OK, I guess I asked for that :-)
Could you reduce it down to the shortest possible program that
reproduces the error? For example, a 2 or 3 line program (including
imports) would be ideal. You'll should also supply the input file,
e.g. a one-molecule sdf file would be ideal.
You also need to supply the versions of your operating system, python,
eric, openbabel.
Since this is an eric bug, rather than in openbabel, you'll probably
have to report it to eric instead, but at least I can help you narrow
down the problem.
- Noel
2009/7/24 Andrew Fant <fa...@mo...>:
> Noel asked me to verify the code was working on the command line and to
> post it to the group.
>
> The following code should be fed two sd formatted files from the command
> line. It works fine from the command line but dies the previously
> mentioned ugly death under eric.
>
> (yes, I know it needs refactoring. this was a cut and paste job to do a
> one-off.)
>
> Andy
>
> #!/usr/bin/env python
>
> import pybel
> import sys
> import os.path
> import numpy
> import scipy
> import scipy.stats
> import string
> import math
> import matplotlib.pyplot as plt
>
> if len(sys.argv) == 3:
> file1=sys.argv[1]
> file2=sys.argv[2]
> if not(os.path.isfile(file1)) or not(os.path.isfile(file2)):
> print sys.argv[0],": input files must exist"
> exit(64)
> else:
> print "Usage:",sys.argv[0]," file1 file2"
> exit(128)
>
> basename1=string.split( (string.split(file1,'_',2)[0]),'.',2 )[0]
> basename2=string.split( (string.split(file2,'_',2)[0]),'.',2 )[0]
>
> set1=[]
> for molecule in pybel.readfile("sdf",file1):
> set1.append(molecule)
>
> set2=[]
> for molecule in pybel.readfile("sdf",file2):
> set2.append(molecule)
>
> #generate data arrays
>
>
> data1=[]
> for molecule in set1:
> mw=molecule.molwt
> logp=molecule.calcdesc()['LogP']
> mr=molecule.calcdesc()['MR']
> tpsa=molecule.calcdesc()['TPSA']
> fp2=molecule.calcfp('FP2')
> fp4=molecule.calcfp('FP4')
> mumble=[mw,logp,mr,tpsa,fp2,fp4]
> data1.append(mumble)
>
> data2=[]
> for molecule in set2:
> mw=molecule.molwt
> logp=molecule.calcdesc()['LogP']
> mr=molecule.calcdesc()['MR']
> tpsa=molecule.calcdesc()['TPSA']
> fp2=molecule.calcfp('FP2')
> fp4=molecule.calcfp('FP4')
> mumble=[mw,logp,mr,tpsa,fp2,fp4]
> data2.append(mumble)
>
> #Generate stats for mw,logP,mr, & tpsa for each set
>
> scratch1=numpy.empty((len(data1),4))
> kount=0
> for line in data1:
> scratch1[kount,0]=line[0]
> scratch1[kount,1]=line[1]
> scratch1[kount,2]=line[2]
> scratch1[kount,3]=line[3]
> kount+=1
>
> scratch2=numpy.empty((len(data2),4))
> kount=0
> for line in data2:
> scratch2[kount,0]=line[0]
> scratch2[kount,1]=line[1]
> scratch2[kount,2]=line[2]
> scratch2[kount,3]=line[3]
> kount+=1
>
> print "Statistical Summaries"
> print "for",basename1
> print "n =",len(set1)
> print "property mean sigma"
> print "Mol. Wt ",numpy.mean(scratch1[:,0])," ",numpy.std(scratch1[:,0])
> print "LogP ",numpy.mean(scratch1[:,1])," ",numpy.std(scratch1[:,1])
> print "Molar Ref. ",numpy.mean(scratch1[:,2])," ",numpy.std(scratch1[:,2])
> print "TPSA ",numpy.mean(scratch1[:,3])," ",numpy.std(scratch1[:,3])
> print
> print "for",basename2
> print "n =",len(set2)
> print "property mean sigma"
> print "Mol. Wt ",numpy.mean(scratch2[:,0])," ",numpy.std(scratch2[:,0])
> print "LogP ",numpy.mean(scratch2[:,1])," ",numpy.std(scratch2[:,1])
> print "Molar Ref. ",numpy.mean(scratch2[:,2])," ",numpy.std(scratch2[:,2])
> print "TPSA ",numpy.mean(scratch2[:,3])," ",numpy.std(scratch2[:,3])
>
> cross_FP2_similar=numpy.empty((len(set1),len(set2)))
> cross_FP4_similar=numpy.empty((len(set1),len(set2)))
> for i in range(len(set1)):
> for j in range(len(set2)):
> cross_FP2_similar[i,j]=data1[i][4] | data2[j][4]
> cross_FP4_similar[i,j]=data1[i][5] | data2[j][5]
>
>
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