Bug: mad interference between matplotlib and openbabel

Community matplotlib-users
1

Hi folks!

I' m working on a code to identify ligand's information from pdb crystal
structures. For this purpose I use the openbabel package. I' m encoding
the ligand's information in smarts.
For checking if the smarts are assigned correctly I 'm writing a sdf
file (to control whether the features are placed correctly).

This part works fine - but I get into deep trouble when I try to plot
simple count statistics of my smarts, when I use the "from pylab
import*" , or "from pylab import matplotlib" statements (trouble appears
just after IMPORTING - I do not use a pylab function in this state of
the program yet):

Smart features are not recognized anymore, the feature coordinates are
shifted and so on - But I don' t know why.

my code snip:

import os
from numpy import*
from time import*

#### SMARTING
import numpy

import openbabel
from openbabel import*
import pybel
from pybel import*

#### LIGAND DETECTION
import Bio.PDB
from Bio.PDB import*
import Numeric
from Bio.PDB.StructureBuilder import *

#from pylab import* --> RAISES THE PROBLEMS !!!!

def projecting_smarts(isolated_ligand, method ,color, output):
   
#### Bio PDB -> 2 get ligand coords
    parser =PDBParser()
   
    structure = parser.get_structure('s', isolated_ligand)
    atom = structure.get_atoms()

···

###

    print "smarting successfully started!"
   
    mol = readfile("pdb", isolated_ligand).next()

    smart_list = []
   
    result_acceptor = method.findall(mol) #finds acceptors
   
    for i in result_acceptor: #Result
Donor= list from tuples
        list_element1 = (list(i)[0]) # ->
resolve hierarchy
        smart_list.append(list_element1)
   
    print smart_list,"ACCEPTOR_LIST" #list of smart features

Maybe one of you might know what to do!

Thanx alot!

flo

2

Hi Florian,
   you should try "import pylab" or "import pylab as P". "from pylab import *" might overwrite some functions or methods ... if a pylab function/method has the same name as one in a module imported with * before.

See the following example:

#file a.py
def foo():
     print "I'm a"

# file b.py
def foo():
     print "I'm b"

# file import_ab.py
from a import *
foo()
from b import *
foo()

The output is:
I'm a
I'm b

as the function foo() is overwritten by the second import...

Manuel

Florian Koelling wrote:

···

Hi folks!

I' m working on a code to identify ligand's information from pdb crystal
structures. For this purpose I use the openbabel package. I' m encoding
the ligand's information in smarts.
For checking if the smarts are assigned correctly I 'm writing a sdf
file (to control whether the features are placed correctly).

This part works fine - but I get into deep trouble when I try to plot
simple count statistics of my smarts, when I use the "from pylab
import*" , or "from pylab import matplotlib" statements (trouble appears
just after IMPORTING - I do not use a pylab function in this state of
the program yet):
Smart features are not recognized anymore, the feature coordinates are shifted and so on - But I don' t know why.

my code snip:

import os
from numpy import*
from time import*

#### SMARTING
import numpy

import openbabel
from openbabel import*
import pybel
from pybel import*

#### LIGAND DETECTION
import Bio.PDB
from Bio.PDB import*
import Numeric
from Bio.PDB.StructureBuilder import *

#from pylab import* --> RAISES THE PROBLEMS !!!!

def projecting_smarts(isolated_ligand, method ,color, output):
   
    parser =PDBParser()
       structure = parser.get_structure('s', isolated_ligand)
    atom = structure.get_atoms() ###

    print "smarting successfully started!"
       mol = readfile("pdb", isolated_ligand).next()

       smart_list =
       result_acceptor = method.findall(mol) #finds acceptors
   
Donor= list from tuples
        list_element1 = (list(i)[0]) # -> resolve hierarchy smart_list.append(list_element1)
       print smart_list,"ACCEPTOR_LIST" #list of smart features

Maybe one of you might know what to do!

Thanx alot!

flo

-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
matplotlib-users List Signup and Options