[r12013]: cdk-qa / trunk / projects / 080813-00001 / README  Maximize  Restore  History

Download this file

53 lines (37 with data), 1.5 kB

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
GOAL
---------------------------------------------

To list the differences in Sybyl atom type perception between the CDK
and ZINC8.

ZINC
---------------------------------------------

OpenBabel 2.2.0 was used.

wget http://zinc8.docking.org/subset1/10/10_p0.1.sdf.gz
gunzip 10_p0.1.sdf.gz
bsh extractZINCmol2AtomTypes.bsh > mol2.zinc.txt

Chemistry Development Kit
---------------------------------------------

CDK from trunk 2008-08-11 (r11998+) was used.

bsh -classpath cdk-svn-20080221.jar extractCDKmol2AtomTypes.bsh > mol2.cdk.txt

Comparison
---------------------------------------------

Number of differences:

bsh diff.bsh | wc -l

Number of ZINC structures with differences:

bsh debug.bsh | cut -d':' -f1 | sort | uniq | wc -l

By difference:

bsh diff.bsh | sort | uniq -c | sort -n -r

    269 N.pl3 -> N.3                                                                                                                           
    228 N.am -> N.pl3                                                                                                                          
    144 N.am -> N.3                                                                                                                            
     86 S.3 -> Any
     86 N.2 -> Any
     66 O.3 -> Any
     60 O.3 -> Het
     50 N.pl3 -> Any
     32 C.cat -> C.2
     16 N.1 -> Any
      4 S.o -> S.O
      2 S.o -> S.O2
      1 ZINC03777711 ->
      1 N.am -> Any
      1 C.3 ->

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks