'cat/sed: concatenation of the fragments of the log filles

I have a folder consisted of many logs. Each log have a similar format.

This is the log1

Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.55 angstroms and 40 degrees
Models used:
    1.1 SarsCov2_Y6A_nsp5holo_rep1.pdb

6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? SER 144 OG   /d UNL 1 S     /? SER 144 HG    3.940  3.529
/? HIS 163 NE2  /d UNL 1 S     no hydrogen      3.821  N/A
/? GLN 189 NE2  /d UNL 1 O     /? GLN 189 1HE2  3.178  2.453
/d UNL 1 N      /? THR 25 OG1  /d UNL 1 HN      2.755  2.270
/d UNL 1 N      /? CYS 44 O    /d UNL 1 HN      3.277  2.501
/d UNL 1 N      /? ARG 188 O   /d UNL 1 HN      3.056  2.055

log2

Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.55 angstroms and 40 degrees
Models used:
    1.1 SarsCov2_06I_nsp5holo_rep1.pdb    
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? THR 26 N     /d UNL 1 O      /? THR 26 H      3.579  2.754
/? ASN 142 ND2  /d UNL 1 O      /? ASN 142 1HD2  3.250  2.324
/d UNL 1 N      /? THR 26 O     /d UNL 1 H       3.458  2.630
/d UNL 1 N      /? HIS 163 NE2  /d UNL 1 HN      3.222  2.456

This is the log 3:

Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.55 angstroms and 40 degrees
Models used:
    1.1 SarsCov2_X7V_nsp5holo_rep1.pdb

2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? GLN 189 NE2  /d UNL 1 O    /? GLN 189 1HE2  3.185  2.258
/d UNL 1 N      /? LEU 141 O  /d UNL 1 HN      2.868  1.958

I need to fuse all the logs together taking only the strings starting from # H-bonds adding the name of the initial file in the same line:

This is fused log produced by combining log1 -log 3:

log 1: 6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? SER 144 OG   /d UNL 1 S     /? SER 144 HG    3.940  3.529
/? HIS 163 NE2  /d UNL 1 S     no hydrogen      3.821  N/A
/? GLN 189 NE2  /d UNL 1 O     /? GLN 189 1HE2  3.178  2.453
/d UNL 1 N      /? THR 25 OG1  /d UNL 1 HN      2.755  2.270
/d UNL 1 N      /? CYS 44 O    /d UNL 1 HN      3.277  2.501
/d UNL 1 N      /? ARG 188 O   /d UNL 1 HN      3.056  2.055


log 2: 4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? THR 26 N     /d UNL 1 O      /? THR 26 H      3.579  2.754
/? ASN 142 ND2  /d UNL 1 O      /? ASN 142 1HD2  3.250  2.324
/d UNL 1 N      /? THR 26 O     /d UNL 1 H       3.458  2.630
/d UNL 1 N      /? HIS 163 NE2  /d UNL 1 HN      3.222  2.456

log3: 2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? GLN 189 NE2  /d UNL 1 O    /? GLN 189 1HE2  3.185  2.258
/d UNL 1 N      /? LEU 141 O  /d UNL 1 HN      2.868  1.958

I've tried trivial solution with CAT but it does not work correcly since in each log I have different number of lines and TAIL could not recognize it correctly:

for log in ${results}/*_rep"${i}".log; do
  log_name=$(basename "$log" .log)
  echo "$log_name" >> ${results}/combined.log
  cat $log | tail -n 10 >> ${results}/combined.log
done

may I use cat in some specific expressin to recognize lines or alternatively I have to use SED before CAT to delete unused lines from each initial log ??

Solution 1:^[1]

USE OF "F" FILENAME OPTION OF SED

sed -i -n -s '1F;/[0-9] H-bonds/,$p' log* | sed -i -s '1N;s/\n/: /' log*

Explanation:
-i ---> inplace
-n ---> disable output
-s ----> treat all input file as seperate
1F ----> Print input filename for 1st line read
/[0-9] H-bonds/,$p ---> prints pattern range N;s/\n: / ---> Merge first two lines adding :

Its a flaw in sed that "F" option directly output filename to stdout and not in pattern space and cannot play with it in one liner

Solution 2:^[2]

Using sed

$ for file in log{1..3}; do echo "${file##*/}: $(sed -n '/[0-9] H-bonds/,$p' "$file")"; echo ""; done
log1: 6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? SER 144 OG   /d UNL 1 S     /? SER 144 HG    3.940  3.529
/? HIS 163 NE2  /d UNL 1 S     no hydrogen      3.821  N/A
/? GLN 189 NE2  /d UNL 1 O     /? GLN 189 1HE2  3.178  2.453
/d UNL 1 N      /? THR 25 OG1  /d UNL 1 HN      2.755  2.270
/d UNL 1 N      /? CYS 44 O    /d UNL 1 HN      3.277  2.501
/d UNL 1 N      /? ARG 188 O   /d UNL 1 HN      3.056  2.055

log2: 4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? THR 26 N     /d UNL 1 O      /? THR 26 H      3.579  2.754
/? ASN 142 ND2  /d UNL 1 O      /? ASN 142 1HD2  3.250  2.324
/d UNL 1 N      /? THR 26 O     /d UNL 1 H       3.458  2.630
/d UNL 1 N      /? HIS 163 NE2  /d UNL 1 HN      3.222  2.456

log3: 2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? GLN 189 NE2  /d UNL 1 O    /? GLN 189 1HE2  3.185  2.258
/d UNL 1 N      /? LEU 141 O  /d UNL 1 HN      2.868  1.958

Solution 3:^[3]

If I'm not misunderstanding the question, a simple grep seems to be what you are after:

grep -EH '^([0-9]+\s+)?H-bonds($| \()|^/' log*

Or if you need that exact format:

for log in log*; do
    sed -n "s/^[0-9]\+\s\+H-bonds$/$log: &/; /^$log: /,\${\$s/\$/\n/;p};" "$log"
done | sed '$d'

But I'm gonna guess the extra row break isn't necessary, and it then becomes simply:

for log in log*; do
    sed -n "s/^[0-9]\+\s\+H-bonds$/$log: &/; /^$log: /,\$p" "$log"
done

I'll happily return to edit this reply if extra explanation is wanted.

Solution 4:^[4]

$ awk 'FNR==1{f=0} /^[0-9]+ H-bonds/{$0=sep FILENAME": " $0; sep=ORS; f=1} f' log?
log1: 6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? SER 144 OG   /d UNL 1 S     /? SER 144 HG    3.940  3.529
/? HIS 163 NE2  /d UNL 1 S     no hydrogen      3.821  N/A
/? GLN 189 NE2  /d UNL 1 O     /? GLN 189 1HE2  3.178  2.453
/d UNL 1 N      /? THR 25 OG1  /d UNL 1 HN      2.755  2.270
/d UNL 1 N      /? CYS 44 O    /d UNL 1 HN      3.277  2.501
/d UNL 1 N      /? ARG 188 O   /d UNL 1 HN      3.056  2.055

log2: 4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? THR 26 N     /d UNL 1 O      /? THR 26 H      3.579  2.754
/? ASN 142 ND2  /d UNL 1 O      /? ASN 142 1HD2  3.250  2.324
/d UNL 1 N      /? THR 26 O     /d UNL 1 H       3.458  2.630
/d UNL 1 N      /? HIS 163 NE2  /d UNL 1 HN      3.222  2.456

log3: 2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? GLN 189 NE2  /d UNL 1 O    /? GLN 189 1HE2  3.185  2.258
/d UNL 1 N      /? LEU 141 O  /d UNL 1 HN      2.868  1.958

Sources

This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.

Source: Stack Overflow

Solution	Source
Solution 1
Solution 2	HatLess
Solution 3	Kaffe Myers
Solution 4	Ed Morton

'cat/sed: concatenation of the fragments of the log filles

Solution 1:[1]

Solution 2:[2]

Solution 3:[3]

Solution 4:[4]

Sources

Related Questions

Solution 1:^[1]

Solution 2:^[2]

Solution 3:^[3]

Solution 4:^[4]