User dd11f4d86b
20-02-2008 20:59:16
Hello,
I would like to use jcsearch (3.0.12) to count the number of hbond donors and the number of hbond acceptors in a molecule. Can anyone suggest how to go about doing this?
All my best,
Peter
ChemAxon e08c317633
21-02-2008 19:29:47
Hi,
You can use
Hydrogen Bond Donor-Acceptor Plugin through
cxcalc command line application to count the number of hbond donors and the number of hbond acceptors in a molecule.
Example:
| Code: |
$ cxcalc acceptorcount demo10.sdf
id acceptorcount
1 3
2 4
3 2
4 5
5 5
6 4
7 4
8 8
9 12
10 2
$ cxcalc donorcount demo10.sdf
id donorcount
1 0
2 3
3 2
4 3
5 0
6 1
7 3
8 7
9 7
10 0 |
Jcsearch can not be used for counting the number of hbond donors / acceptors, however it can be used for filtering hits using a Chemical Terms filtering expression.
Example: | Code: |
$ jcsearch -e "acceptorcount() > 3" demo10.sdf
jcsearch: Warning: no query specified.
OC1C=CC=C(C1O)C(O)=O
NCC(=O)COP(O)(O)=O
[O-][N+](=O)C1=CC(=C(Cl)C=C1)[N+]([O-])=O
CCN1C=NC2=C(N)N=CN=C12
CCC(C)(O)C(O)C(O)=O
OC1C(O)C(O)C(OP(O)(O)=O)C(O)C1O
NC1=NC2=C(NC(CN2)CN(C=O)C2=CC=C(C=C2)C(=O)NC(CCC(O)=O)C(O)=O)C(O)=N1
$ jcsearch -e "donorcount() <= 2" demo10.sdf
jcsearch: Warning: no query specified.
CC(=O)OC(CC([O-])=O)C[N+](C)(C)C
CC(O)CN
[O-][N+](=O)C1=CC(=C(Cl)C=C1)[N+]([O-])=O
CCN1C=NC2=C(N)N=CN=C12
ClCCCl |
For more information see: http://www.chemaxon.com/jchem/doc/user/Jcsearch.html#expression
Regards,
Zsolt