Converting .sdf file to .excel file

Hello,
I am currently working on a research project pertaining to the Corona Virus. I converted a .sdf file containing around 50,00 Anti-Viral Agents to an .csv excel file; however, some of the chemical names seem to have been truncated during the conversion as shown in the image below. How can I prevent shortening of the chemical names during the process of conversion?

Thank you.

Can you post your workflow and dataset so that we can recreate the error?

Here is the workflow and a sample of the data

Workflow
2020-09-21_13-40-23

Sample of Data
3-Quinolinecarboxylic acid, 6-[[3-chloro-2-fluoro-5-(2-oxo-1-pyrrolidinyl)phe…
C27H28ClFN2O6
1000161-54-5 Copyright © 2020 ACS
37 40 0 0 1 0 0 0 0 0999 V2000
65927.051737775.6286 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
73735.838642276.8721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
58118.264742276.8721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
81544.625637775.6286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
73735.838651304.2277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
50284.609037775.6286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
65927.0517 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
32752.141528325.5043 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
32752.141537676.1536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
32727.2727 9425.2556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
82191.2130 9425.2556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
90000.000013951.3678 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
82191.2130 422.7687 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
16438.2426 24.8687 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
149.2125 9425.2556 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
0.000041157.7784 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
57446.808523799.3921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
57446.808513951.3678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
65927.051728748.2730 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
48991.434128748.2730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
48991.4341 9002.4869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
65927.0517 9002.4869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
74382.426123799.3921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
40536.059723799.3921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
40536.059713951.3678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
74382.426113951.3678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
24918.485813951.3678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
24918.485823724.7859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16438.2426 9052.2244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16438.242628623.9293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7957.999413951.3678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7957.999423724.7859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16438.242637651.2849 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8679.193143644.6532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
24545.454543644.6532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11862.392952796.3526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21710.417252796.3526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 19 1 6 0 0 0
2 4 1 0 0 0 0
2 5 1 0 0 0 0
3 6 1 0 0 0 0
7 22 2 0 0 0 0
8 9 1 0 0 0 0
8 24 1 0 0 0 0
10 25 1 0 0 0 0
10 27 1 0 0 0 0
11 12 1 0 0 0 0
11 13 2 0 0 0 0
11 26 1 0 0 0 0
14 29 1 0 0 0 0
15 31 1 0 0 0 0
16 34 2 0 0 0 0
17 18 1 0 0 0 0
17 19 1 0 0 0 0
17 20 2 0 0 0 0
18 21 2 0 0 0 0
18 22 1 0 0 0 0
19 23 1 0 0 0 0
20 24 1 0 0 0 0
21 25 1 0 0 0 0
22 26 1 0 0 0 0
23 26 2 0 0 0 0
24 25 2 0 0 0 0
27 28 2 0 0 0 0
27 29 1 0 0 0 0
28 30 1 0 0 0 0
29 31 2 0 0 0 0
30 32 2 0 0 0 0
30 33 1 0 0 0 0
31 32 1 0 0 0 0
33 34 1 0 0 0 0
33 35 1 0 0 0 0
34 36 1 0 0 0 0
35 37 1 0 0 0 0
36 37 1 0 0 0 0
M END

<cas.rn>
1000161-54-5

<cas.index.name>
3-Quinolinecarboxylic acid, 6-[[3-chloro-2-fluoro-5-(2-oxo-1-pyrrolidinyl)phenyl]methyl]-1,4-dihydro-1-[(1S)-1-(hydroxymethyl)-2-methylpropyl]-7-methoxy-4-oxo-

<molecular.formula>
C27H28ClFN2O6

<molecular.weight>
530.97

<boiling.point.predicted>
798.7±60.0 °C Press: 760 Torr

<density.predicted>
1.393±0.06 g/cm3 Temp: 20 °C; Press: 760 Torr

<pka.predicted>
0.43±0.20 Most Acidic Temp: 25 °C

Just reading the excerpt you posted from the sd file, the text in the molecule name field is already truncated from the start (see the first line).

Assuming you didn’t create the initial sd file, there’s nothing you can do about that, and I’d argue that it’s the least important part of the file anyway.

What does the cas.index.name column look like?

In the future, posting a workflow that we can open ourselves, instead of just a screenshot, would be more helpful.

2 Likes

The first is truncated but the ones that follow that aren’t truncated in the sdf file are further shortened in the file excel file.

The workflow folder is around 60MB. how do i post the workflow over here?

You can upload workflows to your KNIME Hub space: https://hub.knime.com/site/about

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