Change keyword in a file only in the lines that contain another keyword

Question

I have file with lines that start with two possible keywords, ATOM and HETATM. In some of those lines, there is a second keyword HOH, appearing after some other characters. In other lines, there are other 3-character keywords XXX like SOL instead of HOH:

ATOM 1231 O XXX ... HETATM1232 O SOL ... HETATM1233 O HOH ...

What I want to do is to change HETATMs to ATOM only if HOH also appears on the line.

I tried the following:

sed -E '/\(HETATM\)\(.*HOH\)/s//\1ATOM/' file

which gives the illegal byte sequence error. What am I doing wrong?

Cyrus · Accepted Answer · 2015-08-14 19:19:28Z

2

Try this:

sed '/HOH/s/HETATM/ATOM/' file

Output:

 ATOM 1231 O XXX ... HETATM1232 O SOL ... ATOM1233 O HOH ...

Only in lines which contain HOH search HETATM and replace by ATOM.

answered Aug 14, 2015 at 19:19

Cyrus

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3 Comments

sodiumnitrate Over a year ago

It does give the desired output, but also gives the same error at the end.

sodiumnitrate Over a year ago

Actually, it doesn't print all the file. It stops at line 14095.

sodiumnitrate Over a year ago

Ok, I think it was because I have a weird character at that line. When I do head -n10000 file | sed '/HOH/s/HETATM/ATOM/' it works fine. Thanks!

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