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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