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?

score 2 · Accepted Answer · answered Aug 14 '15 at 19:19

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 '15 at 19:19

Cyrus

84,225
14
89
153

It does give the desired output, but also gives the same error at the end. – sodiumnitrate Aug 14 '15 at 19:36
Actually, it doesn't print all the file. It stops at line 14095. – sodiumnitrate Aug 14 '15 at 19:38
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! – sodiumnitrate Aug 14 '15 at 19:41

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

1 Answers1