Shell Programming and Scripting

Hi
I have written a script for automating a program. There is a string in 2 lines that needs altering from input.

The 2 lines are:

prepare_flexreceptor4.py -r rec_rigid.pdbqt -s TYR119_TRP312 -x rec_flex.pdbqt

and

prepare_flexdocking4.py -l ind.pdbqt -r rec_flex.pdbqt -s TYR119_TRP312

It is the TYR119_TRP312 bit that is important.

So I need a script that says 'enter flexible residues seperated by an underscore'. This should be put after the -s. It should accept 1 upwards values. The original script is FLXDOCK. Can this name be retained?
thanks

Yes.

Please post your code so we can take a look.

(and don't forget to use code tags).

Hi the whole script is


#select one of these for the shell you use
#csh
source /usr/local/MGLTools-1.5.2/bin/mglenv.csh
#bash
#source /usr/local/MGLTools-1.5.2/bin/mglenv.sh

#script for autodock4

#ligand prep. Uses 'ind' prefix. The initial ligand must be ind.pdb. This
#generates ind.pdbqt.
prepare_ligand4.py -l ind.pdb -A hydrogens_bonds -U nphs_lps -o ind.pdbqt

#First a 'generic' receptor must be made. Here the molecule should be called
#rec.pdb
#The receptor has ad atom types (t), gasteiger charges (q) added. This also
#adds non-polar hydrogens (nphs) and bonds (bonds) so a torsion root can be
#found. The output is a *pdbqt file ready for dockng. The command is:

prepare_receptor4.py -r rec.pdb -o rec_rigid.pdbqt -A 'bonds'-A 'checkhydrogens' -U 'nphs'
#where *.pdb is input file and the output will be pdbqt.

#The flex and rigid receptors, use the receptor pdbqt made earlier

prepare_flexreceptor4.py -r rec_rigid.pdbqt -s TYR119_TRP312 -x rec_flex.pdbqt

#Movable residue list seperated by underscores.
#-s is the movable residue; this is aswell as the backbone and amide bonds are
#fixed. This makes 2 files, a flexible and a rigid, that is rec_flex.pdbqt and
#rec_rigid.pdbqt. Use the rigid file for grid
#param file.-x flex.pdbqt

#prep of flex docking

prepare_flexdocking4.py -l ind.pdbqt -r rec_flex.pdbqt -s TYR119_TRP312

#To prepare a gpf we use the rigid ligand. Use:ligand_types for hsg1="A_C_HD_N_OA"

prepare_gpf4.py -l ind.pdbqt -r rec_rigid.pdbqt -x rec_flex.pdbqt -p npts="150 150 150" -i ref.grid

#The ligand types are those obtained from, prepare_ligand_dict.py -l ind.pdbqt
#-d ./ligand.types. ref.grid holds the co ordinates for docking.
#making a file called ligand.types containing the types of residues.
#Thes atoms are used in creating the dpf, docking parameter file.
#The docking parameter file contains the information on the docking.

prepare_dpf4.py -l ind.pdbqt -r rec_rigid.pdbqt -i ref.dpf -p flexres=rec_flex.pdbqt -p set_ga=lga -p ga_num_evals=5000000 -o ind_rec_rigid.dpf
#This uses the ligand atoms. Other parameters should be varied. The resulting
#flexres specifies the flexible residue file. dpf is ind_rec_rigid.dpf.

#Now autogrid4 and autodock4 can be used.
autogrid4 -p rec_rigid.gpf -l dock.glg
#this makes the necessary maps and logs. Use the rigid receptor.

autodock4 -p ind_rec_rigid.dpf -l my_docking.dlg &
#the dpf is named after the receptor and ligand. Producing the docking log
#(dlg) which contains any errors and the results.

############################################################################


I specified the portions earlier. It is the capitals after the '-s'. Should 'getlne' be used and how? A big prob is creating a new file. Can a tmp be maded then 'mv' ed?

I have not written a script to do this since 'I don' posses the code' Neo...
gs

Hi I've been away. Is this doable?