I have a number of pdb files and I want to grep only those lines that starts with ^FORMUL and if line has C followed by the number that is larger then (C3,C4,C5,C6 etc) then I should not print it.
I used this one for extracting line that start with FORMUL but don't know how to search trough each of the lines and match it with C followed by 3>.
grep ^FORMUL *pdb (probably here have to put some kind of cutoff that if inside each line C3> is found then don't print it).
3OC2.pdb:FORMUL 3 HOH *207(H2 O) (print it)
3OC7.pdb:FORMUL 2 SF4 FE4 S4 (print it)
3OC8.pdb:FORMUL 3 NIC C5 H7 N O7 (don't print, there is C5)
3OC9.pdb:FORMUL 4 HOH *321(H2 O) (print it)
3OC10.pdb:FORMUL 3 HEM 2(C34 H32 FE N4 O4) (don't print, there is C34)2 Answers
Use two greps:
grep '^FORMUL' *pdb | grep -vE 'C([3-9]|[12][0-9])'The first lists the lines matching ^FORMUL, the second removes (-v inverts the match) those matching C followed by a digit between 3 and 9, or two digit numbers beginning with 1 or 2 (so every number from greater than 3 will be removed).
I think this should work:
awk '/^FORMUL/ && !match($4, /C[3-9]?[0-9]/) {print;}' *.pdb ?: have an online data source we could try?
ref(page 154): ftp://
