[chimerax-users] ChimeraX tool installationg
Yongcheng MU
ymu004 at odu.edu
Thu Feb 4 18:45:07 PST 2021
Hi Eric and Anthony,
Thank you so much for the reply and help.
I modified the files following your instruction. And now it shows me "No
atoms match given atom specifier". I wonder if this means everything is
good now.
Best regards,
Yongcheng
[image: Screen Shot 2021-02-04 at 9.41.03 PM.png]
On Thu, Feb 4, 2021 at 8:15 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Tony's right. Since you explicitly ask for api_version 1,
> register_command gets the three arguments he mentions (I should have
> checked that!). You could follow his advice about how to handle those, or
> you could change to api_version 0, which corresponds to your current
> declaration (command name and logger). Since api_version 0 is the default,
> you could just eliminate setting it at all if you want to use version 0.
>
> --Eric
>
> On Feb 4, 2021, at 5:05 PM, Anthony James Schaefer <tony.schaefer at uga.edu>
> wrote:
>
> Yongcheng,
>
> I think there are some other issues than what Eric mentioned. The
> register_command method of BundleAPI's should take three arguments: bundle
> info, command info, and a logger. Your register_command only has 2
> arguments (CL_Tensorflow, and logger). You'll have to add an argument to
> your function.
>
> You might also want to check the variable names you're using. When you
> call register:
>
> from chimerax.core.commands import register
> register(CL_Tensorflow, desc, cmd.CL_Tensorflow)
>
> The first argument here should be a string (the name of the command). But
> you've got CL_Tensorflow as an argument in your BundleAPI's
> register_command definition. None of the arguments that get passed to the
> BundleAPI's register_command are strings. I think you can change that by
> setting api_version = 0, but I'm not sure. You might want something more
> like:
>
> class CL_Tensorflow(BundleAPI):
> api_version = 1
>
> @statismethod
> def register_command(bundle_info, command_info, logger):
> # I'm going to skip importing the command function and
> # description because I don't know what your code looks like
> # let's just say your CmdDesc was imported as 'desc' and the
> function was
> # imported as 'func'
> # you'll have to fill that in yourself
>
> from chimerax.core.commands import register
> # use the command_info variable given to register_command to
> specify
> # the name of the command
> register(command_info.name, desc, func)
>
> Best,
>
> Tony
> ------------------------------
> *From:* ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of
> Yongcheng MU <ymu004 at odu.edu>
> *Sent:* Thursday, February 4, 2021 5:51 PM
> *To:* ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> *Subject:* Re: [chimerax-users] ChimeraX tool installationg
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
> Hi Eric,
>
> I really appreciate your quick response. It really helps me a lot to
> understand it. But I have another question, following your instructions, I
> modified the _init_.py file but it still holds an error. I attached some
> related information below.
>
> Thank you for your time and help.
>
> Best regards,
> Yongcheng
>
> On Thu, Feb 4, 2021 at 4:09 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> Hi Yongcheng,
> You probably know this, but in order to avoid registering all commands at
> startup, which would involve executing the code from dozens of bundles and
> make startup really slow, ChimeraX uses information from the Toolshed to
> know which bundles implement which commands and only when the time comes to
> actually execute a command does it invoke the bundle's code that fully
> registers the command, which then allows ChimeraX to know what arguments
> and keywords the command allows and what function the command executes so
> that it can parse the command text and call that function.
> So all that error text you got is indicating that there is an error in
> your command-registration function. ChimeraX asks you to register your
> command by calling the register_command() method of your BundleAPI
> subclass. Does the implementation of register_command() in your
> __init__.py look something like this?:
>
> from chimerax.core.toolshed import BundleAPI
>
> class CL_TensorFlowAPI(BundleAPI):
>
> @staticmethod
> def register_command(command_name, logger):
> from . import cmd
> cmd.register_command(command_name, logger)
>
> If it does, then the problem is that you have no cmd.py file in your
> bundle, producing the error:
>
> cannot import name 'cmd' from 'chimerax.CL_Tensorflow'
> (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))
>
> Let me know if you need further clarification.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
> On Feb 4, 2021, at 10:45 AM, Yongcheng MU <ymu004 at odu.edu> wrote:
>
> Hello,
>
> Hope you are doing well. This is Yongcheng. I am writing this email
> because I am trying to install a Deep learning tool in ChimeraX, but I have
> some issues about it.
>
> I built and installed my code following the steps on the Chimera Guide
> website. I installed my code successfully, but when I run using command
> that I created, it hold some errors:
>
> *"RuntimeError: delayed command registration for 'CL_Tensorflow' failed
> (register_command() failed for command CL_Tensorflow in bundle
> ChimeraX-CL-Tensorflow:*
>
>
>
> *cannot import name 'cmd' from 'chimerax.CL_Tensorflow'
> (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))
> File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2142, in lazy_register *
> *raise RuntimeError("delayed command registration for %r failed (%s)" %
> (cmd_name, e))"*
>
> *"During handling of the above exception, another exception occurred:*
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Traceback (most recent call last): File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py",
> line 275, in execute cmd.run(cmd_text) File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2746, in run self._find_command_name(final,
> used_aliases=_used_aliases) File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2489, in _find_command_name what.lazy_register(cmd_name) File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2142, in lazy_register raise RuntimeError("delayed command
> registration for %r failed (%s)" % (cmd_name, e))RuntimeError: delayed
> command registration for 'CL_Tensorflow' failed (register_command() failed
> for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot import
> name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))RuntimeError:
> delayed command registration for 'CL_Tensorflow' failed (register_command()
> failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot
> import name 'cmd' from 'chimerax.CL_Tensorflow'
> (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2142, in lazy_register*
> *raise RuntimeError("delayed command registration for %r failed (%s)" %
> (cmd_name, e))"*
>
> I wonder if you know what's going on here, and how to fix it. Thank you so
> much for your time.
>
> Best regards,
> Yongcheng
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