2005-09-03, Harshal wrote:
hi,
i have two molecular dynamics codes, both of them take the same
input, but the in different format. let me explain,

for one code (named PinyMD) in the input file, we have,

~atom_def[\atom_typ{na}\atom_ind{ 1 } \mass{14.0067}\charge{ 0.15}]
~atom_def[\atom_typ{na}\atom_ind{ 2 } \mass{14.0067}\charge{ 0.15}]
~atom_def[\atom_typ{cr}\atom_ind{ 3 } \mass{12.0107}\charge{-0.11}]
~atom_def[\atom_typ{cw}\atom_ind{ 4 } \mass{12.0107}\charge{-0.13}]
~atom_def[\atom_typ{cw}\atom_ind{ 5 } \mass{12.0107}\charge{-0.13}]
and so on

and for other code (named NMA) the input file,

1 1
2 1
3 2
4 1
5 1
6 2
7 1
8 1
and so on
--
the relation between them is very straightforwd.
what appears in PinyMD's input file as "na" might be an integer 1
or "cr" be integer 2 for NMA.

i am trying to write a bash script, which will read in PinyMD input
file and convert in the NMA file,
--
after reading the line,
~atom_def[\atom_typ{na}\atom_ind{ 1 } \mass{14.0067}\charge{ 0.15}]
~atom_def[\atom_typ{cr}\atom_ind{ 2 } \mass{14.0067}\charge{ 0.15}]
so on
--
it should echo,

1 1
2 3
so on

how do i pick up elements 'na' (which i will replace with some
integer) and atom_ind{ 1 } which i will replace with 1?

awk -F '[{}]' '{ print $2, $4 }' FILENAME

You will need a translation table to replace na, cr, etc with a
number, unless it is a straight sequence.

2 Sep 2005 20:29:09 -0700, Harshal <p.harshal@gmail.comwrote:
| hi,
| i have two molecular dynamics codes, both of them take the same
| input, but the in different format. let me explain,
|
| for one code (named PinyMD) in the input file, we have,
|
| ~atom_def[\atom_typ{na}\atom_ind{ 1 } \mass{14.0067}\charge{ 0.15}]
| ~atom_def[\atom_typ{na}\atom_ind{ 2 } \mass{14.0067}\charge{ 0.15}]
| ~atom_def[\atom_typ{cr}\atom_ind{ 3 } \mass{12.0107}\charge{-0.11}]
| ~atom_def[\atom_typ{cw}\atom_ind{ 4 } \mass{12.0107}\charge{-0.13}]
| ~atom_def[\atom_typ{cw}\atom_ind{ 5 } \mass{12.0107}\charge{-0.13}]
| and so on
|
| and for other code (named NMA) the input file,
|
| 1 1
| 2 1
| 3 2
| 4 1
| 5 1
| 6 2
| 7 1
| 8 1
| and so on
|
|
| the relation between them is very straightforwd.
| what appears in PinyMD's input file as "na" might be an integer 1
| or "cr" be integer 2 for NMA.
|
| i am trying to write a bash script, which will read in PinyMD input
| file and convert in the NMA file,
|
|
| after reading the line,
| ~atom_def[\atom_typ{na}\atom_ind{ 1 } \mass{14.0067}\charge{ 0.15}]
| ~atom_def[\atom_typ{cr}\atom_ind{ 2 } \mass{14.0067}\charge{ 0.15}]
| so on
|
|
| it should echo,
|
| 1 1
| 2 3
| so on
|
| how do i pick up elements 'na' (which i will replace with some
| integer) and atom_ind{ 1 } which i will replace with 1?

$ cat PinyMD
~atom_def[\atom_typ{na}\atom_ind{ 1 } \mass{14.0067}\charge{ 0.15}]
~atom_def[\atom_typ{na}\atom_ind{ 2 } \mass{14.0067}\charge{ 0.15}]
~atom_def[\atom_typ{cr}\atom_ind{ 3 } \mass{12.0107}\charge{-0.11}]
~atom_def[\atom_typ{cw}\atom_ind{ 4 } \mass{12.0107}\charge{-0.13}]
~atom_def[\atom_typ{cw}\atom_ind{ 5 } \mass{12.0107}\charge{-0.13}]

$ awk -F '[{} ]+' '{print $4 " " $2}' PinyMD | sed -e 's/na/1/' -e 's/cr/2/' -e 's/cw/3/'
1 1
2 1
3 2
4 3
5 3

Change the values in the sed substitute commands as appropriate.

Harshal <p.harshal@gmail.comwrote:

after reading the line,
~atom_def[\atom_typ{na}\atom_ind{ 1 } \mass{14.0067}\charge{ 0.15}]
~atom_def[\atom_typ{cr}\atom_ind{ 2 } \mass{14.0067}\charge{ 0.15}]
so on

it should echo,

1 1
2 3
so on

how do i pick up elements 'na' (which i will replace with some
integer) and atom_ind{ 1 } which i will replace with 1?

Parse out '{}', and what you want is first and second elements.

man awk(-F option)
man grep(-o option)