o RÅ€g *ã@sXdZddlmZddlmZGdd„dƒZGdd„dƒZGdd „d ƒZGd d „d ƒZd S) a‹BioPython Pathway module. Bio.Pathway is a lightweight class library designed to support the following tasks: - Data interchange and preprocessing between pathway databases and analysis software. - Quick prototyping of pathway analysis algorithms The basic object in the Bio.Pathway model is Interaction, which represents an arbitrary interaction between any number of biochemical species. Network objects are used to represent the connectivity between species in pathways and reaction networks. For applications where it is not necessary to explicitly represent network connectivity, the specialized classes Reaction and System should be used in place of Interacton and Network. The Bio.Pathway classes, especially Interaction, are intentionally designed to be very flexible. Their intended use are as wrappers around database specific records, such as BIND objects. The value-added in this module is a framework for representing collections of reactions in a way that supports graph theoretic and numeric analysis. Note: This module should be regarded as a prototype only. API changes are likely. Comments and feature requests are most welcome. é)Úreduce)Ú MultiGraphc@sJeZdZdZddd„Zdd„Zd d „Zd d „Zd d„Zdd„Z dd„Z dS)ÚReactiona"Abstraction for a biochemical transformation. This class represents a (potentially reversible) biochemical transformation of the type:: a S1 + b S2 + ... --> c P1 + d P2 + ... where: - a, b, c, d ... are positive numeric stochiometric coefficients, - S1, S2, ... are substrates - P1, P2, ... are products A Reaction should be viewed as the net result of one or more individual reaction steps, where each step is potentially facilitated by a different catalyst. Support for 'Reaction algebra' will be added at some point in the future. Attributes: - reactants -- dict of involved species to their stochiometric coefficients: reactants[S] = stochiometric constant for S - catalysts -- list/tuple of tuples of catalysts required for this reaction - reversible -- true iff reaction is reversible - data -- reference to arbitrary additional data Invariants: - for all S in reactants: reactants[S] != 0 - for all C in catalysts: catalysts[C] != 0 N©rcCsZ|duri|_n| ¡|_| ¡D] \}}|dkr|j|=qtt|ƒƒ|_||_||_dS)z!Initialize a new Reaction object.Nr)Ú reactantsÚcopyÚitemsÚsortedÚsetÚ catalystsÚdataÚ reversible)Úselfrr r r ÚrÚvaluerrúH/var/www/html/myenv/lib/python3.10/site-packages/Bio/Pathway/__init__.pyÚ__init__Hs € zReaction.__init__cCs:t|tƒo|j|jko|j|jko|j|jko|j|jkS)z#Return true iff self is equal to r.)Ú isinstancerrr r r )rrrrrÚ__eq__Ws  ÿ þ ý ûzReaction.__eq__cCst| ¡ƒ}t|ƒS©zReturn a hashcode for self.)ÚtupleÚspeciesÚhash)rÚtrrrÚ__hash__as zReaction.__hash__cCsd|j|j|j|jfS)ú1Return a debugging string representation of self.zReaction(%r, %r, %r, %r))rr r r ©rrrrÚ__repr__fs üzReaction.__repr__cCsÊd}d}t|jƒ}|D]J}|j|}|dkr3|dkr|d}|dkr,|tt|ƒƒd}|t|ƒ}q |dkrR|dkr?|d}|dkrK|t|ƒd}|t|ƒ}q tdƒ‚|jr_|d|S|d |S) ú'Return a string representation of self.Úrz + éÿÿÿÿú éz+Invalid 0 coefficient in Reaction.reactantsz <=> z --> )r rÚstrÚabsÚAttributeErrorr )rÚ substratesÚproductsÚ all_speciesrÚstochrrrÚ__str__os*    zReaction.__str__cCs4i}|jD] }|j| ||<qt||j|j|jƒS)z2Return a new Reaction that is the reverse of self.)rrr r r )rrrrrrÚreverse‹s zReaction.reversecCó t|jƒS)z.Return a list of all Species involved in self.)Úlistrrrrrr’ó zReaction.species)NrrN) Ú__name__Ú __module__Ú __qualname__Ú__doc__rrrrr*r+rrrrrr)s    rc@sReZdZdZddd„Zdd„Zdd„Zd d „Zd d „Zd d„Z dd„Z dd„Z dS)ÚSystemzÚAbstraction for a collection of reactions. This class is used in the Bio.Pathway framework to represent an arbitrary collection of reactions without explicitly defined links. Attributes: - None rcCót|ƒ|_dS)zInitialize a new System object.N)r Ú_System__reactions)rÚ reactionsrrrr¢ózSystem.__init__cCsdd tt|jƒ¡dS)rzSystem(ú,ú))ÚjoinÚmapÚreprr5rrrrr¦szSystem.__repr__cCs*dtt|jƒƒdtt| ¡ƒƒdS)rz System of z reactions involving z species)r#Úlenr5rrrrrr*ªs ÿþýüÿzSystem.__str__cCó|j |¡dS)zAdd reaction to self.N)r5Úadd©rÚreactionrrrÚ add_reaction´ózSystem.add_reactioncCr>)zRemove reaction from self.N)r5Úremover@rrrÚremove_reaction¸rCzSystem.remove_reactioncCr,)z]Return a list of the reactions in this system. Note the order is arbitrary! )r-r5rrrrr6¼s zSystem.reactionscCs&tttdd„dd„| ¡DƒgƒƒƒS)z,Return a list of the species in this system.cSs||S©Nr)ÚsÚxrrrÚÇsz System.species..cSsg|]}| ¡‘qSr)r)Ú.0rHrrrÚ Çsz"System.species..)r r rr6rrrrrÄs ÿzSystem.speciescCsr| ¡}| ¡}gt|ƒ}tt|ƒƒD]}dt|ƒ||<|| ¡D]}||j||| |¡<q$q|||fS)a‹Compute the stoichiometry matrix for self. Returns (species, reactions, stoch) where: - species = ordered list of species in this system - reactions = ordered list of reactions in this system - stoch = 2D array where stoch[i][j] is coef of the jth species in the ith reaction, as defined by species and reactions above r)rr6r=ÚrangerÚindex)rrr6r)ÚirGrrrÚ stochiometryÊs ÿ zSystem.stochiometryN©r) r/r0r1r2rrr*rBrEr6rrOrrrrr3—s   r3c@s0eZdZdZdd„Zdd„Zdd„Zdd „Zd S) Ú Interactiona!An arbitrary interaction between any number of species. This class definition is intended solely as a minimal wrapper interface that should be implemented and extended by more specific abstractions. Attributes: - data -- reference to arbitrary additional data cCs ||_dSrF)r )rr rrrÚ__init_ðs zInteraction.__init_cCr,r)rr rrrrrór.zInteraction.__hash__cCódt|jƒdS)rz Interaction(r9)r<r rrrrr÷ózInteraction.__repr__cCrS)rú<ú>)r#r rrrrr*ûrTzInteraction.__str__N)r/r0r1r2Ú_Interaction__init_rrr*rrrrrQås   rQc@sjeZdZdZddd„Zdd„Zdd„Zd d „Zd d „Zd d„Z dd„Z dd„Z dd„Z dd„Z dd„ZdS)ÚNetworkafA set of species that are explicitly linked by interactions. The network is a directed multigraph with labeled edges. The nodes in the graph are the biochemical species involved. The edges represent an interaction between two species, and the edge label is a reference to the associated Interaction object. Attributes: - None rcCr4)z Initialize a new Network object.N)rÚ_Network__graph©rrrrrr r7zNetwork.__init__cCrS)z9Return a debugging string representation of this network.z)zAdd species to this network.N)rYÚadd_noderZrrrÚ add_speciesrCzNetwork.add_speciescCs|j |||¡dS)z Add interaction to this network.N)rYÚadd_edge)rÚsourceÚsinkÚ interactionrrrÚadd_interaction szNetwork.add_interactioncCó |j |¡S)z*Return list of unique sources for species.)rYÚparentsrZrrrr_$ó zNetwork.sourcecCrc)z7Return list of (source, interaction) pairs for species.)rYÚ parent_edgesrZrrrÚsource_interactions(rezNetwork.source_interactionscCrc)z(Return list of unique sinks for species.)rYÚchildrenrZrrrr`,rez Network.sinkcCrc)z5Return list of (sink, interaction) pairs for species.)rYÚ child_edgesrZrrrÚsink_interactions0rezNetwork.sink_interactionscCó |j ¡S)z+Return list of the species in this network.)rYÚnodesrrrrr4r.zNetwork.speciescCrk)z7Return list of the unique interactions in this network.)rYÚlabelsrrrrr[8r.zNetwork.interactionsNrP)r/r0r1r2rrr*r]rbr_rgr`rjrr[rrrrrXs  rXN) r2Ú functoolsrÚBio.Pathway.Rep.MultiGraphrrr3rQrXrrrrÚs  nN