
sebgg
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Latest (and probably final) version added to top post and to the Google code page. Now works as intended with APBS tools for measuring average external charge and size at the same time - documentation added as well. http://code.google.com/p/rotamol/ Cheers, Sebastian Eves-van den Akker. --------------------------------------------------------------- old downloads --------------------------------------------------------------------------- Attached File RotaMol v1.09 - Lite.au3 25.54KB 101 downloads Attached File RotaMol v1.09 - Lite.exe 456.81KB 16 downloads
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- RotaMol
- Sebastian Eves-van den Akker
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Uploaded a Download link to Google code page for this project where there will be Full .EXE download, as well as all documentation - tutorials - back versions, and a more in depth description of how it works. Changed electrostatics code to include percentage distributions - still need to add documentation on this though. Here: http://code.google.com/p/rotamol/ latest version should be on top Compatibility with some keyboard settings is not good. Currently working on French language keyboard compatibility - and while im at it to change the comments in the source/tutorial to French also. When finished will also upload this to the Google code page but probably not the source here. Got afew more ideas in the pipeline - will post when changes. Again any more suggestions of issues feel free to email me Cheers, Sebastian Eves-van den Akker.
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Couldnt say its not allowed in forum rules but wanted to check: want to post a link to my google code for back versions etc Cheers, Seb.
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yeah its laid out as i edited in the first post, but no there is no shift down commands, (on my english keyboard/system its all works with the numbers and not the other corresponding characters that I have above my numbers.) But I do know that on a french system, the number on the number keys is not the default option, and normally shift is needed to be pressed before they are sent. so maybe i need to add that before the send for any key that isnt a letter? will give this a try next if the ,1) didnt fix it. thanks again for all the help, Seb.
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thanks very much for the fast reply, I shall give this a try. cheers, Seb
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Hi, So send on some non-english language keyboards/computers is sending strange things, for example send("_") sends the number 8 not an undrscore etc, also sending send ("180") sends instead &_à where ona french keyboard the followign is true & é " ' ( - è _ ç à ) 1 2 3 4 5 6 7 8 9 0 ° had a search counldnt find an example - anyone know a fix to this? would sending the ascii code help? cheers, Seb.
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Recieved an Email from someone who had problems with compatability to an older veriosn of PyMOL. (0.99) If anyone else has compatability problems with older veriosns dont hesistate to let me know and Ill see what I can do. The version of RotaMol available here is for PyMol 1.3. Cheers, Sebastian Eves-van den Akker.
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Thanks for the information, I think the reason this has happened is PyMOL can be slow to load surfaces of some proteins. v1.09 is now up that will fix this problem. have added a separate load surface button which as far as I can see should solve this, simply click it first before starting the analysis (or load the relevant surface manually) -also added a feature to measure electrostatics. Thanks again, Sebastian Eves-van den Akker
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@ mat yep thats the basic idea, ive pretty much compiled the 3 x 30 million character lists now, so now thats done its just a case of getting words from my known words list to see how many in there. this tree idea looks really neat, never seen anything like it, will have a nosey. @ jchd so for codon replacement, stringregexp will maybe be tricky? as it wont keep frame. so for the string atgatgatgatgatg frame 1 would be atg atg atg atg atg so if i did stringregexpe for atg to "m" id get m m m m m perfect! but if i did for gat, it would totaly loose frame so i think going through it base by base may be needed here? have actually done this now but would be nice to know anyways of a faster method if you know it? regarding the searching words bit. my shortlist is just 240,000 words ( thanks GEOSoft! http://dundats.mvps.org/autoit/ (under miscelaneous) so my plan here was to just populate an array of the 240 k known words. and for each stringinstr back to the 30mil character string if no error then print word. then i was planning to trim down this list later on. now this for sure will be slow. so a better way will probably useing stringregexp as you said so will try this with mats idea. as far as shortening the short list. for sure that possible. ive ran my script on just the first 0.3% of the file and got up to 6-7 character words already. so i could cut everyuthing from the list shorter than that for sure. will do this now and have a look at the difference. cheers, seb
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advice to solve the problem once i stated what im up to, just like everyone else was doing. i know this project is just for fun, but i dont think the arrays im manipulating are useless. (as the only ones i can manipulate are the ones not too large for autoit) I havent been choosing functions at random, this code is to the best and all of my knowledge about autoit, to repeat, my choices were absolutly not random - i just dont know alot. Having read regexpreplace, i think that really will be usefull for finding the words thansk for that advice. to my knowledge not sure if i can use it do do all the translations? but ill look into it. really the main question was not really How can I find word patterns in a huge string, more best ways to manipulate very large strings. and for that i have some nice answers and have learned alot. apologies if i phrased it badly in the beginning/not at all. hope this has cleared everything up and thanks for the advice. oh and at the time i read youre reply, i interpreted everything in it, on face value, which may or maynot have been a mistake. it clearly was a missenterpretation but i cant assume everything posted on here is a work in progress and to wait for additional edits.
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ahh so i guess this is the problem code was simple $x = Fileread("contig.txt) $y = stringsplit ($x, "") but it dies what ive done is split the 112 million char list into 100 1.12 million char lists, and split these instead. using the code: for $i = 1 to 100 $origional = fileread ("cleaned contig99.txt") $string = fileread("cleaned contig99.txt" ,1121224) filewrite ("section " & $i & ".txt", $string) $new = stringreplace ($origional , $string, "") filedelete ("cleaned contig99.txt") filewrite ("cleaned contig99.txt", $new ) Next this starts slow but gets faster ofc, done in afew mins just for fun im translating a whole transcriptome (transcribed genome) and wanted to see the longest english word spelled out. just for fun mindso next code is to translate each peice into the 3 different frames, so 100 files becomes 300 files wih a 1/3rd less characters (will do reverse 3 later) using this (runnign currently) now this is a really slow one, but i expected it to be, #include <Array.au3> ; Script Start - Add your code below here ;$q7 = FILEREAD("1st frame.txt") $codontable = fileread("fasta codon.txt") ;$w7 = STRINGSPLIT ($q7 , @CR ) $1stframe = "" $2ndframe = "" $3rdframe = "" $x1 = 0 $1x = 0 $1xx = 0 $5x = 0 ;_arraydisplay ($w) ;$line1 = filereadline ("fasta codon.txt",$i+1) ;msgbox(1,"yesy", $line1) ;$x = stringsplit ($line1, " ") ;_arraydisplay ($x) global $arr[68][2] ;_arraydisplay ($arr) for $i = 0 to 67 $line1 = filereadline ("fasta codon.txt",$i+1) ;msgbox(1,"yesy", $line1) $x = stringsplit ($line1, " ") $arr[$i][1] = $x[2] $arr[$i][0] = $x[1] Next for $o = 1 to 100 $string = fileread("section " & $o &".txt") $split = stringsplit ($string , "") $frame = 0 $start =timerinit () for $i = 1 to $split[0]-5 $frame = $frame + 1 $codon = $split[$i] & $split[$i+1] & $split[$i+2] if $frame = 1 then for $u= 0 to 67 if $arr[$u][0] = $codon then $1stframe = $1stframe & $arr[$u][1] EndIf next elseif $frame = 2 then for $u= 0 to 67 if $arr[$u][0] = $codon then $2ndframe = $2ndframe & $arr[$u][1] EndIf next elseif $frame = 3 then for $u= 0 to 67 if $arr[$u][0] = $codon then $3rdframe = $3rdframe & $arr[$u][1] EndIf next $frame = 0 EndIf if $i >$split[0]/1000 and $x1 = 0 then tooltip("section " & $o & " 0.1% complete time : " & (timerdiff($start)/1000),0,0) $x1 = 1 EndIf if $i >$split[0]/100 and $1x = 0 then tooltip("section " & $o & " 1% complete time : " & (timerdiff($start)/1000),0,0) $1x = 1 EndIf if $i >$split[0]/10 and $1xx = 0 then tooltip("section " & $o & " 10% complete time : " & (timerdiff($start)/1000),0,0) $1xx = 1 EndIf if $i >$split[0]/2 and $5x = 0 then tooltip("section " & $o & " 50% complete time : " & (timerdiff($start)/1000),0,0) $5x = 1 EndIf Next $x1 = 0 $1x = 0 $1xx = 0 $5x = 0 filewrite ("translate/section " & $o & " - 1stframe.txt", $1stframe) filewrite ("translate/section " & $o & " - 2ndframe.txt", $2ndframe) filewrite ("translate/section " & $o & " - 3rdframe.txt", $3rdframe) $3rdframe = "" $2ndframe = "" $1stframe = "" next Next
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I need a List of All known english words.
sebgg replied to sebgg's topic in AutoIt General Help and Support
cheers geo, ill try with the updated word list youve got, thanks all for help Seb -
I need a List of All known english words.
sebgg replied to sebgg's topic in AutoIt General Help and Support
i went with this as it was longer than the one on your webpage, but combining them might add afew i have no idea. and yes 170k is far from complete but its a nice start for fun. http://homepage.ntlworld.com/adam.bozon/Dictionary.htm seb -
I need a List of All known english words.
sebgg replied to sebgg's topic in AutoIt General Help and Support
because then i wouldnt have the chance to chat to all you lovely people! thanks all for help. in the end went with a 17x,xxx word list space separated, perfect! sebs -
Pixelsearch making GUI VERY slow, please help!
sebgg replied to Mich9874's topic in AutoIt General Help and Support
Ive found this make a huge difference in performance _DwmEnable(False) Func _DwmEnable($WhatToDo) DllCall("dwmapi.dll", "long", "DwmEnableComposition", "uint", $WhatToDo) EndFunc cant remeber who i got it from but thanks to them not me if it helps seb -
So just a little project I want to do, see the longest/most frequent word in a massive (several billion characters) list of seemingly random letters. so need alist of known words to compare to. wondered if anyone has one compiled already or if anyone knows where i could get a hold of one? Cheers, Sebastian.
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v1.08 is up, Quite Alot of changes: - No need to do manual measurements anymore! its totaly automated calibration functions. - fixed a pause bug -cleaned up the use of globals in script a bit. apparently v1.06 had some issues starting on some computers, Have tested this version on multiple computers with different windows versions and no problems but let me know anyway. Seb.
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come to think of it, will it be faster just to measure the area which isnt protein, if i know the size of the box? (as proteins normally takes up more than half the screen)
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So the code is posted in my sig (or at least the bit which measures area hasnt changed) Doing each face doesent take 10 seconds, it takes a fraction of a second, but i do it for multiple faces, hence the increased time. I dont do multiple pixelsearches. i do 1 for top 1 for bottom. then for every pixel in that square i do pixelgetcolor as its faster. but if you know a way to map edges and work out the area inside without that im all ears. that would inc speed alot i imagine. not sure how to map edges but i can probably work something out. edit that out, dont think thats possible as the perimeter tells you very little about area (hope someone proves me wrong on this one) Seb
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basically this is solved, i mean i know its not possible to change the direction of pixelsearch in the way i like. and each analysis now takes <10 seconds on the heap of shit of a computer im working on at the moment. (normally < 3seconds) so in cutting the top and bottom of the search area off i did save some time, but i dont think there is any more to be saved from pixelsearch. seb edit: and i will upload the latest version once i re-write the instruction manual as ive managed to remove a whole bunch of steps which are now automated.
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well thats always a set color, and it depends what the user set it as, but usually black (default is black) ( the program checks before each protein is measured) seb
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Yes but to do this i would have to check every column of pixels starting from the middle out till i hit the farthest edge (either left and right). whihc would work. but thats what im already doing in order to count each pixel. so it wont save me any time to do it twice. and really diamond is such an oversimplification , they arent even close to that regular. think more like the shape when you shoot a paintball at a wall accept no where near as symmetical, proteins are often very asymmetrical.