Written by: Ira Ungerleider
Transcribed by: Eric Aasen
[Scene: Monica and Rachel's, the whole gang is there, the guys are watching football, the girls are cooking Thanksgiving dinner.]
The Guys: (reacting to a play) Yes! Yes! Yes! Yes! Awww!
Phoebe: Hey, its your Thanksgiving too, y'know, instead of watching football, you could help.
The Guys: We will. (they dont move)
Monica: Okay, Rachel, you wanna put the marshmellows in concentric circles.
Rachel: No Mon, you want to put them in concentric circles. I want to do this.
(Rachel sticks a marshmellow into Monicas nose. Monica takes it out of her nose by closing one nostril, and blowing.)
Monica: Every year.
Opening Credits
[Scene: Monica and Rachel's, continued from earlier.]
Phoebe: Y'know, for once, I am going to sit down and try to watch one of these things. (just as she sits down).
Ross: Halftime.

Rachel: Oh! That would be sooo much fun!
Phoebe: Oh, can I play too? Ive never played football, like ever.
Joey: Great, you can cover Chandler.
Chandler: No, no, no, I dont, I dont really wanna play.
Joey: Come on man! You never want to do anything since you and Janice broke up.
Chandler: Thats not true! I wanted to wear my bathrobe and eat peanut clusters all day. I wanted to start drinking in the morning. Dont say that I dont have goals!
Joey: Chandler, you have to start getting over her. All right, if you play, you get some fresh air, maybe itll take your mind off Janice, and if you dont play, everyone will be mad at you cause the teams wont be even. Come on.
Chandler: Yeah, all right, Ill play.
Phoebe: Yay!!
Rachel: Lets do it! Ross?
Ross: What?
Rachel: Do you wanna play football?
Ross: Um, Monica and I arent supposed to play football.
Joey: Says who? Your mom?
Monica and Ross: Yeah.
Monica: Well, every, every Thanksgiving um, we used to have a touch football game called the Geller Bowl.
Chandler: No, no, no, you say that proudly.
Monica: Anyway, Ross and I were always captains, and um, it got kindve competitive and one year, Geller Bowl VI, I accidentally broke Rosss nose.
Ross: It was soo not an accident.  And just keep running.
Monica: To score the winning touchdown, by the way.
Ross: Whoa, whoa, whoa, ho, ho, ho, you did not win the game, the touchdown didnt count, because of the spectacularly illegal, oh and by the way savage nose breaking.
Monica: (to Chandler and Joey) I won the game.
Ross: Oh yeah! Then how come you didnt get the Geller Cup?
Rachel: Um, there was a Geller Cup?
Ross: Yes, it was the trophy you got if you won the game. But our Dad said, nobody won that game, and he was sick of our fighting, so he took the trophy and.... (pauses to collect himself, as he is on the verge of tears saying this) threw it in the lake.
Chandler: And was the curse lifted?
Ross: Anyway. Thats when our Mom said we were not to play football ever again.
Monica: Y'know what, I think we should play a game. I mean come on, its been twelve years.
Ross: Can I see you for a second?
(they walk over to the sink and discuss it for a moment)
Monica: (shouting) Once!!
Ross: All right, were gonna play.
Chandler: But wait a minute though, how are we gonna get there, though, because my Mom wont let me cross the street.
[Scene: The Park, the gang is warming up for their football game.]
Monica: Okay. Lets bring it in.
Rachel: Wait no, honey, honey throw it to me, throw it to me.
Ross: Here you go. (throws her the ball)
Rachel: (knocking it down instead of catching it) That almost hit me in the face.
Joey: All right, we have to pick captains.
Chandler: And then Tineals.
Phoebe: Okay, so how do we decide that?
Monica: Well, why dont we just bunny up.
Rachel, Chandler, and Joey: What?
Monica and Ross: (holding both of their hands above their heads making rabbit ears with their fingers.) Bunny!
Monica: Okay, looks like Ross and I are captains. Okay, so um, I bunnied first so that means I get to pick first. Joey.
Joey: Thank you.
Rachel: Monica, Im your best friend.
Ross: Sweetie, dont worry youll get picked. Chandler.
Rachel: Ross!
Monica: Phoebe.
(Phoebe kisses Rachel on the cheek, then joins her team.)
Ross: Sweetie, now I pick you.
Rachel: You dont pick me! Youre stuck with me!
Ross: Okay. All right. So lets see, lets play from the trash can, to the lightpost. Right. Two hand touch, well kick off.
Monica: All right people listen, Ive got exactly twenty-eight minutes before I have to baste again.
Chandler: Wow! Just like in the pros.
Monica: Huddle up.
Joey: (to his team) All right, huddle up, right over here.
Phoebe: Wait for me! Wait for me! Wait for me! Oh cool, this is my first huddle.
Monica: Okay.
Phoebe: Okay, so what do you guys really think of Chandler?
Monica: Okay, Phoebe you know what youre doing right?
Phoebe: Yeah.
Monica: Okay, Joeys gonna catch it, and you and I are gonna block.
Phoebe: Whats block?
Monica: Phoebe, I thought you said you know what youre doing?
Phoebe: I thought you meant in life.
Monica: Break.
(Chandler is getting ready to kick off, Ross is holding the ball between his foot and finger.)
Chandler: The ball is Janice. The ball is Janice. (goes to kick the ball but kicks Rosss foot instead.)
Ross: Oww!! Son of a...!! Ow! Come on!
Chandler: Sorry. Im sorry. Y'know what, were just gonna throw it.
(Chandler throws the ball to kick-off.)
Joey: I got it. (catches the ball)
Phoebe: Go! Go! Go!
(Joey runs up field and fakes out Ross and scores a touchdown. His team all celebrates the touchdown.)
Monica: Score!! 7 to nothing!
Rachel: (coming over to Ross, who is just getting up) Are you okay?
Ross: Come on, lets go!
Monica: Losers walk!
Ross: Yeah, losers talk!
Chandler: No, no, no, actually losers rhyme.
[cut to later, Rosss team has the ball.]
Chandler: (coming up under center, just like a real quarterback does, and puts his hands between Rosss legs.) Twenty-three!! Seventy-four!! (Ross stands up and looks at him) You wanna go shotgun?
Ross: Yeah!
Chandler: (from the shotgun) Hike!
Monica and Joey: One-Mississippi. Two-Mississippi. Three-Mississippi.
(Rachel runs a quick slant.)
Rachel: Over here!
(Chandler throws her the ball, which she drops.)
Rachel: (proud of her self) I almost caught that one!
Chandler: Great! Now, the score is 7 to almost 7.
Ross: Okay, (to Chandler) this play, I want you to do a down and out to the right. Okay. Break!
Rachel: Wait, what am I gonna do?

Rachel: Wait, how long?
Ross: Until we start to look very small.
Rachel: Okay.
Ross: Break!!
[cut to later, Monicas team has the ball.]
Joey: Set....hike!
Ross: One-Mississippi, two-Mississippi, switch! Switch! Switch!!
Chandler: No, no, no, no, no!
(Monica throws the ball over Joeys head, its stopped from rolling away by a very beautiful woman.)
Joey: Haaaaa! Hey-hey, thanks for stopping our ball.
Woman: (in a foreign accent) You are playing American football?
Joey: Yeah! Wow, your like from a whole other country.
Woman: Im Dutch.
Joey: Hi-hi, Im Joey.
Woman: Im Margha.
Joey: Im sorry Dutch, I didnt get that last little bit.
Chandler: (running up) Hey Joey, do you wanna play football or you wanna.. (sees Marhan) Hi, Im Chandler.
Margha: Hello, Chandler.
Joey: Her name is Dutch, and also Marklan.
Margha: Margha.
Joey: Mar-klan.
Margha: Mar-gha.
Chandler: Mar-haaaan.
[cut to Ross and Monica.]
Monica: Come on guys! Lets go! Come on, its second down.
Ross: Uh, hello, its third down.
Monica: No its not, its second.
Ross: Wow!
Monica: Wow, what?
Ross: It just amazes me that your still pulling stuff like this.
Monica: Pulling what? Its second down.
Ross: Okay, its second down. (turns away) Take all the second downs you need.
Monica: I heard that!
Ross: Well, I said it loud.
[cut to Chandler, Joey, and Margha.]
Margha: It is okay, if I stay and watch?
Chandler and Joey: Yeah!  You can sit right there.
(she goes and sits down)
Chandler: Well, that went well.
Joey: I think so.
Chandler: Y'know, I was thinking about ah, asking her for her number.
Joey: Thanks man, but I think it makes a stronger statement if I ask for it myself, y'know.
Chandler: Whoa-ho, whoa! No, I was thinking about y'know for me, as a part of that whole getting over Janice thing you were talking about.
Joey: Oh, yeah, that. All right, means that much to ya, Ill let you have her.
Chandler: Thanks. What, let me have her?! What do mean? Like if you didnt I wouldnt have a shot?
Joey: Well I dont like to say it out loud, but, yeah! Dont feel bad man, we all have our strengths. Youre better with numbers and stuff.
Chandler: Math!! Youre giving me math! All right, look y'know what, forget about it, you go for the girl, well see who gets her.
[cut to later, in Rosss huddle.]
Ross: Chandler, I want you to run a post pattern to the left, okay. And sweetie..
Rachel: Yeah, I know, go long. Y'know, its like all Im doing is running back and forth from the huddle.

Rachel: Can I see that for second.
Ross: Yeah.
(Rachel takes the ball from his hands and bounces it off of Rosss forehead and Chandler catches the rebound.)
Ross: Okay. Hut! Hike!
(Chandler runs around behind Ross, who pitches him the ball. Chandler runs upfield, and Joey knocks the ball out of his hands.)
Joey: Fumble!
(Joey starts to return the fumble and Chandler grabs Joeys shirt and rips it off of his back.)
 This is my favourite jersey.
Chandler: Well now you have two. Hey, I am good at math.
Joey: All right, thats it. Y'know I was still gonna let you have her. But now, forget about it. Prepare to feel very bad about yourself.
Chandler: Hey! Well, Ive been preparing for that my entire life! Or something about you thats mean!
Monica: All right, come on guys, lets go! Tie score, and were runnin out of time. Forty-two!! Thirty-eight!! Hike! (the timer sounds as Monica throws the ball to Phoebe.)
Phoebe: Oh I got it!! (catches the ball) Oh! Ew! Broken boob! Ow!
Joey: Pheebs, run!
Monica: Run, Phoebe, run!
(Phoebe runs and scores a touchdown.)
Phoebe: Touchdown!! Touchdown!!
Ross: Uh, hello, the buzzer buzzed. It doesnt count.
Monica: After the snap!
Ross: Before the snap!
Joey: After!!
Chandler: Before!!
Rachel: Now, does it really matter?
All: Yes!!
Phoebe: Well, okay, I made a touchdown. It was my first touchdown. So?
Ross: Oh Pheebs, thats great. It doesnt count.
Monica: Does so count!
Ross: Cheater, cheater, compulsive eater.
Phoebe: Oh my God!
Monica: Y'know what, thats fine, maybe you havent grown up, but I have.
Ross: Oh-ho, okay.
Monica: Dead leg!! (kicks him in the thigh.)
Ross: Ow! Ow! Okay, okay, fine, fine! All right, you wanna win by cheating, go ahead, all right. Phoebe the touchdown does count, you win.
Phoebe: Woo-yay!!
Monica: No!  Just once I wanna beat when you cant blame it on the broken nose, the buzzer, or the fact that you thought you were getting mono. Lets just call this, tie score and its halftime.
Ross: Okay, first of all, I dont play with cheaters, and second of all, you know I had swollen glands!!
Monica: Y'know what? Ill think youll play.
Ross: Oh really! Why is that?
[cut to Monica and Rachels.]
Monica: Because the winner gets this!
Ross: The Geller Cup.
Chandler: Is everybody else seeing a troll doll nailed to a two by four?
All: Yeah.
Chandler: Okay, good.
Commercial Break
[Scene: The park, the gang is returning to play the second half of the game.]
Ross: Okay, where in the hell did you get that?!
Monica: When Mom and Dad drove you to the hospital to get your nose fixed, I swam into the lake and fished it out.
Ross: That cup is mine!
Monica: No its not!
Rachel: All right, so are we not having dinner at all?
Monica: Come on Phoebe, lets go!  Joey, keep your head in the game.
Joey: Its hard, y'know, his huddle is closer to Dutch girl.
Monica: All right look, if I take Chandler out of the running will you be able to focus?
Joey: What are you gonna do?
Monica: All right, you just make sure that Chandler catches the ball, Ill take care of the rest.
Joey: Okay.
Monica: Break!
Joey: Here you go!
(Joey throws the ball to Chandler)
Ross: Chandler! Chandler!
(Chandler catches the ball and starts to run upfield.)
 Whoa!! Tackled by a girl! Bet ya dont see that everyday, do ya?
Ross: Whoa! Whoa! Whoa! Whats with the tackling?
Monica: What?! I just touched him and he went over.
Ross: Okay, you wanna play rough, we can play rough.
(They both stare each other down as we hear Lets get ready to r-r-r-rum-ble!!!)
(A long football sequence follows.)
[Sequence 1: Monica throws the ball over Chandlers head to Joey who catches it for a touchdown, and starts to dance in celebration. Chandler then tackles him, and he starts to dance in celebration.]
[Sequence 2: Monica runs upfield and stops, waiting for a pass. Ross runs over and pulls her pants down, steps in front of her and intercepts the pass.]
[Sequence 3: Chandler throws a pass to Ross, who catches it. Phoebe starts screaming and runs up to him and tries to tackle him. But all she ends up doing is running around his waist and screaming.]
[Sequence 4: Ross hikes the ball to Chandler, and the camera pans down to show Rachel standing deep in the end zone, playing with her gum. Something hits her on the head and she looks up to see where it came from.]
[Sequence 5: Monica hands the ball off to Phoebe, who runs up field and delivers a fore-arm shiver to Chandler, knocking him over and scores the touchdown, and she yells...]
Phoebe: I love this game!!
[cut to Ross who walks up to Rachel who is eating a baked pretzel.]
Ross: Hey, whered you get that?
Rachel: I went really long.
Monica: Forty-two to twenty-one! Like the turkey, Ross is done!
Ross: Its no surprise that your winning, cause you got to pick first, so you got the better team.
Monica: Youre so pathetic!
(Ross makes a Yeah. Right. sound.)
Monica: Oh, what a great argument, exhaling! All right, y'know what, Ill prove it to you, okay. Ill trade you Joey for Rachel, and Ill still win the game.
Ross: What?! The guys against the girls? See, thats ridiculous Monica, because Im only down by three touchdowns.
Monica: Oh, then bring it on!
Ross: Fine, fine, Rachel your with Monica, Joey youre with me.
Rachel: I can not believe your trading me!!
Monica: Come on Rach, come on. Lets see whats it like to be on a winning team for a change.

Monica: All right then.
[cut to the guys team.]
Margha: (coming over) The game is over, we eat now?
Chandler: No-no-no-no, the games not over, were just switching teams.
Joey: Yeah, Chandler finds me so intimdating that its better if were on the same team.
Ross: Right. Okay, lets play. Lets go.
Chandler: No ah, hold on a second Joe, where do Dutch people come from?
Joey: Ah well, the ah, Pennsylvania Dutch, come from Pennsylvania.
Chandler: And the other ah, Dutch people, they come on from somewhere near the Netherlands, right?
Joey: Nice try. (to Margha) See the Netherlands is this make believe place where Peter Pan and Tinker Bell come from.
Margha: Oh, my.
Ross: Enough with geography for the insane, okay? Lets play some ball, guys.
Joey: Whoa, whoa, no, no, I-Im not playing with this guy, now.
Chandler: Fine with me.
Ross: Okay, y'know what, lets just cut to the chase here. Okay? Heidi, which of my boys do you like?
Chandler and Joey: What are you doing? What are you doing? What are you doing?
Margha: Which do I like?
Ross: Yeah, y'know for dating, general merriment, taking back to your windmill...
Margha: Well, if I had to chose right now, which by the way I find really weird, I would have to say, Chandler.
Chandler: Yes!!
Joey: Wait a minute! Wait a minute! She obviously didnt understand the question.
Chandler: Well, you dont you have Captain Hook explain it to her.
Margha: Im sorry, Joey, that is my chose.
Chandler: You hear that! That is her chose, mister Ill let you have her! I win!  I rule all! A mini-wave in celebration of me!! (does the wave.)
Margha: Im now thinking I would like to change my answer to, no one.
Chandler: Wh-what?
Margha: I now find you shallow and um, a dork. All right, bye.
Joey: Nice going.
Chandler: Y'know what, it doesnt matter, cause she picked me. Me! From now on I get the dates and you have to stay home on Saturday nights watching Ready, Set, Cook!
Ross: Save the breakthroughs for therapy, okay. The clock is ticking. We have no time, and we are losing, we are losing to girls.

Ross: Hey! Its 42-21!
Joey: This sucks, I was just up by that much!
Monica: Are we playing football or what? Come on you hairy-backed Marries.
[cut to the girls huddle.]
Monica: We have to do this. We are playing for women everywhere. Okay, just think about every lousy date that you ever had, okay, every guy who kept on the TV while youre making out...
Phoebe: Oh my God! You dated someone with a glass eye too?!

Rachel: Yeah!!! Kill um!!!

(Another football sequence follows)
[Sequence 1: Chandler is running past Phoebe with the ball, Phoebe flashes him, he stops and stares dumbfounded at her. Phoebe then runs up and takes the ball away.]
[Sequence 2: Phoebe throws the ball, and its intercepted by Joey, who starts to run up field. Rachel jumps on his back in order to try and tackle him, but she doesnt slow him down. Monica and Phoebe then both grab her legs in order to stop Joey, who still manages to fight through the tackle and score the touchdown.]
[Sequence 3: Chandler is running with the ball, Phoebe flashes him again, but Chandler covers his eyes, and keeps running. He then runs into a tree at the end of the field.]
[cut to the girls huddle]
Monica: All right, we still have a minute and a half to go, and were down by two points. Two points.... (she gets interrupted by the guys, who are doing a slow-motion high five.) Phoebe you do a button-hook again. Rachel, you go long.
Rachel: No! Come on!  Use me. They never cover me.
Monica: Honey, theres a reason.
Rachel: God, Im not lame, okay. I can do something.
Phoebe: Come on Mon, let her throw the ball.
 All right. Break.
Rachel: Thank you! Break!
Monica: Thirty-two! Seventy-one! Hike!
(Phoebe snaps the ball to Monica, who pitches back to Rachel.)
The Guys: One-Mississippi! Two-Mississippi! Three-Mississippi!
(They all rush toward Rachel, who panics and runs away. She runs out of the park and up along the fence, she then comes back into the park and runs past Monica, as she gets to Monica, she throws the ball at Monica, and it hits her in the eye.)
Rachel: Im so sorry! Are you okay?
Monica: No! Im not okay!
Rachel: Im sorry, they were just all coming at me, and I didnt know what to do.
Joey: (looking at the timer) Thirty seconds left on the timer!

Monica: Come on! Come on! Hurry! Were running out of time! Huddle up!
Phoebe: Okay. Oooh! Oh, this is our last huddle, yeah.
Monica: All right, Phoebe get open. Rachel, go long.
Rachel: (on the verge of tears) Okay.
Monica: Break!
(In slow motion, Phoebe snaps the ball, Rachel goes long. Joey and Chandler and all over Phoebe, leaving Rachel wide open. Ross starts to rush Monica, who sees Phoebe is double covered, in desperation she throws to Rachel. We see flying through the air, and then Rachel running underneath it, then the ball, then Rachel again, then the ball, then Phoebe, Chandler, and Joey staring at it in shock. Then with the grace of Jerry Rice (no offense to Jerry Rice), Rachel catches the ball, and she stops and spikes the ball. Both Phoebe and Monica erupt in celebration.)
Rachel: (in triumph) I got a touchdown! We did it!!
Chandler: Hey-hey-hey Rachel, funny thing. Actually, the ah, end zone starts at that pole, so youre five feet short, so we win!
Phoebe: Wait-wait-wait-wait! So, explain something to me though, if, if nobody tagged Rachel, then isnt the play still going.
(they all start to dive for the ball and Monica and Ross grab it at the same time.)
Ross: Let go! Let go!
Monica: Let go!
Chandler: Guys! Guys! Come on! Its Thanksgiving, its not important who wins or loses. The important thing is, (to Joey) the Dutch girl picked me! Me! Not you! Holland loves Chandler! Thank you, Amsterdam! Good night!!
Monica: Ow!!
Closing Credits
[Scene: Monica and Rachel's, Rachel, Phoebe, Chandler, and Joey are eating Thanksgiving dinner.]
Rachel: We should defiantly play football more often. Maybe theres a like league we could join or something.
Phoebe: Isnt there a national football league.
Chandler: Yes. Yes, there is, they play on Sundays and Monday nights.
Rachel: Oh shoot! I work Monday nights.
Phoebe: Umm, this stuffing is amazing. Do you think we should bring them some?
Joey: When theyre hungry enough, theyll come in.
[Scene: The park, its dark outside and Monica and Ross are still fighting over the ball.]
Monica: Let go!
Ross: No! You let go!
Monica: No!
Ross: How come its always us left in the field holding the ball?
Monica: I dont know. I guess the other people just dont care enough.
(It starts snowing.)
Ross: Hey! Its starting to snow.
(They both look up, and watch it start to snow. Then they both start fighting for the ball again.)
Ross: Gimme the this!
Monica: Let go!
End


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This particular feature (or bug fix, depending on your perspective) may not look all that big or exciting but it made a big difference to my life. Life is better when we limit the 'garbage in' to any system!


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pybilt.bilayer_analyzer package¶
Submodules¶
pybilt.bilayer_analyzer.analysis_protocols module¶
Analysis Protocols
This is a support module that defines a set of classes used to contruct the ‘analysis protocol’ and the ‘analysis’ used in the anlysis implemented by the pybilt.bilayer_analyzer.bilayer_anlayzer.BilayerAnalyzer class. The AnalysisProtocol is the class used to organize and initial the the individual analysis functions/protocols. The individual analysis functions/protocols are derived classes of AnalysisProtocol, and the availabel analysis can be extended by simply defining a new protocol. .. rubric:: Example
# define a new analysis ‘my_analysis’ # add it to the valid_analysis list valid_analysis.append(‘my_analysis’) #add it to analysis_obj_name_dict dictionary with the buildable object (e.g. mda_frame) needed for the analysis. #The buildables are built by the bilayer analyzer and can accessed from it for the analysisanalysis. analysis_obj_name_dict[‘my_analysis’] = ‘mda_frame’ class MyAnalysisProtocol(AnalysisFunctionProtocol):
#minimal def the __init__ and run_analysisfuncions def __init__(self, args):
#define the initialization#The run_analysis function should always take three inputs # of data that is passed in from the BilayerAnalayzer instance # that owns this instance of an analysis protocol. The values are: # ba_settings = BilayerAnalyzer.settings –> The adjustable # settings dictionary which contains data like ‘lateral’, and # ‘norm’. # ba_reps = BilayerAnalyzer.reps –> The dictionary container of # frame representations. e.g. ‘com_frame’ and ‘lipid_grid’ # ba_mda_data = BilayerAnalyzer.mda_data –> An MDAData instance # that contains data like the MDAnalysis universe, trajectory, # bilayer_selection, etc. def run_analysis(self, ba_settings, ba_reps, ba_mda_data):
#............. #doing my analysis #................ return#redefine any other functions from AnalysisProtocol or add new ones.
-
class
pybilt.bilayer_analyzer.analysis_protocols.
ALDProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
APLBoxProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
APLGridProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
Analyses
(analysis_commands)[source]¶ Bases:
object
A class to facilitate analysis of the bilayers via the BilayerAnalyzer
This object stores all the analyses that are being performed by the BilayerAnalyzer class, and it provides functionality to add and remove analyses.
-
use_objects
¶ dict – A dictionary of buildable objects that need to be contructed in the BilayerAnalyzer for the analysis defined in this protocol.
-
in_commands
¶ list – A list of the input strings for the analysis to be used.
-
arguments
¶ list – A list of the arguments for analysis.
-
analysis_keys
¶ list – A list of the keys assigned to analysis.
-
command_protocol
¶ dict – A dictionary of the analysis objects.
-
analysis_ids
¶ list – A list of the ids assigned to analysis.
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n_commands
¶ int – The number of initialized analysis.
-
add_analysis
(inputs)[source]¶ Used to add a new analysis to the internal set of analyses
Parameters: inputs (str, list, tuple, or dict) – The input to parsed for the type of analysis and its settings to be added to set of analyses.
-
dump_data
(path=None)[source]¶ Calls the individual save_data functions of each AnalysisProtocol.
Parameters: path (str, Optional) – The string path where output files should be dumped to disc.
-
-
class
pybilt.bilayer_analyzer.analysis_protocols.
AnalysisProtocol
(args)[source]¶ Bases:
object
Base class for analysis protocols.
-
analysis_key
¶ str – The key name of this analysis.
-
analysis_id
¶ str – The unique id assigned to this analyisis.
-
save_file_name
¶ str – The path and filename for the pickle file output of this analysis’ results.
-
settings
¶ dict – A dict of the internal settings of the analysis.
-
analysis_output
¶ list or list like – Used to store the ouptut of this analysis during the frame loop.
-
run_analysis
(ba_settings, ba_reps, ba_mda_data)[source]¶ Performs the analysis that this protocol represents for the current frame in the external BilayerAnalyzer’s run_analysis function.
Parameters: - ba_settings (dict) – The settings stored in the external BilayerAnalyzer instance.
- ba_reps (dict) – The representation objects stored in the external BilayerAnalyzer instance.
- ba_mda_data (MDAData instance) – The instance of MDAData stored in the external BilayerAnalyzer instance.
-
-
class
pybilt.bilayer_analyzer.analysis_protocols.
AreaCompressibilityModulusProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
AreaCompressibilityProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
BTGridProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
DCClusterProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
DispVecCorrelationProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
DispVecNNCorrelationProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
DispVecProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
FlipFlopProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
HalperinNelsonProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
LateralOrientationAngleProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
LateralOrientationParameterProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
LipidCollinearityProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
LipidLengthProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
LipidTiltProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
MSDMultiProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
MSDProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
MassDensProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
NDCorrProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
NNFProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
class
pybilt.bilayer_analyzer.analysis_protocols.
VolumeCompressibilityModulusProtocol
(args)[source]¶ Bases:
pybilt.bilayer_analyzer.analysis_protocols.AnalysisProtocol
-
pybilt.bilayer_analyzer.analysis_protocols.
word_list_to_string
(word_list, delimeter=' ')[source]¶ Creates a single string from a list of strings
This function can be used to combine words in a list into one long sentence string.
Parameters: - word_list (list/tuple) – A list (or other container) of strings.
- delimeter (str, Optional) – A string to delimit the strings in the list when combining the strings.
Returns: A string.
pybilt.bilayer_analyzer.bilayer_analyzer module¶
The bilayer_analyzer module.
This module defines the BilayerAnalyzer class that can be used to build protocols for analyzing and generating plots for the analysis of a lipid bilayer trajectory.
Example
>> import pybilt.bilayer_analyzer as ba >> analyzer = ba.BilayerAnalyzer(input_file=”setup.in”) >> analyzer.run_analysis() >> analyzer.dump_data() >> analyzer.save_all_plots()
-
class
pybilt.bilayer_analyzer.bilayer_analyzer.
BilayerAnalyzer
(structure=None, trajectory=None, selection=None, input_file=None, input_dict=None)[source]¶ Bases:
object
An object used to implement analyses of the (quasi-)planar bilayers.
This object is used build and implement analysis protocols for quasi-planar lipid bilayer systems. This object currently uses MDAnalysis as the backend for trajectory manipulation.
-
settings
¶ dict – A dictionary of adjustable settings for the analyzer. The dictionary is keyed by setting names and the setting values are stored at that setting key. The following is a list with descriptions of the settings keys:
- frame_range (list): A three element list containing the range
- of frames and the skipping interval for the analysis (i.e. which frames to include in the loop over the trajectory). Structure: [first_frame, last_frame, interval] Default: [0, -1, 1]
- print_interval (int): Set the frame loop interval/frequency for
- outputting some log data to the screen/std out. Default: 5
- norm (int): An integer representing the index of 3 element xyz
- coordinate arrays for the bilayer normal dimension. Default: 2, or the z-dimension/axis
- lateral (list): A two element list of integers representing the
- indices of 3 element xyz coordinate arrays for the bilayer lateral dimensions. Default: [0, 1], or the xy plane.
- normal_dimension (str): A string representing the bilayer’s
- normal dimension (i.e. ‘x’, ‘y’, or ‘z’). This setting corresponds to the ‘norm’ setting by the transformation (‘x’, ‘y’, ‘z’) => (0, 1, 2). Default: ‘z’
- lateral_dimension (str): A string representing the bilayer’s
- lateral dimensions (i.e. ‘xy’, ‘yz’, ‘xz’, etc.). This corresponds to the ‘lateral’ setting by the transformation (‘x’, ‘y’, ‘z’) => (0, 1, 2). Default: ‘xy’
- frame_index (int): An integer used to store the index of the
- current frame in the trajectory during the analysis loop.
-
reps
¶ dict – A dictionary of used to store the different bilayer representations used by the different analyses. The dictionary is keyed by representation names and the representation objects (if used) are stored at that key after construction. The following is a list with descriptions of the rep keys:
- current_mda_frame (MDAnalysis–>Timestep): This key is used to
- store a copy of the current frame from the MDAnalysis trajectory and constitutes the “all atom” representation of the bilayer.
- com_frame (pybilt.bilayer_analyzer.com_frame.COMFrame): This
- key is used to store an instance of the COMFrame object for the current frame during the analysis loop and represents the reduced dimension “centers-of-mass” represetation of the bilayer. i.e. each lipid (or selection from each lipid) is reduced to a single particle located at its center of mass.
- leaflets: (dict of pybilt.bilayer_analyzer.leaflet.Leaflet):
- This key stores a copy of a dictionary containing the Leaflet objects used to store the data about which lipids are in each of the bilayer leaflets. It has the keys ‘upper’ and ‘lower’, which correspond to the upper and lower leaflets of the bilayer respectively.
- lipid_grid (pybilt.lipid_grid.lipid_grid.LipidGrids): This key
- stores a copy of the LipidGrids object for the current frame of the trajectory in the (analysis) loop and represents the “lipid grid” (or GridMAT-MD style) version of the bilayer. i.e., the lipids of each leaflet are mapped /assigned to a 2-dimensional grid (or matrix). There are two grids, one for each leaflet of the bilayer.
- vector_frame (pybilt.bilayer_analyzer.vector_frame.VectorFrame):
- This key is used to store an instance of the VectorFrame object for the current frame during the analysis loop and represents the “lipid vectors” represetation of the bilayer; i.e. each lipid in the bilayer is represented by a vector.
- first_com_frame (pybilt.bilayer_analyzer.com_frame.COMFrame):
- This key is used to store an instance of the COMFrame object for the first frame during the analysis loop and represents the reduced dimension “centers-of-mass” represetation of the bilayer. i.e. each lipid (or selection from each lipid) is reduced to a single particle located at its center of mass.
-
rep_settings
¶ dict – A dictionary of adjustable settings for representatiion used by the analyzer (as stored in the reps dictionary). The dictionary is keyed by rep names and the setting values are stored in a dictionary at that rep name key. The following is a list with descriptions of the rep_settings keys and the subsequent setting keys:
- rep_settings key:setting key (value type): Description and
- Default value. Corresponds to
- –> rep_settings[‘rep_settings key’][‘setting keys’]
- com_frame:dump (bool): A boolean that is used to determine if the
- COMFrame objects should be dumped to disc as a pickle file after each iteration of the analysis loop. Default: False
- com_frame:dump_path (str): A string containing the file path for
- where COMFrame objects are to be dumped. Default: ‘./’
- com_frame:name_dict (dict): A dictionary keyed by residue names of
- specific lipid types and containing a list of atom names to be used when computing the centers-of-mass of lipids of that type. Default: None
- leaflets:dump (bool): Determines whether the leaflets are dumped
- to disc (as pickles) after each frame in the analysis loop. Default: False
- leaflets:dump_path (str): A string file path for where the
- leaflet object dictionaries are dumped. Default: ‘./’
- leaflets:update_interval (int): Determines how ofter to update the
- leaflet assignments. Default: 1, or every frame.
- lipid_grid:dump (bool): Determines wheter the LipidGrids objects
- built during interations of the analysis loop are dumped to disc as pickle files. Default: False
- lipid_grid:dump_path (str): A string containing the path where
- dumped LipidGrids should be written. Default: ‘./’
- lipid_grid:nxbins (int): An integer defining the number of bins to
- use in the ‘x’ dimension of the LipidGrid objects. Default: 10
- lipid_grid:nybins (int): An integer defining the number of bins to
- use in the ‘y’ dimension of the LipidGrid objects. Default: 10
- vector_frame:dump (bool): Determines wheter the VectorFrame objects
- built during interations of the analysis loop are dumped to disc as pickle files. Default: False
- vector_frame:dump_path (str): A string containing the path where
- dumped VectorFrame objects should be written. Default: ‘./’
- vector_frame:ref_atoms (dict): A dictionary of the atom names of
- atoms to be used to compute the vector each lipid type. The dictionary should be keyed by the resname of the lipid types. For each lipid type there should be dictionary with the keys ‘start’ and ‘end’ with lists of the atom names to use when determining the start and end of the vector respectively. Default: None. Example: rep_settings[‘ref_atoms’] = {‘DOPE’:{‘start’:[‘P’], ‘end’:[‘N’]}}
-
add_analysis
(analysis_in)[source]¶ Add a analysis to the analysis protocol. :Parameters: analysis_in (str, list/tuple, or dict) – The inpute defining the
analysis key, analysis id, and settings for the new analysis.
-
add_plot
(plot_string)[source]¶ Add a new plot to the plot protocol. :Parameters: plot_string (str) – A string with the plot key, id, and arguments.
-
static
available_analysis
()[source]¶ Returns the available analysiss. :returns: A list of string keys corresponding to the available
analysis.Return type: (list)
-
static
available_plots
()[source]¶ Returns the list of the keys of the available plot types.
Returns: A list of string keys for available plot types. Return type: (list)
-
generate_plot
(plot_id)[source]¶ Generate the plot image file (.eps) for the specified plot. :Parameters: plot_id (str) – The string plot id for the plot generate.
-
get_analysis_data
(analysis_id)[source]¶ Return the analysis output for the specified analysis. :Parameters: analysis_id (str) – A string analysis id.
Returns: - The analysis output of the specified analysis. The
- type/structure will depend on the analysis.
Return type: Variable
-
get_analysis_ids
()[source]¶ Return the ids of currently initialized analysiss in the analysis protocol. :returns: A list string analysis ids. :rtype: (list)
-
get_plot_ids
()[source]¶ Return the ids of the plots in the plot protocol.
Returns: - A list of string plot ids that have been initialized in
- the plot protocol.
Return type: (list)
-
next
()[source]¶ Runs the analysis as an iterator. The function performs the loop over the trajectory. At each frame it builds the necessary objects (e.g. COMFrame) and then executes the analysis of each analysis that was initialized in the setup.
Parameters: - nprocs (int) – An integer specifying the number of cores to use in
- multithreaded parallelelization.
-
parse_input_script
(input_script_name)[source]¶ Parses input setup scripts. :Parameters: * input_script_name (str) – A string with the file path and name of
- the input script to be parsed.
Returns: - A dictionary containing lists of commands for each type of
- command key (e.g. analysis, plot, etc.).
Return type: (dict) Raises: RuntimeError
– A runtime error is given if there is an invalid command key in the input script. A runtime error is also raised if the required commands are not provided in the input script.
-
remove_analysis
(analysis_id)[source]¶ Remove a specified analysis from the comptue protocol. :Parameters: analysis_id (str) – The string analysis id of the analysis to be
removed from the protocol.
-
remove_plot
(plot_id)[source]¶ Remove the specified plot from the protocol. :Parameters: plot_id (str) – Plot id of the plot to be removed.
-
run_analysis
()[source]¶ Runs the analysis. The function performs the loop over the trajectory. At each frame it builds the necessary objects (e.g. COMFrame) and then executes the analysis of each analysis that was initialized in the setup.
Args:
-
run_analysis_mp
(nprocs=1)[source]¶ Runs the analysis. The function performs the loop over the trajectory. At each frame it builds the necessary objects (e.g. COMFrame) and then executes the analysis of each analysis that was initialized in the setup.
Parameters: - nprocs (int) – An integer specifying the number of cores to use in
- multithreaded parallelelization.
-
set_dump_com_frame
(on=True, path='./')[source]¶ Turn on (or off) the dumping of COMFrame objects built during analysis. :Parameters: * on (bool, optional) – Defines whether the COMFrame objects should be
dumped (as pickle files) after each frame in the analysis loop. Defaults to True- path (str, optional) – Sets the path where the COMFrame objects are dumped. Defaults to ”./”
-
set_dump_leaflet
(on=True, path='./')[source]¶ Turn on (or off) the dumping of leaflet objects built during analysis. :Parameters: * on (bool, optional) – Defines whether the COMFrame objects should be
- dumped (as pickle files) after each frame in the analysis loop.
- Defaults to True
- path (str, optional) – Sets the path where the COMFrame objects are dumped. Defaults to ”./”
-
set_dump_lipid_grid
(on=True, path='./')[source]¶ Turn on (or off) the dumping of LipidGrid objects built during analysis. :Parameters: * on (bool, optional) – Defines whether the COMFrame objects should be
dumped (as pickle files) after each frame in the analysis loop. Defaults to True.- path (str, optional) – Sets the path where the COMFrame objects are dumped. Defaults to ”./”
-
set_frame_range
(first=0, last=-1, interval=1)[source]¶ Set the frame range and interval to use in the analysis. :Parameters: * first (int) – The first frame.
- last (int) – The last frame.
- interval (int) – The interval to skip between frames in the analysis loop.
-
-
pybilt.bilayer_analyzer.bilayer_analyzer.
print_analysis_settings
(analysis_key)[source]¶ Print to std out the adjustable settings of analyses available to the BilayerAnalyzer.
-
pybilt.bilayer_analyzer.bilayer_analyzer.
print_available_plots
()[source]¶ Print to std out the valid plotting protocols available to the BilayerAnalyzer.
pybilt.bilayer_analyzer.com_frame module¶
-
class
pybilt.bilayer_analyzer.com_frame.
COMFrame
(mda_frame, mda_bilayer_selection, unwrap_coords, name_dict=None)[source]¶ Bases:
object
A molecular dynamics style Frame object for LipidCOM objects.
- Atrributes:
- lipidcom (list of obj:LipidCOM): A list of the LipidCOM objects assigned to the COMFrame. box (np.array): A 3 element vector containing the (rectangular) xyz box edge lengths. time (float): The simulation time that this Frame represents. number (int): The frame number of this Frame. mdnumber (int): The corresponding frame number in the original MD trajectory
-
com
(wrapped=True)[source]¶ Computes the center of mass (COM) for the Frame
This member function is used to compute the overall center of mass (COM) of the COMFrame using the LipidCOM object coordinates and masses.
Parameters: wrapped (bool, optional) – Define which set of coordinates to use in the computation. True (default) - The wrapped LipidCOM coordinates are used to compute the COM of the frame. False - The unwrapped LipidCOM coordinates are used to compute the COM of the frame. Returns: A 3 element vector containing the xyz coordinates of the Frame’s COM Return type: np.array
-
set_box
(box_lengths)[source]¶ Set the rectangular xyz box edge lengths.
Parameters: box_lengths (numpy.array) – A 1d, 3 element numpy.array containing the x,y,z box sizes (or edge lengths)
-
class
pybilt.bilayer_analyzer.com_frame.
LipidCOM
[source]¶ Bases:
object
A lipid center of mass (COM) object.
This object stores the COM coordinates of a lipid (or other molecule or group of atoms) computed from both the wrapped and unwrapped atomic coordinates. This object also stores information about the type of lipid as well as the total mass of the lipid.
-
extract
(mda_residue, unwrap=False, box=None, name_dict=None)[source]¶ Get the center of mass coordinates from an MDAnalysis residue
This function calls the MDAnalysis member function center_of_mass() of the residue to compute the center of mass of the atoms constituting the residue.
Parameters: - mda_residue (MDAnalysis.residue) – An MDAnalysis residue object from which to extract a center of masss coordinates.
- unwrap (bool, optional) – Define which com container to store coordiates in. False (default) - The COM coordinates are stored in the container designated for the wrapped coordinate representation. True - The COM coordinates are stored in the container designated for the unwrapped coordinate representation.
-
pybilt.bilayer_analyzer.leaflet module¶
-
class
pybilt.bilayer_analyzer.leaflet.
Leaflet
(name)[source]¶ Bases:
object
Create a bilayer Leaflet representation. This class object is used to group lipids together according to their bilayer leaflet. It is primarily meant to store the indices of LipidCOMs as they are in a Frame.lipidcom list. This class also creates sub-groups within the Leaflet based on the LipidCOM.type using LipidGroup objects. Instances of Leaflet are created by the MemSys class.
-
add_member
(com_index, resname, resid)[source]¶ Add new lipids to the Leaflet.
This function is meant to be used to add new lipids according to their Frame.lipidcom index to the Leaflet and to a LipidGroup according resname/type/name. :Parameters: * com_index (int) – The COMFrame.lipidcom index of the lipid being added to the Leaflet.
- resname (str) – The resname (or LipidCOM.type) of the lipid being added.
- resid (int) – The topological resid of the lipid being added to the leaflet.
-
get_group_indices
(group_name)[source]¶ Get the indices of lipids in the Leaflet belonging to a specific LipidGroup.
Args: group_name (string): The name of the LipidGroup pull LipidCOM indices from.
Passing the string ‘all’ will return indices of all the lipids assigned to the Leaflet instance. If the group_name is not recognised (i.e. is not in the group_dict) The function defaults to ‘all’.Returns: - A list containing the integer indices of lipids in the Leaflet that
- belong to the specified LipidGroup.
Return type: list of int
-
get_group_names
()[source]¶ Get the names of all the LipidGroup objects in the Leaflet
Returns: list of str: A list of the names of current LipidGroup objects.
-
get_member_indices
()[source]¶ Get the indices of all lipids (LipidCOM) in the Leaflet. This member function Returns: the list of indices for the lipids grouped in the Leaflet instance.
Returns: A list of integer indices of the lipids associated with the Leaflet instance. Return type: list of int
-
get_member_resids
()[source]¶ Get the ‘resid’s of all lipids in the Leaflet. This member function Returns: the list of resid for the lipids grouped in the Leaflet instance.
Returns: A list of integer ‘resid’s of the lipids associated with the Leaflet instance. Return type: list of int
-
get_member_resnames
()[source]¶ Get the ‘resname’s of all lipids in the Leaflet. This member function Returns: the list of resnames for the lipids grouped in the Leaflet instance.
Returns: A list of ‘resname’s of the lipids associated with the Leaflet instance. Return type: list of int
-
-
class
pybilt.bilayer_analyzer.leaflet.
LipidGroup
(name)[source]¶ Bases:
object
Object to group lipid indices by type/resname/name. Instances of this object are created by the Leaflet class.
pybilt.bilayer_analyzer.mda_data module¶
Defines the MDAData class that is used to store the MDAnalysis objects built from the structure and trajectory file.
pybilt.bilayer_analyzer.plot_protocols module¶
-
class
pybilt.bilayer_analyzer.plot_protocols.
APLPlotProtocol
(args, analysis_keys, analysis_ids)[source]¶ Bases:
pybilt.bilayer_analyzer.plot_protocols.PlotFunctionProtocol
-
class
pybilt.bilayer_analyzer.plot_protocols.
BTPlotProtocol
(args, analysis_keys, analysis_ids)[source]¶ Bases:
pybilt.bilayer_analyzer.plot_protocols.PlotFunctionProtocol
-
class
pybilt.bilayer_analyzer.plot_protocols.
DispVecPlotProtocol
(args, analysis_keys, analysis_ids)[source]¶ Bases:
pybilt.bilayer_analyzer.plot_protocols.PlotFunctionProtocol
-
class
pybilt.bilayer_analyzer.plot_protocols.
MSDPlotProtocol
(args, analysis_keys, analysis_ids)[source]¶ Bases:
pybilt.bilayer_analyzer.plot_protocols.PlotFunctionProtocol
pybilt.bilayer_analyzer.prefab_analysis_protocols module¶
Prefab analysis protocols for lipid bilayers.
This module defines a set of functions that perform bilayer analysis using pre-designed (prefab) protocols that automatically setup and run the analyses, extract and output data, and generate plots. Most of these protocols make use of the BilayerAnalyzer class, but some use tools from the mda_tools package. These analyses are meant for quasi-planar lipid bilayer systems.
Example
>> from pybilt.bilayer_analyzer import prefab_analysis_protocols as ba_pap >> ba_pap.msd_diffusion(structure_file=’my_structure’, ... trajectory_file=’my_trajectory’, selection_string=’resname DOPE POPC’, ... dump_path=’./my_output_directory/’)
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
PN_orientational_angle
(structure_file, trajectory_file, selection_string, lipid_resnames, PN_names='default', frame_start=0, frame_end=-1, frame_interval=1, dump_path=None)[source]¶ Protocol to compute PN orientational angles.
This function uses the BilayerAnalyzer with the analysis ‘loa’ to compute the PN orientational angles of the specified lipids (by resname). Reports of data are printed to standard out, while pickled data (numpy array) is dumped to disk. The pickle data files have prefix ‘loa’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- lipid_resnames (list) – A list of lipid types as specified by their resnames.
- PN_names (Optional(dict)) – A dictionary specifying the atom names for the phosphorous and nitrogen atoms to use for the PN vector. This should have the format {‘lipid_resname_1’:(‘phosphorous_name’, nitrogen_name)}. Defaults to ‘default’, which uses (‘P’, ‘N’) for all lipid types.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
Returns: void
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
area_per_lipid
(structure_file, trajectory_file, selection_string, frame_start=0, frame_end=-1, frame_interval=1, dump_path=None, n_xbins=100, n_ybins=100)[source]¶ Protocol to compute area per lipid.
This function uses the BilayerAnalyzer with the analyses ‘apl_box’ and ‘apl_grid’ to estimate the area per lipid using two estimators: the lateral area method (composite) and lipid grid approach. Reports of data are printed to standard out, while pickled data is dumped to disk and plots are generated and also dumped to disk. The generated files have the prefix ‘apl’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
- n_xbins (Optional[int]) – Specify the number of bins in the ‘x’ direction to use in the lipid grid. Defaults to 100.
- n_ybins (Optional[int]) – Specify the number of bins in the ‘y’ direction to use in the lipid grid. Defaults to 100.
Returns: void
Notes
The lipid grid will have dimensions of n_xbins by n_ybins.
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
bilayer_thickness
(structure_file, trajectory_file, selection_string, frame_start=0, frame_end=-1, frame_interval=1, dump_path='./', name_dict=None, n_xbins=100, n_ybins=100, plot_grid_map=True)[source]¶ Protocol to compute the bilayer thickness.
This function uses the BilayerAnalyzer with the analysis ‘bilayer_thickness’ to estimate the the thickness of the bilayer via the lipid grid approach. Reports of data are printed to standard out, while pickled data (numpy array) is dumped to disk and plots are generated and also dumped to disk. The generated files have the prefix ‘bt’ and the grid maps have the prefix ‘thickness_grid’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
- name_dict (Optional[dict]) – A dictionary that defines atoms to use for each lipid type when computing the center of mass, which is then mapped to the lipid grid. The dictionary should have structure {‘lipid_resname_1’:[‘atom_a’, ‘atom_b’], ‘lipid_resname_2’:[‘atom_c’]}. Defaults to None, which means the center of mass of the whole lipid is used.
- n_xbins (Optional[int]) – Specify the number of bins in the ‘x’ direction to use in the lipid grid. Defaults to 100.
- n_ybins (Optional[int]) – Specify the number of bins in the ‘y’ direction to use in the lipid grid. Defaults to 100.
- plot_grid_map (Optional[bool]) – Specify whether the 2d grid heat map of of the thickness should be generated and output for each analyzed frame. Defaults to True.
Returns: void
Notes
The lipid grid will have dimensions of n_xbins by n_ybins.
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
compressibility
(structure_file, trajectory_file, selection_string, frame_start=0, frame_end=-1, frame_interval=1, dump_path=None, temperature=298.15)[source]¶ Protocol to compute the compressibilities.
This function uses the BilayerAnalyzer with the analyses ‘acm’, ‘vcm’, and ‘ac’ to estimate the area compressibility modulus, volume compressibility modulus, and area compressibility of the system. Reports of data are printed to standard out, while pickled data is dumped to disk. The generated files have the prefixes ‘acm’, ‘vcm’, and ‘ac’ for area compressibility modulus, volume compressibility modulus, and area compressibility respectively.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
- temperature (Optional[float]) – Set the temperature (in Kelvin) used in the simulation. Defaults to 298.15.
Returns: void
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
dispvector_correlation
(structure_file, trajectory_file, selection_string, frame_start=0, frame_end=-1, frame_interval=1, dump_path=None)[source]¶ Protocol to compute lipid displacement vector maps and correlations.
This function uses the BilayerAnalyzer with the analyses ‘disp_vec’, ‘disp_vec_corr’, and ‘disp_vec_nncorr’ to compute the lipid displacement vectors and their correlations (i.e. cos(theta)). The displacement vectors are used to generate the vector map plots. Reports of data are printed to standard out, while pickled data is dumped to disk and plots are generated and also dumped to disk. The generated pickle data files have the prefix ‘disp_vec’ and the vector map plots have prefix ‘step_vector_map’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
Returns: void
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
distance_cutoff_clustering
(structure_file, trajectory_file, selection_string, resnames, frame_start=0, frame_end=-1, frame_interval=1, dump_path='./')[source]¶ Protocol to compute hiearchical distance cutoff clusters.
This function uses the BilayerAnalyzer to determine the hiearchical distance cutoff clusters of lipids in the lateral dimensions; clustering is performed between lipids of the same type using a distance cutoff of 12.0*distance_units (assumed to be Angstroms). The protocol extracts the number of clusters and average cluster size for each lipid type in both the ‘upper’ and ‘lower’ leaflets. Reports of data are printed to standard out, while pickled data is dumped to disk and plots are generated and also dumped to disk. The generated files have the prefix ‘dc_cluster’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
Returns: void
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
lipid_grid_maps
(structure_file, trajectory_file, selection_string, frame_start=0, frame_end=-1, frame_interval=1, dump_path='./', name_dict=None, n_xbins=100, n_ybins=100, type_colors='auto')[source]¶ Protocol to generate lipid grid map plots.
This function uses the BilayerAnalyzer with the ‘lipid_grid’ reprentation to estimate the the thickness of the bilayer via the lipid grid approach. Grid map lots are generated and dumped to disk. The generated files have the prefix ‘lipid_grid’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
- name_dict (Optional[dict]) – A dictionary that defines atoms to use for each lipid type when computing the center of mass, which is then mapped to the lipid grid. The dictionary should have structure {‘lipid_resname_1’:[‘atom_a’, ‘atom_b’], ‘lipid_resname_2’:[‘atom_c’]}. Defaults to None, which means the center of mass of the whole lipid is used.
- n_xbins (Optional[int]) – Specify the number of bins in the ‘x’ direction to use in the lipid grid. Defaults to 100.
- n_ybins (Optional[int]) – Specify the number of bins in the ‘y’ direction to use in the lipid grid. Defaults to 100.
- type_colors (Optional[dict]) – Specify the colors to use for for each lipid type when generating the 2d grid map plot. The dictionary should be keyed by the lipid types’ resnames. Defaults to ‘auto’, which automatically assigns colors for each lipid type.
Returns: void
Notes
The lipid grid will have dimensions of n_xbins by n_ybins.
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
msd_diffusion
(structure_file, trajectory_file, selection_string, resnames=None, frame_start=0, frame_end=-1, frame_interval=1, dump_path=None)[source]¶ Protocol to compute MSD curves and estimate diffusion coefficents.
This function uses the BilayerAnalyzer with the analysis ‘msd’ to compute the time series curves for the mean squared displacements of lipids in the selection and then uses tools from the diffusion package to estimate the diffusion coefficents via three different estimators; i.e., the Einstein relation, linear (least squares) line fit, and a non-linear anomalous diffusion model fit. The protocol uses two different time ranges for the diffusion coefficent estimations: 0 (or first frame) to 10000.0 (assumed to be 10000 ps or 10 ns) and 10000.0 to 100000.0 (assumed to 10000 ps or 10 ns to 100000 ps or 100 ns). Reports of data are printed to standard out, while pickled data is dumped to disk and MSD time series plots are generated and also dumped to disk. The output files have the prefix ‘msd’.
- Args:
structure_file (str): The path and filename of the structure file. trajectory_file (str, list): The path and filename of the trajectory
file. Also accepts a list of path/filenames.- selection_string (str): The MDAnalysis compatible string used to select
- the bilayer components.
- resnames (Optional[str, list]): Specify the resnames of the lipid types
- that are to be included in this analysis. Defaults to None, which includes all lipid types.
- frame_start (Optional[int]): Specify the index of the first frame
- of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]): Specify the index of the last frame
- of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]): Specify the interval between frames of
- the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]): Specify a file path for the output files.
- Defaults to None, which outputs in the current directory.
Returns: void Notes
This function summarizes the diffusion coefficent estimates by printing to the std out, which could be redirected into a file.
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
nearest_neighbor_fraction
(structure_file, trajectory_file, selection_string, lipid_resnames, frame_start=0, frame_end=-1, frame_interval=1, dump_path=None)[source]¶ Protocol to compute the nearest neigbor fraction.
This function uses the BilayerAnalyzer with analysis ‘nnf’ to estimate the nearest neighbor fractions (also known as fractional interactions) of the specified lipids (by resname). Reports of data are printed to standard out, while pickled data is dumped to disk and plots are generated and also dumped to disk. The generated files have the prefix ‘nnf’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- lipid_resnames (list) – A list of lipid types as specified by their resnames.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
Returns: void
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
normal_displacement_lipid_type_correlation
(structure_file, trajectory_file, selection_string, frame_start=0, frame_end=-1, frame_interval=1, dump_path=None, com_sub_selection_dict=None)[source]¶ Protocol for correlation between the normal dimension displacement and lipid type.
This function uses the BilayerAnalyzer with the analysis ‘ndcorr’ to do a local grid analysis to estimate the correlation between between lipid types and their deflection along the bilayer normal; this analysis includes all lipid types. Reports of data are printed to standard out, while pickled data is dumped to disk and plots are generated and also dumped to disk. The generated pickle files have the prefix ‘norm_disp_correlation’ while the plots have the prefix ‘ndcorr’.
Parameters: - structure_file (str) – The path and filename of the structure file.
- trajectory_file (str, list) – The path and filename of the trajectory file. Also accepts a list of path/filenames.
- selection_string (str) – The MDAnalysis compatible string used to select the bilayer components.
- frame_start (Optional[int]) – Specify the index of the first frame of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]) – Specify the index of the last frame of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]) – Specify the interval between frames of the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]) – Specify a file path for the output files. Defaults to None, which outputs in the current directory.
Returns: void
-
pybilt.bilayer_analyzer.prefab_analysis_protocols.
position_density_maps_2d
(structure_file, trajectory_file, bilayer_selection_string, resnames, frame_start=0, frame_end=-1, frame_interval=1, dump_path='./')[source]¶ Protocol to compute the 2d positional densities and its plots.
This function uses the mda_tools.mda_density_map.position_density_map_2d_leaflet_simple function to compute the 2d positional densities of lipids in the lateral dimensions and generates their plots. Separate plots are generated for each lipid type, denoted by their resnames. The plots are generated and dumped to disk. The output files have the prefix ‘position_density_2d’.
- Args:
structure_file (str): The path and filename of the structure file. trajectory_file (str, list): The path and filename of the trajectory
file. Also accepts a list of path/filenames.- selection_string (str): The MDAnalysis compatible string used to select
- the bilayer components.
- resnames (list): Specify the resnames of the lipid types
- that are to be included in this analysis.
- frame_start (Optional[int]): Specify the index of the first frame
- of the trajectory to include in the analysis. Defaults to 0, which is the first frame of the trajectory.
- frame_end (Optional[int]): Specify the index of the last frame
- of the trajectory to include in the analysis. Defaults to -1, which is the last frame of the trajectory.
- frame_interval (Optional[int]): Specify the interval between frames of
- the trajectory to include in the analysis, or the frame frequency. Defaults to 1, which includes all frames [frame_start, frame_end].
- dump_path (Optional[str]): Specify a file path for the output files.
- Defaults to None, which outputs in the current directory.
Returns: void
pybilt.bilayer_analyzer.vector_frame module¶
-
class
pybilt.bilayer_analyzer.vector_frame.
LipidVec
[source]¶ Bases:
object
A lipid vector object.
This object stores the coordinates corresponding to a vector representation of a lipid (e.g. the PN vector); the object uses the wrapped coordinates. This object also stores information about the type of lipid as well as the total mass of the lipid.
-
extract
(mda_residue, ref_atoms)[source]¶ Get the center of mass coordinates from an MDAnalysis residue
This function calls the MDAnalysis member function center_of_mass() of the residue to compute the center of mass of the atoms constituting the residue.
Parameters: - mda_residue (MDAnalysis.residue) – An MDAnalysis residue object from which to extract (build) a vector representation.
- ref_atoms (dict) – A dictionary storing the references atoms to be used in building the vector representation. The outer keys of ref_atoms should be the resnames of the lipids.
-
-
class
pybilt.bilayer_analyzer.vector_frame.

- Atrributes:
- lipidvec (list of obj:LipidVec): A list of the LipidVec objects assigned to the COMFrame. box (np.array): A 3 element vector containing the (rectangular) xyz box edge lengths. time (float): The simulation time that this Frame represents. number (int): The frame number of this Frame. mdnumber (int): The corresponding frame number in the original MD trajectory
-
set_box
(box_lengths)[source]¶ Set the rectangular xyz box edge lengths.
Parameters: box_lengths (numpy.array) – A 1d, 3 element numpy.array containing the x,y,z box sizes (or edge lengths)


--- layout: post title: A behind-the-scenes look at the Rails Tutorial published: true ---
As part of gearing up for full screencast production and as a teaser for what's to come, I've made a short screencast with a special behing-the-scenes look at how I produce both the Rails Tutorial sample app and the Rails Tutorial book itself. You can find it on YouTube here. (For best viewing, increase the resolution to HD and run it in full-screen mode.)


Level:
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double shoot:
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large ship:
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super speed:
Designed & programmed by
rtCoder
Play
Controls
Equipment
Credits
<-
Keyboard
Mouse
Gamepad
<-


{% extends "base.html" %} {% block app_content %}
Subitizing is the rapid, accurate, and confident judgments of numbers performed for small numbers of items.


Welcome to Jonathan's Homepage
Class-One: How to set up a website;
Here's the passage from Pearlescent
This is a list of assignment
week1
week2
week3


Now anyone can start business online!
Take your business online with us
Promote contact free delivery mechanism in COVID-19
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Customer can use this app to order necessary items and goods right from their place and get it delivered at their doorstep
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We provide on demand online payment gateways to pay contactless, Go cashless and prevent Corona
Read moreNow order needful items at your doorstep
Customer Mobile App
Mobile App
Simple to use Mobile App with easy and clear user interface for easy shopping
Admin Panel
Vendors can easily manage orders, items, store items, users, customers with fully functional dashboard
Online Ordering
Developed to avoid visiting to corona prone areas to get essential items and grocery at your doorstep
Notification and Support
Secure OTP authentication and easy user management with live status of orders, also receive timely notifications


Submitting Titanium Desktop Apps to the Mac App Store
With the new Mac App Store, many Mac OS X developers are taking advantage of the frictionless distribution mechanism of the Mac App Store to distribute and monetize desktop applications. In fact, some top Mac App Store apps have been written and distributed using Titanium! In this multi-part series, we will explore the APIs and techniques necessary to build and distribute an application to the Mac App Store using Titanium Desktop.
Episode Resources:


Boogie Nights
Chad'z rating: ***1/2 (out of 4 = very good)
1997, R, 152 minutes [2 hours, 32 minutes]
[drama/crime]
starring: Mark Wahlberg (Eddie Adams/Dirk Diggler), Burt Reynolds (Jack Horner), Julianne Moore (Amber Waves), Heather Graham (Rollergirl); produced by Paul Thomas Anderson, Lloyd Levin, John Lyons, Joanne Sellar; written and directed by Paul Thomas Anderson.
Seen Saturday, November 1, 1997 at 3:15 p.m. at Mohawk Mall (Schenectady, NY) for $4.25 by myself.
There's been a number of epic, "The Rise and Fall of..." films released in the last few years. It's a formula that's guaranteed for success if the characters are developed well enough so that when they "fall" it's effective. Most films using this formula are about low and/or high class criminals, but what makes "Boogie Nights" so original and daring is the fact it's about people who produce pornography. Yet this isn't a film about freedom of speech and ethics (a la "The People Vs. Larry Flynt"), it's just a detailed study of characters most mainstream films wouldn't dare deal with.
I'm sure everyone has wondered make kind of people are involved in the porn industry.  Are they exploiting their wild sexuality with porn, or does porn make them sexually wild? It's a classic case of "the chicken and the egg," and the film leaves it up to us to answer those questions.
This idea is perfectly illustrated through the main character, Eddie Adams (Wahlberg), a busboy who's very well-endowed and doesn't consider himself a stud, or at least realize he is and what he could do. He is approached by Jack Horner (Reynolds), an adult filmmaker who takes his profession seriously and knows Eddie could be a major star. Eddie comes from a dysfunctional family, and when his mother kicks him out, he takes up Horner's offer not knowing whether he'll enjoy it or not.
Although Eddie (who changes his name to Dirk Diggler) is the film's protagonist, Horner is the catalyst around whom everything revolves. The film takes place in the late 1970s and early 80s when porn was moving from theaters to home video, but Horner insists on shooting all his movies on film since he considers it an artform. This fact on its own makes it seem as if Horner is one sick puppy, but within the film's context it makes sense because we get to know him well enough to understand his rationalization, yet we're not asked to condone or condemn him.
In fact, that idea symbolizes the film's usage of characterization and theme. It delves deep into the industry, creating for an extremely nihilistic, almost anarchic lifestyle (it's surprising this wasn't rated NC-17). Many of the "actors" are drug addicts who do it for the money, while others are seemingly normal people who just happen to be porn stars. The business is such a part of their daily routine and their overall lifestyle there's almost no distinction between the characters' personal lives and professional lives. For example, consider the starlet Rollergirl (Graham) who is called by that name at all times because nobody even knows her real name. Or Amber Waves (Moore), a starlet who tries to be something of a mother to the actors - someone they can look to for support.... among other things.
The first half documents the rise of Diggler from a nobody to a somebody, and in the process does a good job in defining atmosphere and character. But history proves fame can be taken away just as quickly as it was given, and this happens here as Diggler (along with some of his co-stars) becomes a drug addict. At first, he was coerced into drug use, but eventually he seemed to genuinely enjoy it - so whose fault is it?
By the two-thirds point the film becomes more of a straight crime story showing Diggler's attempts to get by using any means necessary. At the same time, Horner starts losing his edge because he's so adamantly opposed to switching to the mass market appeal of VHS home video ("Like any amateur can just pick up a camera and make a movie!?"). I didn't like the gloomy direction the story takes at this point. I felt as if I had seen most of it before, in films such as "Trainspotting," "GoodFellas," and "Casino." The story wanders a bit more than it needs to and I found myself becoming a little restless. However, the ending is clever and poetic.
There's much to commend "Boogie Nights" for, mostly for the chance it takes in telling the story it does, but also for its use of open-ended themes so everyone will leave without feeling as if they'd been preached to, just intellectually stimulated.
e-mail<EMAIL_ADDRESS>(C) 1997 Chad Polenz
The review above was posted to the
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The Handmaid’s Tale author Margaret Atwood to visit Perth on In Conversation with Margaret Atwood tour
From Gilead to Australia — famed author Margaret Atwood is headed Down Under.
The Handmaid’s Tale author will appear live on stage early next year as part of her In Conversation with Margaret Atwood tour, including a date at Perth’s Riverside Theatre on March 1.
The visit comes after the publication of The Testaments, the much-hyped sequel to her seminal novel.
It comes 34 years after The Handmaid’s Tale, which remains a symbol of women’s rights and inspired the Emmy-winning TV series.
Atwood said the tour would include the stories behind her diverse works and her latest project.
“I am so happy to be returning to Australia ... where readers have always been so warm and welcoming,” she said.
Ticket pre-sales begin a week today before the general release on November 29. See margaretatwoodlive.com.au.


NB: This interview was recorded in May 2021. (Audio Transcript)
In this episode, I had the pleasure to talk to @Jillian Augustine, Ph.D.! Jillian Augustine, is a British-Grenadian data scientist living in Vienna, Austria. She was born and grew up in West Yorkshire in the north of England whilst also (thankfully) spending many school summer vacations on Carriacou, Grenada. Jillian received a Bachelor’s degree from the University of Leeds, in the UK during which she also spent time at McGill University, Canada. In 2018 she received a doctorate in Molecular Biology from the University of Vienna. Since then she has been working in a range of large and mid-sized companies in various AI/digitalization teams and is currently a Senior Data Scientist in the AI Centre of Excellence at Crayon.
Making the career jump from academia to industry and the intrinsic value of inclusiveness
On the show today, I have the pleasure to talk to Jillian Augustine. Jillian is currently working as a Data Scientist in the Digital Excellence Team of the international paper and packaging manufacturer Mondi, but has received your Phd in Molecular Biology. On the show we are discussing Jillian experience working in academia and private industry. She is contrasting the mindset prominent on both sides, and what is needed to be successful, as well what industry can learn from academia, and vice versa. In addition we briefly discuss different ways how domain experts and data scientists work together most efficiently, and how improvements of tooling and software might change this relationship in the future. We end this episode, talking about diversity and inclusiveness. Jillian shares with us, what it means, and how it feels to be part of an underrepresented group. The importance of role models, and the intrinsic value of inclusiveness.
Moving in to Data Science from Non-CS Academia (Audio Transcript)
Working in academia provides a solid foundation on which you can build data science skills. But if you are outside of an advanced mathematical or informatics field, knowing exactly where your strengths lie and what you need to work on can be unclear. In this talk I will answer questions from an open survey of people who want to transition into data science. I will talk about the requirements for your first data science job, what hiring managers look out for and my personal learning path.
the art, science and maths of doing data science
A short promotion of Mondi’s paricipation in WeAreDevelopers 2019.
DATA SKILLS: HOW MONDI DOES DIGITAL
Talk Description: Organisations are becoming more aware of the importance of data in their daily business. But hiring people with the right skills is only part of the process. Building a Digital Transformation team in a traditional, multinational industry comes with its own challenges. How do you integrate specialists into teams across the globe whilst ensuring they stay connected and work as one unit? In this talk I will introduce our Digital Transformation team, our extended data community and how Mondi does digital.
From Test Tube to Data Lake
Talk Description: When I tell people where I work and what I studied, the response is always one of surprise. If you were to say that molecular biology research and telecommunications data science have nothing to do with each other, you’d be right… but also wrong. In my talk I will share with you my take on careers and answer some of the career-related questions that are often posed to me on this topic. I will talk about my transition from academia in the life sciences, into the telecommunications industry, and my experiences along the way. I will introduce you to the world of data science at A1 Telekom Austria, how we manage and protect your data, and how we use it to improve the user experience of our customers. Using examples from my current day-to-day work, I will show you how the two worlds are more similar than you might think.


Troon boss quits after nightmare start to the season
The 34-year-old had been in charge of the West Premiership outfit since June but announced his departure on twitter this morning.
by Eric McGowan, https://www.dailyrecord.co.uk/authors/eric-mcgowan/Jonathan Baillie has stepped down as Troon manager after a nightmare start to the season.
The 34-year-old had been in charge of the West Premiership outfit since June but announced his departure on twitter this morning.
His resignation comes on the back of a 1-0 defeat at Rossvale on Saturday which left Troon languishing second bottom of the table.
The Portland Park side have lost 10 of their 13 league games played so far.
Baillie admitted he feared the axe in an interview with Ayrshire Juniors reporter Lewis Moynihan after the latest defeat.
He said: "Absolutely there's worry, we are getting beat every week.
"We've lost three on the spin in the league – I've got to be under pressure as we are down at the bottom of the table.
"If the club feel the need to make a change then that's fine, I'm not going to have any complaints; the results speak for themselves."
And this morning, posting on his personal twitter page Baillie said: "Monday night I left my position as manager of Troon. Many mitigating factors but ultimately results not been good enough."


EE expands 5G network to 14 new towns and cities
The operator has expanded its 5G network to Liverpool, Glasgow and Huddersfield as well as a number of other towns in the UK.
EE has announced the expansion of its 5G network to 14 new towns and cities, including Liverpool, Glasgow and Huddersfield for the first time.
The mobile operator said independent tests by network performance firm RootMetrics had also found its network now covered 60% of London.
As part of the new expansion, EE said it had introduced 5G in Castlereagh, Guildford, Hamilton, Harlow, Hoddesdon, Kimberley, Lisburn, Maidstone, Sydenham, Watford and Wolverhampton.
5G is the next generation of mobile data network, offering speeds several times that of current-generation 4G.
EE – which is owned by BT – began its 5G network rollout in May, initially launching coverage in London, Edinburgh, Belfast, Cardiff, Birmingham and Manchester.
Fellow operators Vodafone, O2 and Three have since begun their own introductions of 5G coverage.
BT consumer division chief executive Marc Allera said of the update: “Switching on 5G in more places is helping us deliver the best mobile experience to our customers, keeping them connected to the things that matter most.
“RootMetrics’ early 5G testing shows that we are a long way ahead in terms of 5G performance and our engineers are continuing to build new sites every day, on our journey to keeping our customers connected 100% of the time.”
EE said its latest rollout also included introducing 5G to new areas of high football, including Bristol Parkway, Cardiff Castle and Camden Market and Carnaby Street in London.


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Manages all Timers
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responsible for updating all Timers whenever it ticks.
It is owned by the Director. cocosCairo was designed to have one Scheduler per Director (and one Director per application), so this method should be indirectly accessed through the Director.
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timeScale Modifies the time scale of all scheduled timers. |
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Registers a timer to be notified when the Scheduler ticks.
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Unregisters a timer to be notified when the Scheduler ticks.
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Called whenever a small amount of time has progressed and notifies all registered timers of the tick. This method should not generally be called manually. The Scheduler is ticked once per main loop iteration in Director.
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timeScaleModifies the time scale of all scheduled timers. Setting a value less
than the current one will create a "slow motion" effect, while
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| Generated by Epydoc 3.0.1 on Fri Apr 9 14:54:59 2010 | http://epydoc.sourceforge.net |


I am a Business Analyst in HealthCare as well as Automation Tester in Selenium who works at Cognizant Tech Solutions servicing Health Care Clients in buliding framework for Claims Processing and Payment.
Skills i have
- Selenium
- Core-Java
- 837,835 EDI Processing
- Cucumber
- HealthCareClaimsProcessing
- Gherkin


This page summarizes the code fragments that have been found to be replicated in the code.
Only those fragments longer than 30 lines of code are shown.
# duplications
Total lines
Total tokens
Approx # bytes
1
33
239
956
You expand and collapse the code fragments using the + buttons. You can also navigate to the source code by clicking
on the file names.