can’t find toolbox module

[Anonymous]

 

Hi!

I was not sure if this is ‘build/install’ question, but it seems that ‘general’ forum is for more advanced issues..

I’m a beginner in PyRosetta and not really a “tech” person, more wet biologist so sorry if the question is stupid..

Currently using tutorial from http://graylab.jhu.edu/pyrosetta/downloads/documentation/Workshop2_PyRosetta_Intro.pdf to try basics of PyRosetta.

When running pose = pose_from_pdb(“1yy8.clean.pdb”) got unknown exception error.

Using Ubuntu 16.04.1 LTS 64-bit, python, pyrosetta versions may be seen from log below (is there a way to hide it behind a cut?)

 

I would be grateful for your advice!

Python 2.7.12 (default, Jul  1 2016, 15:12:24)

Type "copyright", "credits" or "license" for more information.



IPython 2.4.1 -- An enhanced Interactive Python.

?         -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help      -> Python's own help system.

object?   -> Details about 'object', use 'object??' for extra details.



In [1]: from pyrosetta import *



In [2]: pyrosetta.init()

NameError                                 Traceback (most recent call last)

<ipython-input-2-34444050a08f> in <module>()

----> 1 pyrosetta.init()



NameError: name 'pyrosetta' is not defined



In [3]: import pyrosetta



In [4]: pyrosetta.init()

Found rosetta database at: /usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/database; using it....

PyRosetta-4 2016 [Rosetta 2016 unknown:caf3ac9d7450e125941c5e85236b57d398680305 2016-10-22 12:28:39 -0700] retrieved from: git@github.com:RosettaCommons/main.git

(C) Copyright Rosetta Commons Member Institutions.

Created in JHU by Sergey Lyskov and PyRosetta Team.



core.init: Rosetta version  from

core.init: command: PyRosetta -ex1 -ex2aro -database /usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/database

core.init: 'RNG device' seed mode, using '/dev/urandom', seed=396660147 seed_offset=0 real_seed=396660147

core.init.random: RandomGenerator:init: Normal mode, seed=396660147 RG_type=mt19937



In [5]: pose = pose_from_pdb("1yy8.clean.pdb")



RuntimeError                              Traceback (most recent call last)

<ipython-input-5-c5fc8cfb3b2d> in <module>()

----> 1 pose = pose_from_pdb("1yy8.clean.pdb")



/usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/pyrosetta/__init__.pyc in pose_from_pdb(filename)

327 # because otherwise, it wrecks a lot of people's scripts.  ~Labonte

328 def pose_from_pdb(filename):

--> 329     return pose_from_file(filename)

330

331



RuntimeError: Caught an unknown exception!

 

[Anonymous]

sorry, the previous was just because of wrong working directory…

now pose_from_pdb works…

but now I’ve got an ImportError, can’t find toolbox module..

In [18]: from toolbox import get_struct

ImportError                               Traceback (most recent call last)

<ipython-input-18-4c061d2704b0> in <module>()

----> 1 from toolbox import get_struct



ImportError: No module named toolbox

 

[Anonymous]

sorry, the previous was just because of wrong working directory…

now pose_from_pdb works…

but now I’ve got an ImportError, can’t find toolbox module..

In [18]: from toolbox import get_struct

ImportError                               Traceback (most recent call last)

<ipython-input-18-4c061d2704b0> in <module>()

----> 1 from toolbox import get_struct



ImportError: No module named toolbox

 

[Anonymous]

sorry, the previous was just because of wrong working directory…

now pose_from_pdb works…

but now I’ve got an ImportError, can’t find toolbox module..

In [18]: from toolbox import get_struct

ImportError                               Traceback (most recent call last)

<ipython-input-18-4c061d2704b0> in <module>()

----> 1 from toolbox import get_struct



ImportError: No module named toolbox

 

[Anonymous]

Well, the log file in your post clearly says that PDB file is not there:

In [5]: pose = pose_from_pdb("1yy8.clean.pdb")

core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 455 residue types

core.chemical.ResidueTypeSet: Total time to initialize 0.493135 seconds.

core.import_pose.import_pose: File: 1yy8.clean.pdb not found!

 

[Anonymous]

Well, the log file in your post clearly says that PDB file is not there:

In [5]: pose = pose_from_pdb("1yy8.clean.pdb")

core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 455 residue types

core.chemical.ResidueTypeSet: Total time to initialize 0.493135 seconds.

core.import_pose.import_pose: File: 1yy8.clean.pdb not found!

 

[Anonymous]

Well, the log file in your post clearly says that PDB file is not there:

In [5]: pose = pose_from_pdb("1yy8.clean.pdb")

core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 455 residue types

core.chemical.ResidueTypeSet: Total time to initialize 0.493135 seconds.

core.import_pose.import_pose: File: 1yy8.clean.pdb not found!

 

[Anonymous]

Re toolbox module: in PyRosetta-4 it location is changed to pyrosetta.toolbox, please try to import it instead.

[Anonymous]

Re toolbox module: in PyRosetta-4 it location is changed to pyrosetta.toolbox, please try to import it instead.

[Anonymous]

Re toolbox module: in PyRosetta-4 it location is changed to pyrosetta.toolbox, please try to import it instead.

[Anonymous]

Just thought it may be informative, regarding PyMOL_Mover issue,

error happened in the same session, after everything “above” worked (import pyrosetta, pyrosetta.init(), import pyrosetta.toolbox, protein geometry manipulation, pose.dump_pdb. … PyMOLPyRosettaServer.py worked in PyMOL).

I appreciate your help!

[Anonymous]

Just thought it may be informative, regarding PyMOL_Mover issue,

error happened in the same session, after everything “above” worked (import pyrosetta, pyrosetta.init(), import pyrosetta.toolbox, protein geometry manipulation, pose.dump_pdb. … PyMOLPyRosettaServer.py worked in PyMOL).

I appreciate your help!

[Anonymous]

Just thought it may be informative, regarding PyMOL_Mover issue,

error happened in the same session, after everything “above” worked (import pyrosetta, pyrosetta.init(), import pyrosetta.toolbox, protein geometry manipulation, pose.dump_pdb. … PyMOLPyRosettaServer.py worked in PyMOL).

I appreciate your help!

[Anonymous]

We changed implementation of PyMOL mover from python to C++. So now you need to use something like this:

pymol = pyrosetta.PyMolMover()

 

[Anonymous]

We changed implementation of PyMOL mover from python to C++. So now you need to use something like this:

pymol = pyrosetta.PyMolMover()

 

[Anonymous]

We changed implementation of PyMOL mover from python to C++. So now you need to use something like this:

pymol = pyrosetta.PyMolMover()

 

[Anonymous]

Hi,

I have the PyRosetta4.MinSizeRel.python27.linux.release-140 installed on my Windows 8 platform. So far I have been able to pose a pdb structure and am looking forward linking PyMol to Pyrosetta through pymover. I found a post that says that implementation of the pymover is now pymol = pyrosetta.PyMolMover() due to the change from python to C++. However when I enter this command in ipython, I get the AttributeError: “module” object has no attribute “PyMolMover”. I will really appreciate any assistance to solve this issue.

Thanks.

[Anonymous]

Hi,

I have the PyRosetta4.MinSizeRel.python27.linux.release-140 installed on my Windows 8 platform. So far I have been able to pose a pdb structure and am looking forward linking PyMol to Pyrosetta through pymover. I found a post that says that implementation of the pymover is now pymol = pyrosetta.PyMolMover() due to the change from python to C++. However when I enter this command in ipython, I get the AttributeError: “module” object has no attribute “PyMolMover”. I will really appreciate any assistance to solve this issue.

Thanks.

[Anonymous]

Hi,

I have the PyRosetta4.MinSizeRel.python27.linux.release-140 installed on my Windows 8 platform. So far I have been able to pose a pdb structure and am looking forward linking PyMol to Pyrosetta through pymover. I found a post that says that implementation of the pymover is now pymol = pyrosetta.PyMolMover() due to the change from python to C++. However when I enter this command in ipython, I get the AttributeError: “module” object has no attribute “PyMolMover”. I will really appreciate any assistance to solve this issue.

Thanks.

[Anonymous]

Thank’s a lot!

You’re right, it was my mistake  when creating pose.

pyrosetta.toolbox import worked, thank you.

now I’ve lost PyMOL_mover..

In [21]: pymol = PyMOL_Mover()

NameError                                 Traceback (most recent call last)

<ipython-input-21-d991403572a8> in <module>()

----> 1 pymol = PyMOL_Mover()



NameError: name 'PyMOL_Mover' is not defined

Am I doing smth wrong? I didn’t find an answer in pymol_mover tutorial..

[Anonymous]

Thank’s a lot!

You’re right, it was my mistake  when creating pose.

pyrosetta.toolbox import worked, thank you.

now I’ve lost PyMOL_mover..

In [21]: pymol = PyMOL_Mover()

NameError                                 Traceback (most recent call last)

<ipython-input-21-d991403572a8> in <module>()

----> 1 pymol = PyMOL_Mover()



NameError: name 'PyMOL_Mover' is not defined

Am I doing smth wrong? I didn’t find an answer in pymol_mover tutorial..

[Anonymous]

Thank’s a lot!

You’re right, it was my mistake  when creating pose.

pyrosetta.toolbox import worked, thank you.

now I’ve lost PyMOL_mover..

In [21]: pymol = PyMOL_Mover()

NameError                                 Traceback (most recent call last)

<ipython-input-21-d991403572a8> in <module>()

----> 1 pymol = PyMOL_Mover()



NameError: name 'PyMOL_Mover' is not defined

Am I doing smth wrong? I didn’t find an answer in pymol_mover tutorial..

[Anonymous]

It works. Thank you!

[Anonymous]

It works. Thank you!

[Anonymous]

It works. Thank you!

[Anonymous]

Be careful of capitalization: I believe it’s pyrosetta.PyMOLMover()

[Anonymous]

Be careful of capitalization: I believe it’s pyrosetta.PyMOLMover()

[Anonymous]

Be careful of capitalization: I believe it’s pyrosetta.PyMOLMover()

[Author]

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