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Methods defined here:
- __init__(self, nid='')
- create a Fraglets interpreter and reaction vessel with node id
'nid'
- add_cnx(self, dst, addr)
- add a link between this vessel and another vessel: 'dst' is the
tag that identifies the link; 'addr' is the reference to the
Fraglets object corresponding to the destination vessel
- del_cnx(self, dst)
- delete a link given its tag id 'dst'
- getmethod(self, mol)
- get method that implements the instruction at the head
(first symbol) of fraglet 'mol'
- getname(self, op)
- get human-friendly name for an instruction in character-encoded
format
- inert(self)
- true if reactor is inert: there are no more reactions to fire
- inject(self, mol, mult=1)
- inject 'mult' copies of fraglet 'mol' in the reactor
- inject_list(self, mlist)
- inject the list of fraglets 'mlist' in the reactor
- interpret(self, fname='')
- interpret a file containing fraglet code for a single vessel
- isbimol(self, mol)
- true if fraglet 'mol' starts with a bimolecular reaction rule
- ismatchp(self, mol)
- true if fraglet 'mol' starts with a matchp instruction
- ispassive(self, mol)
- true if fraglet 'mol' does not start with a reaction rule
- isunimol(self, mol)
- true if fraglet 'mol' starts with a unimolecular reaction rule
- iterate(self)
- one iteration of fraglets for single-vessel configuration
- mol2fraglet(self, mol, mult=1)
- convert a 'character-encoded' molecule into a human-readable
fraglet
- parse(self, frag)
- parse fraglet, converting it to a condensed 'character-encoded'
string with one character per symbol
- propensity(self)
- calculate all propensities of bimolecular reactions
- r_dup(self, mol)
- fire a 'dup' fraglet: duplicate 3rd symbol
- r_exch(self, mol)
- fire an 'exch' fraglet: exchange symbols n. 3 and 4
- r_fork(self, mol)
- fire a 'fork' fraglet that duplicates its tail
- r_match(self, mol1, mol2)
- fire a 'match' fraglet: merge 2 fraglets
- r_matchp(self, mol1, mol2)
- fire a 'matchp' fraglet: merge 2 fraglets, while keeping a
copy of the original matchp fraglet
- r_nop(self, mol)
- fire a 'nop' fraglet: consume 'nop' symbol
- r_nul(self, mol)
- fire a 'nul' fraglet: delete the fraglet
- r_pop(self, mol)
- fire a 'pop' fraglet: consume 'nop' symbol plus 3rd symbol
- r_send(self, mol)
- fire a 'send' fraglet by consuming the header symbols and
injecting the remaining tail in the destination vessel
- r_split(self, mol)
- fire a 'split' fraglet: split at the first occurrence of a '*'
symbol
- react(self, w)
- perform the selected reaction pointed to by the dice position w
(typically involked from the hierarchical Gillespie SSA
implementation in Cell.py)
- react1(self, mol)
- fire unimolecular reaction involving molecule 'mol'
- react2(self, mol1, mol2)
- fire bimolecular reaction between mol1 and mol2
- run(self, niter)
- run for 'niter' iterations, or until the reactor is inert
- run_bimol(self)
- pick one bimolecular reaction using Gillespie's SSA;
assumes propensities are up to date;
for single reactor only:
if more than one reactor, use react() within Cell instead
- run_unimol(self)
- run all unimolecular transformations at once
- set_nodeid(self, tag)
- assign nodeid 'tag' to this vessel
- trace(self)
- print all fraglets in the vessel, in human-readable format
- trace_all_msets(self)
- print all fraglets in the vessel, in 'compiled' character-code
format (for debugging purposes)
- trace_mlist(self, mlist)
- print a list of fraglets
- trace_mol(self, mol, mult=1)
- print a given fraglet, in human-readable format
- trace_reaction(self, mlist1, mlist2)
- print reaction in the form [frag1], [frag2] --> [frag3]
(doesn't work for the send reaction)
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