#-------------------------------------------------------------------------------
# Name:        Explanation_1_13CMFA_toymodel_model.txt
#              Model definition file for Explanation_1_13CMFA_toymodel.py of mfapy
#
# Author:      Fumio_Matsuda
#
# Created:     12/06/2018
# Copyright:   (c) Fumio_Matsuda 2021
# Licence:     MIT license
#-------------------------------------------------------------------------------
#
#  Any texts after "#" are ignored as comment
#
# Definition of metabolic reactions
# 1. id, text
#	Please use alphabet (+ number) as ids. Do not use space and special characters to avoid unexpected errors.
# 2. Stoichiometry for the construicton of stoichiometry matrix, text
#	All id of metabolites must be defined in //Metabolites
#	Only "+" and "-->" are accpectable separators.
#	Here, expression of reaction using coefficient such as  "Fumx --> {2}OA" is allowed.
#	"nd" means this reaction is an "pseudo" reaction and ignored in the flux calculation of substrate by stoichiometry matrix.
# 3. Stoichiometry for the construicton of atom mapping, text
#	Only "+" and "-->" are accpectable separators.
#	Here, expression of reaction without using coefficient is needed such as  "Fumx --> OA+OA".
#	"nd" means this reaction is an excretion reaction and ignored in the MDV calculation
# 4. Atom mapping, text
#	Only "+" and "-->" are accpectable separators. Please use A-Z to express carbon atom.
#	"nd" means this reaction is an excretion reaction and ignored in the MDV calculation
# 5. Links to external ids (Optional)
#	Links to external ids can be described here
# 6. Lower boundary of metabolic flux level, float (Optional)
#	Value must be more than zero
# 7. Upper boundary of metabolic flux level, float (Optional)
#	Value must be more than zero
//Reactions
v1	AcCoA + OAC --> Cit	AcCoA + OAC --> Cit	AB + CDEF --> FEDBAC	(kegg:R00351)	0.1	300
v2	Cit --> AKG + CO2ex	Cit --> AKG + CO2ex	ABCDEF --> ABCDE + F	(kegg:R00709)	0.1	300
v3	AKG --> Glu	AKG --> Glu	ABCDE --> ABCDE 	(kegg:R00243)	0.1	300
v4	AKG --> Suc + CO2ex	AKG --> Suc + CO2ex	ABCDE --> BCDE + A	(kegg:R01197)	0.1	300
v5	Suc --> Fum	Suc --> Fum	ABCD --> ABCD	(kegg:R02164)	0.1	300
v6	Fum --> OAC	Fum --> OAC	ABCD --> ABCD	(kegg:R01082)	0.1	300
v7	OAC --> Fum	OAC --> Fum	ABCD --> ABCD	(kegg:R01082)	0.1	300
v8	Asp --> OAC	Asp --> OAC	ABCD --> ABCD	(kegg:R00355)	0.1	300
v9	Suc --> Sucex	nd	nd	noid	0.1	300
e1	Glu --> Gluex	nd	nd 	noid	0.1	300
v10	OAC --> OACx	OAC --> OACx	ABCD --> ABCD	noid	0.1	300
v11	OACs --> OACx	OACs --> OACx	ABCD --> ABCD	noid	0.001	300
v12	OACx --> OACe	nd	nd	noid	0.1	300
v13	OAC+OAC --> Fumx	OAC+OAC --> Fumx	ABCD+EFGH --> EFAB	noid	0.1	300
v14	OA --> Fume	nd	nd	noid	0.1	300
v15	OAC+Fum+Suc --> Tx	OAC+Fum+Suc --> Tx	ABCD+EFGH+IJKL --> CDHL	noid	0.1	300
v16	Tx --> Te	nd	nd	noid	0.1	300
v17	Fumx --> {2}OA	Fumx --> OA+OA	ABCD --> AB+CD	noid	0.1	300
#
# Definition of metabolites
# 1. id, text
#	Please use alphabet and numbers. Do not use space, "_", and other special characters to avoid unexpected errors.
#	Initial character must be alphabet. The id "6PG" was not allowed. Please convert to "m6PG" or other names
# 2. Carbon number, int
#   Max number of carbon in "carbonsource" metabolites are 8.
# 3. symmetry, text
#	Set "symmetry" metabolites such as fumarete and succinate
# 4. corbon source, text
#	Set "carbonsource" metabolites
# 5. excretion, text
#	Set "excreted" metabolites
# 6. Links to external ids (Optional)
#	Links to external ids can be described here
# 7. Lower boundary of metabolite pool size, float (Optional)
#	Value must be more than zero
#	Required for INST-MFA mode
# 8. Upper boundary of metabolite pool size, float (Optional)
#	Value must be more than zero
#	Required for INST-MFA mode
#
//Metabolites
CO2ex	1	no	no	excreted	(kegg:C00011)	0.0	300
AcCoA	2	no	carbonsource	no	(kegg:C00024)	0.0	300
OAC	4	no	no	no	(kegg:C00036)	0.0	300
OACs	4	no	carbonsource	no	noid	0.0	300
OACx	4	no	no	no	noid	0.0	300
OACe	4	no	no	excreted	noid	0.0	300
Fumx	4	no	no	no	noid	0.0	300
OA	2	no	no	no	noid	0.0	300
Fume	4	no	no	excreted	noid	0.0	300
Tx	4	no	no	no	noid	0.0	300
Te	4	no	no	excreted	noid	0.0	300
Cit	6	no	no	no	(kegg:C00158)	0.0	300
AKG	5	no	no	no	(kegg:C00026)	0.0	300
Suc	4	symmetry	no	no	(kegg:C00042)	0.0	300
Fum	4	symmetry	no	no	(kegg:C00122)	0.0	300
Glu	5	no	no	no	(kegg:C00025)	0.0	300
Gluex	5	no	no	excreted	noid	0.0	300
Sucex	4	no	no	excreted	noid	0.0	300
Asp	4	no	carbonsource	no	(kegg:C00049)	0.0	300
#
# Definition of reversible reactions
# Reversible reaction is used for
#	(i) output of metabolic flux distribution data
#	(ii) constrain metabolic flux
# 	(iii) investigate confidence intervals
# 	(iii) Composition of two or more reactions such as for the calculation of total ATP producton is supported.
# 1. Id, text
#	Please use alphabet and numbers. Please do not use space and special characters to avoid unexpected errors.
# 2. Dorward reaction, text
#	Reacton id
#	Composition of reacton ids such as "v9+e1" is also supported.
#	Only "+" is accpectable separator.
# 3. Reverse reaction, text
#	Reacton id
#	Set "nothing" if there is no data
# 4. Links to external ids (Optional)
#	Links to external ids can be described here
# 5. Lower boundary of metabolic flux level, float (Optional)
#	Value must be more than zero
# 6. Upper boundary of metabolic flux level, float (Optional)
#	Value must be more than zero
#
//Reversible_reactions
FUM	v6	v7	(kegg:R01082)	-300	300
Input	v9+e1	nothing	(kegg:R01082)	-300	300
#
# Definition of Target fragments
# Target fragments are metabolite out side of the metabolic model whose MDV are generarted by the calmdv function.
# 1. id, text
#	Please use alphabet and numbers. Please do not use space, "_" and other special characters to avoid unexpected errors.
# 2. type, text
#	"gcms" is supported.
# 3. Carbon composition, text
#	"Glu_12345" indicated that the target compound has five carbons derived from 1-5th carbons of metabolite id "Glu".
#	In the "gcms"mode, "OAC_12+OAC_12" indicated that the target compound has for carbons derived from 1-2th carbons of metabolite id "OAC".
# 4. Usage, text
#	"use" means this target fragment is used in the analysis.
# 5. Formula, text
#	Experimental, Chemical formula of target compound
//Target_fragments
Glue	gcms	Glu_1:2:3:4:5	use	C5H10N2O3
AKGe	gcms	AKG_1:2:3:4:5	use	C5H10N2O3
OACo	gcms	OACx_1:2:3:4	use	C5H10N2O3
OACi	gcms	OAC_1:2:3:4	use	C5H10N2O3
OACt	gcms	Fumx_1:2:3:4	use	C5H10N2O3
OACc	gcms	OAC_1:2+OAC_1:2	use	C5H10N2O3
Txt	gcms	Tx_1:2:3:4	use	C5H10N2O3
Txc	gcms	OAC_3:4+Fum_4+Suc_4	use	C5H10N2O3
Gluf	gcms	Glu_1:2+Glu_3:4:5	no	C5H10N2O3
AKGms	gcms	AKG_1:2:3:4:5	no
AKGc	gcms	AKG_1:2+AKG_3:4:5	no	C5H10N2O3
//End
