python program that allows to change residues's atomtypes in PDB files and then perform click
DEPENDENCIES
This python script needs the next files in the same script folder:
*Click binary
*Parameters.inp
*table file specifing new atomtypes
*optional: Another Parameters file
*optional: table file with PDB, chain, resnum specification
*optional: list with pdb1,pdb2 superposition pairs
Additionally you need parallel python module to run several click
instances using more than one core in a multicore system.
MINIMAL USAGE:
python modclick.py mobile.pdb target.pdb -t tableFile
OPTIONS:
-t [file] modclick realize superpositions with the new atomnames specified
in the table [file] with resname:atomname:new_atomname specifitacions.
modclick changes the typeAtom record of Parameters.inp file by the atom
types of this table automatically
-i [file] modclick uses the [file] parameters to run click superpositions
-f [file] modclick uses the [file] table with PDB:chain:resnumber fields that
shows only the residues wich you want to change atom types
-l [file] modclick runs click over a pair list of PDB files separated by
comma ',' from [file]. For all those PDB files the same table of atom
types will be applied and click will run with the same parameters
-m modclick mantains *.clique file. Merged pdb file is mantains too except if
-s flag is chosen
-s modclick runs click with -s 0 flag. With this flag click doesn't create
transformation pdb files, therefore Merged pdb file is not created
-p [nCPUs] modclick try to run superpositions with parallel python module using
a given number of cores. If no number is specified, or 0 number is given,
modclick uses the maximun machine available cores
-o [file] modclick writes summary [file] with pdb1,pdb2,RMSD records. If not
[file] name is given or this flag is not used, results.out file will be
written
EXAMPLE:
python modclick.py -t MyAtomtypesTable -l MyList -s -p 4 -o MyOutput
this line runs click on each superposition pair in MyList with MyParameters
Parameters using MyAtomtypesTable using 4 cores. Results RMSD will be written in MyOutput file
OUTPUTS:
mobile_target_Merged.pdb: this file contain the 2 click's outputs merged
in a single pdb file separating with MODEL records. MODEL 1 contain
coordenates for mobile superposed on target, and MODEL 2 the target
coordenates
mobileMod-targetMod.pdb.1.clique: It's the same click's output but the
"Mod" word is added because click was running with modified pdb files.
If both pdbs are in different folders, this file will be written in the
folder of first pdb file
[[file]|results].out: This file contains a summary with pdb pairs superposed
and RMSD values obtained by click. If click doesn't report RMSD, 'NA' field is used. If
no RMSD is reported by problem in a file, this file will be written in parentheses () symbols.