PDBParser + VMD installation problems

[Andy Anker]

Hi,

I am fairly new to FullRMC and trying to model amorphous bismuth oxide, however, facing some problems which seem to be related to the installation of VMD and the PDBParser.

The first issue is when I am trying to install fullrmc on new computers, it gives me a PDBParser issue, which I did not receive a month ago. I have tried to install it with different python versions, different control systems and followed the different ways to install fullrmc. However, every time I get the error shown in attached picture 1.

The second issue is happening on a computer, where I successfully installed fullrmc 2 months ago and also managed to do some refinements. When I want to use the visualization script in the examples, it gives me an error related to VMD (attached picture 2). I have tried to install VMD, but maybe this was not successful? 

Have any of you seen any of these two problems before?

Best,

Andy

[Bachir Aoun]

Hi Andy,

how did you install fullrmc on the new computers ? did you use pip command ?

you seem to have an old version of fullrmc and pdbparser because pdbparser is spelled all lowercase

using the same python installtion can you try the following

python-m pip install fullrmc --upgrade

then open your terminal and try the following 

import pdbparser
import fullrmc

as for VMD it's a third party application, if it's a windows machine that you have you should have an alias for the installation, try launching and see if it works.

thanks

[Mikkel Juelsholt]

Hi Bachir

I have the exact same problem with PDBparser on a Windows machine. I have installed fullRMC using pip

When I run the upgrade command I get a message saying that all the packages already are up to date. And then when I try to run fullRMC I still get the error messaging saying it cannot find PDBparser. 

The weird thing is I had fullRMC up running on the same computer around 1 month ago and then 1 day it suddenly stopped working. I have reinstalled both python and fullRMC multiple times, but I cannot solve the problem. 

I don't know where things go wrong, but hope it can be solved somehow.

Thanks for a nice program!

Mikkel 

[Bachir Aoun]

Hello Mikkel,

Saying that suddenly fullrmc stopped working suggests that you either have python path problem or you are now using a different python.

If you have different python installation, you can be using the wrong pip to do the installations.

please do me this favor and get me screen shot of your terminal. start python and do the following

from __future__ import print_function
import sys
print(sys.path)

import pdbparser
print(pdbparser)

import fullrmc
print(fullrmc)
print(fullrmc.get_version())

this is what i need from you

thank you

[Andy Anker]

Hi Bachir,

Thanks for the quick response!

The upgrade did not work for me either. I tried running the above-mentioned lines in the terminal, at different computers I get the same error message. It seems like you are right regarding the lower/upper case letters in pdbparser, because when I change this in the engine.py file, it solves this problem, whereafter it gives me another, which is probably due to the same reason of a wrong version.

['', '/env/python', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/local/lib/python2.7/dist-packages/IPython/extensions', '/root/.ipython']
<module 'pdbparser' from '/usr/local/lib/python2.7/dist-packages/pdbparser/__init__.pyc'>

ImportErrorTraceback (most recent call last)

<ipython-input-3-060a7db6cbf4> in <module>()
      7 print(pdbparser)
      8 
----> 9 import fullrmc
     10 print(fullrmc)
     11 print(fullrmc.get_version())

---

1 frames

---

/usr/local/lib/python2.7/dist-packages/fullrmc/__init__.py in <module>()
    322 # import package info
    323 from __pkginfo__ import __version__, __author__, __email__, __onlinedoc__, __repository__, __pypi__
--> 324 from Engine import Engine
    325 
    326 def get_version():

/usr/local/lib/python2.7/dist-packages/fullrmc/Engine.py in <module>()
     25 except:
     26     import pickle
---> 27 from pdbParser.pdbParser import pdbParser
     28 from pdbParser.Utilities.BoundaryConditions import InfiniteBoundaries, PeriodicBoundaries
     29 from pyrep import Repository

ImportError: No module named pdbParser.pdbParser

When I use conda list to see the version of the fullrmc, it says that I have fullrmc version 3.3.0.

Andy

[Leon Wang]

Hi, everyone,

 

I believe what you have is the improper environment setting.  You may install those packages or modules, but you or Anaconda does not configure them properly so you get those error/warning message.

 

Here is my experience. Hope it would be helpful. I have to point out that I am new to fullRMC. If I say something wrong or silly, please forgive me.

 

I use fullRMC on Linux system. I was struggling the conflicts and issues of file/module not found. Finally, I noticed that I did not figure out the Python environment properly. DO NOT USE CONDA TO UPDATE OR INSTALL fullRMC AND REQUIRED PACKAGES. If you did, you would receive the error message you had.

 

Just remind, fullRMC requires Python (>= 2.7 and < 3).

 

Here is what I did on Linux. I believe it is same thing for Windows.

1. Create a new environment only for fullRMC. It may cost some diskspace, but you would get rid of those error messages.

“conda env list”                  # check what kind of environment you are using

“conda create --name=py27 python=2.7”      #create python 2.7 environment

“conda activate py27”      #activate py27 environment, install everything based in this environment

 

2. If you do want to use your current environment, you can manually find those files location and add the paths into ~/.local/lib/python2.7/site-packages/*.pth where you can use any name to replace the star (*). EACH PATH TAKES ONE LINE.

For Windows, I guess you need add those path into your environment in a similar way. Please google it.

           

            e.g. Andy’s computer cannot find pdbParser. You can check your anaconda2 directory. For me, it looks like “…/apps/anaconda2/lib/python2.7/site-packages/pdbParser”. If you could not find it, try to find it and copy or move it to this directory. Or you can add the path to your *.pth file.

 

3. If you do want to use VMD on Linux, please make sure the configuration of SSH Tunneling correctly to visualize your structure. If fullRMC needs to run it, you have to set the path for VMD as well.

 

Good Luck,

Liaoyuan (Leon) Wang

[Peter Metz]

Hi Andy,

You mentioned that you used `conda list`, but the Python path returned by `sys.path` usually includes things like ... ~/anaconda3/lib/python3.7 .... for a vanilla Anaconda install. 

I wonder if your system had a default Python installation, and whether your system PATH points to a different Python installation than conda. If you enter 'which python' and 'which conda' in your linux terminal, do you get different file paths?

-Peter

[Bachir Aoun]

Hi All,

I am glad to see active responders to this post.

@Leon, you are spot on. I am not fan of anaconda because packages path can get messed up sometimes. I personally use traditional pip installations and fullrmc is not a (or i didn't make it) available on conda installer.

Also, fullrmc is python3 compliant but not all its dependencies are. Version 4.0 of fullrmc will be fully supported on python 3 as well as python 2.

version 3.3 of fullrmc would work on python 3 but you guys have to install it's dependencies manually.

hope that helps   

[Mikkel Juelsholt]

First thank you for the help to everyone.

I have tried using both anaconda and a regular python installation on windows. And I get the same error. 

Bachir I have done as requested and attached the screenshot. I cleaned my windows of any python installation (hopefully) and installed a fresh one. 

I cannot import fullrmc as it gives me the error that it cannot find pdbparser.

My fullrmc folder is: C:\Python27\Lib\site-packages\fullrmc

My pdbparser folder is: C:\Python27\Lib\site-packages\pdbparser. This is also the path the terminal prints

[Mikkel Juelsholt]

And when I try to run the upgrade command I get: "Requirement already up-to-date: fullrmc in c:\python27\lib\site-packages (3.3.0)

                                                                                        Requirement already satisfied, skipping upgrade: #Some-python package"

[Bachir Aoun]

Hello Mikkel,

Shoot now i know what your issue is.

i bet you have a newer pdbparser verison than 0.1.5.

it's all on me, I updated pdbparser on pypi before pushing the new fullrmc version.

you might want to pip install this

python -m pip install 'pdbParser==0.1.5'

then make sure pdbParser is in your python path and everything would work for you

import sys
print(sys.path)

I was waiting to finish some work prior to publishing fullrmc 4.0.0 but i think it's now time to ..

thanks

[Mikkel Juelsholt]

Okay, so this works. Both with and without anaconda. I can now import fullrmc, however when I try to run a script I get the following error regarding 'ACID'. This is from my spyder console, but same error other places as well. 

Thank you for the help so far. 

Okay, thats great! I did that it solves it, I can now import fullrmc. But if I try to run a script I

[Bachir Aoun]

My pleasure.

you now have to do the same for pyrep.

python -m pip install 'pyrep==1.0.4'

all of that is happening because I modified pyrep and pdbparser for fullrmc 4.0

this new version of fullrmc I will be hosting it on a cloud service at some point to leverage super computers and scale up fullrmc.

bachir

[Mikkel Juelsholt]

Hi Bachir

Yes, now it runs! Thanks for all the help, sorry if it stresses you with releasing fullrmc 4.0. Looking forward to it, thoug!

Best Mikkel

[Bachir Aoun]

Happy to help. that was a great exercise for all of us. I wasn't aware that my late side packages early release might affect others work

regards

[Andy Anker]

It also worked for me! Thanks a lot for the help.

Best

Andy

[Leon Wang]

Hi, Bachir,

Thanks for your effort and support to us!

Cheers,

Leon

[Bachir Aoun]

My pleasure.

I uploaded fullrmc 4.0 earlier than i what i anticipated for you all because there some discrepancy in the libraries version.
To avoid any conflict, install it with python 3 and test it out. I added more features and fixed some bugs of previous versions.

Regards