forked from jczech/mcellRules
/
grammar_definition.py
164 lines (128 loc) · 8.88 KB
/
grammar_definition.py
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from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore, Keyword, Literal, \
CaselessLiteral, nums, Combine, alphas, nestedExpr, cppStyleComment, OneOrMore, \
quotedString, LineEnd, StringEnd, restOfLine, delimitedList, dictOf, Forward, Dict
lbrace = Suppress("{")
rbrace = Suppress("}")
lbracket = Suppress("[")
rbracket = Suppress("]")
lparen = Suppress("(")
rparen = Suppress(")")
equal = Suppress("=")
comma = Suppress(",")
point = Literal('.')
tilde = ('~')
bang = ('!')
e = CaselessLiteral('E')
plusorminus = Literal('+') | Literal('-')
hashsymbol = Suppress("#")
dbquotes = '"'
uni_arrow = Literal("->")
bi_arrow = Literal("<->")
#system keywords
system_constants_ = Keyword("SYSTEM_CONSTANTS")
# molecule keywords
define_molecules_ = Keyword("DEFINE_MOLECULES")
define_functions_ = Keyword("DEFINE_FUNCTIONS")
diffusion_constant_3d_ = Keyword("DIFFUSION_CONSTANT_3D")
diffusion_constant_2d_ = Keyword("DIFFUSION_CONSTANT_2D")
diffusion_function_ = Keyword("DIFFUSION_FUNCTION")
#reaction keywords
define_reactions_ = Keyword("DEFINE_REACTIONS")
#seed species keywords
instantiate_ = Keyword("INSTANTIATE")
object_ = Keyword("OBJECT")
parent_ = Keyword("PARENT")
release_site_ = Keyword("RELEASE_SITE")
#observables keywords
reaction_data_output_ = Keyword("REACTION_DATA_OUTPUT")
step_ = Keyword("STEP")
count_ = Keyword("COUNT")
#keywords inherited from bng
species_ = Keyword("Species")
molecules_ = Keyword("Molecules")
#misc
number = Word(nums)
integer = Combine(Optional(plusorminus) + number)
real = Combine(integer +
Optional(point + Optional(number)) +
Optional(e + integer))
numarg = (real | integer)
identifier = Word(alphas + "_", alphanums + "_")
dotidentifier = Word(alphas, alphanums + "_" + ".")
bracketidentifier = identifier + lbracket + Word(alphas) + rbracket
statement = Group(identifier + equal + (quotedString | restOfLine))
#math
mathElements = (numarg | ',' | '+' | '-' | '*' | '/' | '^' | '&' | '>' | '<' | '=' | '|' | identifier)
nestedMathDefinition = nestedExpr( '(', ')', content=mathElements)
mathDefinition = OneOrMore(mathElements)
section_enclosure2_ = nestedExpr( '{', '}')
section_enclosure_ = Forward()
nestedBrackets = nestedExpr('[', ']', content=section_enclosure_)
nestedCurlies = nestedExpr('{', '}', content=section_enclosure_)
section_enclosure_ << (statement | Group(identifier + ZeroOrMore(identifier) + nestedCurlies) | Group(identifier + '@' + restOfLine) | Word(alphas, alphanums + "_[]") | identifier | Suppress(',') | '@' | real)
function_entry_ = Suppress(dbquotes) + Group(identifier.setResultsName('functionName') + Suppress(lparen) +
delimitedList(Group(identifier.setResultsName('key') + Suppress(equal) + (identifier | numarg).setResultsName('value')), delim=',').setResultsName('parameters') + Suppress(rparen)) + Suppress(dbquotes)
name = Word(alphanums + '_')
species = Suppress('()') + Optional(Suppress('@' + Word(alphanums + '_-'))) + ZeroOrMore(Suppress('+') + Word(alphanums + "_" + ":#-")
+ Suppress("()") + Optional(Suppress('@' + Word(alphanums + '_-'))))
# bng pattern definition
component_definition = Group(identifier.setResultsName('componentName') + Optional(Group(Suppress(tilde) + delimitedList(identifier|integer,delim='~')).setResultsName('state')))
component_statement = Group(identifier.setResultsName('componentName') + Optional(Group(Suppress(tilde)+ (identifier | integer)).setResultsName('state')) + \
Optional(Group(Suppress(bang) + (numarg | '+' | '?')).setResultsName('bond'))
)
molecule_definition = Group(identifier.setResultsName('moleculeName') +
Optional((lparen + Optional(delimitedList(component_definition, delim=',').setResultsName('components')) + rparen)) +
Optional(Group('@' + Word(alphanums + '_-')).setResultsName('moleculeCompartment')))
molecule_instance = Group(identifier.setResultsName('moleculeName') +
Optional((lparen + Optional(delimitedList(component_statement, delim=',').setResultsName('components')) + rparen)) +
Optional(Group('@' + Word(alphanums + '_-')).setResultsName('moleculeCompartment')))
species_definition = Group(Optional(Group('@' + Word(alphanums + '_')).setResultsName('speciesCompartment') + Suppress('::')) +
delimitedList(molecule_instance, delim='.').setResultsName('speciesPattern'))
reaction_definition = Group(Group(delimitedList(species_definition, delim='+')).setResultsName('reactants') + (uni_arrow | bi_arrow) +
Group(delimitedList(species_definition, delim='+')).setResultsName('products') +
Group(lbracket + (numarg | (identifier + Suppress(Optional('()')))) + Optional(comma + (numarg| (identifier + Suppress(Optional('()'))))) + rbracket).setResultsName('rate'))
# generic hash section grammar
hashed_section = (hashsymbol + Group(OneOrMore(name) + section_enclosure2_))
#hash system_constants
#system_constants = Group()
hashed_system_constants = Group(hashsymbol + Suppress(system_constants_) + lbrace + OneOrMore(statement) + rbrace)
# hash molecule_entry
diffusion_entry_ = Group((diffusion_constant_2d_.setResultsName('2D') | diffusion_constant_3d_.setResultsName('3D')) + Suppress(equal) + (function_entry_.setResultsName('function') | (identifier | numarg).setResultsName('variable')))
molecule_entry = Group(molecule_definition + Optional(Group(lbrace + Optional(diffusion_entry_.setResultsName('diffusionFunction')) + (ZeroOrMore(statement)).setResultsName('moleculeParameters') + rbrace)))
hashed_molecule_section = Group(hashsymbol + Suppress(define_molecules_) + lbrace + OneOrMore(molecule_entry) + rbrace)
#hash function entry
function_name = Group(identifier + '()')
math_function_entry = Group(function_name.setResultsName('functionName') + Suppress(equal) + Group(restOfLine).setResultsName('functionBody'))
hashed_function_section = Group(hashsymbol + Suppress(define_functions_) + lbrace + ZeroOrMore(math_function_entry) +rbrace)
# hash reaction entry
hashed_reaction_section = Group(hashsymbol + Suppress(define_reactions_) + lbrace + OneOrMore(reaction_definition) + rbrace)
# hash observable entry
count_definition = Group(count_ + lbracket + species_definition.setResultsName('speciesPattern') + Suppress(',') + identifier + rbracket)
observable_entry = Group(lbrace + Group(delimitedList(count_definition, delim='+')).setResultsName('patterns') + rbrace + Suppress('=>') + quotedString.setResultsName('outputfile'))
bngobservable_entry = Group((species_ | molecules_).setResultsName('obskey') + identifier.setResultsName('obsname') + Group(delimitedList(species_definition, delim=',')).setResultsName('obspatterns'))
hashed_observable_section = Group(hashsymbol + Suppress(reaction_data_output_) + lbrace + OneOrMore(statement).setResultsName('statements') + ZeroOrMore(observable_entry).setResultsName('mdlobs') + ZeroOrMore(bngobservable_entry).setResultsName('bngobs') + rbrace)
# hash initialization entry
key = identifier + Suppress('=')
value = restOfLine
release_site_definition = Group(identifier.setResultsName('name') + release_site_ + lbrace + dictOf(key,value).setResultsName('entries') + rbrace)
object_definition = Group(identifier.setResultsName('compartmentName') + Suppress(object_) + (bracketidentifier | identifier) + (nestedExpr('{', '}',content=statement)).setResultsName('compartmentOptions'))
hashed_initialization_section = Group(hashsymbol + Suppress(instantiate_) + identifier.setResultsName('name') +
identifier.setResultsName('type') + lbrace + Group(ZeroOrMore(release_site_definition | object_definition)).setResultsName('entries') + rbrace )
other_sections = section_enclosure_
#statement = Group(identifier + equal + (quotedString | OneOrMore(mathElements))) + Suppress(LineEnd() | StringEnd())
grammar = ZeroOrMore(Suppress(other_sections) | Suppress(statement) | hashed_system_constants.setResultsName('systemConstants')
| hashed_molecule_section.setResultsName('molecules') | hashed_reaction_section.setResultsName('reactions')
| hashed_observable_section.setResultsName('observables')
| hashed_initialization_section.setResultsName('initialization')
| hashed_function_section.setResultsName('math_functions')
#| Suppress(hashed_section)
)
nonhashedgrammar = ZeroOrMore(Suppress(statement) | Suppress(hashed_section) | Dict(other_sections))
statementGrammar = ZeroOrMore(statement | Suppress(other_sections) | Suppress(hashed_section))
singleLineComment = "//" + restOfLine
grammar.ignore(singleLineComment)
grammar.ignore(cppStyleComment)
nonhashedgrammar.ignore(singleLineComment)
nonhashedgrammar.ignore(cppStyleComment)
statementGrammar.ignore(singleLineComment)
statementGrammar.ignore(cppStyleComment)