scripting biomolecular simulations with tcl part of cs590v
DESCRIPTION
Scripting Biomolecular Simulations with Tcl part of CS590v. Michael McLennan Senior Research Scientist Rosen Center for Advanced Computing, Purdue University [email protected]. Biomolecular Simulation. - PowerPoint PPT PresentationTRANSCRIPT
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Scripting Biomolecular Simulations with TclScripting Biomolecular Simulations with Tclpart of CS590v
Michael McLennanSenior Research Scientist
Rosen Center for Advanced Computing, Purdue [email protected]
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Biomolecular SimulationBiomolecular Simulation
developed by the Theoretical and Computational
Biophysics Group in the Beckman Institute for Advanced Science and
Technology at the University of Illinois at
Urbana-Champaign
Download from http://www.ks.uiuc.edu/Research/vmd/
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What is scripting?What is scripting?
Type in commands Write little programs Like Unix “shell” scripts
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What is Tcl?What is Tcl?
Developed by John Ousterhout at UC Berkeley Released in 1989, currently maintained as Open Source Millions of users worldwide Used in commercial CAD tools and products (TiVo!) More info: http://www.tcl.tk/
Tcl: language
button .b –text “Hello, World!”pack .b –pady 8
Tk: widget toolkit
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Application: UbiquitinApplication: Ubiquitin
Ubiquitin660 atoms
Carbon backbone drawn in green
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Application: UbiquitinApplication: Ubiquitin
Ubiquitin660 atoms
Carbon backbone drawn in green(tube method)
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Application: UbiquitinApplication: Ubiquitin
Ubiquitin660 atoms
= starting point= after simulation
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Application: UbiquitinApplication: Ubiquitin
Ubiquitin660 atoms
= small change= medium change= large change
Movement after simulation:
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Coloring script for comparing moleculesColoring script for comparing molecules
A little script to color according to atomic movements:proc tutorialcoloring {} { set mol1 [lindex [molinfo list] 0] set mol2 [lindex [molinfo list] 1] set sel0 [atomselect $mol1 "alpha and protein"] ;# crystal set sel1 [atomselect $mol2 "alpha and protein"] ;# simulation
set mylist {} foreach v0 [$sel0 get {x y z}] v1 [$sel1 get {x y z}] { set dx [expr [lindex $v0 0] - [lindex $v1 0]] set dy [expr [lindex $v0 1] - [lindex $v1 1]] set dz [expr [lindex $v0 2] - [lindex $v1 2]] set disp [expr ($dx*$dx + $dy*$dy + $dz*$dz)] lappend mylist $disp } $sel0 set beta $mylist}
Tcl code!
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unix> tclsh
% puts “Hello, World!”Hello, World!
% puts –nonewline “hello”hello% %% exitunix>
unix> tclsh
% puts “Hello, World!”Hello, World!
% puts –nonewline “hello”hello%
““Hello, World!” in TclHello, World!” in Tcl
Start up a Tcl application:unix> tclsh
unix> wish
unix> vmd
oror
Like Unix shell, but speaks Tcltclsh + widgetsVMD molecular visualization
unix> tclsh
% puts “Hello, World!”Hello, World!%
For example:
Command to write out a stringOutput written on stdout by defaultAdd options to commandsOutput written without trailing newline
Exit tclsh
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Tcl command syntaxTcl command syntax
puts –nonewline “Hello, World!”
command arg arg …
First word is the command name Remaining arguments depend on command syntax Use double-quotes (“”) to wrap up text strings Any line starting with hash (#) is a comment Use semicolon (;) to separate multiple commands on same line Use backslash (\) to extend a command onto multiple lines
# this is a commentputs “Hello”; puts “World!”puts –nonewline \ “Hello, World!”
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Tcl DocumentationTcl Documentation
http://www.tcl.tk/doc/
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Tcl VariablesTcl Variables
Variables hold numbers, strings, and other values: set x “World” puts “Hello, $x!” Hello, World!
Uses the value of variable named x
set pi 3.14159 puts “Value of pi is $pi” Value of pi is 3.14159
Value can be a number
set cmd puts $cmd “Hello, World!” Hello, World!
Value can be a command name
set var x set $var “Universe” puts “Hello, $x!” Hello, Universe!
Value can be a variable name
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Doing Math in TclDoing Math in Tcl
Mathematical Expressions: set pi 3.14159 set r 10 puts “Circumference is 2*$pi*$r”
Why didn’t we get a number here? Circumference is 2*3.14159*10
expr 2+2 4
Use the expr command to do math
expr 2*$pi*$r 62.8318
The right way to get circumference
puts “Circumference is expr 2*$pi*$r”Oops! Still not quite right! Circumference is expr 2*3.14159*10
puts “Circumference is [expr 2*$pi*$r]”
Execute command and substitute result in its place Circumference is 62.8318
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Tcl Versus Other LanguagesTcl Versus Other Languages
Pythagorean Theorem expressed in Tcl:
ab c
c = a2+b2
set a 3
set b 4
set c [expr sqrt($a*$a + $b*$b)]
Use ()’s for functions/grouping Use C-like math functions
In C you might say… In Tcl you say…x = x + 1; set x [expr $x + 1]
x += 2; incr x 2 set x [expr $x+2]
Y = sin(2*x/(x-1)); set y [expr sin(2*$x/($x-1))]
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Tcl Quoting RulesTcl Quoting Rules
Tcl also supports {} quotes: puts “Hello, World!” puts {Hello, World!} Both keep text together
puts “Hello, World!”
puts {Hello, World!}
Both handle multi-line strings
The difference is important when you have substitutions: set x “World” puts “Hello, $x!” Hello, World!
set x “World” puts {Hello, $x!} Hello, $x!
Curly braces prevent substitutions!
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QuizQuiz
Problem #1 set x 10 puts x x
Problem #2 set set set puts $set set
Problem #3 set pi 3.14159 set area {expr $pi*$r*$r} puts “Area is: $area” Area is: expr $pi*$r*$r
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Command ScriptsCommand Scripts
Save a series of commands in a command script file:
# This is a command scriptputs –nonewline “What’s your name?”set name [gets stdin]puts “Hello, $name!”
File: hello.tcl
unix> tclsh% source hello.tclWhat’s your name? FredHello, Fred!
% source hello.tclWhat’s your name?
Load the script interactively: Run as a program:unix> tclsh hello.tclWhat’s your name? FredHello, Fred!
unix>
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Programming StatementsProgramming Statements
Conditionals: if {$x > 0} { statements }
if {$x > 0} { statements } elseif {$x < 0} { statements } else { statements }
switch -regexp $x { a.*z { statements } [0-9]+ { statements } foo – bar { statements } }
Looping: while {$x != 0} { statements }
for {set x 0} {$x < 10} {incr x} { statements }
foreach x {a b c d e} { statements }
break
continue
Break out of loop
Go back to top of loop
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Lists of ValuesLists of Values
Variables can hold lists of values set x {a b c d e} llength $x 5
Space-separated list of values
set x “a b c d e” llength $x 5
Nothing special about quotes
lappend x f lappend x g h puts $x a b c d e f g h
Add to list stored in variable x
lindex $x 0 a lindex $x 1 b lindex $x end h
Extract an element from a list
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proc lreverse {list} {
set rlist “”
set max [expr [llength $list]-1]
for {set i $max} {$i >= 0} {incr i -1} {
set v [lindex $list $i]
lappend rlist $v
}
return $rlist
}
set x {a b c d e f g}
set rx [lreverse $x]
Empty list
Get element from listAdd to end of return list
proc lreverse {list} { set rlist “” set max [expr [llength $list]-1]
for {set i $max} {$i >= 0} {incr i -1} {
set v [lindex $list $i] lappend rlist $v
} return $rlist}
set x {a b c d e f g}
set rx [lreverse $x]
i = max; i >= 0; i--
proc lreverse {list} { set rlist “”
set max [expr [llength $list]-1]
for {set i $max} {$i >= 0} {incr i -1} { set v [lindex $list $i] lappend rlist $v
} return $rlist}
set x {a b c d e f g}
set rx [lreverse $x]
Substitutions(innermost to outermost)
proc lreverse {list} {
set rlist “” set max [expr [llength $list]-1] for {set i $max} {$i >= 0} {incr i -1} { set v [lindex $list $i] lappend rlist $v } return $rlist
}
set x {a b c d e f g}
set rx [lreverse $x]
name argument list
Procedure declaration
Return value from procedure call
Functions and ProceduresFunctions and Procedures
Reverse a list:
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VMD CommandsVMD Commands
VMD is just like tclsh, but with extra Tcl commands: vmd > molinfo list 0 1
vmd > atomselect0 num 660 top molecule vmd > atomselect0 set radius 10
vmd > atomselect0 set radius 2
vmd > atomselect top all atomselect0
molecules
vmd > atomselect top alpha atomselect1 vmd > atomselect1 set radius 5
vmd > atomselect top hydrophobic atomselect2 vmd > atomselect2 set radius 10
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VMD CommandsVMD Commands
Use variables to store selections: vmd > set s [atomselect top all]
vmd > $s num 660 vmd > $s set radius 2
vmd > set s2 [atomselect top alpha]
vmd > $s2 set radius 5
vmd > $s2 num 76
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Coloring script for comparing moleculesColoring script for comparing molecules
A little script to color according to atomic movements:proc tutorialcoloring {} { set mol1 [lindex [molinfo list] 0] set mol2 [lindex [molinfo list] 1] set sel0 [atomselect $mol1 "alpha and protein"] ;# crystal set sel1 [atomselect $mol2 "alpha and protein"] ;# simulation
set mylist {} foreach v0 [$sel0 get {x y z}] v1 [$sel1 get {x y z}] { set dx [expr [lindex $v0 0] - [lindex $v1 0]] set dy [expr [lindex $v0 1] - [lindex $v1 1]] set dz [expr [lindex $v0 2] - [lindex $v1 2]] set disp [expr ($dx*$dx + $dy*$dy + $dz*$dz)] lappend mylist $disp } $sel0 set beta $mylist}