text stringlengths 25 2.19k | embedding listlengths 768 768 |
|---|---|
def black _ check ( session, dilibraries = dilibraries ) : session. log ( f'run black _ check for { lib _ name }') standard _ di _ black _ check ( session, dilibraries = dilibraries ) | [
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def min ( self, start = 0, end = none ) : return super ( minsegmenttree, self ). reduce ( start, end ) | [
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def load _ more _ reviews _ url ( review _ page, data _ ajaxurl ) : load _ more = review _ page ( '. load - more - data') data _ key = load _ more. attr ('data - key') if data _ key is none : return none data _ url = imdb _ url + data _ ajaxurl + '? ref _ = undefined & paginationkey ='+ data _ key return data _ url | [
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def get _ enum ( self, enum ) : curves = [ ] for afmdata in self. _ mmlist : if afmdata. enum = = enum : curves. append ( afmdata ) if len ( curves ) = = 0 : raise keyerror ( f " could not find dataset with enum'{ enum } '! " ) elif len ( curves ) = = 1 : return curves [ 0 ] else : raise valueerror ( f " multiple curve... | [
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def configure ( self, servers ) : nodes = [ ] log. debug ( " configuring servers { 0 } ". format ( servers ) ) # format server info into a dict for server in servers : nodes. append ( {'name': server. name,'ip': server. ip } ) # create the inventory file inventoryfile. create ( self. _ inventory _ path, nodes ) # run a... | [
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def _ bnd _ hub ( self, n, hub ) : # index of face ( up or down ) face = 4 if hub = ='hub'else 5 # the easy part for attr in self. components ( ) : n. addtopologyset ( hub, ( flatten _ objects ( getattr ( self, attr ) ),'face ', face ) ) # utility function for adding edges edge _ add = 2 if hub = ='antihub'else 0 def e... | [
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def _ handle _ create ( databases, database, force, output _ type, include, exclude ) : if database = ='-': # must write bytes to stdout ; use sys. stdout. buffer. fd = sys. stdout. buffer elif not force and os. path. exists ( database ) : raise fileexistserror ( f'the file { database } already exists! use - - force to... | [
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def read _ xyz ( self, eleme1, eleme2, clay, clayao, perion ) : num _ h2o = 0 water _ o = [ 0 ] * 3 while 1 : line = self. file. readline ( ) if line : linesep = line. split ( ) if linesep [ 0 ]! = " item : " : if linesep [ 0 ] in self. ele1 : water _ o [ num _ h2o % 3 ] = [ float ( linesep [ 1 ] ), float ( linesep [ 2... | [
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def create _ logger ( level ='debug ', handler _ type ='stream ', path ='' ) : # recover the associate value to the specified level level _ value = getattr ( logging, level, 0 ) logger = logging. getlogger ('simple _ example') logger. name = " _ name _ " logger. setlevel ( level _ value ) # create the handler depengin ... | [
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def array ( self ) : return np. array ( self. value ) | [
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def _ ensure _ leading _ sample _ dim ( arr, sample _ dim = 0 ) : if is _ xarray _ object ( arr ) and is _ integer ( sample _ dim ) : # find name of dimension corresponding to integer # axis dimension. dims = list ( arr. dims ) axis _ nums = [ arr. get _ axis _ num ( d ) for d in dims ] sample _ dim = dims [ axis _ num... | [
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def _ get _ driver ( self, mocked _ browser ) : driver = splinterbrowserdriver ( ) driver. _ browser = mocked _ browser return driver | [
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def find _ material ( self, mat : union [ int, str, material ] ) : if isinstance ( mat, int ) : return self. find _ material _ from _ id ( mat ) elif isinstance ( mat, str ) : return self. find _ material _ from _ name ( mat ) elif isinstance ( mat, material ) : return mat | [
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def get _ clone _ expression ( self, define ='v _ j _ cdr3') : clone _ expression = { } for i in self. data : vgene = i ['vgene'] jgene = i ['jgene'] cdr3 = i ['cdr3'] count = i ['count'] expression = count / self. total if define = ='v _ j _ cdr3': index ='_ '. join ( [ vgene, jgene, cdr3 ] ) elif define = ='cdr3': in... | [
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def exit ( self, error ) : self. error = error exit ( error ) | [
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def get _ md _ entry ( db, entry, bibfile, add _ comments = true ) : md _ str = " " md _ str + = " - * * " + entry ['title'] + " * * " md _ str + = ", ( " + entry ['year'] + " ) " if'url'in entry. keys ( ) : md _ str + = " [ [ paper ] ] ( " + entry ['url'] + " ) " md _ str + = " [ [ bib ] ] ( " + create _ bib _ link ( ... | [
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def testpubmedfieldblanksearch ( self ) : form = self. form form. enter _ value ('accids ','j : 23094') form. click _ search ( ) # finds the results table and iterates through the table table _ element = self. driver. find _ element ( by. id, " resultstable " ) table = table ( table _ element ) # finds the pmid column ... | [
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def creation _ timestamp ( self ) - > optional [ pulumi. input [ str ] ] : return pulumi. get ( self, " creation _ timestamp " ) | [
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def _ _ init _ _ ( _ _ self _ _, resource _ name : str, args : optional [ accountargs ] = none, opts : optional [ pulumi. resourceoptions ] = none ) :... | [
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def imag ( input, name = none ) : with ops. name _ scope ( name, " imag ", [ input ] ) as name : input = ops. convert _ to _ tensor ( input, name = " input " ) if input. dtype. is _ complex : return gen _ math _ ops. imag ( input, tout = input. dtype. real _ dtype, name = name ) else : return array _ ops. zeros _ like ... | [
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def is _ prime ( n ) : prime = true for num in range ( 2, int ( n * * 0. 5 ) + 2 ) : if n % num = = 0 : prime = false break return prime | [
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def _ gridsearch ( self, x, y ) : self. model _ = gridsearchcv ( estimator = self. _ estimator, param _ grid = self. _ param _ grid, scoring = self. _ scoring, n _ jobs = self. _ n _ jobs, cv = self. _ cv, refit = self. _ refit, verbose = self. _ verbose ) self. model _. fit ( x, y ) # save key cv results on attributes... | [
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def send ( self, request, pk = none ) : receiver = user. objects. get ( pk = pk ) message = chatmessage ( sender = request. user, receiver = receiver, text = request. data. get ('text') ) message. save ( ) return response ( { " code " : 1 }, status = status. http _ 201 _ created ) | [
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def generate ( self, x : np. ndarray, y : optional [ np. ndarray ] = none, * * kwargs ) - > np. ndarray : mask = kwargs. get ( " mask " ) x _ adv = x. astype ( art _ numpy _ dtype ) y = check _ and _ transform _ label _ format ( y, self. estimator. nb _ classes ) if y is none : y = get _ labels _ np _ array ( self. est... | [
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def command _ blog ( self, brain, arg ) : pattern = " ". join ( arg ) blog _ re = re. compile ( '. * % s. *'% pattern, re. i ) url = " http : / / sa. seoblogs. ops. yahoo. net / feed / " content = self. fetchurl ( url ) rss = xml. etree. elementtree. fromstring ( content. read ( ) ) channel = rss. find ( " channel " ) ... | [
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def testsendrequestconnectionerror ( self ) : self. client. sock. connect _ fail = true self. assertequal ( self. client. send _ request ( 9 ), ( 400, 2 ) ) | [
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def load _ hr _ config ( config ) : logger = logging. getlogger ( _ _ name _ _ ) start _ hr = 8 end _ hr = 23 section _ name = " start _ end " if section _ name in config. sections ( ) : start _ hr _ config = config [ section _ name ]. get ( " start _ hr " ) if start _ hr _ config : logger. debug ( f " using start hr f... | [
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def temporalblock ( input _ layer, out _ channel, filter _ size, stride, dilation _ rate, counters, dropout, use _ highway = false, gated = false, reuse = false, normalization ='weight _ norm ', is _ training = false, init = false ) : keep _ prob = 1. 0 - dropout in _ channel = input _ layer. get _ shape ( ) [ - 1 ] na... | [
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def get _ gene _ expression ( self, gene _ class, normailze _ by _ gene _ length = false, drop _ allele _ info = true, gene _ segment _ reference _ dirpath ='/ users / nstrauli / data / ref _ seqs / ig / from _ imgt _ appended / human /') : # check if gene _ class is a string ( i. e. singular ) if isinstance ( gene _ c... | [
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def test _ atomic _ base64 _ binary _ max _ length _ 1 _ nistxml _ sv _ iv _ atomic _ base64 _ binary _ max _ length _ 2 _ 2 ( mode, save _ output, output _ format ) : assert _ bindings ( schema = " nistdata / atomic / base64binary / schema + instance / nistschema - sv - iv - atomic - base64binary - maxlength - 2. xsd ... | [
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def test _ atomic _ base64 _ binary _ pattern _ 1 _ nistxml _ sv _ iv _ atomic _ base64 _ binary _ pattern _ 2 _ 4 ( mode, save _ output, output _ format ) : assert _ bindings ( schema = " nistdata / atomic / base64binary / schema + instance / nistschema - sv - iv - atomic - base64binary - pattern - 2. xsd ", instance ... | [
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def find _ k _ closest _ elements _ to _ pivot ( input _ numbers : list [ int ], k : int, pivot : int ) - > list [ int ] : if len ( input _ numbers ) < k : raise runtimeerror ('there is not enough input numbers in { } to return { } elements. '. format ( input _ numbers, k ) ) else : number _ lists _ by _ distances : di... | [
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def css2xpath ( css ) : sel = scrapy. selector ( ) return sel. _ css2xpath ( css ) | [
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def moore _ penrose _ pinv ( x, num _ iter = 6 ) : abs _ x = torch. abs ( x ) col = abs _ x. sum ( dim = - 1 ) row = abs _ x. sum ( dim = - 2 ) z = x. transpose ( - 1, - 2 ). contiguous ( ) z = z / ( torch. max ( col ) * torch. max ( row ) ) i = torch. eye ( x. shape [ - 1 ], device = x. device ). unsqueeze ( 0 ) for _... | [
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def get _ status ( self ) : return self. _ request ('get ','/ status') | [
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def bias ( measured, observed ) : assert len ( measured. shape ) = = 2, " need 2 - d input " assert len ( observed. shape ) = = 2, " need 2 - d input " if measured. shape! = observed. shape : print ( f " regrid required. will interpolate observed { observed. shape } to measured grid { measured. shape }. " ) observed = ... | [
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def database ( self ) : return self. m _ database | [
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def id ( self ) - > int : return self. member. id | [
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def squashrngcython ( rng, apermol ) : if not checksymmetry ( rng ) : raise runtimeerror ( " graph is non - symmetrical " ) sh = rng. shape rng = rng. toarray ( ) newsh = ( int ( sh [ 0 ] / apermol ), int ( sh [ 1 ] / apermol ) ) # pdb. set _ trace ( ) # molrng = lil _ matrix ( newsh ) molrng = np. zeros ( newsh ) molr... | [
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def segment _ data ( data, example _ size, seq _ len ) : data = ( data - sum ( data ) / len ( data ) ) / ( max ( data ) - min ( data ) ) num _ seq = int ( len ( data ) / ( example _ size * seq _ len ) ) data = data [ : num _ seq * seq _ len * example _ size ] return np. array ( data ). reshape ( num _ seq, seq _ len, e... | [
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def delete ( self, bucket _ name : str, object _ name : str ) - > none : client = self. get _ conn ( ) bucket = client. bucket ( bucket _ name ) blob = bucket. blob ( blob _ name = object _ name ) blob. delete ( ) self. log. info ( " blob % s deleted. ", object _ name ) | [
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def comp _ external _ contour ( orig, thresh ) : # get the dimension and color channel of the input image img _ height, img _ width, img _ channels = orig. shape # initialize parameters trait _ img = orig. copy ( ) area = 0 w = h = 0 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ... | [
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def itksubtractconstantfromimagefilteriul3diul3 _ superclass _ cast ( * args ) : return _ itksubtractconstantfromimagefilterpython. itksubtractconstantfromimagefilteriul3diul3 _ superclass _ cast ( * args ) | [
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def download ( url, data _ path ) : if not os. path. exists ( data _ path ) : os. makedirs ( data _ path ) url _ parse = urlparse ( url ) file _ name = os. path. join ( data _ path, url _ parse. path. split ('/') [ - 1 ] ) if not os. path. exists ( file _ name. replace ( '. gz ','' ) ) : logging. info ( " downloading %... | [
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def test _ atomic _ boolean _ pattern _ 2 _ nistxml _ sv _ iv _ atomic _ boolean _ pattern _ 3 _ 4 ( mode, save _ output, output _ format ) : assert _ bindings ( schema = " nistdata / atomic / boolean / schema + instance / nistschema - sv - iv - atomic - boolean - pattern - 3. xsd ", instance = " nistdata / atomic / bo... | [
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def quick _ select ( unsorted _ list, start, end, k ) : if start = = end : return unsorted _ list [ start ] left, right = start, end pivot = unsorted _ list [ left + ( ( right - left ) > > 1 ) ] while left < = right : while left < = right and unsorted _ list [ left ] < pivot : left + = 1 while left < = right and unsort... | [
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0.3604044616... |
def render _ object ( self, obj _ id, r, t, fx, fy, cx, cy ) : raise notimplementederror | [
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def guess _ storage ( self ) : # build lookups by name and id storage _ by _ id = { } storage _ by _ name = { } # the storages may change as new storages are added manually so we do # this each time this is called storages = self. _ storage _ model. storages for storage in storages : # store lower case names so we can ... | [
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def make _ coord _ dict ( subs, subscript _ dict, terse = true ) : sub _ elems _ list = [ y for x in subscript _ dict. values ( ) for y in x ] coordinates = { } for sub in subs : if sub in sub _ elems _ list : name = find _ subscript _ name ( subscript _ dict, sub ) coordinates [ name ] = [ sub ] elif not terse : coord... | [
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def test _ update _ market _ value _ of _ asset _ not _ in _ list ( ) : start _ dt = pd. timestamp ('2017 - 10 - 05 08 : 00 : 00 ', tz = pytz. utc ) later _ dt = pd. timestamp ('2017 - 10 - 06 08 : 00 : 00 ', tz = pytz. utc ) port = portfolio ( start _ dt ) asset = equity ( " acme inc. ", " aaa ", tax _ exempt = false ... | [
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def exp ( x ) : try : return variable ( x. name, np. exp ( x. val ), { k : v * np. exp ( x. val ) for ( k, v ) in x. der. items ( ) }, false ) except attributeerror : return np. exp ( x ) | [
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def _ withdraw _ funds ( amount, person ) : fund _ service. remove _ funds ( amount, person ) withdrawal = model. bankwithdrawals ( person _ id = person. id, amount = amount ) model. db. session. add ( withdrawal ) model. db. session. commit ( ) | [
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def close _ position ( self, instrument ) : url = " { 0 } / { 1 } / accounts / { 2 } / positions / { 3 } ". format ( self. domain, self. api _ version, self. account _ id, instrument ) try : return self. _ client _ _ call ( uri = url, method = " delete " ) except requestexception : return false except assertionerror : ... | [
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def get _ iv ( self, protocol _ version ='1. 0') : print ( " [ + ] start getting iv... " ) msg = protocol. encode _ request _ iv ( protocol _ version ) self. _ write _ characteristic _ and _ wait ( msg ) return self. _ iv | [
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def events _ to _ timestamp _ image _ torch ( xs, ys, ts, ps, device = none, sensor _ size = ( 180, 240 ), clip _ out _ of _ range = true, interpolation ='bilinear ', padding = true, timestamp _ reverse = false ) : if device is none : device = xs. device xs, ys, ps, ts = xs. squeeze ( ), ys. squeeze ( ), ps. squeeze ( ... | [
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def on _ pushbutton _ ssdaddata _ clicked ( self ) : # todo : not implemented yet self. sendcmdssd _ ad _ data ( ) # receive data global gsocketbufsize gsocketbufsize = 32 * 1024 + 24 + 16 self. udpsocketclient. receivedata ( ) data = self. udpsocketclient. mdata # print ( " receive total length : ", len ( data ) ) dat... | [
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def _ generate _ lease _ requests _ for _ new _ machines ( machine _ type, swarming _ server ) : lease _ requests = [ ] request _ number = machine _ type. request _ count for _ in xrange ( machine _ type. target _ size - machine _ type. current _ size ) : request _ number + = 1 request _ id ='% s - % d'% ( machine _ ty... | [
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def run ( self ) : self. setup ( ) while self. _ looping : try : self. processing ( ) except keyboardinterrupt : return 0 return 0 | [
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def get _ tensor _ accuracy ( self, logits : torch. tensor, targets : torch. tensor ) - > tuple [ torch. tensor, torch. tensor ] : preds = torch. argmax ( logits, dim = - 1 ) # ( batch, len _ tokens ) masked _ tokens = targets. ne ( self. alphabet. padding _ idx ) masked _ preds = torch. masked _ select ( preds, masked... | [
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... |
def load _ testconditions ( self ) : # initializes arrays for conditions for each test self. capimages = np. zeros ( ( 1, self. n ) ) self. capdiamvals = np. zeros ( ( 1, self. n ) ) self. pressdiffvals = np. zeros ( ( 1, self. n ) ) self. height = np. zeros ( ( 1, self. n ) ) self. width = np. zeros ( ( 1, self. n ) )... | [
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0.662767827510833... |
def test _ error ( self ) : self. assertnotidentical ( self. root. find ('error'), none ) | [
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0.3... |
def enter _ to _ clear ( ) : input ( " \ n - - > appuyez sur entree pour continuer : " ) os. system ('cls') | [
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... |
def ln _ likelihood _ det ( model _ plasma, det, data, sigma, labels = none ) : try : model _ data = det. take _ data ( model _ plasma ) except : return - np. inf if labels is none : ln _ p = gaussian _ likelihood ( data, model _ data, sigma ) else : ln _ p = 0. 0 for label in labels : ln _ p + = gaussian _ likelihood ... | [
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0.07962080091238... |
def test _ list _ decimal _ enumeration _ 2 _ nistxml _ sv _ iv _ list _ decimal _ enumeration _ 3 _ 4 ( mode, save _ output, output _ format ) : assert _ bindings ( schema = " nistdata / list / decimal / schema + instance / nistschema - sv - iv - list - decimal - enumeration - 3. xsd ", instance = " nistdata / list / ... | [
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def change _ led ( led, state, led _ state ) : led _ state = led _ state & masks [ led ] if state : led _ state = led _ state | bits [ led ] # print ( led _ state ) update _ leds ( led _ state ) | [
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def _ _ init _ _ ( self ) : self. ftp _ settings = read _ backend _ config ( self. get _ id ( ) ) self. verify _ dir = self. ftp _ settings [ " verify _ dir " ] self. archive _ staging _ dir = self. ftp _ settings [ " archive _ staging _ dir " ] self. connection _ pool = connectionpool ( ) self. download _ threads = [ ... | [
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def taketest ( ) : user = getuser ( request, session ) problem = request. args. get ( " problem " ) questions = db. gettestquestions ( problem ) return render _ template ('test. html ', learningstyle = " visual ", user = user, problem = problem, questions = questions ) | [
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def batting _ heuristic ( player ) : score = player [ " strike _ rate " ] * 20 + \ player [ " average " ] * 200 + \ player [ " sixes " ] * 10 + \ player [ " boundaries " ] * 5 - \ player [ " ducks " ] * 10 + \ player [ " not _ out " ] * 5 + \ player [ " innings " ] * 10 + \ player [ " runs " ] * 5 + \ player [ " centur... | [
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def navigate _ to ( self, path, dont _ wait = none ) : links = path. split ('>') for link in links : self. click _ link ( link ) self. wait _ for _ page _ loaded ( dont _ wait ) | [
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def pandas _ series _ to _ arrow _ array ( series : pd. series ) - > pa. array : if hasattr ( series, " cat " ) : return pa. dictionaryarray. from _ arrays ( # pandas categorical value " - 1 " means none pa. array. from _ pandas ( series. cat. codes, mask = ( series. cat. codes = = - 1 ) ), pandas _ series _ to _ arrow... | [
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def hyper _ operator ( x, y, op ) : def hypop ( a, b, c ) : if c = = 0 : return a + 1 else : return hypop ( hypop ( a, b - 1, c ), a, c - 1 ) \ if ( c = = 1 and b > 0 ) or ( b > 1 ) else a print ( hypop ( x, y, op ) ) | [
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async def charge _ port _ door _ close ( self ) - > none : data = await self. _ send _ command ( " charge _ port _ door _ close " ) if data and data [ " response " ] [ " result " ] is true : params = { " charge _ port _ door _ open " : false } self. _ vehicle _ data [ " charge _ state " ]. update ( params ) | [
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def _ _ translate ( self, parameter _ values ) : template _ copy = self. template sam _ parser = parser ( ) sam _ translator = translator ( managed _ policy _ map = self. _ _ managed _ policy _ map ( ), sam _ parser = sam _ parser, # default plugins are already initialized within the translator plugins = self. extra _ ... | [
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def cancel ( self, cr, uid, ids, context = none ) : self. write ( cr, uid, ids, {'state':'cancel'}, context = context ) return true | [
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def decode ( self, probs, sizes = none, num _ results = 1 ) : out, scores, offsets, seq _ lens = self. _ decoder. decode ( probs. cpu ( ), sizes ) strings = self. convert _ to _ strings ( out, seq _ lens ) offsets = self. convert _ tensor ( offsets, seq _ lens ) return strings, offsets, scores | [
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def filter _ stack ( stacks : iterable, f : callable ) - > none : for s in stacks : if f ( s ) : yield s | [
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def testgetinstance ( self, mock _ list _ instances ) : mock _ list _ instances. return _ value = mock _ list _ instances found _ instance = fake _ source _ project. compute. getinstance ( fake _ instance. name ) self. assertisinstance ( found _ instance, compute. googlecomputeinstance ) self. assertequal ( fake _ sour... | [
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def save ( self, * args, * * kwargs ) : if self. profile _ pic : im = img. open ( self. profile _ pic ) im. thumbnail ( ( 200, 200 ), img. antialias ) output = bytesio ( ) im. save ( output, format ='jpeg') output. seek ( 0 ) self. profile _ pic = inmemoryuploadedfile ( output,'imagefield ', " % s. jpg " \ % self. prof... | [
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def unset _ eventid ( self ) : self. eventid = none | [
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def read _ json ( self, filename ) : with open ( filename,'r') as f : json _ data = eval ( f. read ( ) ) self. menu _ text = json _ data [ " menu _ text " ] self. new _ game _ text = json _ data [ " new _ game _ text " ] self. starting _ node = json _ data [ " starting _ node " ] self. continue _ text = json _ data [ "... | [
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def get _ pipeline ( ) : extra _ trees _ classifier = extratreesclassifier ( n _ estimators = 100, criterion ='entropy ', max _ features = 0. 15, n _ jobs = - 1 ) rfe = rfe ( extra _ trees _ classifier, step = 0. 35 ) naive _ bayes = bernoullinb ( alpha = 0. 01, fit _ prior = true ) return pipeline ( [ ('feature _ sele... | [
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def _ _ init _ _ ( self, config _ path, proc _ id ) : super ( self. _ _ class _ _, self ). _ _ init _ _ ( config _ path ) self. proc _ id = proc _ id self. payload = emoppayload ( self. settings, proc _ id ) self. scheduler = emopscheduler. get _ scheduler _ instance ( name = self. settings. scheduler, settings = self.... | [
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def get _ db _ session ( self ) : database. initialize ( ) return database. get _ session ( ) | [
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def test _ atomic _ qname _ min _ length _ 1 _ nistxml _ sv _ iv _ atomic _ qname _ min _ length _ 2 _ 2 ( mode, save _ output, output _ format ) : assert _ bindings ( schema = " nistdata / atomic / qname / schema + instance / nistschema - sv - iv - atomic - qname - minlength - 2. xsd ", instance = " nistdata / atomic ... | [
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... |
def _ map _ projection ( self, lat, lon, anchor _ lat, anchor _ lon ) : sin _ lat = np. sin ( lat ) cos _ lat = np. cos ( lat ) cos _ d _ lon = np. cos ( lon - anchor _ lon ) sin _ anchor _ lat = np. sin ( anchor _ lat ) cos _ anchor _ lat = np. cos ( anchor _ lat ) arg = sin _ anchor _ lat * sin _ lat + cos _ anchor _... | [
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1... |
def inline _ equation ( self ) : return'\ n '. join ( [ r'\ begin { math } ', self. latex. get ( ), r'\ end { math }'] ) | [
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def download _ extract _ cars ( cars _ dir, cars _ url, cars _ annotations _ url ) : download _ url ( cars _ annotations _ url, root = cars _ dir ) download _ url ( cars _ url, root = cars _ dir ) filename = os. path. join ( cars _ dir, os. path. basename ( cars _ url ) ) with tarfile. open ( filename, " r : gz " ) as ... | [
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def is _ moderator ( self ) : return self. role = = self. permissionchoice. moderator | [
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def serialise _ system ( self ) : modeller = app. modeller ( self. molecule. to _ openmm _ topology ( ), self. molecule. openmm _ coordinates ( ) ) forcefield = app. forcefield ( self. xml ) # check for virtual sites try : system = forcefield. createsystem ( modeller. topology, nonbondedmethod = app. nocutoff, constrai... | [
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def make _ complete _ graph ( num _ nodes ) : graph = { } nodes = range ( num _ nodes ) for node in nodes : graph [ node ] = set ( range ( num _ nodes ) ) ( graph [ node ] ). remove ( node ) return graph | [
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def start ( self ) : self. log. info ( " start : running < % s > in < % s >. " % ( self. cmd, self. test _ dir ) ) # spawn as a process and then wait until # the web server is ready to accept requests. # self. serverprocess = subprocess. popen ( args = self. cmd, shell = true, cwd = self. test _ dir, ) pid = self. serv... | [
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... |
def csv _ print ( module _ name, server _ list, directory ) : full _ file _ path = directory + " / " + module _ name print ( " # # creating { } file. ". format ( full _ file _ path ) ) with open ( full _ file _ path,'w ', newline ='' ) as f : fieldnames = server _ list [ 0 ]. keys ( ) thewriter = csv. dictwriter ( f, f... | [
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def dis _ between _ authors ( author1, author2 ) : metric = author. ametrictype if metric = = authormetric. centroiddis : return author2. distance _ to ( author1. get _ center ( ) ) temp = [ author1. distance _ to ( author2works ) for author2works in author2. get _ matrices ( ) ] if metric = = authormetric. averagedis ... | [
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... |
def get _ rois _ mask _ in _ native _ space ( sub _ id ) : roi _ dir = os. path. join ('pipelines ','rois') # get all roi file paths anat _ roi _ images = glob. glob ( os. path. join ( roi _ dir,'anatomical ','*. nii *') ) func _ roi _ images = glob. glob ( os. path. join ( roi _ dir,'functional ','* ','*. nii *') ) su... | [
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def test _ atomic _ any _ uri _ enumeration _ nistxml _ sv _ iv _ atomic _ any _ uri _ enumeration _ 1 _ 4 ( mode, save _ output, output _ format ) : assert _ bindings ( schema = " nistdata / atomic / anyuri / schema + instance / nistschema - sv - iv - atomic - anyuri - enumeration - 1. xsd ", instance = " nistdata / a... | [
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0.146039485931396... |
def test _ atomic _ language _ length _ nistxml _ sv _ iv _ atomic _ language _ length _ 1 _ 5 ( mode, save _ output, output _ format ) : assert _ bindings ( schema = " nistdata / atomic / language / schema + instance / nistschema - sv - iv - atomic - language - length - 1. xsd ", instance = " nistdata / atomic / langu... | [
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-0.0800323560833931,
0.47781461477279663... |
def _ _ init _ _ ( self, t, trajectory, ats, molno ) : self. timestep = t self. ats = ats self. box = none self. rng = none if type ( trajectory ) is np. ndarray : carray = trajectory self. timestep = int ( carray [ 0 ] ) self. ats = int ( carray [ 2 ] ) self. nclusts = carray [ 1 ] pend = 4 + 3 * ats * molno self. pos... | [
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0.516655445098877,
-0.017846645787358... |
def thetafrombot _ locuc ( self, theta, noblock = false ) : return float ( theta ) | [
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-... |
def remove _ site _ effects ( self ) : assert ( self. regrs _ site _ effects is not none ), " run regr _ model _ site _ effects ( ) first. " roi _ gs _ df = self. roi _ df. copy ( ) def apply _ model ( y ) : " " " returns data corrected for site effects. " " " return ( y - b0 ) / b1 # apply appropriate correction for e... | [
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def checkclick ( self, pos ) : if self. die1. checkclick ( pos ) or self. die2. checkclick ( pos ) : self. handlemouserelease ( ) | [
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0.1957254260778427,
... |
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