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FoldIt Lua Library

2009-11-28T17:39:54Z

← Older revision		Revision as of 17:39, November 28, 2009
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	end		end
	print(txt)		print(txt)
		+	end
		+
		+	=== table:insert ===
		+
		+
		+	=== table:remove ===
		+
		+
		+	=== table:push ===
		+
		+
		+	=== table:pop ===
		+
		+
		+	=== table:find ===
		+
		+
		+	=== table:sort ===
		+
		+
		+	=== mergeTables(t, u) ===
		+
		+
		+
		+	== Randomization Functions ==
		+	I'm just listing some functions we already have (implemented in existing scripts) -- will go in and fill in code later.
		+
		+
		+
		+	=== getRandomSegment() ===
		+	gets a random seg between 1 and end of protein.
		+
		+	=== getRandomInt(a, b) ===
		+	gets a random integer in the range of a and b
		+
		+	=== setRandomBand([s1][,e1][,s2],[e2]) ===
		+	sets a random band somewhere in the segment.  If called with no parameters, sets a random band between any two segs.  If called with s1, e1, sets a random band between two segments in the range s1, e1.  If called with all parameters, sets a random band between a segment in the range s1, e1 and a segment in the range s2, e2.
		+
		+
		+
		+	== Ptable Functions ==
		+	We can build a "Ptable" which is a table filled with all the information we can pull out of a protein, segment by segment.  Included will be amino acid,  secondary structure, segment score, all the segment score parts (backbone, clashing, packing, etc.).  We can also derive some other data, such as distance to start/end
		+
		+
		+
		+
		+
		+	== Banding Functions ==
		+
		+
		+	== bandEveryN(n [,s][,e]) ==
		+	bands every n segments.  If s and e are specified, bands every n segments between s and e.  Otherwise, does it to the whole protein.
		+	function bandEveryN(n, s, e)
		+	if (s==null) or (e==null) then
		+	s = 1
		+	e = get_segment_count()
		+	end
		+
		+	for i = s, e, n do
		+	if (i+n <= get_segment_count()) then
		+	band_add_segment_segment(i, i+n)
		+	end
		+	end
	end		end

Testing

2009-11-28T08:13:36Z

marked problem #26086 as "Fixed"

New page

Testing

2009-11-28T08:13:34Z

deleted "[[Testing]]" Author request: content was: 'testing to see if I can mark it as draft' (and the only contributor was 'Themarquis')

New page

FoldIt Lua Library

2009-11-28T08:12:28Z

← Older revision		Revision as of 08:12, November 28, 2009
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	These two functions return information about secondary structures.  getStructIndices takes an index and returns the start and end points of that index's structure.  For example, if we have a loop from segments 5 -10 and you call getStructIndices(3), the result would be 5, 10 (note that in Lua we can return multiple results!).		These two functions return information about secondary structures.  getStructIndices takes an index and returns the start and end points of that index's structure.  For example, if we have a loop from segments 5 -10 and you call getStructIndices(3), the result would be 5, 10 (note that in Lua we can return multiple results!).

-	function getStructIndices (i) -- i is an index to any segment in the protein	+	function getStructIndices (i) -- i is an index to any segment in the protein s = i -- initialize start segment e = i -- initialize end segment -- look forward to find end point for j = i+1, get_segment_count() do if get_ss(j) ~= get_ss(i) then break -- we hit a new structure type; we're done. end e = j end -- look back to find start point for k = i-1, 1, -1 do if get_ss(k) ~= get_ss(i) then break end s = k end return s, e end
-
-	s = i -- initialize start segment
-	e = i -- initialize end segment
-
-	-- look forward
-	to find end point
-	for j = i+1, get_segment_count() do
-	if get_ss(j) ~= get_ss(i) then
-	break -- we hit a new structure type; we're done.
-	end
-	e = j
-
-	end
-	-- look back
-	to find start point
-	for k = i-1, 1, -1 do
-
-	if get_ss(k) ~= get_ss(i) then
-	break
-	end
-	s = k
-
-	end
-	return s, e
-
-	end


Line 122:		Line 122:
	do_global_wiggle_all(10)		do_global_wiggle_all(10)
	deselect_all()		deselect_all()
		+	end
		+
		+	== Some really simple functions ==
		+	These ones fit into the "duh" category, but could they be useful?
		+
		+	=== abs(n) ===
		+	Return the absolute value of n.
		+	function abs(n)
		+	if n >= 0 then
		+	return n
		+	else
		+	return -n
		+	end
		+	end
		+
		+	=== printTable(t) ===
		+	print out contents of a table (formatted nicely!)
		+	function printTable(t)
		+	txt = ""
		+	for i = 1, # t do
		+	txt = txt .. " " .. i .. " " .. t[i] .. "\n"
		+	end
		+	print(txt)
	end		end

User:AndrewBuck

2009-11-27T23:04:56Z

New user account

New page

FoldIt Lua Library

2009-11-26T21:28:06Z

← Older revision		Revision as of 21:28, November 26, 2009
Line 19:		Line 19:
	Or make new pages for each function (users can cut and paste into their game clients).		Or make new pages for each function (users can cut and paste into their game clients).

-	==Integer==
-	function int(x) -- integer function
-	temp=x-x%1
-	if temp<1 then temp=temp+1 end
-	return temp
-	end

-	==proportional function==	+
-	function proportional(a,b,x) -- If a is proportional to b, what is x? use b=100 for percent.	+
-	temp=x*b/a	+
-	return temp	+	== Integer ==
		+
		+	function int(x) -- integer function
		+
		+	temp=x-x%1
		+
		+	if temp<1 then temp=temp+1 end
		+
		+	return temp
		+
	end		end

-	==Rescale function==	+
-	function rescale(x,x1,x2,y1,y2) -- x is a value in a scale between x1-x2. what would x be within a scale of y1-y2?	+
-	y=(y2-y1)/(x2-x1)*(x-x1)+y1	+
-	return y	+
		+	== proportional function ==
		+
		+	function proportional(a,b,x) -- If a is proportional to b, what is x? use b=100 for percent. temp=x*b/a
		+
		+	return temp
		+
		+	end
		+
		+
		+
		+
		+
		+	== Rescale function ==
		+
		+	function rescale(x,x1,x2,y1,y2) -- x is a value in a scale between x1-x2. what would x be within a scale of y1-y2? y=(y2-y1)/(x2-x1)*(x-x1)+y1 return y
		+
	end		end

	For example, if there is a value x which only moves between 130 and 297, and we want to stretch it to 0 and 100, we can use rescale(x,130,297,1,100)		For example, if there is a value x which only moves between 130 and 297, and we want to stretch it to 0 and 100, we can use rescale(x,130,297,1,100)
-	Useful for percentage when you run a loop running backwards and/or starting at with an offset.	+	Useful for percentage when you run a loop running backwards and/or starting at with an offset.

-	You can also use it to morph values:
-	Morph -100 to 236, where x=0 -> y=-100; and at x=1 -> y=236 use

-	rescale (x,0,1,-100,236)	+	You can also use it to morph values: Morph -100 to 236, where x=0 -> y=-100; and at x=1 -> y=236 use
-	Increasing x in fine values form 0 to 1 will give you values between -100 and 236	+
		+	rescale (x,0,1,-100,236
		+	Increasing x in fine values form 0 to 1 will give you values between -100 and 236
		+
		+
		+
		+
		+
		+
		+
		+
		+	== Get Structure functions ==
		+	These two functions return information about secondary structures.  getStructIndices takes an index and returns the start and end points of that index's structure.  For example, if we have a loop from segments 5 -10 and you call getStructIndices(3), the result would be 5, 10 (note that in Lua we can return multiple results!).
		+
		+	function getStructIndices (i) -- i is an index to any segment in the protein
		+
		+	s = i -- initialize start segment
		+	e = i -- initialize end segment
		+
		+	-- look forward
		+	to find end point
		+	for j = i+1, get_segment_count() do
		+	if get_ss(j) ~= get_ss(i) then
		+	break -- we hit a new structure type; we're done.
		+	end
		+	e = j
		+
		+	end
		+	-- look back
		+	to find start point
		+	for k = i-1, 1, -1 do
		+
		+	if get_ss(k) ~= get_ss(i) then
		+	break
		+	end
		+	s = k
		+
		+	end
		+	return s, e
		+
		+	end
		+
		+
		+	To use getStructIndices, simply call it with a whole number as a parameter (index to a segment in the protein).  It will return two values, a start index and and end index.  Below are some examples of how you might use the functions and the values it returns.
		+
		+
		+	-- Example of use for getStructIndices()
		+
		+	s, e = getStructIndices(5) -- get indices for struct at index 5 and store as s (start) and e (end)
		+	print("start = " , s , " end = " , e) -- print start and end points
		+	select_index_range(s, e) -- another way to use s and e. Send them to a function of your choice.
		+	do_global_wiggle_all(5) -- you can wiggle that whole structure by itself!
		+	Next, we have a related function: getStructTable().  Note that getStructTable depends on getStructIndices, so that means you'll need to paste both functions into your script if you wish to use getStructTable() (note that if you just want getStructIndices, it will work fine by itself).  getStructTable() takes no parameters and iterates through the whole protein, calling getStructIndices() several times to compile a table of all of the start and end points of structures.  For example, a table is returned with values {1, 5, 6, 9, 10, 10} for a protein that has a loop in indices 1 - 5 inclusive, a helix structure in 6 - 9 inclusive, and another loop at segment 10.  Note this is a bit redundant and we might want to improve the efficiency (we don't need both start and end points for each).  But it is useful if we want to feed the table into a function that wiggles each structure in turn, for example.
		+	function getStructTable()
		+
		+	structTable = {} -- our empty table of values
		+	curSeg, tableIndex = 1
		+
		+	while curSeg <= get_segment_count() do
		+	s, e = getStructIndices(curSeg) -- dependent on getStructIndices
		+	structTable[tableIndex], structTable[tableIndex + 1] = s, e
		+	tableIndex = tableIndex + 2 -- we're filling pairs of values
		+	curSeg = e + 1 -- next point to look at is seg after e
		+	end
		+
		+	return structTable
		+	end
		+	To use getStructTable, make sure to include the code for the function it's dependent on, getStructIndices().  It needs no parameters and returns a table.  In Lua, tables are similar to arrays.  The examples below will show you how to use getStructTable and access its table.
		+	myTable = getStructTable(
		+	) -- it's convenient to assign the table to a variable so we can easily access it.
		+	printStr = " "
		+
		+	-- print table
		+	for i = 1, # myTable do
		+	-- # means "size of"
		+	printStr = printStr .. "table entry " .. i .. " " .. myTable[i]
		+	-- .. means "concatenate"
		+	end
		+
		+	print(printStr)
		+
		+	-- wiggle each structure in turn
		+	for i = 1, # myTable, 2 do
		+	select_index_range(myTable[i], myTable[i+1])
		+	do_global_wiggle_all(10)
		+	deselect_all()
		+	end

Lua Scripting

2009-11-25T04:07:18Z

RESOURCES:

← Older revision		Revision as of 04:07, November 25, 2009
Line 47:		Line 47:

	[http://www.youtube.com/watch?v=7y43yYUA4mE Foldit Cookbook Scripting]		[http://www.youtube.com/watch?v=7y43yYUA4mE Foldit Cookbook Scripting]
		+
		+	[http://www.wowwiki.com/Lua Lua Wiki for WOW (WOW-specific but contains a lot of useful resources)]
		+
		+	[http://www.lua.org/pil/index.html Programming in Lua Book (First Edition)]

	== LUA INTERFACE ==		== LUA INTERFACE ==

FoldIt Lua Library

2009-11-23T10:17:07Z

← Older revision		Revision as of 10:17, November 23, 2009
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	Or make new pages for each function (users can cut and paste into their game clients).		Or make new pages for each function (users can cut and paste into their game clients).
		+
		+	==Integer==
		+	function int(x) -- integer function
		+	temp=x-x%1
		+	if temp<1 then temp=temp+1 end
		+	return temp
		+	end
		+
		+	==proportional function==
		+	function proportional(a,b,x) -- If a is proportional to b, what is x? use b=100 for percent.
		+	temp=x*b/a
		+	return temp
		+	end
		+
		+	==Rescale function==
		+	function rescale(x,x1,x2,y1,y2) -- x is a value in a scale between x1-x2. what would x be within a scale of y1-y2?
		+	y=(y2-y1)/(x2-x1)*(x-x1)+y1
		+	return y
		+	end
		+
		+	For example, if there is a value x which only moves between 130 and 297, and we want to stretch it to 0 and 100, we can use rescale(x,130,297,1,100)
		+	Useful for percentage when you run a loop running backwards and/or starting at with an offset.
		+
		+	You can also use it to morph values:
		+	Morph -100 to 236, where x=0 -> y=-100; and at x=1 -> y=236 use
		+
		+	rescale (x,0,1,-100,236)
		+	Increasing x in fine values form 0 to 1 will give you values between -100 and 236

Lua Scripting Tutorial (Beginner 3)

2009-11-22T05:32:34Z

Starting a New Script:

← Older revision		Revision as of 05:32, November 22, 2009
Line 19:		Line 19:

	== Starting a New Script ==		== Starting a New Script ==
-	coming soon ...!	+	In [[Lua Scripting Tutorial (Beginner 2)]], you learned how to load a pre-existing script and modify it.  Now it's time to learn how to make a brand new script from scratch.
		+
		+
		+
		+
		+	#Click on "Open Recipe Editor" on the cookbook bar.  Click on "New (Script)" at the bottom of the recipe editor window.
		+	#You should see a blank screen pop up.  This is where you'll type your script.
		+	#To get started with your new script, cut and paste the following text into the script window:
		+
		+	-- Automatic Rebuild script by your name here
		+
		+	print("My first script!")
		+	print ("Score before rebuilding is ", get_score())
		+
		+	deselect_all() -- deselect everything, just in case anything is selected by mistake.
		+	select_index_range(1, 10) -- select segments 1 through 10
		+
		+	do_local_rebuild(1) -- rebuild the selected segments for 1 round
		+	do_shake(2) -- shake for 2 rounds
		+	do_global_wiggle_all(10) -- wiggle it out for 10 rounds
		+
		+	print("Score after rebuilding is ", get_score())
		+	Although not everything in this script will make sense, you should be able to recognize some components.  For example, you already know all about print statements, deselect_all() and select_index_range().  Can you figure out what the rest of the script does?  Fortunately, there's an easy way to find out if you're correct -- let's go ahead and run this script!
		+
		+
		+	#Save the script by clicking "Save as" and writing a title and description.  Note that you will have to save your script under a new name and/or description each time you modify it ("save" is not currently working properly), so you may want to title it something like Automatic Rebuild Script 1.00.  Using numbers like 1.00, 1.01, 1.02 each time you make a minor revision or  2.00, 3.00, and so on when you make a major revision will help you keep track of all the versions you will save.
		+	#Go ahead and open an output window and run your script.
		+
		+	Hopefully, as you already guessed, the Automatic Rebuild script takes the first ten segments of the protein, rebuilds it, and then shakes and wiggles out -- fairly similar to the beginner scripts you've already run.  It also calculates the score before and after the rebuild and prints it out for your information.  Although it doesn't do anything exciting, you're eventually going to turn this script into one that rebuilds each part of the protein in turn, shakes and wiggles out, and then determines whether the rebuild was successful or not.  By doing this several times, it will eventually pick a rebuild that is highest in points.

Lua Scripting

2009-11-21T13:56:53Z

← Older revision		Revision as of 13:56, November 21, 2009
(One intermediate revision not shown)
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	As you may know, the newest Fold-it update includes support for '''Lua Scripting'''. In very basic terms, '''Lua''' is a simple '''programming language''' that we can use to manipulate proteins and automate repetitive tasks -- much like we already do with the''' Cookbook'''		As you may know, the newest Fold-it update includes support for '''Lua Scripting'''. In very basic terms, '''Lua''' is a simple '''programming language''' that we can use to manipulate proteins and automate repetitive tasks -- much like we already do with the''' Cookbook'''

-	.[[File:Output.png\|thumb\|Running a script with output!]]	+	.[[File:Output.png\|thumb\|Running a script with output!]]

	A '''script '''is actually quite similar to a Cookbook recipe (as well as to a real-life recipe for say, a cake) -- it contains a series of '''instructions''' (called '''commands''') that tell Foldit what to do with your protein (just as a real-life recipe has step by step instructions about how to combine ingredients to create a cake!)		A '''script '''is actually quite similar to a Cookbook recipe (as well as to a real-life recipe for say, a cake) -- it contains a series of '''instructions''' (called '''commands''') that tell Foldit what to do with your protein (just as a real-life recipe has step by step instructions about how to combine ingredients to create a cake!)
Line 10:		Line 10:
	Lua scripting adds an exciting new layer of gameplay to Foldit!  Fortunately, lua is easy enough to learn that everyone can use it, even people who have never programmed or scripted before.  The best place to get started if you don't have any programming experience is to work through the [[Lua Scripting Tutorial (Beginner 1)]] (followed by [[Lua Scripting Tutorial (Beginner 2)]] and the upcoming [[Lua Scripting Tutorial (Beginner 3)]]		Lua scripting adds an exciting new layer of gameplay to Foldit!  Fortunately, lua is easy enough to learn that everyone can use it, even people who have never programmed or scripted before.  The best place to get started if you don't have any programming experience is to work through the [[Lua Scripting Tutorial (Beginner 1)]] (followed by [[Lua Scripting Tutorial (Beginner 2)]] and the upcoming [[Lua Scripting Tutorial (Beginner 3)]]

-	). If you're not interested in scripting yourself but just want to download and run other people's scripts, Beginner 1 is all you need!  But if you want to go a bit further and modify scripts and write your own, you can move onto Beginner 2 and 3.[[File:Multitool.png\|thumb\|Viewing code: Crashguard's Multitool script]]	+	). If you're not interested in scripting yourself but just want to download and run other people's scripts, Beginner 1 is all you need!  But if you want to go a bit further and modify scripts and write your own, you can move onto Beginner 2 and 3.[[File:Multitool.png\|thumb\|Viewing code: Crashguard's Multitool script]]

	If, on the other hand, you have some programming experience or want to get a quicker start, begin with [[Lua Scripting Tutorial (Intermediate)]].  This intermediate tutorial starts from the ground up and assumes no prior knowledge but moves through material at a more rapid pace, including basics about how to run and modify scripts as well as core programming concepts like looping and variables.		If, on the other hand, you have some programming experience or want to get a quicker start, begin with [[Lua Scripting Tutorial (Intermediate)]].  This intermediate tutorial starts from the ground up and assumes no prior knowledge but moves through material at a more rapid pace, including basics about how to run and modify scripts as well as core programming concepts like looping and variables.

Simplified List of Lua Commands

2009-11-21T07:06:35Z

← Older revision		Revision as of 07:06, November 21, 2009
(One intermediate revision not shown)
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-	=== ''' [http://wiki/Get_segment_score_part get_segment_score_part](''score_part, segment1[, ... segment_n]'')''' ===	+	=== ''' get_segment_score_part(''score_part, segment1[, ... segment_n]'')''' ===
-	<br />This command is a bit tricky (click above on the command to link to a more detailed description!)  We can use it to give us '''part''' of the current backbone score of segment1, and optionally, segment 2, segment 3, and so on.  The parameter ''score_part ''refers to a particular part of the segment's score -- possibilities include "clashing", "packing", "hiding", "bonding, "backbone", "sidechain", "reference", "disulfides" and "other".  These are the same as the individual components of a score that pop up if you tab over a segment in the game.	+	<br />This command is a bit tricky (see [[Get segment score part]] for a more detailed description!)  We can use it to give us '''part''' of the current backbone score of segment1, and optionally, segment 2, segment 3, and so on.  The parameter ''score_part ''refers to a particular part of the segment's score -- possibilities include "clashing", "packing", "hiding", "bonding, "backbone", "sidechain", "reference", "disulfides" and "other".  These are the same as the individual components of a score that pop up if you tab over a segment in the game.
	print(get_segment_score_part("clashing", 5)) -- prints the "clashing" part of the score of segment 5		print(get_segment_score_part("clashing", 5)) -- prints the "clashing" part of the score of segment 5
	print(get_segment_score_part("bonding", 20, 30, 40)) -- prints the "bonding" part of the score of segment 20, segment		print(get_segment_score_part("bonding", 20, 30, 40)) -- prints the "bonding" part of the score of segment 20, segment

Lua Scripting

2009-11-21T07:02:45Z

← Older revision		Revision as of 07:02, November 21, 2009
Line 2:		Line 2:
	As you may know, the newest Fold-it update includes support for '''Lua Scripting'''. In very basic terms, '''Lua''' is a simple '''programming language''' that we can use to manipulate proteins and automate repetitive tasks -- much like we already do with the''' Cookbook'''		As you may know, the newest Fold-it update includes support for '''Lua Scripting'''. In very basic terms, '''Lua''' is a simple '''programming language''' that we can use to manipulate proteins and automate repetitive tasks -- much like we already do with the''' Cookbook'''

-	.[[File:Output.png\|thumb\|Running a script with output!]]	+	.[[File:Output.png\|thumb\|Running a script with output!]]

	A '''script '''is actually quite similar to a Cookbook recipe (as well as to a real-life recipe for say, a cake) -- it contains a series of '''instructions''' (called '''commands''') that tell Foldit what to do with your protein (just as a real-life recipe has step by step instructions about how to combine ingredients to create a cake!)		A '''script '''is actually quite similar to a Cookbook recipe (as well as to a real-life recipe for say, a cake) -- it contains a series of '''instructions''' (called '''commands''') that tell Foldit what to do with your protein (just as a real-life recipe has step by step instructions about how to combine ingredients to create a cake!)
Line 10:		Line 10:
	Lua scripting adds an exciting new layer of gameplay to Foldit!  Fortunately, lua is easy enough to learn that everyone can use it, even people who have never programmed or scripted before.  The best place to get started if you don't have any programming experience is to work through the [[Lua Scripting Tutorial (Beginner 1)]] (followed by [[Lua Scripting Tutorial (Beginner 2)]] and the upcoming [[Lua Scripting Tutorial (Beginner 3)]]		Lua scripting adds an exciting new layer of gameplay to Foldit!  Fortunately, lua is easy enough to learn that everyone can use it, even people who have never programmed or scripted before.  The best place to get started if you don't have any programming experience is to work through the [[Lua Scripting Tutorial (Beginner 1)]] (followed by [[Lua Scripting Tutorial (Beginner 2)]] and the upcoming [[Lua Scripting Tutorial (Beginner 3)]]

-	). If you're not interested in scripting yourself but just want to download and run other people's scripts, Beginner 1 is all you need!  But if you want to go a bit further and modify scripts and write your own, you can move onto Beginner 2 and 3.[[File:Multitool.png\|thumb\|Viewing code: Crashguard's Multitool script]]	+	). If you're not interested in scripting yourself but just want to download and run other people's scripts, Beginner 1 is all you need!  But if you want to go a bit further and modify scripts and write your own, you can move onto Beginner 2 and 3.[[File:Multitool.png\|thumb\|Viewing code: Crashguard's Multitool script]]

	If, on the other hand, you have some programming experience or want to get a quicker start, begin with [[Lua Scripting Tutorial (Intermediate)]].  This intermediate tutorial starts from the ground up and assumes no prior knowledge but moves through material at a more rapid pace, including basics about how to run and modify scripts as well as core programming concepts like looping and variables.		If, on the other hand, you have some programming experience or want to get a quicker start, begin with [[Lua Scripting Tutorial (Intermediate)]].  This intermediate tutorial starts from the ground up and assumes no prior knowledge but moves through material at a more rapid pace, including basics about how to run and modify scripts as well as core programming concepts like looping and variables.
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	[[Lua Scripting Tutorial (Advanced)]]		[[Lua Scripting Tutorial (Advanced)]]
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		+	[[Simplified List of Lua Commands]]

	[[Lua Export and Import of Scripts\|Lua Export and Import of Scripts using Text and HEX editor]]		[[Lua Export and Import of Scripts\|Lua Export and Import of Scripts using Text and HEX editor]]
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	== LUA INTERFACE ==		== LUA INTERFACE ==
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		+	For a version of this interface more appropriate for beginners, as well as code snippets, see the [[Simplified List of Lua Commands]].

Simplified List of Lua Commands

2009-11-21T06:01:20Z

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