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multiscalegui.tcl
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multiscalegui.tcl
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##
## Gui for CG/Hybrid Builder
##
## Authors: Lemmin Thomas && Christophe Bovigny
##
##
##
## Tell Tcl that we're a package and any dependencies we may have
package provide multiscalegui 0.11
package require multiscaletools 0.11
package require readParTop 0.11
package require writelammps 0.11
namespace eval ::multiscalegui:: {
# window handle
variable w
variable toCGResidueFrame
variable fromCGFrame
variable toCGShapeFrame
variable toResCGMenu
variable toShapeCGMenu
variable fromMolMenu
variable fromAAMolMenu
variable cgpath
variable toCGoutpdbfile
variable toCGoutallpdbfile
variable toCGouttopfile
variable toCGoutparmfile
variable fromCGoutpdbfile
variable revcgfile
#LBM STUFF
variable pdbpath
variable psfpath
variable CG_name "CG_model"
variable CG_rev "cgrev"
variable Hybrid_name "Hybrid_model"
variable Hybrid_rev "hybridrev"
variable toCGResidueHybrid 0
variable toCGshapeMass
variable drawn 0
variable drawnlbm
variable hybridChoice "0"
variable CG_model 0
# kAtomsPerDXPoint chosen to make hook.dx generate 15 beads.
# taken from the number of points in the file (listed as the last
# integer in the object 3 line). 24955 / 550 / 3 => 15, which is what
# we want
variable menuChoice 0
}
# -------------------------------------------------------------------------
# should the user be able to pick 'next'
proc ::multiscalegui::toggleNextButton { a b c } {
variable menuChoice
variable w
if { $menuChoice > 0 } {
$w.chooseFrame.next configure -state normal
} else {
$w.chooseFrame.next configure -state disabled
}
}
# -------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# LBM Hybrid Box
proc ::multiscalegui::toggleHybridBox { a b c } {
variable toCGResidueHybrid
variable toCGResidueFrame
#variable drawnlbm
#if { $drawnlbm == 0 } {
# return
# }
if { $toCGResidueHybrid == 1 } {
$toCGResidueFrame.hybrid.hybcutoffAA configure -state normal
$toCGResidueFrame.hybrid.cutoffAA configure -state normal
$toCGResidueFrame.hybrid.hybcutoffCG configure -state normal
$toCGResidueFrame.hybrid.cutoffCG configure -state normal
$toCGResidueFrame.hybrid.hybcenter configure -state normal
$toCGResidueFrame.hybrid.center configure -state normal
$toCGResidueFrame.hybrid.preview configure -state normal
$toCGResidueFrame.hybrid.explaintexthybrid configure -state normal
} else {
$toCGResidueFrame.hybrid.hybcutoffAA configure -state disabled
$toCGResidueFrame.hybrid.cutoffAA configure -state disabled
$toCGResidueFrame.hybrid.hybcutoffCG configure -state disabled
$toCGResidueFrame.hybrid.cutoffCG configure -state disabled
$toCGResidueFrame.hybrid.hybcenter configure -state disabled
$toCGResidueFrame.hybrid.center configure -state disabled
$toCGResidueFrame.hybrid.preview configure -state disabled
$toCGResidueFrame.hybrid.explaintexthybrid configure -state disabled
}
}
# -------------------------------------------------------------------------
### LBM STUFF
proc ::multiscalegui::calcCutoffValues { } {
#if {[string trim $::multiscalegui::tohybridcutoffAA] == "" || \
# ! [string is double $::multiscalegui::tohybridcutoffAA] || \
# $::multiscalegui::tohybridcutoffAA < 1 || [string trim $::multiscalegui::tohybridcutoffCG] == "" || \
# ! [string is double $::multiscalegui::tohybridcutoffCG] || \
# $::multiscalegui::tohybridcutoffCG < 1 } {
# return 0
# }
}
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# --LBM-----------------------------------------------------------------------
proc ::multiscalegui::hybridSourceChoice { } {
variable toCGResidueFrame
variable hybridChoice
variable toCGResidueHybrid
if { $hybridChoice == "0" } {
# molecule
$toCGResidueFrame.hybrid.hybcutoffAA configure -state disabled
$toCGResidueFrame.hybrid.cutoffAA configure -state disabled
$toCGResidueFrame.hybrid.hybcutoffCG configure -state disabled
$toCGResidueFrame.hybrid.cutoffCG configure -state disabled
$toCGResidueFrame.hybrid.hybcenter configure -state disabled
$toCGResidueFrame.hybrid.center configure -state disabled
$toCGResidueFrame.hybrid.preview configure -state disabled
$toCGResidueFrame.hybrid.explaintexthybrid configure -state disabled
# $toCGShapeFrame.mol.menu configure -state normal
set toCGResidueHybrid 0
} elseif { $hybridChoice == "1" } {
# # EDM
$toCGResidueFrame.hybrid.hybcutoffAA configure -state normal
$toCGResidueFrame.hybrid.cutoffAA configure -state normal
$toCGResidueFrame.hybrid.hybcutoffCG configure -state normal
$toCGResidueFrame.hybrid.cutoffCG configure -state normal
$toCGResidueFrame.hybrid.hybcenter configure -state normal
$toCGResidueFrame.hybrid.center configure -state normal
$toCGResidueFrame.hybrid.preview configure -state normal
$toCGResidueFrame.hybrid.explaintexthybrid configure -state normal
set toCGResidueHybrid 0
}
}
# -------------------------------------------------------------------------
#
# Create the window and initialize data structures
#
proc ::multiscalegui::multiscalegui {} {
# puts "very beginning of ::multiscalegui::cggui";
variable toResCGMenu
variable toShapeCGMenu
variable w
variable chooseFrame
variable chooseCGFrame
variable toCGResidueFrame
variable toCGShapeFrame
variable fromCGFrame
# ::multiscalegui::init_vars
# puts "before everything starts\n";
#trace add variable ::multiscalegui::currentToCGMol write ::multiscalegui::tomolmenuaux
#trace add variable ::multiscalegui::currentFromCGMol write ::multiscalegui::frommolmenuaux
#trace add variable ::multiscalegui::currentFromCGAAMol write ::multiscalegui::fromaamolmenuaux
#trace add variable ::multiscalegui::currentMapCGMol write ::multiscalegui::mapcgmenuaux
#trace add variable ::multiscalegui::currentMapAAMol write ::multiscalegui::mapaamenuaux
#trace add variable ::multiscalegui::currentMapRefMol write ::multiscalegui::maprefmenuaux
#trace add variable ::multiscalegui::ljparamCurrentMol write ::multiscalegui::ljparammenuaux
trace remove variable ::multiscalegui::menuChoice write ::multiscalegui::toggleNextButton
trace add variable ::multiscalegui::menuChoice write ::multiscalegui::toggleNextButton
#trace add variable ::multiscalegui::toCGShapeUseMass write ::multiscalegui::toggleMassBox
#LBM STUFF
trace add variable ::multiscalegui::toCGResidueHybrid write ::multiscalegui::toggleHybridBox
# If already initialized, just turn on
if { [winfo exists .multiscalegui] } {
wm deiconify $w
return
}
set w [toplevel ".multiscalegui"]
wm title $w "Multiscale Builder - Main Menu"
#Add a menubar
frame $w.menubar -relief raised -bd 2
#grid $w.menubar -padx 1 -column 0 -columnspan 5 -row 0 -sticky ew
pack $w.menubar -padx 1 -fill x
menubutton $w.menubar.help -text "About Authors" -underline 0 \
-menu $w.menubar.help.menu
$w.menubar.help config -width 12
pack $w.menubar.help -side right
## help menu
menu $w.menubar.help.menu -tearoff no
$w.menubar.help.menu add command -label "LBM" \
-command {tk_messageBox -type ok -title "LBM" \
-message "This tools was implemented by Lemmin/Bovigny Modeling (LBM) Compagny"}
$w.menubar.help.menu add command -label "Laboratory of Biomolecular Modeling" \
-command "vmd_open_url http:https://lbm.epfl.ch"
# now, we define a few frames
## ---------------------------------------------------------------------------
## ---------------------- START choose order FRAME ---------------------------
set chooseFrame [frame $w.chooseFrame]
set row 0
#puts "before intro text"
# intro text
grid [label $chooseFrame.introText -text "Coarse Graining"] \
-row $row -column 0 -columnspan 2 -sticky ew
incr row
# -----------------------------------------------
grid [labelframe $chooseFrame.resCg -bd 2 -relief ridge \
-text "Coarse Grain and Hybrid Plugin : " \
-padx 1m -pady 1m] -row $row -column 0 -columnspan 2 -sticky nsew
incr row
grid [radiobutton $chooseFrame.resCg.r1 -text \
"Create a Coarse Grain or Hybrid Model for LAMMPS " \
-variable ::multiscalegui::menuChoice -value 1 ] \
-row 0 -column 0 -sticky ew
grid [radiobutton $chooseFrame.resCg.r2 -text \
"Write Lammps data from pdb/psf" \
-variable ::multiscalegui::menuChoice -value 3 ] \
-row 1 -column 0 -sticky w
# ---
#grid [labelframe $chooseFrame.sCg -bd 2 -relief ridge \
# -text "Hybrid CG-AA Tools" \
# -padx 1m -pady 1m] -row $row -column 0 -columnspan 2 -sticky nsew
#incr row
#grid [radiobutton $chooseFrame.sCg.r1 -text \
# "Create CG-AA Model" \
# -variable ::multiscalegui::menuChoice -value 2 ] \
# -row 0 -column 0 -sticky w
grid [button $chooseFrame.next -text "Next ->" -state disabled \
-command {
if { $::multiscalegui::menuChoice > 0 } {
pack forget $::multiscalegui::chooseFrame
if { $::multiscalegui::menuChoice == 1 } {
pack $::multiscalegui::toCGResidueFrame
wm title $::multiscalegui::w "CG Builder - LBM Based"
# } elseif { $::multiscalegui::menuChoice == 2 } {
#pack $::multiscalegui::toCGResidueFrame
# pack $::multiscalegui::toCGShapeFrame
# wm title $::multiscalegui::w "CG Builder - Shape-Based CG"
} elseif { $::multiscalegui::menuChoice == 3} {
pack $::multiscalegui::fromCGFrame
wm title $::multiscalegui::w "Reverse LBM-BASED CG"
# } elseif { $::multiscalegui::menuChoice == 4 } {
# pack $::multiscalegui::mapSBFrame
# wm title $::multiscalegui::w "Map Shaped-Based CG To All Atom"
#} elseif { $::multiscalegui::menuChoice == 5 } {
# pack $::multiscalegui::ljParamFrame
# wm title $::multiscalegui::w "Get Lennard-Jones Params for CG model"
#} elseif { $::multiscalegui::menuChoice == 6 } {
# pack $::multiscalegui::baFromSimFrame
# wm title $::multiscalegui::w "Extract Bond/Angle Params from AA Sim"
#} elseif { $::multiscalegui::menuChoice == 7 } {
# pack $::multiscalegui::scaleBAFrame
# wm title $::multiscalegui::w "Scale Bond/Angle Spring Constants"
} else {
tk_messageBox -type ok -message \
"Unknown Menu Choice. Contact Developers" -title "Error!"
}
}
}] \
-row $row -column 0 -columnspan 2 -sticky ew
incr row
## ---------------------- END choose order FRAME ---------------------------
## ---------------------------------------------------------------------------
# ::multiscalegui::createToCGResidueFrame {}
#puts "before doing residue TO frame"
## ---------------------------------------------------------------------------
## ---------------------- START to CG via RESIDUE FRAME ---------------------
set toCGResidueFrame [frame $w.toCGResidueFrame]
set row 0
#puts "before intro text"
# intro text
grid [label $toCGResidueFrame.introText -text "Coarse Grain / Hybrid Plugin"] \
-row $row -column 0 -columnspan 2 -sticky w
incr row
grid [label $toCGResidueFrame.introTextDesc1 -text \
"Convert All Atom pdb/psf files to CG/Hybrid pdb/psf and mapping files"] \
-row $row -column 0 -columnspan 2 -sticky w
incr row
grid [label $toCGResidueFrame.introTextDesc2 -text \
"If you're vegetarian : close this plugin, it could be dangerous for you !!!"] \
-row $row -column 0 -columnspan 2 -sticky w
incr row
grid [labelframe $toCGResidueFrame.inp -bd 2 -relief ridge \
-text "Input" \
-padx 1m -pady 1m] -row $row -column 0 -columnspan 2 -sticky nsew
incr row
grid [label $toCGResidueFrame.inp.inpdblabel -text "input PDB"] \
-row $row -column 0 -sticky w
grid [entry $toCGResidueFrame.inp.inpdbpath -width 56 \
-textvariable ::multiscalegui::pdbpath ] \
-row $row -column 1 -sticky ew
grid [button $toCGResidueFrame.inp.inpdbbutton -text "Browse" \
-command {
set tempfile [tk_getOpenFile]
if {![string equal $tempfile ""]} { set ::multiscalegui::pdbpath $tempfile }
}] -row $row -column 2 -sticky w
incr row
grid [label $toCGResidueFrame.inp.inpsflabel -text "input PSF"] \
-row $row -column 0 -sticky w
grid [entry $toCGResidueFrame.inp.inpsfpath -width 56 \
-textvariable ::multiscalegui::psfpath ] \
-row $row -column 1 -sticky ew
grid [button $toCGResidueFrame.inp.inpsfbutton -text "Browse" \
-command {
set tempfile [tk_getOpenFile]
if {![string equal $tempfile ""]} { set ::multiscalegui::psfpath $tempfile }
}] -row $row -column 2 -sticky w
incr row
#puts "before cg database"
# -----------------------------------------------
# deal with the CG database
grid [labelframe $toCGResidueFrame.database -bd 2 -relief ridge \
-text "CG Database" \
-padx 1m -pady 1m] -row $row -column 0 -columnspan 2 -sticky nsew
incr row
set rowDB 0
grid [label $toCGResidueFrame.database.pLabel -text "Proteins"] \
-row $rowDB -column 0 -sticky w
grid [label $toCGResidueFrame.database.pPath \
-text "([file join $::env(MULTISCALE) lbm.cgc])"] \
-row $rowDB -column 1 -columnspan 2 -sticky w
grid [button $toCGResidueFrame.database.paddbutton -text "Add" \
-command {
::multiscaletools::read_db [file join $::env(MULTISCALE) lbm.cgc]
$::multiscalegui::numBeadsLabel configure \
-text "[llength $::multiscaletools::convbeads]"
$::multiscalegui::toCGResidueFrame.database.paddbutton \
configure -state disabled
$::multiscalegui::toCGResidueFrame.database.paddbutton \
configure -text "Added!"
}] -row $rowDB -column 3 -sticky e
incr rowDB
grid [label $toCGResidueFrame.database.wLabel -text "Water"] \
-row $rowDB -column 0 -sticky w
grid [label $toCGResidueFrame.database.wPath \
-text "([file join $::env(CGTOOLSDIR) water.cgc])"] \
-row $rowDB -column 1 -columnspan 2 -sticky w
grid [button $toCGResidueFrame.database.waddbutton -text "Add" \
-command {
::multiscaletools::read_db [file join $::env(CGTOOLSDIR) water.cgc]
$::multiscalegui::numBeadsLabel configure \
-text "[llength $::multiscaletools::convbeads]"
$::multiscalegui::toCGResidueFrame.database.waddbutton \
configure -state disabled
$::multiscalegui::toCGResidueFrame.database.waddbutton \
configure -text "Added!"
}] -row $rowDB -column 3 -sticky e
incr rowDB
grid [label $toCGResidueFrame.database.udLabel -text "User Defined"] \
-row $rowDB -column 0 -sticky w
grid [entry $toCGResidueFrame.database.udpath -width 46 \
-textvariable ::multiscalegui::cgpath ] \
-row $rowDB -column 1 -sticky ew
grid [button $toCGResidueFrame.database.udbutton -text "Browse" \
-command {
set tempfile [tk_getOpenFile]
if {![string equal $tempfile ""]} { set ::multiscalegui::cgpath $tempfile }
}] -row $rowDB -column 2 -sticky w
grid [button $toCGResidueFrame.database.udaddbutton -text "Add" \
-command {
::multiscaletools::read_db $::multiscalegui::cgpath
$::multiscalegui::numBeadsLabel configure \
-text "[llength $::multiscaletools::convbeads]"
}] -row $rowDB -column 3 -sticky e
incr rowDB
grid [label $toCGResidueFrame.database.beadsText \
-text "Bead Definitions Currently Loaded:"] \
-row $rowDB -column 1 -sticky w
set ::multiscalegui::numBeadsLabel [label $toCGResidueFrame.database.beadsNum \
-text "[llength $::multiscaletools::convbeads]"]
grid $::multiscalegui::numBeadsLabel -row $rowDB -column 2 -sticky e
incr rowDB
#### LBM LAB HYBRID PART
# deal with the Hybrid System
grid [labelframe $toCGResidueFrame.hybrid -bd 2 -relief ridge \
-text "Hybrid Part" \
-padx 1m -pady 1m] -row $row -column 0 -columnspan 5 -sticky nsew
incr row
set rowHB 0
grid [checkbutton $toCGResidueFrame.hybrid.choiceButton -variable \
[namespace current]::toCGResidueHybrid] -row 0 -column 0 -sticky w
incr rowHB
grid [label $toCGResidueFrame.hybrid.hybcutoffAA -state disabled -text \
"Cutoff All Atom :"] -row $rowHB -column 0 -sticky w
grid [entry $toCGResidueFrame.hybrid.cutoffAA -state disabled -width 7 \
-textvariable ::multiscalegui::tohybridcutoffAA ] \
-row $rowHB -column 1 -sticky e
incr rowHB
grid [label $toCGResidueFrame.hybrid.hybcutoffCG -state disabled -text \
"Cutoff Coarse Grain :"] -row $rowHB -column 0 -sticky w
grid [entry $toCGResidueFrame.hybrid.cutoffCG -state disabled -width 7 \
-textvariable ::multiscalegui::tohybridcutoffCG] \
-row $rowHB -column 1 -sticky e
incr rowHB
grid [label $toCGResidueFrame.hybrid.explaintexthybrid -state disabled -text "Give a selection to center your hybrid system (ex : resid 5 and backbone)"] \
-row $rowHB -column 1 -sticky e
incr rowHB
grid [label $toCGResidueFrame.hybrid.hybcenter -state disabled -text \
"Center :" ] -row $rowHB -column 0 -sticky w
grid [entry $toCGResidueFrame.hybrid.center -state disabled -width 46 \
-textvariable ::multiscalegui::tohybridcenter] \
-row $rowHB -column 1 -sticky e
incr rowHB
#grid [label $toCGResidueFrame.hybrid.void -text " "] -row $rowHB -column 2
grid [button $toCGResidueFrame.hybrid.preview -state disabled -text "Preview For Hybrid" \
-command ::multiscalegui::buildHybridExecute] \
-row $rowHB -column 1 -sticky e
incr row
incr rowHB
# Output filenames
grid [label $toCGResidueFrame.outpdblabel -text "Output PDB: "] \
-row $row -column 0 -sticky w
grid [entry $toCGResidueFrame.toCGoutpdbfile -width 30 -textvariable ::multiscalegui::toCGoutpdbfile] \
-row $row -column 1 -sticky ew
incr row
grid [label $toCGResidueFrame.revcglabel -text "Rev CG File: "] -row $row \
-column 0 -sticky w
grid [entry $toCGResidueFrame.revcgfile -width 30 \
-textvariable ::multiscalegui::revcgfile] -row $row -column 1 -sticky ew
incr row
grid [button $toCGResidueFrame.back -text "Back To Previous Screen" \
-command { \
pack forget $::multiscalegui::toCGResidueFrame
set ::multiscalegui::menuChoice 0
wm title $::multiscalegui::w "CG Builder - Method Selection"
pack $::multiscalegui::chooseFrame }] \
-row $row -column 0 -sticky w
grid [button $toCGResidueFrame.applyDB -text "Build Model" \
-command ::multiscalegui::build_model] \
-row $row -column 1 -sticky e
incr row
## ---------------------- END to residue CG rep FRAME -------------------
## ---------------------------------------------------------------------------
## ---------------------------------------------------------------------------
## ---------------------- START fromCGFrame ---------------------
set fromCGFrame [frame $w.fromCGFrame]
set row 0
#puts "before intro text"
# intro text
grid [label $fromCGFrame.introText -text "Convert pDB/PSF to Lammps data"] \
-row $row -column 0 -columnspan 2 -sticky w
incr row
grid [label $fromCGFrame.introTextDesc1 -text \
"Creation of data files for LAMMPS, from CoarseGrained files pdb, psf"] \
-row $row -column 0 -columnspan 2 -sticky w
incr row
grid [labelframe $fromCGFrame.inp -bd 2 -relief ridge \
-text "Input" \
-padx 1m -pady 1m] -row $row -column 0 -columnspan 2 -sticky nsew
incr row
grid [label $fromCGFrame.inp.inpdblabel -text "input PDB"] \
-row $row -column 0 -sticky w
grid [entry $fromCGFrame.inp.inpdbpath -width 56 \
-textvariable ::multiscalegui::pdbpath ] \
-row $row -column 1 -sticky ew
grid [button $fromCGFrame.inp.inpdbbutton -text "Browse" \
-command {
set tempfile [tk_getOpenFile]
if {![string equal $tempfile ""]} { set ::multiscalegui::pdbpath $tempfile }
}] -row $row -column 2 -sticky w
incr row
grid [label $fromCGFrame.inp.inpsflabel -text "input PSF"] \
-row $row -column 0 -sticky w
grid [entry $fromCGFrame.inp.inpsfpath -width 56 \
-textvariable ::multiscalegui::psfpath ] \
-row $row -column 1 -sticky ew
grid [button $fromCGFrame.inp.inpsfbutton -text "Browse" \
-command {
set tempfile [tk_getOpenFile]
if {![string equal $tempfile ""]} { set ::multiscalegui::psfpath $tempfile }
}] -row $row -column 2 -sticky w
incr row
# Output filenames
grid [label $fromCGFrame.outpdblabel -text "Output Lammps: "] \
-row $row -column 0 -sticky w
grid [entry $fromCGFrame.toCGoutpdbfile -width 30 -textvariable ::multiscalegui::toCGoutpdbfile] \
-row $row -column 1 -sticky ew
incr row
grid [button $fromCGFrame.back -text "Back To Previous Screen" \
-command { \
pack forget $::multiscalegui::fromCGFrame
set ::multiscalegui::menuChoice 0
wm title $::multiscalegui::w "CG Builder - Method Selection"
pack $::multiscalegui::chooseFrame }] \
-row $row -column 0 -sticky w
grid [button $fromCGFrame.applyDB -text "Build DataFile" \
-command ::multiscalegui::build_data] \
-row $row -column 1 -sticky e
incr row
## ---------------------- END to residue CG rep FRAME -------------------
## ---------------------------------------------------------------------------
pack $chooseFrame
# this trace lets the plugin determine when you have loaded a molecule
# in VMD
trace add variable ::vmd_initialize_structure write \
::multiscalegui::vmd_init_struct_trace
}
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
proc ::multiscalegui::addStatusLine {strText} {
variable toCGShapeFrame
::multiscalegui::addGenericStatusLine $toCGShapeFrame $strText
}
# -------------------------------------------------------------------------
proc ::multiscalegui::addGenericStatusLine {frameName strText} {
$frameName.statFrame.statBox configure -state normal
$frameName.statFrame.statBox insert end "$strText\n"
$frameName.statFrame.statBox see end
update idletask
$frameName.statFrame.statBox configure -state disabled
}
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
proc multiscalegui_tk {} {
# puts "before invoking the constructor";
::multiscalegui::multiscalegui
# puts "after invoking the constructor";
# READ PARAMETERS and TOPOLOGY files
::readParTop::read_topology $::env(MULTISCALE)/top_lbm.rtf
::readParTop::read_topology $::env(MULTISCALE)/top_K51.rtf
::readParTop::read_topology $::env(MULTISCALE)/top_amber2charmm.inp
::readParTop::read_parameters $::env(MULTISCALE)/par_lbm.prm
#AA Amber parameters
#::readParTop::read_topology $::env(MULTISCALE)/top_amber2charmm.inp
::readParTop::read_parameters $::env(MULTISCALE)/par_amber_lammps.inp
# parameters and topology of ligand K49
::readParTop::read_parameters $::env(MULTISCALE)/par_K51.inp
set ::multiscaletools::DEBUG 0
return $::multiscalegui::w
}
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
proc ::multiscalegui::viewAA { molid atom1 cutoff} {
set sel [atomselect $molid "same residue as within $cutoff of ($atom1)"]
#mol delrep 0 top
mol selection "[$sel text]"
mol color Type
mol representation CPK
mol material Opaque
mol addrep top
#mol selupdate 0 top 0
#mol colupdate 0 top 0
#mol showrep top 0 0
}
proc ::multiscalegui::viewCG { molid atom1 cutoff } {
set sel [atomselect $molid "same residue as (not within $cutoff of ($atom1))"]
#mol delrep 0 top
mol selection "[$sel text]"
mol color ColorID 9
mol material Transparent
mol representation Beads 0.9 8
mol addrep top
#mol selupdate 1 top 0
#mol colupdate 1 top 0
#mol showrep top 1 0
}
proc ::multiscalegui::viewHybrid {molid atom1 cutoffAA cutoffCG } {
set pure_AA [atomselect $molid "same residue as within $cutoffAA of ($atom1)"]
set pure_CG [atomselect $molid "same residue as (not within $cutoffCG of ($atom1))"]
set hybrid [atomselect $molid "not (index [$pure_CG get index] [$pure_AA get index])"]
#mol selection "[$pure_CG text]"
#mol representation licorice
#mol addrep top
#mol selection "[$pure_AA text]"
#mol color type
#mol representation CPK
#mol addrep top
mol selection "[$hybrid text]"
#mol color ColorID 7
mol color Type
mol material Steel
mol representation licorice
mol addrep top
}
proc ::multiscalegui::view { molidAA atomAA cutoffAA cutoffCG } {
viewAA $molidAA $atomAA $cutoffAA
viewCG $molidAA $atomAA $cutoffCG
viewHybrid $molidAA $atomAA $cutoffAA $cutoffCG
}
proc ::multiscalegui::test { } {
mol delrep 0 top
mol delrep 0 top
mol delrep 0 top
set molidAA 0
set atomAA "resid 5 and backbone"
set cutoffAA 5
set cutoffCG 10
::multiscalegui::view $molidAA $atomAA $cutoffAA $cutoffCG
}
proc ::multiscalegui::build_model { } {
# Test if output or not
set outpdb $::multiscalegui::toCGoutpdbfile
if { [string trim $::multiscalegui::toCGoutpdbfile] == "" } {
tk_messageBox -message "Put an output \n Gerce ignoble" \
-type ok -title "Error!"
return
}
# Test if rcg or not
set outrevcg $::multiscalegui::revcgfile
if { [string trim $::multiscalegui::revcgfile] == "" } {
tk_messageBox -message "Put a REVCG => " \
-type ok -title "Error!"
return
}
if { $::multiscalegui::toCGResidueHybrid == 1 } {
file delete $::multiscalegui::Hybrid_name.pdb $::multiscalegui::Hybrid_name.psf $::multiscalegui::Hybrid_rev
set ::multiscalegui::Hybrid_rev $::multiscalegui::revcgfile
set ::multiscalegui::Hybrid_name $::multiscalegui::toCGoutpdbfile
::multiscalegui::build_hybrid
set hyb [mol new $::multiscalegui::Hybrid_name.psf]
mol addfile $::multiscalegui::Hybrid_name.pdb
mol addfile $::multiscalegui::Hybrid_name.psf
set id [[atomselect top "all"] molid]
puts $id
set all [atomselect top "all"]
set triplet [::multiscaletools::write_dipole $id [topo -molid $id getanglelist] $::readParTop::patches]
::multiscaletools::set_connectivitytype $id $::readParTop::parameters $triplet
::writelammps::writelammpsdata $id $::multiscalegui::Hybrid_name.data multiscale $all $::readParTop::parameters $::multiscaletools::dipoles $::multiscaletools::ellipsoids
::multiscaletools::set_group $id
::writelammps::writelammpsinput $::multiscalegui::Hybrid_name.data $::multiscaletools::sc_dipole $::multiscaletools::standard
} else {
file delete $::multiscalegui::CG_name.pdb $::multiscalegui::CG_name.psf $::multiscalegui::CG_rev
set ::multiscalegui::CG_rev $::multiscalegui::revcgfile
set ::multiscalegui::CG_name $::multiscalegui::toCGoutpdbfile
::multiscalegui::build_CG
set CG [mol new $::multiscalegui::CG_name.psf]
mol addfile $::multiscalegui::CG_name.pdb
mol addfile $::multiscalegui::CG_name.psf
set idCG [[atomselect top "all"] molid]
set allCG [atomselect top "all"]
[atomselect top "all"] set occupancy 3
set triplet [::multiscaletools::write_dipole $idCG [topo -molid $idCG getanglelist] $::readParTop::patches]
::multiscaletools::set_connectivitytype $idCG $::readParTop::parameters $triplet
::writelammps::writelammpsdata $idCG $::multiscalegui::CG_name.data multiscale $allCG $::readParTop::parameters $::multiscaletools::dipoles $::multiscaletools::ellipsoids
::multiscaletools::set_group $idCG
::writelammps::writelammpsinput $::multiscalegui::CG_name.data $::multiscaletools::sc_dipole $::multiscaletools::standard
}
}
###################################################################################
# Coarse grained procs #
# #
###################################################################################
proc ::multiscalegui::build_CG { } {
set AA [mol new $::multiscalegui::psfpath]
mol addfile $::multiscalegui::pdbpath
#::multiscaletools::read_db $CG_topology
::multiscaletools::apply_database $AA $::multiscalegui::CG_name.pdb $::multiscalegui::CG_rev 1
::multiscaletools::psfgen $::multiscalegui::CG_name.pdb $AA $::multiscalegui::CG_name.psf $::multiscalegui::CG_rev $::readParTop::topology
mol delete $AA
}
proc ::multiscalegui::load_AA_CG {psfAA pdbAA pdbCG psfCG} {
set AA [mol new $psfAA]
mol addfile $pdbAA
set CG [mol new $psfCG]
mol addfile $pdbCG
return [list $AA $CG]
}
proc ::multiscalegui::display_hybrid {psfhybrid pdbhybrid} {
mol delete all
set current [mol new $psfhybrid]
mol addfile $pdbhybrid
mol delrep 0 $current
#pure AA
mol selection "occupancy 0"
mol color ColorID 1
mol material Opaque
mol representation CPK 1.0 0.3 8 6
mol addrep $current
#hybrid AA
mol selection "occupancy 1"
mol color ColorID 8
mol material Opaque
mol representation Licorice
mol addrep $current
#hybrid CG
mol selection "occupancy 2"
mol color ColorID 8
mol material Transparent
mol representation CPK 3.0 1.5 8.0 8.0
mol addrep $current
#pure CG
mol selection "occupancy 3"
mol color ColorID 19
mol material Opaque
mol representation CPK 3.0 1.5 8.0 8.0
mol addrep $current
}
###################################################################################
# Hybrid procs #
# #
###################################################################################
proc ::multiscalegui::buildHybridExecute { } {
if { $::multiscalegui::CG_model == 0 } {
::multiscalegui::build_CG
set ::multiscalegui::CG_model 1
}
set cutAA -1
# need to have a positive value for the CA cutoff
if {[string trim $::multiscalegui::tohybridcutoffAA] == "" || \
! [string is double $::multiscalegui::tohybridcutoffAA] || \
$::multiscalegui::tohybridcutoffAA < 0 } {
tk_messageBox -message "Cutoff AA must be an double or a pokemon." \
-type ok -title "Error!"
return
}
set cutAA $::multiscalegui::tohybridcutoffAA
set cutCG -1
# need to have a positive value for the CG cutoff
if {[string trim $::multiscalegui::tohybridcutoffCG] == "" || \
! [string is double $::multiscalegui::tohybridcutoffCG] || \
$::multiscalegui::tohybridcutoffCG < 0 } {
tk_messageBox -message "Cutoff CG must be an double or a pokemon." \
-type ok -title "Error!"
return
}
set cutCG $::multiscalegui::tohybridcutoffCG
if { $cutCG < $cutAA } {
tk_messageBox -message "Cut off CG has to be greater than cut off all atom!" \
-type ok -title "Error!"
return
}
set center -1
if { [string trim $::multiscalegui::tohybridcenter] == "" } {
tk_messageBox -message "Center selection is not defined. Encule!" \
-type ok -title "Error!"
return
}
set center $::multiscalegui::tohybridcenter
if { [::multiscalegui::build_hybrid]==0 } {
::multiscalegui::display_hybrid $::multiscalegui::Hybrid_name.psf $::multiscalegui::Hybrid_name.pdb
}
}
proc ::multiscalegui::build_hybrid { } {
set l [load_AA_CG $::multiscalegui::psfpath $::multiscalegui::pdbpath $::multiscalegui::CG_name.pdb \
$::multiscalegui::CG_name.psf]
lassign $l idAA idCG
set out [::multiscaletools::select_multiscale $::multiscalegui::CG_rev $::multiscalegui::tohybridcenter \
$::multiscalegui::tohybridcutoffAA $::multiscalegui::tohybridcutoffCG \
$idAA $idCG $::multiscalegui::Hybrid_rev $::multiscalegui::Hybrid_name $::readParTop::topology]
if { $out == -1 } {
tk_messageBox -message "Unvalid selection Do not bullshit with me, man!" \
-type ok -title "Error!"
return -1
}
if { $out == -2 } {
tk_messageBox -message "No atoms in hybrid selection. Change cutoffs." \
-type ok -title "Error!"
return -1
}
return 0
}
proc ::multiscalegui::build_data { } {
# Test if pdb or not
set outrevcg $::multiscalegui::pdbpath
if { [string trim $::multiscalegui::pdbpath] == "" } {
tk_messageBox -message "YOU HAVE TO PUT A PDB FILE IN, OTHERWISE THOMAS LEMMIN COMES AND BEAT YOU => http:https://www.facebook.com/#!/profile.php?id=573598702 " \
-type ok -title "!!!!!!!INPUT PDB ERROR!!!!!!!"
return
}
set outpsf $::multiscalegui::psfpath
if { [string trim $::multiscalegui::psfpath] == "" } {
tk_messageBox -message "YOU HAVE TO PUT A PSF FILE IN, OTHERWISE THOMAS LEMMIN COMES AND BEAT YOU => http:https://www.facebook.com/#!/profile.php?id=573598702 " \
-type ok -title "!!!!!!!INPUT PSF ERROR!!!!!!"
return
}
# Test if output or not
set outpdb $::multiscalegui::toCGoutpdbfile
if { [string trim $::multiscalegui::toCGoutpdbfile] == "" } {
tk_messageBox -message "PUT AN OUTPUT FILENAME, PLEASE. WE ARE SURE THAT YOU ARE \n Une Gerce Ignoble" \
-type ok -title "!!!!!!!OUTPUT ERROR!!!!!!"
return
}
set CG [mol new $::multiscalegui::psfpath]
mol addfile $::multiscalegui::pdbpath
mol addfile $::multiscalegui::psfpath
set id [[atomselect top "all"] molid]
puts $id
set all [atomselect top "all"]
set triplet [::multiscaletools::write_dipole $id [topo -molid $id getanglelist] $::readParTop::patches]
::multiscaletools::set_connectivitytype $id $::readParTop::parameters $triplet
::writelammps::writelammpsdata $id $::multiscalegui::toCGoutpdbfile.data multiscale $all $::readParTop::parameters $::multiscaletools::dipoles $::multiscaletools::ellipsoids
::multiscaletools::set_group $id
::writelammps::writelammpsinput $::multiscalegui::toCGoutpdbfile.data $::multiscaletools::sc_dipole $::multiscaletools::standard
}