diff --git a/DESCRIPTION b/DESCRIPTION
index bc7a4d2cf6e6ef3da728e4f944db641d2809569d..3d90c4d2362e59cbb820b0e790dbc304ce0c9f03 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling in R
-Version: 2.0.3
-Date: 2017-04-20
+Version: 2.0.4
+Date: 2017-07-21
Authors@R: c(
person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut")),
@@ -21,7 +21,8 @@ URL:
Description: This Systems Biology Library for R implements algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). Most of the current LP/MILP solvers are supported via additional packages.
LazyLoad: yes
License: GPL-3 | file LICENSE
-Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
+Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R
+ reactClass.R
validreactId_Exch.R validsysBiolAlg.R addAlgorithm.R
addExchReact.R addReact.R addSolver.R blockedReact.R
bracket_pairs.R ceilValues.R changeBounds.R changeGPR.R
@@ -53,7 +54,7 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R
-Packaged: 2017-04-20 12:34:14 UTC; jonathan
+Packaged: 2017-07-21 12:34:14 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
diff --git a/NAMESPACE b/NAMESPACE
index e782ef4835465a07be574fe5c2c7610ae3cb85da..faaef08ab95c9700db55d457e6fe661d1a6090d1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -30,6 +30,7 @@ optsol_robAna,
optsol,
pointerToProb,
ppProc,
+react,
reactId,
sybilError,
sybilLog
diff --git a/R/generics.R b/R/generics.R
index af64b93398d579728264339f40fbcd40d648d6bd..9ba875409869a84ed6f650ef0c00d2e17d50302e 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -351,6 +351,10 @@ setGeneric(name = "getObjVal",
def = function(lp) { standardGeneric("getObjVal") }
)
+setGeneric(name = "getReaction",
+ def = function(X, ...) { standardGeneric("getReaction") }
+)
+
setGeneric(name = "getRedCosts",
def = function(lp) { standardGeneric("getRedCosts") }
)
@@ -389,6 +393,13 @@ setGeneric(name = "gprRules<-",
def = function(object, value) { standardGeneric("gprRules<-") }
)
+setGeneric(name = "gprRule",
+ def = function(object) { standardGeneric("gprRule") }
+)
+setGeneric(name = "gprRule<-",
+ def = function(object, value) { standardGeneric("gprRule<-") }
+)
+
setGeneric(name = "hasEffect",
def = function(object) { standardGeneric("hasEffect") }
)
@@ -869,6 +880,13 @@ setGeneric(name = "S<-",
def = function(object, value) { standardGeneric("S<-") }
)
+setGeneric(name = "s",
+ def = function(object) { standardGeneric("s") }
+)
+setGeneric(name = "s<-",
+ def = function(object, value) { standardGeneric("s<-") }
+)
+
setGeneric(name = "scaleProb",
def = function(lp, ...) { standardGeneric("scaleProb") }
)
diff --git a/R/modelorgClass.R b/R/modelorgClass.R
index 5cd4063e5cd24ab01b9f406e35558bea526576d4..a8da37cc8627a08dafdc603d0bacd476722dbb14 100644
--- a/R/modelorgClass.R
+++ b/R/modelorgClass.R
@@ -965,7 +965,44 @@ setMethod("printMetabolite", signature(object = "modelorg"),
}
)
+#------------------------------------------------------------------------------#
+setMethod("getReaction", signature(X = "modelorg"),
+ function(X, j = NULL, drop=T, tol = SYBIL_SETTINGS("TOLERANCE")) {
+ # translate reaction id's to indices
+ cj <- checkReactId(X, react = j)
+ if (!is(cj, "reactId")) {
+ stop("check argument j")
+ }
+ else {
+ cn <- react_pos(cj)
+ }
+ rl <- lapply(cn, function(r){
+ s <- S(X)[,r]
+ new("react",
+ id=react_id(X)[r],
+ name=react_name(X)[r],
+ rev=react_rev(X)[r],
+ met_id=met_id(X)[abs(s) > tol],
+ met_name=met_name(X)[abs(s) > tol],
+ met_comp=met_comp(X)[abs(s) > tol],
+ s=s[abs(s) > tol],
+ lowbnd=lowbnd(X)[r],
+ uppbnd=uppbnd(X)[r],
+ obj_coef=obj_coef(X)[r],
+ gprRule=gprRules(X)[r],
+ genes=genes(X)[[r]],
+ gpr = gpr(X)[r],
+ subSys = colnames(subSys(X))[subSys(X)[r,]]
+ )
+ })
+
+ if(length(rl) == 1 && drop){
+ return(rl[[1]])
+ }
+ return(rl)
+ }
+)
#------------------------------------------------------------------------------#
diff --git a/R/reactClass.R b/R/reactClass.R
new file mode 100644
index 0000000000000000000000000000000000000000..13c7337870810314d3d7e06f570128f4d0819f03
--- /dev/null
+++ b/R/reactClass.R
@@ -0,0 +1,421 @@
+# reactClass.R
+# FBA and friends with R.
+#
+# Copyright (C) 2010-2017 Claus Jonathan Fritzemeier, Dpt. for Computational Cell Biology,
+# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+# All right reserved.
+# Email: clausjonathan.fritzemeier@uni-duesseldorf.de
+#
+# This file is part of sybil.
+#
+# Sybil is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Sybil is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with sybil. If not, see <http://www.gnu.org/licenses/>.
+
+
+# reactClass
+
+
+#------------------------------------------------------------------------------#
+# definition of the class react #
+#------------------------------------------------------------------------------#
+
+setClass("react",
+ representation(
+ react_rev = "logical", # vector reversibilities
+ react_id = "character", # reaction id
+ react_name = "character", # reaction name
+ react_single = "logical", # reaction using metabolites appearing only once in S
+ react_de = "logical", # reaction using dead end metabolites
+ met_id = "character", # metabolites used in this reaction
+ met_comp = "integer", # compartments of metabolites
+ met_name = "character", # metabolite names
+ s = "numeric", # matrix S
+ lowbnd = "numeric", # reaction lower bound
+ uppbnd = "numeric", # reaction upper bound
+ obj_coef = "numeric", # objective coefficient
+ gprRule = "character",
+ genes = "character",
+ gpr = "character",
+ subSys = "character"
+
+ ),
+ validity = .validreact
+)
+
+
+#------------------------------------------------------------------------------#
+# default constructor #
+#------------------------------------------------------------------------------#
+
+setMethod(f = "initialize",
+ signature = "react",
+ definition = function(.Object,
+ id,
+ name="",
+ rev=TRUE,
+ single=NA,
+ de=NA,
+ met_id,
+ met_name=NULL,
+ met_comp=NULL,
+ s,
+ lowbnd=-1000,
+ uppbnd=1000,
+ obj_coef=0,
+ gprRule=NULL,
+ genes=NULL,
+ gpr = NULL,
+ subSys = NULL
+ ) {
+ stopifnot(!missing(id))
+ stopifnot(!missing(met_id))
+ stopifnot(!missing(s))
+
+ .Object@react_id <- id
+ .Object@react_name <- name
+ .Object@react_rev <- rev
+ .Object@react_single <- single
+ .Object@react_de <- de
+ .Object@met_id <- met_id
+ .Object@met_comp <- met_comp
+ .Object@met_name <- met_name
+ .Object@s <- s
+ .Object@lowbnd <- lowbnd
+ .Object@uppbnd <- uppbnd
+ .Object@obj_coef <- obj_coef
+ .Object@gprRule <- gprRule
+ .Object@genes <- genes
+ .Object@gpr <- gpr
+ .Object@subSys <- subSys
+ return(.Object)
+ }
+)
+
+
+#------------------------------------------------------------------------------#
+# setters and getters #
+#------------------------------------------------------------------------------#
+
+# metabolite id's
+setMethod("met_id", signature(object = "react"),
+ function(object) {
+ return(object@met_id)
+ }
+)
+
+setReplaceMethod("met_id", signature(object = "react"),
+ function(object, value) {
+ object@met_id <- value
+ return(object)
+ }
+)
+
+
+# metabolite names
+setMethod("met_name", signature(object = "react"),
+ function(object) {
+ return(object@met_name)
+ }
+)
+
+setReplaceMethod("met_name", signature(object = "react"),
+ function(object, value) {
+ object@met_name <- value
+ return(object)
+ }
+)
+
+
+# metabolites compartments
+setMethod("met_comp", signature(object = "react"),
+ function(object) {
+ return(object@met_comp)
+ }
+)
+
+setReplaceMethod("met_comp", signature(object = "react"),
+ function(object, value) {
+ object@met_comp <- value
+ return(object)
+ }
+)
+
+
+# reversibilities
+setMethod("react_rev", signature(object = "react"),
+ function(object) {
+ return(object@react_rev)
+ }
+)
+
+setReplaceMethod("react_rev", signature(object = "react"),
+ function(object, value) {
+ object@react_rev <- value
+ return(object)
+ }
+)
+
+
+# reaction id's
+setMethod("react_id", signature(object = "react"),
+ function(object) {
+ return(object@react_id)
+ }
+)
+
+setReplaceMethod("react_id", signature(object = "react"),
+ function(object, value) {
+ object@react_id <- value
+ return(object)
+ }
+)
+
+
+# reaction names
+setMethod("react_name", signature(object = "react"),
+ function(object) {
+ return(object@react_name)
+ }
+)
+
+setReplaceMethod("react_name", signature(object = "react"),
+ function(object, value) {
+ object@react_name <- value
+ return(object)
+ }
+)
+
+
+# singletons
+setMethod("react_single", signature(object = "react"),
+ function(object) {
+ return(object@react_single)
+ }
+)
+
+setReplaceMethod("react_single", signature(object = "react"),
+ function(object, value) {
+ object@react_single <- value
+ return(object)
+ }
+)
+
+
+# dead ends
+setMethod("react_de", signature(object = "react"),
+ function(object) {
+ return(object@react_de)
+ }
+)
+
+setReplaceMethod("react_de", signature(object = "react"),
+ function(object, value) {
+ object@react_de <- value
+ return(object)
+ }
+)
+
+
+# stoichiometric matrix
+setMethod("s", signature(object = "react"),
+ function(object) {
+ return(object@s)
+ }
+)
+
+setReplaceMethod("s", signature(object = "react"),
+ function(object, value) {
+ object@s <- value
+ return(object)
+ }
+)
+
+# lower bounds
+setMethod("lowbnd", signature(object = "react"),
+ function(object) {
+ return(object@lowbnd)
+ }
+)
+
+setReplaceMethod("lowbnd", signature(object = "react"),
+ function(object, value) {
+ object@lowbnd <- value
+ return(object)
+ }
+)
+
+# upper bounds
+setMethod("uppbnd", signature(object = "react"),
+ function(object) {
+ return(object@uppbnd)
+ }
+)
+
+setReplaceMethod("uppbnd", signature(object = "react"),
+ function(object, value) {
+ object@uppbnd <- value
+ return(object)
+ }
+)
+
+
+# objective coefficient
+setMethod("obj_coef", signature(object = "react"),
+ function(object) {
+ return(object@obj_coef)
+ }
+)
+
+setReplaceMethod("obj_coef", signature(object = "react"),
+ function(object, value) {
+ object@obj_coef <- value
+ return(object)
+ }
+)
+
+
+# gprRules
+setMethod("gprRule", signature(object = "react"),
+ function(object) {
+ return(object@gprRule)
+ }
+)
+
+setReplaceMethod("gprRule", signature(object = "react"),
+ function(object, value) {
+ object@gprRule <- value
+ return(object)
+ }
+)
+
+
+# genes
+setMethod("genes", signature(object = "react"),
+ function(object) {
+ return(object@genes)
+ }
+)
+
+setReplaceMethod("genes", signature(object = "react"),
+ function(object, value) {
+ object@genes <- value
+ return(object)
+ }
+)
+
+
+# gpr associations
+setMethod("gpr", signature(object = "react"),
+ function(object) {
+ return(object@gpr)
+ }
+)
+
+setReplaceMethod("gpr", signature(object = "react"),
+ function(object, value) {
+ object@gpr <- value
+ return(object)
+ }
+)
+
+
+# reaction sub systems
+setMethod("subSys", signature(object = "react"),
+ function(object) {
+ return(object@subSys)
+ }
+)
+
+setReplaceMethod("subSys", signature(object = "react"),
+ function(object, value) {
+ object@subSys <- value
+ return(object)
+ }
+)
+
+
+#------------------------------------------------------------------------------#
+# other methods #
+#------------------------------------------------------------------------------#
+
+setMethod("show", signature(object = "react"),
+ function(object) {
+ cat("react id: ", react_id(object), "\n")
+ cat("react name: ", react_name(object), "\n")
+ cat("stoichiometry:\n")
+ print(data.frame(met_id=met_id(object), s_coef=s(object)))
+ cat("lower bound: ", lowbnd(object), "\n")
+ cat("upper bound: ", uppbnd(object), "\n")
+ cat("objective function: ", obj_coef(object), "\n")
+ }
+)
+
+
+#------------------------------------------------------------------------------#
+
+# print reactions
+setMethod("printReaction", signature(object = "react"),
+ function(object, printOut = TRUE, ...) {
+
+ mat <- s(object)
+ reaction <- character(1)
+
+ for (j in seq(along = cind)) {
+
+ met <- met_id(object)
+ nzv <- mat
+
+ ed <- nzv < 0
+ pd <- nzv > 0
+
+ if (sum(ed) > 0) {
+ educt <- paste(paste("(", abs(nzv[ed]), ")", sep = ""),
+ met[ed], collapse = " + ")
+ }
+ else {
+ educt = ""
+ }
+
+ if (sum(pd) > 0) {
+ product <- paste(paste("(", nzv[pd], ")", sep = ""),
+ met[pd], collapse = " + ")
+ }
+ else {
+ product = ""
+ }
+
+ arrow <- ifelse(react_rev(object)[cind[j]], " <==> ", " --> ")
+
+ reaction[j] <- paste(react_id(check)[j],
+ paste(educt, product, sep = arrow), sep = "\t")
+ }
+
+ if (isTRUE(printOut)) {
+ cat("abbreviation\tequation", reaction, sep = "\n", ...)
+ }
+
+ return(invisible(reaction))
+
+ }
+)
+
+
+
+
+
+
+
+
+
+
+
diff --git a/R/validreact.R b/R/validreact.R
new file mode 100644
index 0000000000000000000000000000000000000000..0036dd2923c5e198c89c3f2053862ee09d1a6752
--- /dev/null
+++ b/R/validreact.R
@@ -0,0 +1,112 @@
+# validreact.R
+# FBA and friends with R.
+#
+# Copyright (C) 2010-2017 Claus Jonathan Fritzemeier, Dpt. for Computational Cell Biology,
+# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+# All right reserved.
+# Email: clausjonathan.fritzemeier@uni-duesseldorf.de
+#
+# This file is part of sybil.
+#
+# Sybil is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Sybil is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with sybil. If not, see <http://www.gnu.org/licenses/>.
+
+
+# validreact
+
+
+################################################
+# Function: .validreact
+#
+# Validity checking of an object of class react.
+#
+# Returns TRUE if the model is valid, otherwise
+# a character String containing a description of
+# the error.
+
+
+.validreact <- function(object) {
+ # data has to have the same length or to be NULL
+ if(!is(object, "react")){
+ "object is not of react class"
+ }
+
+ if(length(object@id) != 1){
+ return("id has to be length 1")
+ }
+ if(length(object@name) != 1){
+ return("id has to be length 1")
+ }
+
+ met_count <- length(object@s)
+ if(met_comp < 1){
+ return("reactions have to have at least one metabolite")
+ }
+ if(length(object@met_id) == met_count){
+ return("s, met_id, met_name, and met_comp have to have the same length")
+ }
+ if(length(object@met_name) == met_count && !is.null(object@met_name)){
+ return("s, met_id, met_name, and met_comp have to have the same length")
+ }
+ if(length(object@met_comp) == met_count && !is.null(object@met_comp)){
+ return("s, met_id, met_name, and met_comp have to have the same length")
+ }
+
+ if(length(object@id)!=1){
+ return("length of id has to be 1")
+ }
+ if(length(object@rev)!=1){
+ return("length of rev has to be 1")
+ }
+ if(length(object@name)!=1){
+ return("length of name has to be 1")
+ }
+ if(length(object@lowbnd)!=1){
+ return("length of lowbnd has to be 1")
+ }
+ if(length(object@uppbnd)!=1){
+ return("length of uppbnd has to be 1")
+ }
+ if(length(object@obj_coef)!=1){
+ return("length of obj_coef has to be 1")
+ }
+
+ if(!is.null(gprRule) && length(object@gprRule)!=1){
+ return("if not NULL, the length of gprRule has to be 1")
+ }
+ if(!is.null(genes) && length(object@genes)!=1){
+ return("if not NULL, the length of genes has to be 1")
+ }
+ if(!is.null(gpr) && length(object@gpr)!=1){
+ return("if not NULL, the length of gpr has to be 1")
+ }
+ if(!is.null(subSys) && length(object@subSys)!=1){
+ return("if not NULL, the length of subSys has to be 1")
+ }
+
+ return(TRUE)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+