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):
>
>
> #### 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
>
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