTableFilter': {'': (432, 315, 576, 270), '$': <enthought.traits.ui.key_bindings.KeyBindings object at 0xcf931dc>, 'rules_table': {'widths': [142, 142, 142, 143], 'filters': [], 'columns': ['', 'Name', 'Operation', 'Value']}}}> ignored
Exception IOError: (13, 'Permission denied', '/home/aneesh/.enthought/traits/traits_ui.dir') in <bound method _Database.close of {'enthought.traits.ui.table_filter.MenuTableFilter': '\x80\x02}q\x01(U\x00(M\xb0\x01M;\x01M@\x02M\x0e\x01tq\x02U\x01$centhought.traits.ui.key_bindings\nKeyBindings\nq\x03)\x81q\x04}q\x05(U\x12__traits_version__q\x06U\x053.3.0q\x07U\x08bindingsq\x08centhought.traits.trait_handlers\nTraitListObject\nq\t)\x81q\n}q\x0b(U\nname_itemsq\x0cU\x0ebindings_itemsq\rU\x06objectq\x0eh\x04U\x04nameq\x0fh\x08ubU\x06prefixq\x10U\x00U\x06suffixq\x11U\x00ubU\x0brules_tableq\x12}q\x13(U\x06widthsq\x14]q\x15(K\x8eK\x8eK\x8eK\x8feU\x07columnsq\x16]q\x17(U\x00U\x04Nameq\x18U\tOperationq\x19U\x05Valueq\x1aeU\x07filtersq\x1b]q\x1cuu.'}> ignored
*********************************************************************************************

Am I did any mistake during installaiton? If so, please help me to solve it.

Moreover, I have two more quick quries here....

1. How should I set the environment varible so that I can invoke PyRx from terminal itself?

2. How to screen ligand library with 'Lipinski rule' and other criterias? Is there way to do in PyRx?

Many thanks in advance

Sincerely
Aneesh
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aneeshcna
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Re: Error message pop-up while invoking PyRx from Destop ico

Postby sargis » Thu Jan 30, 2014 9:58 pm

aneeshcna wrote:Dear Users,

I have just installed PyRx in my Ubuntu system. As a trail run, when I invoke PyRx from the the Destop icon, a wxPython stdout/stderr window pop-up with following error -

********************************************************************************************
Exception IOError: (13, 'Permission denied', '/home/aneesh/.enthought/traits/traits_ui.dir') in <bound method DbfilenameShelf.__del__ of {'enthought.traits.ui.table_filter.MenuTableFilter': {'': (432, 315, 576, 270), '$': <enthought.traits.ui.key_bindings.KeyBindings object at 0xcf931dc>, 'rules_table': {'widths': [142, 142, 142, 143], 'filters': [], 'columns': ['', 'Name', 'Operation', 'Value']}}}> ignored
Exception IOError: (13, 'Permission denied', '/home/aneesh/.enthought/traits/traits_ui.dir') in <bound method _Database.close of {'enthought.traits.ui.table_filter.MenuTableFilter': '\x80\x02}q\x01(U\x00(M\xb0\x01M;\x01M@\x02M\x0e\x01tq\x02U\x01$centhought.traits.ui.key_bindings\nKeyBindings\nq\x03)\x81q\x04}q\x05(U\x12__traits_version__q\x06U\x053.3.0q\x07U\x08bindingsq\x08centhought.traits.trait_handlers\nTraitListObject\nq\t)\x81q\n}q\x0b(U\nname_itemsq\x0cU\x0ebindings_itemsq\rU\x06objectq\x0eh\x04U\x04nameq\x0fh\x08ubU\x06prefixq\x10U\x00U\x06suffixq\x11U\x00ubU\x0brules_tableq\x12}q\x13(U\x06widthsq\x14]q\x15(K\x8eK\x8eK\x8eK\x8feU\x07columnsq\x16]q\x17(U\x00U\x04Nameq\x18U\tOperationq\x19U\x05Valueq\x1aeU\x07filtersq\x1b]q\x1cuu.'}> ignored
*********************************************************************************************
Am I did any mistake during installation? If so, please help me to solve it.


Dear Aneesh,

Thank you for the message. What version of Ubuntu system are you using and for how long? I have successfully run PyRx-0.9-Linux-x86-Install on 12.04 and 13.04. Do 'ls -al '/home/aneesh/' to see if you have a write access to your home folder. I haven't seen the error message you are getting; not sure what's causing it.

aneeshcna wrote:1. How should I set the environment varible so that I can invoke PyRx from terminal itself?

To invoke PyRx from terminal itself run ~/PyRx-0.9/run.sh. Have a look at that file to see what environment variables it sets.
aneeshcna wrote:2. How to screen ligand library with 'Lipinski rule' and other criterias? Is there way to do in PyRx?

You can filter ligand library by mass, but there is no 'Lipinski rule' filter implemented in PyRx yet. You'll need to write one yourself or use third party package that do that.

Sincerely,
Sargis
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Re: Error message pop-up while invoking PyRx from Destop ico

Postby aneeshcna » Fri Jan 31, 2014 6:09 am

Dear Sargis,

Thanks a lot the quick and prompt reply. I have changed the file permission and it worked fine. But, When I try to invoke PyRx from terminal, as u suggested, a warning message pop-up in the terminal, as follows...

***************************************************************************************************************************************
(python:3442): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python:3442): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python:3442): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 17
*****************************************************************************************************************************************

Do I need to worry about this message?

Thanks in advance

Reagrds
Aneesh
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Re: Error message pop-up while invoking PyRx from Destop ico

Postby sargis » Fri Jan 31, 2014 8:29 pm

Dear Aneesh,

You are welcome. No need to worry about Gtk-WARNING.

Regards,
Sargis
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