Output problems for example.py and import problems for dbmol.py

[qfyu]

Dear Lomap,

I had some problems when I tried to run the python scripts of lomap, please see the following for detial.

(1) #LINUX VERSION LSB Version: core-2.0-noarch:core-3.2-noarch:core-4.0-noarch:core-2.0-x86_64:core-3.2-x86_64:core-4.0-x86_64:desktop-4.0-amd64:desktop-4.0-noarch:graphics-2.0-amd64:graphics-2.0-noarch:graphics-3.2-amd64:graphics-3.2-noarch:graphics-4.0-amd64:graphics-4.0-noarch Distributor ID: SUSE LINUX Description: SUSE Linux Enterprise Server 11 (x86_64) Release: 11 Codename: n/a

(2) #LOMAP INSTALLATION conda config --add channels nividic conda create -c nividic -n my-lomap lomap source activate my-lomap

all prerequisites were installed

conda list boost 1.56.0 py34_1 nividic graphviz 2.38.0 1 mobleylab lomap 0.0.0 py34_0 nividic pygraphviz 1.4rc1 py34_0 nividic rdkit 2015.09.2 np110py34_0 nividic matplotlib 1.5.1 np110py34_0 networkx 1.11 py34_0 pyqt 4.11.4 py34_4 …..

(3) python example.py

basic or radial

db_mol = lomap.DBMolecules('test/basic/', output=True)

db_mol = lomap.DBMolecules('test/radial/', output=True)

outputs are as following

out.txt out_score_with_connection.txt mcs.png

Question One: Why didn’t the script output all results? Such as out.png, out.pickle, out.pdf, out.eps, and out.doc?

(4) #open dbmol.py and input commands python

from lomap import mcs Traceback (most recent call last): File "", line 1, in ImportError: cannot import name 'mcs' from lomap import graphgen Traceback (most recent call last): File "", line 1, in ImportError: cannot import name 'graphgen'

Question Two: What caused these problems and how to solve them?

Thank you and look forward to your reply.

[davidlmobley]

@nividic @shuail any insights?

I'll try and see if I can reproduce your issue.

[davidlmobley]

@qfyu - I've reproduced a problem with this (installing in a clean conda environment), though I'm not sure it's the same as your problem; I'm getting an issue with libc++abi.dylib throwing an uncaught exception; if I had to guess my particular issue looks like it's a problem with graphics libraries.

Did you get any error messages when you attempted this? And what platform are you on?

Probably we need to get #34 merged in and then go through and make sure we have a build that is compatible with the latest versions of the relevant packages. We haven't been using this very much lately and I think things may have gotten a bit outdated.

[shuail]

@qfyu @davidlmobley I tried to reproduce the errors from a clean conda env. Here are steps I performed:

conda create --no-default-packages -n test-lomap-clean python source activate test-lomap-clean conda config --add channels nividic conda install lomap conda install networkx=1.11 (here since #34 is not merged yet, just manually downgrade networkx.)

After all, I go to the Lomap folder and run "python example.py", it gives me all the results.

Here is the list of relevant packages in the conda list

boost 1.56.0 py27_3 nividic graphviz 2.38.0 5
lomap 0.0.0 py27_0 nividic matplotlib 1.5.0 np110py27_0
networkx 1.11 py27_1
numpy 1.10.4 py27_2
pygraphviz 1.3.1 py27_3 nividic pyqt 4.11.4 py27_4
python 2.7.15 h1571d57_0
qt 4.8.7 4
rdkit 2016.03.1 np110py27_0 nividic

Comparing with @qfyu your installed packages, the version of some packages are different. Then I realized that you are using python 3.4.

So I create another python 3.4 env as below: conda create --no-default-packages -n test-lomap-python3 python=3.4 source activate test-lomap-python3 conda config --add channels nividic conda install lomap

Here is the key package list in this python3.4 env

boost 1.56.0 py34_1 nividic graphviz 2.38.0 5
lomap 0.0.0 py34_0 nividic matplotlib 1.5.1 np110py34_0
networkx 1.11 py34_0
numpy 1.10.4 py34_2
pygraphviz 1.4rc1 py34_0 nividic pyqt 4.11.4 py34_4
python 3.4.5 0
qt 4.8.7 4
rdkit 2015.09.2 np110py34_0 nividic

Using this python, I could also get the correct results. My conda version is 4.5.1. So @qfyu I suggest that you create a new empty conda environment and try again. If there is still a problem, could you post the error message here.

[shuail]

@davidlmobley I got the same error message as you did when I use my Mac to install lomap, it seems to be the graphviz compatible issue with Mac OS.

[davidlmobley]

Thanks, @shuail ! So it sounds like we have a separate issue to resolve relating to OS X then...?

[shuail]

@davidlmobley yes, I think graphviz may fail on certain OS X at least the latest OS X. Specifically it fails when graphviz try to convert the dot file (networkx output) to png file. Maybe we could either fix the compatible issue between graphviz and Mac, or find another package to convert the file format.

[qfyu]

@davidlmobley, I didn't get your error messages, and I am using ubuntu 14. @shuail, I tried to create a new conda environment "test-lomap-python3" with your commands, the packages were same as yours, and the conda version was 4.2.9. However, the problems shown in (3) and (4) still existed.

[shuail]

@qfyu If the packages are all identical, I am not sure what could cause your problems at this point. For your problem 3, when you run the program, what is the printed out messages? Could you paste the message here.

[qfyu]

@shuail, I found the graphviz was a bit different: graphviz 2.38.0 1 mobleylab.

When I run the command "python example.py", no messages printed out on the screen, and I got some result files: out.txt, out_score_with_connection.txt, mcs.png, mcsmapping_.

out.txt

ID FileName

0 1,3,7-trimethylnaphthalene.mol2 1 1-butyl-4-methylbenzene.mol2 2 2,6-dimethylnaphthalene.mol2 3 2-methyl-6-propylnaphthalene.mol2 4 2-methylnaphthalene.mol2 5 2-naftanol.mol2 6 methylcyclohexane.mol2 7 toluene.mol2

out_score_with_connection.txt

Index_1 ,Index_2 ,Filename_1 ,Filename_2 ,Erc_sim ,Str_sim ,Loose_sim ,Connect 0 ,1 ,1,3,7-trimethylnaphthalene.mol2,1-butyl-4-methylbenzene.mol2,1.00 ,0.11080 ,0.11080 ,No 0 ,2 ,1,3,7-trimethylnaphthalene.mol2,2,6-dimethylnaphthalene.mol2,1.00 ,0.90484 ,0.90484 ,Yes ...

mcs_mapping_0_5

1 1 10 2 9 3 8 4 3 9 2 10 4 8 5 7 6 6 7 5 0 0

Thanks for the comments.

[shuail]

@qfyu I am not sure if the difference of graphviz would affect the result while I think it worth to try again with exact command (with the same order) of I did and see if you could get the identical packages.

[qfyu]

@shuail, the packages and results were obtained form the same order of your commands for the environment "test-lomap-python3".

[davidlmobley]

Closing this; maintenance moved to github.com/OpenFreeEnergy/Lomap.