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Merge pull request #1809 from opencobra/develop
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Develop
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@rmtfleming
rmtfleming authored Sep 23, 2021
2 parents 5ea3f81 + 9ae11fc commit 2acd2f7
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19 changes: 17 additions & 2 deletions .gitmodules
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path = external/base/solvers/lusol
url = https://github.com/nwh/lusol.git
ignore = dirty
branch = master
[submodule "pdco"]
path = external/base/solvers/pdco
url = https://github.com/mxsaunders/pdco.git
ignore = dirty
branch = master
[submodule "Smith-Decomposition"]
path = external/base/utilities/Smith-Decomposition
url = https://github.com/nbfigueroa/Smith-Decomposition.git
ignore = dirty
branch = master
[submodule "binary"]
path = binary
url = https://github.com/opencobra/COBRA.binary.git
ignore = none
branch = master
[submodule "gaimc"]
path = external/analysis/gaimc
url = https://github.com/dgleich/gaimc.git
ignore = dirty
branch = master
[submodule "models"]
path = test/models
url = https://github.com/opencobra/COBRA.models
ignore = none
ignore = dirty
branch = master
[submodule "Volume-and-Sampling"]
path = external/analysis/Volume-and-Sampling
url = https://github.com/Bounciness/Volume-and-Sampling.git
ignore = dirty
branch = master
[submodule "CnaCobraInterface"]
path = external/analysis/CnaCobraInterface
url = https://github.com/SteffKlamt/CnaCobraInterface.git
ignore = dirty
branch = master
[submodule "tutorials"]
path = tutorials
url = https://github.com/opencobra/COBRA.tutorials.git
ignore = none
ignore = dirty
branch = master
[submodule "papers"]
path = papers
url = https://github.com/opencobra/COBRA.papers.git
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path = external/analysis/octave-networks-toolbox
url = https://github.com/aeolianine/octave-networks-toolbox.git
ignore = dirty
branch = master
[submodule "looplessFluxSampler"]
path = external/base/samplers/looplessFluxSampler
url = https://github.com/rmtfleming/looplessFluxSampler
ignore = dirty
branch = master
[submodule "external/base/utilities/condalab"]
path = external/base/utilities/condalab
url = https://github.com/sg-s/condalab
ignore = dirty
branch = master
[submodule "external/analysis/PolytopeSamplerMatlab"]
path = external/analysis/PolytopeSamplerMatlab
url = https://github.com/ConstrainedSampler/PolytopeSamplerMatlab
ignore = dirty
branch = master
44 changes: 22 additions & 22 deletions src/analysis/topology/conservedMoieties/identifyConservedMoieties.m
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% * .Nodes.MoietyIndex - numeric id of the corresponding moiety (arm.MTG.Nodes.MoietyIndex)
% * .Nodes.Component - numeric id of the corresponding connected component (rows of C2A)
% * .Nodes.IsomorphismClass - numeric id of the corresponding isomprphism class (rows of I2C)
% * .Nodes.IsFirst - boolean, true if atom is within first component of an isomorphism class
% * .Nodes.IsCanonical - boolean, true if atom is within first component of an isomorphism class
%
% * .Edges — Table of edge information, with `u` rows, one for each atom transition instance.
% * .Edges.EndNodes - numeric id of head and tail atoms that defines the graph edges
Expand All @@ -87,7 +87,7 @@
% * .Edges.TransIndex - unique numeric id for each atom transition
% * .Edges.Component - numeric id of the corresponding connected component (columns of T2C)
% * .Edges.IsomorphismClass - numeric id of the corresponding isomprphism class (columns of T2I)
% * .Edges.IsFirst - boolean, true if atom transition is within first component of an isomorphism class
% * .Edges.IsCanonical - boolean, true if atom transition is within first component of an isomorphism class
%
% arm.M2A: `m x a` matrix mapping each metabolite to one or more atoms in the (undirected) atom transition graph
% arm.A2R: `u x n` matrix that maps atom transitions to reactions. An atom transition can map to multiple reactions and a reaction can map to multiple atom transitions
Expand All @@ -105,9 +105,9 @@
% arm.MTG: (undirected) moitey transition graph, as a MATLAB graph structure with the following tables and variables:
%
% * .Nodes — Table of node information, with `p` rows, one for each moiety instance.
% * .Nodes.MoietyIndex - unique numeric id of the moiety
% * .Nodes.MoietyIndex - unique numeric id of the moiety instance
% * .Nodes.Formula - chemical formula of the moiety (Hill notation)
% * .Nodes.Met - representative metabolite containing the moiety
% * .Nodes.Met - metabolite containing the moiety instance
% * .Nodes.Component - numeric id of the corresponding connected component (rows of C2M)
% * .Nodes.IsomorphismClass - numeric id of the corresponding isomprphism class (rows of I2M)

Expand All @@ -117,7 +117,7 @@
% * .Edges.Rxn - the reaction from which this moiety transition was derived
% * .Edges.Component - numeric id of the corresponding connected component (columns of M2C)
% * .Edges.IsomorphismClass - numeric id of the corresponding isomprphism class (columns of M2I)
% * .Edges.IsFirst - boolean, true if moiety transition is within first component of an isomorphism class
% * .Edges.IsCanonical - boolean, true if moiety transition is within first component of an isomorphism class
% Note that M = incidence(arm.MTG); gives the p x q incidence matrix of the moitey transition graph
%
% arm.I2M Matrix to map each isomorphism class to one or more moiety instances
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% arm.ATG.Edges.orientationATM2dATM - orientation of edge with respect to the reaction from which this atom transition was derived
% arm.ATG.Edges.Rxn - the reaction from which this atom transition was derived
%
% arm.MTG.Nodes.IsFirst - boolean, true if moiety corresponds to the first component of an isomorphism class (should be all true)
% arm.MTG.Nodes.IsCanonical - boolean, true if moiety corresponds to the first component of an isomorphism class (should be all true)
% arm.MTG.Nodes.Atom - alphanumeric id of the corresponding atom in the first component of an isomorphism class
% arm.MTG.Nodes.AtomIndex - numeric id of the corresponding atom in the first component of an isomorphism class
% arm.MTG.Edges.orientationATM2dATM - orientation of moiety transition with respect to the reaction from which this moiety transition was derived
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%% Moiety transition graph
%create the moiety transition graph explicitly as a
%subgraph of the atom transition graph
[isFirst, moiety2isomorphismClass] = ismember(atoms2component,firstSubgraphIndices);
moiety2isomorphismClass = moiety2isomorphismClass(isFirst);
[isCanonical, moiety2isomorphismClass] = ismember(atoms2component,firstSubgraphIndices);
moiety2isomorphismClass = moiety2isomorphismClass(isCanonical);

if sanityChecks
moiety2isomorphismClass2 = atoms2isomorphismClass(isFirst);
moiety2isomorphismClass2 = atoms2isomorphismClass(isCanonical);
if any(moiety2isomorphismClass~=moiety2isomorphismClass2)
error('Inconsistent moiety2isomorphismClass vector')
end
end

ATG.Nodes = addvars(ATG.Nodes,isFirst,'NewVariableNames','IsFirst');
ATG.Nodes = addvars(ATG.Nodes,isCanonical,'NewVariableNames','IsCanonical');
%size of the moiety instance transition graph
nMoieties=nnz(isFirst);
isFirstTransition = any(A(isFirst, :), 1)';
nMoietyTransitions = nnz(isFirstTransition);
nMoieties=nnz(isCanonical);
isCanonicalTransition = any(A(isCanonical, :), 1)';
nMoietyTransitions = nnz(isCanonicalTransition);

if 0
ATG.Edges = addvars(ATG.Edges,isFirstTransition,'NewVariableNames','IsFirst');
ATG.Edges = addvars(ATG.Edges,isCanonicalTransition,'NewVariableNames','IsCanonical');
else
ATG.Edges.IsFirst = isFirstTransition;
ATG.Edges.IsCanonical = isCanonicalTransition;
end

%draft moiety transition graph, before editing node and
%edge information
MTG = subgraph(ATG,isFirst);
MTG = subgraph(ATG,isCanonical);
M = incidence(MTG);

MTG.Nodes.MoietyIndex = (1:nMoieties)';
Expand All @@ -752,7 +752,7 @@
end

%add moiety specific information
MTG.Nodes = removevars(MTG.Nodes,{'AtomNumber','Element','IsFirst','Atom','AtomIndex'});
MTG.Nodes = removevars(MTG.Nodes,{'AtomNumber','Element','IsCanonical','Atom','AtomIndex'});
MTG.Nodes = addvars(MTG.Nodes,moietyFormulae(moiety2isomorphismClass),'NewVariableNames','Formula','After','MoietyIndex');

% * .Edges.HeadAtom - head Nodes.Atom
Expand All @@ -767,7 +767,7 @@
if 1
%graph.Edges cannot be directly edited in a graph object, so extract,
%edit and regenerate the graph
Edges = removevars(MTG.Edges,{'Trans','TransIndex','TransInstIndex','OrigTransInstIndex','HeadAtomIndex','TailAtomIndex','HeadAtom','TailAtom','orientationATM2dATM','IsFirst','Rxn'});
Edges = removevars(MTG.Edges,{'Trans','TransIndex','TransInstIndex','OrigTransInstIndex','HeadAtomIndex','TailAtomIndex','HeadAtom','TailAtom','orientationATM2dATM','IsCanonical','Rxn'});
%add variables
Edges = addvars(Edges,MTG.Nodes.Formula(Edges.EndNodes(:,1)),'NewVariableNames','Formula');
%reorder the variables
Expand Down Expand Up @@ -796,7 +796,7 @@
% Extract moiety graph directly from atom transition
% graph incidence matrix
[isFirstAlso, ~] = ismember(atoms2component,firstSubgraphIndices);
if ~all(isFirst == isFirstAlso)
if ~all(isCanonical == isFirstAlso)
error('moiety incidence matrix does not match first component')
end
A = incidence(ATG);
Expand Down Expand Up @@ -824,7 +824,7 @@
%add the moiety indices for the first atoms in each moiety
moietyInd=1;
for i=1:nAtoms
if ATG.Nodes.IsFirst(i)
if ATG.Nodes.IsCanonical(i)
ATG.Nodes.MoietyIndex(i)=moietyInd;
moietyInd = moietyInd + 1;
end
Expand Down Expand Up @@ -880,7 +880,7 @@

%% Map between moiety graph and metabolic network
%map metabolite to moieties
moieties2mets = atoms2mets(isFirst);
moieties2mets = atoms2mets(isCanonical);

%matrix to map each metabolite to one or more moieties
M2M = sparse(moieties2mets,(1:nMoieties)', 1,nMappedMets,nMoieties);
Expand Down Expand Up @@ -919,7 +919,7 @@
%matrix to map moiety transitions to reactions. Multiple moiety
%transitions can map to multiple reactions.
%A2R = A2Ti*Ti2R;
M2R = A2R(isFirstTransition,:);
M2R = A2R(isCanonicalTransition,:);

if 0
%in general it is not possible to specify the mapping from moiety
Expand Down

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