One-Liners
==========

A collection of potentially useful one-liners.

Gathering .db2 files from and .sdi list
---------------------------------------

``while read line; do name=$(echo $line | awk -F'/' '{print $NF}'); echo $name; cp $line  GZ/$RANDOM-$RANDOM-$name;  done <working/enrichment_sdi``

Repacking from .db2.gz to .tgz
---------------------------------------

``echo "Gunzipping files..."; files=$(ls *db2.gz); for file in $files; do echo $file;  gunzip $file; done; echo "Making tgz archives..."; files1=$(ls *db2); for file1 in $files1; do  tar -czvf  $file1.tgz $file1; done``

Gathering and renaming db2 files
---------------------------------------

``files=$(find . -name "*db2*"); for file in $files; do id=$(echo $file | awk -F"/" '{print $(NF-1)}'); echo $id; filename=$(echo $file | awk -F"/" '{print $NF}'); echo $filename; cp $file $id-$filename;  done``

``while read line; do filename=$(echo $line | awk -F"/" '{print $(NF-1)"_"$NF}'); echo $filename; cp -v $line $filename; done <actives.list``

db2.gz to names
---------------------------------------

``files=$(ls *db2.gz); for file in $files; do zcat $file | head -n 1; done | awk '{print $2}' | sort -u > ../ligands.names``

gather decoys to decoys.names
---------------------------------------

``ll decoys | awk '{print $9}' | awk 'FS="." {print $1}' > decoys.names``

then examine file content and delete not needed lines to get ligands.names use ligands.smi

copy decoy files listed in decoys_sdi
---------------------------------------

``while read -u 9 line; do echo $line; name=$(echo $line | awk -F'\/' '{print $(NF-1) "-" $NF}'); echo $name "\n"; cp -v $line $name; done 9<../decoys/decoys_sdi``

Getting names from .mol2
---------------------------------------
.. code:: bash

   grep Name nsp14-frags-sel.mol2 | grep -v fake | grep -v Long | awk '{print $3}' | awk -F'.' '{print $1}' | sort -u

Make subset mol2 from larger mol2 file:
---------------------------------------

on gimel5 or dev nodes

``python ~ttummino/zzz.scripts/misc/lc_blazing_fast_collect_mol2.py list_of_ids input_mol2 output_mol2``

Add data to MOL2 header
-----------------------

``python ~stefan/zzz.scripts/add_stuff_to_mol2_header_tc.py`` 

The inputs are: the mol2 file a 2-columns list of ZINC-ID and Variables you want to add to the mol2 (ZINC ID tab variable) output file name Name of variable you add to the mol2


Purchasability: search zinc-22.py
---------------------------------
https://wiki.docking.org/index.php/Search_zinc22.py

.. code:: bash

   ssh n-1-17
   source /nfs/soft/zinc22/search_zinc/miniconda/bin/activate /nfs/soft/zinc22/search_zinc/miniconda/envs/zinc22_search
   python /nfs/soft/zinc22/search_zinc/search_zinc22.py --get-vendors input_zinc_ids.txt output_vendor_ids.txt


Get output as a table
---------------------

``file_name="pkd2-zinc22a-hac13-20-jji.out"; ids=$(awk '{print $2}' $file_name | sort -u); echo $ids; for id in $ids; do grep -m 1 $id $file_name | awk '{print $1}' | tr "\n" "\t"; echo -ne $id "\t";  grep --color $id $file_name | awk '{print $4}' |  grep -v ZINC | sort -u | tr "\n" "\t"; echo ; done``

with HAC
''''''''

``file_name="pkd2-down-sel-jji.out"; ids=$(awk '{print $2}' $file_name | sort -u); echo $ids; for id in $ids; do grep -m 1 $id $file_name | awk '{print $1}' | tr "\n" "\t"; echo -ne $id "\t";  hac=$(grep -m 1 $id $file_name | awk '{print $3}'); out_line=$(grep --color $id $file_name | awk '{print $4}' |  grep -v ZINC | sort -u | tr "\n" "\t"; echo); echo -e $hac $out_line ; done``

Rigid ligand docking
--------------------

On Gimel
Prepare a mol2 files corresponding to your ligands, then run 

.. code:: bash

   #!/bin/tcsh
   # set mols= ( ls *mol2 )
   setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/
   source $DOCKBASE/env.csh
   foreach f ( `ls *mol2` )
       set NAME = `basename $f .mol2`
       echo "name.txt 1 $NAME CCCCCCCCCCCC | NO_LONG_NAME" > name.txt
       python /mnt/nfs/home/ak87/PROGRAM/RIGID/convert.py --i=$f --o=$f-conv.mol2 
       $DOCKBASE/ligand/amsol/calc_solvation.csh $f-conv.mol2
       $DOCKBASE/ligand/mol2db2/mol2db2.py -v --mol2=output.mol2 --solv=output.solv --db=$NAME.db2.gz
   end