Hi,
External tool node is a wonderful KNIME feature that extends its functionality and flexibility almost indefinately. However, there is a problem with the input file for the node. Each row in the file which is passed onto the External tool from any previous node gets “double-quoted”, which possesses certain problems for the software used in the core of the external tool. For example, in sdf file each compound gets double-quoted like here:
"MOLECULE_1
Marvin 04240916152D
25 26 0 0 0 0 999 V2000
1.8076 -4.5022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5227 -4.9123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2342 -4.5022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9460 -4.9172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6694 -4.5082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6694 -3.6799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9530 -3.2601 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.2342 -3.6737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 17 1 0 0 0 0
4 18 1 0 0 0 0
5 19 1 0 0 0 0
10 20 1 0 0 0 0
11 21 1 0 0 0 0
11 22 1 0 0 0 0
12 23 1 0 0 0 0
12 24 1 0 0 0 0
15 25 1 0 0 0 0
M END
$$$$"
"MOLECULE_2
Marvin 04240916152D
25 26 0 0 0 0 999 V2000
1.8076 -4.5022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5227 -4.9123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2342 -4.5022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9460 -4.9172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6694 -4.5082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6694 -3.6799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9530 -3.2601 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.2342 -3.6737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 17 1 0 0 0 0
4 18 1 0 0 0 0
5 19 1 0 0 0 0
10 20 1 0 0 0 0
11 21 1 0 0 0 0
11 22 1 0 0 0 0
12 23 1 0 0 0 0
12 24 1 0 0 0 0
15 25 1 0 0 0 0
M END
$$$$"
etc. So before I can use any kind of software which operates on sdf files I have to remove the quotes by some script. This actually applies to any file format, e.g. smiles or plain text. Is there any solution how to avoid getting double-quoted files in the input of the external tool? Many thanks for suggestions!
/Aleks