Gfilui

I have a 23 folders and each folder has two subfolders (always same name) and each subfolder has exactly two files (always same name). So it looks like this:

Folder1/BindingDB/chiral.smi
 nochiral.smi
Folder1/Xray/chiral.smi
 nochiral.smi

 Folder2/BindingDB/chiral.smi
 nochiral.smi
 Folder2/Xray/chiral.smi
 nochiral.smi

For example chiral.smi file looks like this:

COCCNC(=O)[C@H]1[C@@H]([C@H]2CN3C(=O)C=CC=C3[C@@H]1N2C4=NC(=C(S4)C5=CC=CC=C5)C6=CC=C(C=C6)Cl)CO K00000004
C1[C@H]2[C@H](C=C([C@H]3[C@@H]2[C@H]4[C@@H]1[C@@H]([C@H]4C=C3)CC/C=C/CC5=CC=C(C=C5)O)C(=O)O)O K00000005
C[C@]12CCC[C@@]([C@@H]1CC[C@@]34[C@H]2C[C@H]5[C@@H](C3)[C@]5(C4)CO)(C)C(=O)O K00000006

So here, last two lines K00000005 and K00000006 have double space and I want to match these two lines.

I am trying to double check all chiral.smi and nochiral.smi files in my folders if they have lines that have double space (I should only have one space in each line of each file).

I have tried in bash something like this:

for i in */*/*.smi ; do sed -e "s/s2,/ /g" $i; done but it is not working. Also, when I run sed -e "s/s3,/ /g" *smi in subfolder (BindingDB or Xray) it prints all the lines that have only one space. Can anyone help me since I cannot figure out whats the problem?

You can list the names of any .smi files in which any line contains two adjacent spaces with

grep --include='*.smi' -rl ' ' .

If you want to output the lines themselves, then remove the l option.

If I understand it correctly, something like

grep -l ' ' */*/*.smi

will print the "double space" filenames

If you want do normalize spaces (' ' -> ' ') you can try to

sed -ri.bak 's/s2,/ /g' */*/*.smi

and remove the backup files if all went well

rm /*/*.smi.bak