Package schrodinger :: Package application :: Package matsci :: Module amorphous :: Class Moieties

Class Moieties

object --+
         |
        Moieties

A holder and manager for the various moieties that make up the polymer

Instance Methods

[hide private]

__init__(self, filename, logger, structs=[])
Create a Moieties object

bool

hasCascader(self)
Has a cascader been defined?

bool

hasBrancher(self)
Has a brancher been defined?

bool

hasRings(self)
Do any moieties have rings?

Monomer

getMonomer(self, letter)
Get the monomer with the given one-letter code

Monomer, Initiator, Cascader, or Terminator

getMoiety(self, letter)
Get the get one single moiety based on 'INI', 'TRM', 'CAS' or monomer one-letter code.

list

getOneLetterCodes(self)
Get all the allowed one-letter codes

bool

checkValidOneLetterCodes(self, codes)
Check that all the codes in the given string are valid

bool

checkValidWeights(self, weights)
Validate the given weights

int

getCascadeGenerations(self)
Get the number of cascade generations

list

getAllMoietyNames(self)
Get the names of all Moieties - initiator, terminator, monomers, etc.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, filename, logger, structs=`[]`)
(Constructor)

Create a Moieties object

Parameters:

filename (str) - The path to the file that holds the moiety structures
logger (logging.Logger) - The logger for this builder

Overrides: object.__init__

hasCascader(self)

Has a cascader been defined?

Returns: bool: Whether a cascader was defined

hasBrancher(self)

Has a brancher been defined?

Returns: bool: Whether a brancher was defined

hasRings(self)

Do any moieties have rings?

Returns: bool: Whether any of the moieties have rings

getMonomer(self, letter)

Get the monomer with the given one-letter code

Parameters:

letter (str) - The one-letter code for the desired monomer

Returns: Monomer

The monomer with the given one-letter code

getMoiety(self, letter)

Get the get one single moiety based on 'INI', 'TRM', 'CAS' or monomer one-letter code.

Parameters:

letter (str) - The one-letter code for the desired monomer

Returns: Monomer, Initiator, Cascader, or Terminator

the initiator, cascader, terminat or one nonomer find by the one letter code

getOneLetterCodes(self)

Get all the allowed one-letter codes

Returns: list: All the defined one-letter codes

checkValidOneLetterCodes(self, codes)

Check that all the codes in the given string are valid

Parameters:

codes (str) - A string with a series of one-letter codes

Returns: bool

Whether all the one-letter codes are associated with a Monomer

checkValidWeights(self, weights)

Validate the given weights

Parameters:

weights (dict) - Keys are one-letter codes, values are integer weights for that monomer in a random copolymer

Returns: bool

Whether all the one-letter codes in weights are valid

getCascadeGenerations(self)

Get the number of cascade generations

Returns: int: The number of cascade generations (0 if none)

getAllMoietyNames(self)

Get the names of all Moieties - initiator, terminator, monomers, etc.

Returns: list: A list of all moiety names. Monomers first, then initiator, terminator and cascader (if defined)

Class Moieties

__init__(self, filename, logger, structs=[]) (Constructor)

hasCascader(self)

hasBrancher(self)

hasRings(self)

getMonomer(self, letter)

getMoiety(self, letter)

getOneLetterCodes(self)

checkValidOneLetterCodes(self, codes)

checkValidWeights(self, weights)

getCascadeGenerations(self)

getAllMoietyNames(self)

init(self, filename, logger, structs=`[]`)
(Constructor)