idx int64 0 251k | question stringlengths 53 3.53k | target stringlengths 5 1.23k | len_question int64 20 893 | len_target int64 3 238 |
|---|---|---|---|---|
248,100 | def decrypt ( self , encrypted ) : fernet = Fernet ( self . decryption_cipher_key ) return fernet . decrypt ( encrypted ) | decrypts the encrypted message using Fernet | 34 | 9 |
248,101 | def create_subject ( self , authc_token = None , account_id = None , existing_subject = None , subject_context = None ) : if subject_context is None : # this that means a successful login just happened # passing existing_subject is new to yosai: context = self . create_subject_context ( existing_subject ) context . aut... | Creates a Subject instance for the user represented by the given method arguments . | 246 | 15 |
248,102 | def login ( self , subject , authc_token ) : try : # account_id is a SimpleIdentifierCollection account_id = self . authenticator . authenticate_account ( subject . identifiers , authc_token ) # implies multi-factor authc not complete: except AdditionalAuthenticationRequired as exc : # identity needs to be accessible f... | Login authenticates a user using an AuthenticationToken . If authentication is successful AND the Authenticator has determined that authentication is complete for the account login constructs a Subject instance representing the authenticated account s identity . Once a subject instance is constructed it is bound to the... | 238 | 61 |
248,103 | def ensure_security_manager ( self , subject_context ) : if ( subject_context . resolve_security_manager ( ) is not None ) : msg = ( "Subject Context resolved a security_manager " "instance, so not re-assigning. Returning." ) logger . debug ( msg ) return subject_context msg = ( "No security_manager found in context. A... | Determines whether there is a SecurityManager instance in the context and if not adds self to the context . This ensures that do_create_subject will have access to a SecurityManager during Subject construction . | 105 | 41 |
248,104 | def resolve_session ( self , subject_context ) : if ( subject_context . resolve_session ( ) is not None ) : msg = ( "Context already contains a session. Returning." ) logger . debug ( msg ) return subject_context try : # Context couldn't resolve it directly, let's see if we can # since we have direct access to the sess... | This method attempts to resolve any associated session based on the context and returns a context that represents this resolved Session to ensure it may be referenced if needed by the invoked do_create_subject that performs actual Subject construction . | 182 | 43 |
248,105 | def resolve_identifiers ( self , subject_context ) : session = subject_context . session identifiers = subject_context . resolve_identifiers ( session ) if ( not identifiers ) : msg = ( "No identity (identifier_collection) found in the " "subject_context. Looking for a remembered identity." ) logger . debug ( msg ) ide... | ensures that a subject_context has identifiers and if it doesn t will attempt to locate them using heuristics | 165 | 23 |
248,106 | def logout ( self , subject ) : if ( subject is None ) : msg = "Subject argument cannot be None." raise ValueError ( msg ) self . before_logout ( subject ) identifiers = copy . copy ( subject . identifiers ) # copy is new to yosai if ( identifiers ) : msg = ( "Logging out subject with primary identifier {0}" . format (... | Logs out the specified Subject from the system . | 199 | 10 |
248,107 | def is_permitted ( self , identifiers , permission_s ) : identifier = identifiers . primary_identifier for required in permission_s : domain = Permission . get_domain ( required ) # assigned is a list of json blobs: assigned = self . get_authzd_permissions ( identifier , domain ) is_permitted = False for perms_blob in ... | If the authorization info cannot be obtained from the accountstore permission check tuple yields False . | 121 | 17 |
248,108 | def has_role ( self , identifiers , required_role_s ) : identifier = identifiers . primary_identifier # assigned_role_s is a set assigned_role_s = self . get_authzd_roles ( identifier ) if not assigned_role_s : msg = 'has_role: no roles obtained from account_store for [{0}]' . format ( identifier ) logger . warning ( m... | Confirms whether a subject is a member of one or more roles . | 138 | 14 |
248,109 | def on_start ( self , session , session_context ) : session_id = session . session_id web_registry = session_context [ 'web_registry' ] if self . is_session_id_cookie_enabled : web_registry . session_id = session_id logger . debug ( "Set SessionID cookie using id: " + str ( session_id ) ) else : msg = ( "Session ID coo... | Stores the Session s ID usually as a Cookie to associate with future requests . | 125 | 16 |
248,110 | def is_session_storage_enabled ( self , subject = None ) : if subject . get_session ( False ) : # then use what already exists return True if not self . session_storage_enabled : # honor global setting: return False # non-web subject instances can't be saved to web-only session managers: if ( not hasattr ( subject , 'w... | Returns True if session storage is generally available ( as determined by the super class s global configuration property is_session_storage_enabled and no request - specific override has turned off session storage False otherwise . | 126 | 40 |
248,111 | def default_marshaller ( obj ) : if hasattr ( obj , '__getstate__' ) : return obj . __getstate__ ( ) try : return obj . __dict__ except AttributeError : raise TypeError ( '{!r} has no __dict__ attribute and does not implement __getstate__()' . format ( obj . __class__ . __name__ ) ) | Retrieve the state of the given object . | 86 | 9 |
248,112 | def default_unmarshaller ( instance , state ) : if hasattr ( instance , '__setstate__' ) : instance . __setstate__ ( state ) else : try : instance . __dict__ . update ( state ) except AttributeError : raise TypeError ( '{!r} has no __dict__ attribute and does not implement __setstate__()' . format ( instance . __class_... | Restore the state of an object . | 95 | 8 |
248,113 | def do_authenticate_account ( self , authc_token ) : try : realms = self . token_realm_resolver [ authc_token . __class__ ] except KeyError : raise KeyError ( 'Unsupported Token Type Provided: ' , authc_token . __class__ . __name__ ) if ( len ( self . realms ) == 1 ) : account = self . authenticate_single_realm_account... | Returns an account object only when the current token authenticates AND the authentication process is complete raising otherwise | 366 | 19 |
248,114 | def extra_from_record ( self , record ) : return { attr_name : record . __dict__ [ attr_name ] for attr_name in record . __dict__ if attr_name not in BUILTIN_ATTRS } | Returns extra dict you passed to logger . | 57 | 8 |
248,115 | def save ( self , subject ) : if ( self . is_session_storage_enabled ( subject ) ) : self . merge_identity ( subject ) else : msg = ( "Session storage of subject state for Subject [{0}] has " "been disabled: identity and authentication state are " "expected to be initialized on every request or " "invocation." . format... | Saves the subject s state to the subject s Session only if session storage is enabled for the subject . If session storage is not enabled for the specific Subject this method does nothing . | 91 | 36 |
248,116 | def create_manager ( self , yosai , settings , session_attributes ) : mgr_settings = SecurityManagerSettings ( settings ) attributes = mgr_settings . attributes realms = self . _init_realms ( settings , attributes [ 'realms' ] ) session_attributes = self . _init_session_attributes ( session_attributes , attributes ) se... | Order of execution matters . The sac must be set before the cache_handler is instantiated so that the cache_handler s serialization manager instance registers the sac . | 207 | 33 |
248,117 | def check_permission ( self , identifiers , permission_s , logical_operator ) : self . assert_realms_configured ( ) permitted = self . is_permitted_collective ( identifiers , permission_s , logical_operator ) if not permitted : msg = "Subject lacks permission(s) to satisfy logical operation" raise UnauthorizedException... | like Yosai s authentication process the authorization process will raise an Exception to halt further authz checking once Yosai determines that a Subject is unauthorized to receive the requested permission | 77 | 35 |
248,118 | def by_type ( self , identifier_class ) : myidentifiers = set ( ) for identifier in self . source_identifiers . values ( ) : if ( isinstance ( identifier , identifier_class ) ) : myidentifiers . update ( [ identifier ] ) return set ( myidentifiers ) | returns all unique instances of a type of identifier | 63 | 10 |
248,119 | def create ( self , session ) : sessionid = super ( ) . create ( session ) # calls _do_create and verify self . _cache ( session , sessionid ) return sessionid | caches the session and caches an entry to associate the cached session with the subject | 40 | 16 |
248,120 | def start ( self , session_context ) : # is a SimpleSesson: session = self . _create_session ( session_context ) self . session_handler . on_start ( session , session_context ) mysession = session_tuple ( None , session . session_id ) self . notify_event ( mysession , 'SESSION.START' ) # Don't expose the EIS-tier Sessi... | unlike shiro yosai does not apply session timeouts from within the start method of the SessionManager but rather defers timeout settings responsibilities to the SimpleSession which uses session_settings | 125 | 38 |
248,121 | def _setup ( self , name = None ) : envvar = self . __dict__ [ 'env_var' ] if envvar : settings_file = os . environ . get ( envvar ) else : settings_file = self . __dict__ [ 'file_path' ] if not settings_file : msg = ( "Requested settings, but none can be obtained for the envvar." "Since no config filepath can be obtai... | Load the settings module referenced by env_var . This environment - defined configuration process is called during the settings configuration process . | 132 | 24 |
248,122 | def remember_encrypted_identity ( self , subject , encrypted ) : try : # base 64 encode it and store as a cookie: encoded = base64 . b64encode ( encrypted ) . decode ( 'utf-8' ) subject . web_registry . remember_me = encoded except AttributeError : msg = ( "Subject argument is not an HTTP-aware instance. This " "is req... | Base64 - encodes the specified serialized byte array and sets that base64 - encoded String as the cookie value . | 118 | 24 |
248,123 | def get_remembered_encrypted_identity ( self , subject_context ) : if ( self . is_identity_removed ( subject_context ) ) : if not isinstance ( subject_context , web_subject_abcs . WebSubjectContext ) : msg = ( "SubjectContext argument is not an HTTP-aware instance. " "This is required to obtain a web registry " "in ord... | Returns a previously serialized identity byte array or None if the byte array could not be acquired . | 241 | 19 |
248,124 | def _get_settings_class ( ) : if not hasattr ( django_settings , "AUTH_ADFS" ) : msg = "The configuration directive 'AUTH_ADFS' was not found in your Django settings" raise ImproperlyConfigured ( msg ) cls = django_settings . AUTH_ADFS . get ( 'SETTINGS_CLASS' , DEFAULT_SETTINGS_CLASS ) return import_string ( cls ) | Get the AUTH_ADFS setting from the Django settings . | 99 | 12 |
248,125 | def build_authorization_endpoint ( self , request , disable_sso = None ) : self . load_config ( ) redirect_to = request . GET . get ( REDIRECT_FIELD_NAME , None ) if not redirect_to : redirect_to = django_settings . LOGIN_REDIRECT_URL redirect_to = base64 . urlsafe_b64encode ( redirect_to . encode ( ) ) . decode ( ) qu... | This function returns the ADFS authorization URL . | 263 | 9 |
248,126 | def create_user ( self , claims ) : # Create the user username_claim = settings . USERNAME_CLAIM usermodel = get_user_model ( ) user , created = usermodel . objects . get_or_create ( * * { usermodel . USERNAME_FIELD : claims [ username_claim ] } ) if created or not user . password : user . set_unusable_password ( ) log... | Create the user if it doesn t exist yet | 115 | 9 |
248,127 | def update_user_attributes ( self , user , claims ) : required_fields = [ field . name for field in user . _meta . fields if field . blank is False ] for field , claim in settings . CLAIM_MAPPING . items ( ) : if hasattr ( user , field ) : if claim in claims : setattr ( user , field , claims [ claim ] ) logger . debug ... | Updates user attributes based on the CLAIM_MAPPING setting . | 254 | 15 |
248,128 | def update_user_groups ( self , user , claims ) : if settings . GROUPS_CLAIM is not None : # Update the user's group memberships django_groups = [ group . name for group in user . groups . all ( ) ] if settings . GROUPS_CLAIM in claims : claim_groups = claims [ settings . GROUPS_CLAIM ] if not isinstance ( claim_groups... | Updates user group memberships based on the GROUPS_CLAIM setting . | 434 | 16 |
248,129 | def update_user_flags ( self , user , claims ) : if settings . GROUPS_CLAIM is not None : if settings . GROUPS_CLAIM in claims : access_token_groups = claims [ settings . GROUPS_CLAIM ] if not isinstance ( access_token_groups , list ) : access_token_groups = [ access_token_groups , ] else : logger . debug ( "The config... | Updates user boolean attributes based on the BOOLEAN_CLAIM_MAPPING setting . | 396 | 20 |
248,130 | def get ( self , request ) : code = request . GET . get ( "code" ) if not code : # Return an error message return render ( request , 'django_auth_adfs/login_failed.html' , { 'error_message' : "No authorization code was provided." , } , status = 400 ) redirect_to = request . GET . get ( "state" ) user = authenticate ( r... | Handles the redirect from ADFS to our site . We try to process the passed authorization code and login the user . | 374 | 24 |
248,131 | def authenticate ( self , request ) : auth = get_authorization_header ( request ) . split ( ) if not auth or auth [ 0 ] . lower ( ) != b'bearer' : return None if len ( auth ) == 1 : msg = 'Invalid authorization header. No credentials provided.' raise exceptions . AuthenticationFailed ( msg ) elif len ( auth ) > 2 : msg... | Returns a User if a correct access token has been supplied in the Authorization header . Otherwise returns None . | 203 | 20 |
248,132 | def molecular_orbital ( coords , mocoeffs , gbasis ) : # Making a closure def f ( x , y , z , coords = coords , mocoeffs = mocoeffs , gbasis = gbasis ) : # The other functions take nanometers return sum ( c * bf ( x * 10 , y * 10 , z * 10 ) for c , bf in zip ( mocoeffs , getbfs ( coords * 10 , gbasis ) ) ) return f | Return a molecular orbital given the nuclei coordinates as well as molecular orbital coefficients and basis set specification as given by the cclib library . | 118 | 28 |
248,133 | def getbfs ( coords , gbasis ) : sym2powerlist = { 'S' : [ ( 0 , 0 , 0 ) ] , 'P' : [ ( 1 , 0 , 0 ) , ( 0 , 1 , 0 ) , ( 0 , 0 , 1 ) ] , 'D' : [ ( 2 , 0 , 0 ) , ( 0 , 2 , 0 ) , ( 0 , 0 , 2 ) , ( 1 , 1 , 0 ) , ( 0 , 1 , 1 ) , ( 1 , 0 , 1 ) ] , 'F' : [ ( 3 , 0 , 0 ) , ( 2 , 1 , 0 ) , ( 2 , 0 , 1 ) , ( 1 , 2 , 0 ) , ( 1 , 1... | Convenience function for both wavefunction and density based on PyQuante Ints . py . | 308 | 20 |
248,134 | def A_term ( i , r , u , l1 , l2 , PAx , PBx , CPx , gamma ) : return pow ( - 1 , i ) * binomial_prefactor ( i , l1 , l2 , PAx , PBx ) * pow ( - 1 , u ) * factorial ( i ) * pow ( CPx , i - 2 * r - 2 * u ) * pow ( 0.25 / gamma , r + u ) / factorial ( r ) / factorial ( u ) / factorial ( i - 2 * r - 2 * u ) | THO eq . 2 . 18 | 127 | 7 |
248,135 | def A_array ( l1 , l2 , PA , PB , CP , g ) : Imax = l1 + l2 + 1 A = [ 0 ] * Imax for i in range ( Imax ) : for r in range ( int ( floor ( i / 2 ) + 1 ) ) : for u in range ( int ( floor ( ( i - 2 * r ) / 2 ) + 1 ) ) : I = i - 2 * r - u A [ I ] = A [ I ] + A_term ( i , r , u , l1 , l2 , PA , PB , CP , g ) return A | THO eq . 2 . 18 and 3 . 1 | 134 | 11 |
248,136 | def _normalize ( self ) : l , m , n = self . powers self . norm = np . sqrt ( pow ( 2 , 2 * ( l + m + n ) + 1.5 ) * pow ( self . exponent , l + m + n + 1.5 ) / fact2 ( 2 * l - 1 ) / fact2 ( 2 * m - 1 ) / fact2 ( 2 * n - 1 ) / pow ( np . pi , 1.5 ) ) return | Normalize basis function . From THO eq . 2 . 2 | 104 | 13 |
248,137 | def hide ( self , selections ) : if 'atoms' in selections : self . hidden_state [ 'atoms' ] = selections [ 'atoms' ] self . on_atom_hidden_changed ( ) if 'bonds' in selections : self . hidden_state [ 'bonds' ] = selections [ 'bonds' ] self . on_bond_hidden_changed ( ) if 'box' in selections : self . hidden_state [ 'box... | Hide objects in this representation . BallAndStickRepresentation support selections of atoms and bonds . | 200 | 19 |
248,138 | def change_radius ( self , selections , value ) : if 'atoms' in selections : atms = selections [ 'atoms' ] . mask if value is None : self . radii_state . array [ atms ] = [ vdw_radii . get ( t ) * 0.3 for t in self . system . type_array [ atms ] ] else : self . radii_state . array [ atms ] = value self . update_scale_f... | Change the radius of each atom by a certain value | 113 | 10 |
248,139 | def paintGL ( self ) : if self . post_processing : # Render to the first framebuffer glBindFramebuffer ( GL_FRAMEBUFFER , self . fb0 ) glViewport ( 0 , 0 , self . width ( ) , self . height ( ) ) status = glCheckFramebufferStatus ( GL_FRAMEBUFFER ) if ( status != GL_FRAMEBUFFER_COMPLETE ) : reason = dict ( GL_FRAMEBUFFE... | GL function called each time a frame is drawn | 648 | 9 |
248,140 | def toimage ( self , width = None , height = None ) : from . postprocessing import NoEffect effect = NoEffect ( self ) self . post_processing . append ( effect ) oldwidth , oldheight = self . width ( ) , self . height ( ) #self.initializeGL() if None not in ( width , height ) : self . resize ( width , height ) self . r... | Return the current scene as a PIL Image . | 236 | 10 |
248,141 | def _real ( coords1 , charges1 , coords2 , charges2 , rcut , alpha , box ) : n = coords1 . shape [ 0 ] m = coords2 . shape [ 0 ] # Unit vectors a = box [ 0 ] b = box [ 1 ] c = box [ 2 ] # This is helpful to add the correct number of boxes l_max = int ( np . ceil ( 2.0 * rcut / np . min ( np . trace ( box ) ) ) ) result... | Calculate ewald real part . Box has to be a cuboidal box you should transform any other box shape to a cuboidal box before using this . | 329 | 32 |
248,142 | def _reciprocal ( coords1 , charges1 , coords2 , charges2 , kmax , kappa , box ) : n = coords1 . shape [ 0 ] m = coords2 . shape [ 0 ] result = np . zeros ( n , dtype = np . float64 ) need_self = np . zeros ( n , dtype = np . uint8 ) # Reciprocal unit vectors g1 , g2 , g3 = reciprocal_vectors ( box ) V = box_volume ( b... | Calculate ewald reciprocal part . Box has to be a cuboidal box you should transform any other box shape to a cuboidal box before using this . | 476 | 32 |
248,143 | def update_bounds ( self , bounds ) : starts = bounds [ : , 0 , : ] ends = bounds [ : , 1 , : ] self . bounds = bounds self . lengths = np . sqrt ( ( ( ends - starts ) ** 2 ) . sum ( axis = 1 ) ) vertices , normals , colors = self . _process_reference ( ) self . tr . update_vertices ( vertices ) self . tr . update_norm... | Update cylinders start and end positions | 102 | 6 |
248,144 | def make_trajectory ( first , filename , restart = False ) : mode = 'w' if restart : mode = 'a' return Trajectory ( first , filename , mode ) | Factory function to easily create a trajectory object | 40 | 8 |
248,145 | def has_key ( self , key ) : k = self . _lowerOrReturn ( key ) return k in self . data | Case insensitive test whether key exists . | 27 | 7 |
248,146 | def update_positions ( self , positions ) : sphs_verts = self . sphs_verts_radii . copy ( ) sphs_verts += positions . reshape ( self . n_spheres , 1 , 3 ) self . tr . update_vertices ( sphs_verts ) self . poslist = positions | Update the sphere positions . | 70 | 5 |
248,147 | def isnamedtuple ( obj ) : return isinstance ( obj , tuple ) and hasattr ( obj , "_fields" ) and hasattr ( obj , "_asdict" ) and callable ( obj . _asdict ) | Heuristic check if an object is a namedtuple . | 48 | 12 |
248,148 | def running_coordination_number ( coordinates_a , coordinates_b , periodic , binsize = 0.002 , cutoff = 1.5 ) : x , y = rdf ( coordinates_a , coordinates_b , periodic = periodic , normalize = False , binsize = binsize , cutoff = cutoff ) y = y . astype ( 'float32' ) / len ( coordinates_a ) y = np . cumsum ( y ) return ... | This is the cumulative radial distribution function also called running coordination number | 99 | 12 |
248,149 | def update_colors ( self , colors ) : colors = np . array ( colors , dtype = np . uint8 ) self . _vbo_c . set_data ( colors ) self . _vbo_c . unbind ( ) | Update the colors | 53 | 3 |
248,150 | def frames ( skip = 1 ) : from PyQt4 import QtGui for i in range ( 0 , viewer . traj_controls . max_index , skip ) : viewer . traj_controls . goto_frame ( i ) yield i QtGui . qApp . processEvents ( ) | Useful command to iterate on the trajectory frames . It can be used in a for loop . | 66 | 20 |
248,151 | def display_system ( system , autozoom = True ) : viewer . clear ( ) viewer . add_representation ( BallAndStickRepresentation , system ) if autozoom : autozoom_ ( ) viewer . update ( ) msg ( str ( system ) ) | Display a ~chemlab . core . System instance at screen | 58 | 13 |
248,152 | def display_molecule ( mol , autozoom = True ) : s = System ( [ mol ] ) display_system ( s , autozoom = True ) | Display a ~chemlab . core . Molecule instance in the viewer . | 36 | 16 |
248,153 | def load_molecule ( name , format = None ) : mol = datafile ( name , format = format ) . read ( 'molecule' ) display_system ( System ( [ mol ] ) ) | Read a ~chemlab . core . Molecule from a file . | 45 | 15 |
248,154 | def write_system ( filename , format = None ) : datafile ( filename , format = format , mode = 'w' ) . write ( 'system' , current_system ( ) ) | Write the system currently displayed to a file . | 40 | 9 |
248,155 | def write_molecule ( filename , format = None ) : datafile ( filename , format = format , mode = 'w' ) . write ( 'molecule' , current_system ( ) ) | Write the system displayed in a file as a molecule . | 44 | 11 |
248,156 | def load_trajectory ( name , skip = 1 , format = None ) : df = datafile ( name , format = format ) dt , coords = df . read ( 'trajectory' , skip = skip ) boxes = df . read ( 'boxes' ) viewer . current_traj = coords viewer . frame_times = dt viewer . traj_controls . set_ticks ( len ( dt ) ) def update ( index ) : f = co... | Load a trajectory file into chemlab . You should call this command after you load a ~chemlab . core . System through load_system or load_remote_system . | 233 | 37 |
248,157 | def from_arrays ( cls , * * kwargs ) : if 'mol_indices' in kwargs : raise DeprecationWarning ( 'The mol_indices argument is deprecated, use maps instead. (See from_arrays docstring)' ) return super ( System , cls ) . from_arrays ( * * kwargs ) | Initialize a System from its constituent arrays . It is the fastest way to initialize a System well suited for reading one or more big System from data files . | 78 | 31 |
248,158 | def minimum_image ( self ) : if self . box_vectors is None : raise ValueError ( 'No periodic vectors defined' ) else : self . r_array = minimum_image ( self . r_array , self . box_vectors . diagonal ( ) ) return self | Align the system according to the minimum image convention | 60 | 10 |
248,159 | def where ( self , within_of = None , inplace = False , * * kwargs ) : masks = super ( System , self ) . where ( inplace = inplace , * * kwargs ) def index_to_mask ( index , n ) : val = np . zeros ( n , dtype = 'bool' ) val [ index ] = True return val def masks_and ( dict1 , dict2 ) : return { k : dict1 [ k ] & index_t... | Return indices that met the conditions | 360 | 6 |
248,160 | def _gser ( a , x ) : ITMAX = 100 EPS = 3.e-7 gln = lgamma ( a ) assert ( x >= 0 ) , 'x < 0 in gser' if x == 0 : return 0 , gln ap = a delt = sum = 1. / a for i in range ( ITMAX ) : ap = ap + 1. delt = delt * x / ap sum = sum + delt if abs ( delt ) < abs ( sum ) * EPS : break else : print ( 'a too large, ITMAX too smal... | Series representation of Gamma . NumRec sect 6 . 1 . | 160 | 12 |
248,161 | def _gcf ( a , x ) : ITMAX = 100 EPS = 3.e-7 FPMIN = 1.e-30 gln = lgamma ( a ) b = x + 1. - a c = 1. / FPMIN d = 1. / b h = d for i in range ( 1 , ITMAX + 1 ) : an = - i * ( i - a ) b = b + 2. d = an * d + b if abs ( d ) < FPMIN : d = FPMIN c = b + an / c if abs ( c ) < FPMIN : c = FPMIN d = 1. / d delt = d * c h = h *... | Continued fraction representation of Gamma . NumRec sect 6 . 1 | 218 | 13 |
248,162 | def dmat ( c , nocc ) : return np . dot ( c [ : , : nocc ] , c [ : , : nocc ] . T ) | Form the density matrix from the first nocc orbitals of c | 35 | 13 |
248,163 | def geigh ( H , S ) : A = cholorth ( S ) E , U = np . linalg . eigh ( simx ( H , A ) ) return E , np . dot ( A , U ) | Solve the generalized eigensystem Hc = ESc | 49 | 13 |
248,164 | def _check_periodic ( periodic ) : periodic = np . array ( periodic ) # If it is a matrix if len ( periodic . shape ) == 2 : assert periodic . shape [ 0 ] == periodic . shape [ 1 ] , 'periodic shoud be a square matrix or a flat array' return np . diag ( periodic ) elif len ( periodic . shape ) == 1 : return periodic el... | Validate periodic input | 109 | 4 |
248,165 | def count_neighbors ( coordinates_a , coordinates_b , periodic , r ) : indices = nearest_neighbors ( coordinates_a , coordinates_b , periodic , r = r ) [ 0 ] if len ( indices ) == 0 : return 0 if isinstance ( indices [ 0 ] , collections . Iterable ) : return [ len ( ix ) for ix in indices ] else : return len ( indices ... | Count the neighbours number of neighbors . | 90 | 7 |
248,166 | def change_default_radii ( def_map ) : s = current_system ( ) rep = current_representation ( ) rep . radii_state . default = [ def_map [ t ] for t in s . type_array ] rep . radii_state . reset ( ) | Change the default radii | 63 | 5 |
248,167 | def add_post_processing ( effect , * * options ) : from chemlab . graphics . postprocessing import SSAOEffect , OutlineEffect , FXAAEffect , GammaCorrectionEffect pp_map = { 'ssao' : SSAOEffect , 'outline' : OutlineEffect , 'fxaa' : FXAAEffect , 'gamma' : GammaCorrectionEffect } pp = viewer . add_post_processing ( pp_m... | Apply a post processing effect . | 149 | 6 |
248,168 | def unit_vector ( x ) : y = np . array ( x , dtype = 'float' ) return y / norm ( y ) | Return a unit vector in the same direction as x . | 30 | 11 |
248,169 | def angle ( x , y ) : return arccos ( dot ( x , y ) / ( norm ( x ) * norm ( y ) ) ) * 180. / pi | Return the angle between vectors a and b in degrees . | 37 | 11 |
248,170 | def metric_from_cell ( cell ) : cell = np . asarray ( cell , dtype = float ) return np . dot ( cell , cell . T ) | Calculates the metric matrix from cell which is given in the Cartesian system . | 35 | 17 |
248,171 | def add_default_handler ( ioclass , format , extension = None ) : if format in _handler_map : print ( "Warning: format {} already present." . format ( format ) ) _handler_map [ format ] = ioclass if extension in _extensions_map : print ( "Warning: extension {} already handled by {} handler." . format ( extension , _ext... | Register a new data handler for a given format in the default handler list . | 106 | 15 |
248,172 | def minimum_image ( coords , pbc ) : # This will do the broadcasting coords = np . array ( coords ) pbc = np . array ( pbc ) # For each coordinate this number represents which box we are in image_number = np . floor ( coords / pbc ) wrap = coords - pbc * image_number return wrap | Wraps a vector collection of atom positions into the central periodic image or primary simulation cell . | 77 | 18 |
248,173 | def subtract_vectors ( a , b , periodic ) : r = a - b delta = np . abs ( r ) sign = np . sign ( r ) return np . where ( delta > 0.5 * periodic , sign * ( periodic - delta ) , r ) | Returns the difference of the points vec_a - vec_b subject to the periodic boundary conditions . | 57 | 20 |
248,174 | def add_vectors ( vec_a , vec_b , periodic ) : moved = noperiodic ( np . array ( [ vec_a , vec_b ] ) , periodic ) return vec_a + vec_b | Returns the sum of the points vec_a - vec_b subject to the periodic boundary conditions . | 49 | 20 |
248,175 | def distance_matrix ( a , b , periodic ) : a = a b = b [ : , np . newaxis ] return periodic_distance ( a , b , periodic ) | Calculate a distrance matrix between coordinates sets a and b | 38 | 13 |
248,176 | def geometric_center ( coords , periodic ) : max_vals = periodic theta = 2 * np . pi * ( coords / max_vals ) eps = np . cos ( theta ) * max_vals / ( 2 * np . pi ) zeta = np . sin ( theta ) * max_vals / ( 2 * np . pi ) eps_avg = eps . sum ( axis = 0 ) zeta_avg = zeta . sum ( axis = 0 ) theta_avg = np . arctan2 ( - zeta_... | Geometric center taking into account periodic boundaries | 156 | 8 |
248,177 | def radius_of_gyration ( coords , periodic ) : gc = geometric_center ( coords , periodic ) return ( periodic_distance ( coords , gc , periodic ) ** 2 ) . sum ( ) / len ( coords ) | Calculate the square root of the mean distance squared from the center of gravity . | 53 | 17 |
248,178 | def find ( query ) : assert type ( query ) == str or type ( query ) == str , 'query not a string object' searchurl = 'http://www.chemspider.com/Search.asmx/SimpleSearch?query=%s&token=%s' % ( urlquote ( query ) , TOKEN ) response = urlopen ( searchurl ) tree = ET . parse ( response ) elem = tree . getroot ( ) csid_tags... | Search by Name SMILES InChI InChIKey etc . Returns first 100 Compounds | 159 | 20 |
248,179 | def imageurl ( self ) : if self . _imageurl is None : self . _imageurl = 'http://www.chemspider.com/ImagesHandler.ashx?id=%s' % self . csid return self . _imageurl | Return the URL of a png image of the 2D structure | 56 | 13 |
248,180 | def loadextendedcompoundinfo ( self ) : apiurl = 'http://www.chemspider.com/MassSpecAPI.asmx/GetExtendedCompoundInfo?CSID=%s&token=%s' % ( self . csid , TOKEN ) response = urlopen ( apiurl ) tree = ET . parse ( response ) mf = tree . find ( '{http://www.chemspider.com/}MF' ) self . _mf = mf . text if mf is not None els... | Load extended compound info from the Mass Spec API | 612 | 9 |
248,181 | def image ( self ) : if self . _image is None : apiurl = 'http://www.chemspider.com/Search.asmx/GetCompoundThumbnail?id=%s&token=%s' % ( self . csid , TOKEN ) response = urlopen ( apiurl ) tree = ET . parse ( response ) self . _image = tree . getroot ( ) . text return self . _image | Return string containing PNG binary image data of 2D structure image | 93 | 12 |
248,182 | def mol ( self ) : if self . _mol is None : apiurl = 'http://www.chemspider.com/MassSpecAPI.asmx/GetRecordMol?csid=%s&calc3d=false&token=%s' % ( self . csid , TOKEN ) response = urlopen ( apiurl ) tree = ET . parse ( response ) self . _mol = tree . getroot ( ) . text return self . _mol | Return record in MOL format | 103 | 6 |
248,183 | def mol3d ( self ) : if self . _mol3d is None : apiurl = 'http://www.chemspider.com/MassSpecAPI.asmx/GetRecordMol?csid=%s&calc3d=true&token=%s' % ( self . csid , TOKEN ) response = urlopen ( apiurl ) tree = ET . parse ( response ) self . _mol3d = tree . getroot ( ) . text return self . _mol3d | Return record in MOL format with 3D coordinates calculated | 111 | 11 |
248,184 | def update_positions ( self , r_array ) : self . ar . update_positions ( r_array ) if self . has_bonds : self . br . update_positions ( r_array ) | Update the coordinate array r_array | 47 | 7 |
248,185 | def concatenate_attributes ( attributes ) : # We get a template/ tpl = attributes [ 0 ] attr = InstanceAttribute ( tpl . name , tpl . shape , tpl . dtype , tpl . dim , alias = None ) # Special case, not a single array has size bigger than 0 if all ( a . size == 0 for a in attributes ) : return attr else : attr . value ... | Concatenate InstanceAttribute to return a bigger one . | 122 | 13 |
248,186 | def concatenate_fields ( fields , dim ) : if len ( fields ) == 0 : raise ValueError ( 'fields cannot be an empty list' ) if len ( set ( ( f . name , f . shape , f . dtype ) for f in fields ) ) != 1 : raise ValueError ( 'fields should have homogeneous name, shape and dtype' ) tpl = fields [ 0 ] attr = InstanceAttribute ... | Create an INstanceAttribute from a list of InstnaceFields | 153 | 15 |
248,187 | def normalize_index ( index ) : index = np . asarray ( index ) if len ( index ) == 0 : return index . astype ( 'int' ) if index . dtype == 'bool' : index = index . nonzero ( ) [ 0 ] elif index . dtype == 'int' : pass else : raise ValueError ( 'Index should be either integer or bool' ) return index | normalize numpy index | 87 | 5 |
248,188 | def to_dict ( self ) : ret = merge_dicts ( self . __attributes__ , self . __relations__ , self . __fields__ ) ret = { k : v . value for k , v in ret . items ( ) } ret [ 'maps' ] = { k : v . value for k , v in self . maps . items ( ) } return ret | Return a dict representing the ChemicalEntity that can be read back using from_dict . | 81 | 17 |
248,189 | def from_json ( cls , string ) : exp_dict = json_to_data ( string ) version = exp_dict . get ( 'version' , 0 ) if version == 0 : return cls . from_dict ( exp_dict ) elif version == 1 : return cls . from_dict ( exp_dict ) else : raise ValueError ( "Version %d not supported" % version ) | Create a ChemicalEntity from a json string | 88 | 8 |
248,190 | def copy ( self ) : inst = super ( type ( self ) , type ( self ) ) . empty ( * * self . dimensions ) # Need to copy all attributes, fields, relations inst . __attributes__ = { k : v . copy ( ) for k , v in self . __attributes__ . items ( ) } inst . __fields__ = { k : v . copy ( ) for k , v in self . __fields__ . items ... | Create a copy of this ChemicalEntity | 166 | 7 |
248,191 | def copy_from ( self , other ) : # Need to copy all attributes, fields, relations self . __attributes__ = { k : v . copy ( ) for k , v in other . __attributes__ . items ( ) } self . __fields__ = { k : v . copy ( ) for k , v in other . __fields__ . items ( ) } self . __relations__ = { k : v . copy ( ) for k , v in other... | Copy properties from another ChemicalEntity | 145 | 6 |
248,192 | def update ( self , dictionary ) : allowed_attrs = list ( self . __attributes__ . keys ( ) ) allowed_attrs += [ a . alias for a in self . __attributes__ . values ( ) ] for k in dictionary : # We only update existing attributes if k in allowed_attrs : setattr ( self , k , dictionary [ k ] ) return self | Update the current chemical entity from a dictionary of attributes | 82 | 10 |
248,193 | def subentity ( self , Entity , index ) : dim = Entity . __dimension__ entity = Entity . empty ( ) if index >= self . dimensions [ dim ] : raise ValueError ( 'index {} out of bounds for dimension {} (size {})' . format ( index , dim , self . dimensions [ dim ] ) ) for name , attr in self . __attributes__ . items ( ) : ... | Return child entity | 427 | 3 |
248,194 | def sub_dimension ( self , index , dimension , propagate = True , inplace = False ) : filter_ = self . _propagate_dim ( index , dimension , propagate ) return self . subindex ( filter_ , inplace ) | Return a ChemicalEntity sliced through a dimension . If other dimensions depend on this one those are updated accordingly . | 50 | 21 |
248,195 | def expand_dimension ( self , newdim , dimension , maps = { } , relations = { } ) : for name , attr in self . __attributes__ . items ( ) : if attr . dim == dimension : newattr = attr . copy ( ) newattr . empty ( newdim - attr . size ) self . __attributes__ [ name ] = concatenate_attributes ( [ attr , newattr ] ) for na... | When we expand we need to provide new maps and relations as those can t be inferred | 393 | 17 |
248,196 | def concat ( self , other , inplace = False ) : # Create new entity if inplace : obj = self else : obj = self . copy ( ) # Stitch every attribute for name , attr in obj . __attributes__ . items ( ) : attr . append ( other . __attributes__ [ name ] ) # Stitch every relation for name , rel in obj . __relations__ . items ... | Concatenate two ChemicalEntity of the same kind | 209 | 11 |
248,197 | def sub ( self , inplace = False , * * kwargs ) : filter_ = self . where ( * * kwargs ) return self . subindex ( filter_ , inplace ) | Return a entity where the conditions are met | 42 | 8 |
248,198 | def sub ( self , index ) : index = np . asarray ( index ) if index . dtype == 'bool' : index = index . nonzero ( ) [ 0 ] if self . size < len ( index ) : raise ValueError ( 'Can\'t subset "{}": index ({}) is bigger than the number of elements ({})' . format ( self . name , len ( index ) , self . size ) ) inst = self . ... | Return a sub - attribute | 135 | 5 |
248,199 | def resolve ( input , representation , resolvers = None , * * kwargs ) : resultdict = query ( input , representation , resolvers , * * kwargs ) result = resultdict [ 0 ] [ 'value' ] if resultdict else None if result and len ( result ) == 1 : result = result [ 0 ] return result | Resolve input to the specified output representation | 74 | 8 |
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