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Extract paragraph that contains a value x<-30

 
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# 1  
Old 04-06-2016
Extract paragraph that contains a value x<-30
I am using OSX. I have a multi-mol2 file (text file with coordinates and info for several molecules). An example of two molecules in the file is given below for molecule1 and molecule 2. The total file contains >50,000 molecules.

I would like to extract out and write to another file only the molecules that have a Grid Score < -30.0000. For the case below, it should only write for molecule1 (Grid Score = -43.6), but not molecule2 (Grid Score = -13.6).

Looking through the forum, I realized I need to do a paragraph grep or something analogous. The best I could determine is that I could use the awk command. But, I have no idea how to put in the condition for Grid Score < -30.

This is my first post, and I am very much an amateur. Any help to get me going in the right direction would be greatly appreciated. Forgive me if my post is not formatted correctly. Happy to take any criticism. Thanks.



Code:
########## Name:                molecule1
##########    Grid Score:          -43.616261
##########      Grid_vdw:          -38.348866
##########       Grid_es:           -5.267394
##########    Int_energy:            7.004528

@<TRIPOS>MOLECULE
molecule1
 50 50 1 0 0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C1         23.3017   18.5209   24.1009 C.3     1  <0>        -0.1533
      2 C2         21.8869   18.3400   23.5472 C.3     1  <0>        -0.1225
      3 C3         21.8457   18.8065   22.0906 C.3     1  <0>        -0.1318
@<TRIPOS>BOND
     1     1     2    1
     2     1    21    1
@<TRIPOS>SUBSTRUCTURE
     1 <0>         1 TEMP              0 ****  ****    0 ROOT


########## Name:                molecule2
##########    Grid Score:          -13.616261
##########      Grid_vdw:          -18.348866
##########       Grid_es:           -1.267394
##########    Int_energy:            5.004528

@<TRIPOS>MOLECULE
molecule2
 50 50 1 0 0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C1         23.3017   18.5209   24.1009 C.3     1  <0>        -0.1533
      2 C2         21.8869   18.3400   23.5472 C.3     1  <0>        -0.1225
      3 C3         21.8457   18.8065   22.0906 C.3     1  <0>        -0.1318
@<TRIPOS>BOND
     1     1     2    1
     2     1    21    1
@<TRIPOS>SUBSTRUCTURE
     1 <0>         1 TEMP              0 ****  ****    0 ROOT

# 2  
Old 04-06-2016
a little bit verbose with some assumptions based on a sample, but....
awk -f egy.awk Mymulti-mol2File where egy.awk is:
Code:
BEGIN {
  if (!grid) grid=-30.0000
}
/Name:/ {flag=0;block=$0;next}
/Grid Score:/  && $NF<grid {
      flag=1;
      print block ORS $0
      next
}
flag

Last edited by vgersh99; 04-06-2016 at 06:55 PM..
This User Gave Thanks to vgersh99 For This Post:
Egy
# 3  
Old 04-06-2016
Works great. I added the following to write to a separate file:

Code:
awk -f egy.awk Mymulti-mol2File > output.mol2

Much appreciated!
 
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