54fbedbaf256ab429c34a1e22431a387 *DESCRIPTION
784d7dc7357bd924e8d5642892bf1b6b *LICENSE
a0057ebdd98c02282ccde8e5106b3480 *NAMESPACE
90ecac75949618855d37c9257cd3f6ba *R/addAlgorithm.R
8308e92d9fa5642ee9c53541989b0161 *R/addExchReact.R
87f91c76ef82858f58db32fc3259ecda *R/addReact.R
b6fc85a91c57ad8233c9065711aaaf00 *R/addSolver.R
2a1c0a2be52da03b060fcb34af46ac2a *R/blockedReact.R
2c645acea7585b67c1d1820a1baee4fe *R/bracket_pairs.R
38743161b198e109f7c0a1f9657228d1 *R/ceilValues.R
ef427931942d9332a49254a720da8a23 *R/changeBounds.R
8f4d03faa34f40d81b9001264fbe222b *R/changeGPR.R
45f775f7c87d97030186555701ebd1a2 *R/changeObjFunc.R
4a76a6d8aae7c018117bec725b850c12 *R/checkAlgorithm.R
e3a4d2f9fd12ef86b792f5915813ae95 *R/checkDefaultMethod.R
afcf332a2a1832a6e6e8aa17890e8e03 *R/checkEmptyField.R
3fdc8bfb51a143f19e4fc66b62ac367d *R/checkReactId.R
1a025d46fa4f48abacbd0c3b73f59919 *R/check_brackets.R
0bf802cf611985868a5d0e757a4f8a32 *R/checksolClass.R
37cbc341d4ad73c05681b0d41960bf5e *R/createReactionString.R
44f1ea333d3837da3a462d98925c7d4b *R/deadEndMetabolite.R
563bed0f47351cf36e30310efb0f9a0c *R/doInRound.R
9856be12647a6aa75e24be484a7e0892 *R/doubleFluxDel.R
d8485a1f9ed4373e44f5bc8302910eea *R/doubleGeneDel.R
b93928569f7b0c04a66c971f62a2ad35 *R/doubleReact.R
e4cc6e7aaed353eae3ef9cff55baa72c *R/editEnvir.R
d90269aa0cd1c7bd0525f345a1930b4e *R/findExchReact.R
6919dd17bfcfa206d62c6dc7008cb1fa *R/floorValues.R
dcc687dab70707bcb67771ee1f6a42b9 *R/fluxDistributionClass.R
47be7ca4522a71d3fc7a213215f0fc33 *R/fluxVar.R
25f400593cad446ea6407b51d1e89270 *R/geneDel.R
54155cafbd020f506529f1d3b09712db *R/geneDeletion.R
0991ea1d270faf4fb8c17a95b3f9d696 *R/generateFluxdels.R
6a9ec13e76ac04adcee61d137c8e04c4 *R/generateModKey.R
eeff891a92637e0388e98296bc7e52a0 *R/generateWT.R
fbdd7547d4dac50193999a7c92ad79e9 *R/generics.R
161f081b5e0e4ab9c6760b6c10f68d68 *R/getsybilenv.R
c9871521aa40b4ff5ef0366e25b99d14 *R/makeLPcompatible.R
9fe159e369938336f80657771a0481be *R/mergeReact2Modelorg.R
cd80dbd650f7cb83681bc0648a0feda4 *R/mod2irrev.R
48057c793465f42492bfa86e38eca2de *R/modelorg2ExPA.R
ff95c8bba67c0872032c138e21917198 *R/modelorg2text.R
0008835ef92bd9dfc6cdfcb1c1e37a8d *R/modelorg2tsv.R
5e1c37e636b57d878f0421b7a39eb4e9 *R/modelorgClass.R
76daff0a28b2ce1d628fbd55804effe0 *R/modelorg_irrevClass.R
261781f2a650538647dd3c6324c6d0ce *R/multiDel.R
27038f668dfc3ddf3fc5b7625cf6625d *R/netFluxClass.R
6fa896a4d254f3712dd2d6d8b9e99836 *R/oneFluxDel.R
2108d061d378328fee160e9f34219b6a *R/oneGeneDel.R
7bdc0491ddfe80cf84232c80a279522d *R/onlyChangeGPR.R
2bf00b25107e3454ad17c4210d428ce9 *R/onlyCheckGPR.R
b9b397908dfcc9d0e67f3f5b11152d20 *R/optObjClass.R
1e2353b32882d92b998de47e4d75c261 *R/optObj_basicfunc.R
031717b9dd5f23ecd7ea9aff32d27c36 *R/optObj_clpAPIClass.R
9ef89d87cdc1352513d851312528d96a *R/optObj_cplexAPIClass.R
85ac1dfaf016d674471aae080132a1bd *R/optObj_glpkAPIClass.R
50c8e6e21f2cfe0d19282532c298029e *R/optObj_lpSolveAPIClass.R
6c54af969a8d735a0f2ab0efbb3847b6 *R/optObj_lpSolveAPIcompat.R
13d8595ffa2e6698dcbb24d7b1829ba1 *R/optObj_pointer.R
d6d5067479ef8669bec1ed3b017143e5 *R/optimizer.R
7b6ccea4b68c89a01f01207878faf184 *R/optsolClass.R
85319118ce31a706c4f136c2959744b3 *R/optsol_blockedReactClass.R
fac3d3b256ede37569d1182df0875855 *R/optsol_fluxVarClass.R
bcf4e52fd4b5ebe55988a1a2cad39dea *R/optsol_fluxdelClass.R
f116c47fcd6d582632dfddfa27af048a *R/optsol_genedelClass.R
a0615a915293ec9b892342c6a7748106 *R/optsol_optimizeProbClass.R
74308b9dd44d0541bbf73c3d38d23345 *R/optsol_phppClass.R
65a70792a1d656fe3eacb2847a769365 *R/optsol_robAnaClass.R
64ddbba173b8655222ce625121c1e8df *R/parseBoolean.R
4bcfa4434e025e5cf8acaf833aa544b9 *R/phpp.R
7bd65887a4d6eabf6dd4dc240b70ad00 *R/ppProcClass.R
f121516c97606ece165c12fb90c40c8f *R/ppProcessing.R
824360522eddac0a8f23671af4115cca *R/prepareSubSysMatrix.R
75de08d58a12bfb6c75e3ee4640f611b *R/printLogComment.R
3cdeb4684cdde1ad915dc908de501c3a *R/printNamedList.R
725991084b78416f2909dce9f7f4bcfd *R/progress.R
59445a53f70600ed558deefee8d16ee3 *R/promptSysBiolAlg.R
8c3c00b1f691472604bbb7d26f22b190 *R/reactClass.R
7f78125bbebbd423578165991bd01ef2 *R/reactIdClass.R
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4f28ba60325a56db6b28574f9d11594f *R/readTEXTmod.R
828fb55b036b026ba1cfaa2b7d5f7e46 *R/readTSVmod.R
2333f0e4415c6d759231f47091dbbf93 *R/reassignFwBwMatch.R
7be0d1c8f0aeb3ee77d934c87dfdb16e *R/recodeMatrix.R
96529cf6505d1848a608789d654d0872 *R/rmReact.R
85ee480ef1164d83e4321ff56bac3aff *R/robAna.R
a7b8feac6869afc4f4fd0332cfb0ec90 *R/settings.R
7021a4fdac1e26a687f3132087efc747 *R/singletonMetabolite.R
ba98dd07dcf9d7bf2389d9b3fb39069a *R/summaryOptsolClass.R
474f5824d454b9e07b0828b7ef89a984 *R/sybilErrorClass.R
d9b5c25b4e3592096f8e8a55e2c2cc61 *R/sybilLogClass.R
d6d5eb8a09894326bb10f7132e757c2a *R/sybilStack.R
19da023860c82719ef99bd36ffeb5b7e *R/sysBiolAlgClass.R
2f995f47ac07359ba07824eb2e48ebcd *R/sysBiolAlg_fbaClass.R
cf0b1562804d4518145cee37e49b083b *R/sysBiolAlg_fbaEasyConstraintClass.R
6f9b45a4726bf832be14cc56118b2d28 *R/sysBiolAlg_fvClass.R
03fa130843af0c3b8f98a0097ae2c697 *R/sysBiolAlg_lmomaClass.R
1e274ec357de9c6f3f660e91445e73d6 *R/sysBiolAlg_momaClass.R
086ed8679d6df46ea294beb9c4e88359 *R/sysBiolAlg_mtfClass.R
688b11570c03c34811fe58668a778857 *R/sysBiolAlg_mtfEasyConstraintClass.R
7486b073ca76fbb5b4d1eecf92d844c4 *R/sysBiolAlg_roomClass.R
1f5a28241ac469bf3318c58921536c32 *R/upgradeModelorg.R
95404327ccf1220466bf8660239ed82e *R/validmodelorg.R
581b6740b46f3230ea6b70225adb5baf *R/validoptsol.R
cec3c6af43cb39dc7da1c0d8743e8227 *R/validreact.R
4bf1eb49479dde86718fc4257b3049d0 *R/validreactId.R
f9253acaee4e2dae34d57291e0471248 *R/validreactId_Exch.R
723c6b1fa7a331c280ca8b049396b6c8 *R/validsysBiolAlg.R
94eef6e16843a2cd6cf543132f24f8cd *R/ypd.R
42dab78122a95222825a810ee795ca0f *R/zzz.R
9369963bbd3323c0f9c3407e7998a49c *README.md
d1e2ccd86bc4515035114524affabd1a *build/vignette.rds
c3a4955df966f86bd01b43aef1f93ad8 *data/Ec_core.RData
dcb1bdb0b852efeed6c4633f10aa2fd0 *inst/CITATION
a0569f7dda243faefb4937e49b3946d3 *inst/NEWS.Rd
23d1433e302a9eba8ef18916b190c9d2 *inst/doc/sybil.R
24e6cf8fb9f47f6aa6c8b7bdf3957ca5 *inst/doc/sybil.Rnw
58676f126a2fdefdce614c8344e9f42c *inst/doc/sybil.pdf
57349ddd1c5292698b4f40828fb0a4c8 *inst/extdata/Ec_core_desc.tsv
a087d5c12df926906688674ba133e6a9 *inst/extdata/Ec_core_met.tsv
5e592ee880a444834fca2de9f320367a *inst/extdata/Ec_core_react.tsv
c94a9ca15e74ec5de8c7be9976faeaed *man/Ec_core.Rd
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14ab03155ccfdef3e08be59b7061eec4 *man/addCols-methods.Rd
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3422f576308e3bd1a9e9886739fa0acc *man/applyChanges-methods.Rd
206d92669e7b3c9ac487e898f719a251 *man/backupProb-methods.Rd
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9f81284beebc224e7d079a2e4bc6d5be *man/changeBounds.Rd
09d34392325a20a27127c7f2df195e14 *man/changeColsBnds-methods.Rd
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db51a9eb1effebbdddb3c7ef69c61190 *man/changeGPR.Rd
660f3123273b750f98b05704a820afb4 *man/changeMatrixRow-methods.Rd
8adb5b17afe732819b7b0ee48a91de50 *man/changeObjCoefs-methods.Rd
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c6958244524e3df2437c9172011c253c *man/changeRowsBnds-methods.Rd
38186ec69234adb184e6cd9e8c3589a8 *man/changeUptake-methods.Rd
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95ab37fb8517a99f4f3078e1f8098aa8 *man/checkDefaultMethod.Rd
875d823be078a73755e420610485e6d7 *man/checkOptSol-methods.Rd
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9b0befab257c18b90d203e1a3ce21462 *man/checkVersion-methods.Rd
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9dcfb4d294e27e815c50754c609f4a98 *man/deadEndMetabolites-methods.Rd
9a89d92a9e698ac57c195a5aa110c717 *man/delProb-methods.Rd
ec9ee63fb5b374445346188c5e2d19ce *man/deprecated.Rd
5c845239985edd90703fec4eeb5867f6 *man/doubleFluxDel.Rd
7faefaf770ef8a36d24ff23410af994f *man/doubleGeneDel.Rd
190d26c7735a8efd4b0dbff8ce3757b1 *man/doubleReact.Rd
b8c5de342b4db848046419bb94ca5c0d *man/editEnvir.Rd
ec861b708294cecfbdef4a98638e5242 *man/findExchReact.Rd
262850c04c44fcd3b17c969832de2229 *man/fluxDistribution-class.Rd
c9d19467a7bb33fa01f571976062ed2f *man/fluxVar.Rd
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38e181c869185cf8ff2fc55bc646e1e2 *man/geneDeletion.Rd
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9e97f12bbeaaaa8db31be0acbf932867 *man/getColsLowBnds-methods.Rd
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18a1103e42f8fe5ca6ba8c1109e3dee5 *man/getColsUppBnds-methods.Rd
cf7c199dcef57accf859fe33aae1d92d *man/getFluxDist-methods.Rd
c1228dfdd4bebf1298134b10b6e3ef1b *man/getNumCols-methods.Rd
1b4108419e0864c4c9cc7c90a96b76f6 *man/getNumNnz-methods.Rd
f86f7df11c15c4250e935352bc54f9f9 *man/getNumRows-methods.Rd
11c3651fe989fecd339c1504474c01fe *man/getObjCoefs-methods.Rd
9124944b213a82b09c0f76522b4fbe44 *man/getObjDir-methods.Rd
cfec843eab5afcbb027ce51c23ea0e82 *man/getObjVal-methods.Rd
4bcc8313bc83932239c251013fb126c7 *man/getRedCosts-methods.Rd
ec9b2846fc044472aa79443462f78abf *man/getRowsLowBnds-methods.Rd
22519c54adee1532294a8fb70b0b44c0 *man/getRowsNames-methods.Rd
3f8186fa4d3f43ac661038ca2c9e18f5 *man/getRowsUppBnds-methods.Rd
5a0332ac47da86ce0a2d3acab24df721 *man/getSolStat-methods.Rd
2e7eb4ab98735451461ccb93ab524630 *man/getSolverParm-methods.Rd
70a2290d937401faa1381e2854a0b36b *man/getsybilenv.Rd
92329739fd82e345e4424bfaba459b74 *man/initProb-methods.Rd
55b7ffbf45d2007cdef95325d151e557 *man/loadLPprob-methods.Rd
125274e3486d2b8459e5e5f261a041af *man/loadQobj-methods.Rd
24478dc94580fa98c2303da7533f5348 *man/makeOptsolMO.Rd
6e2ee239b2e37aa93613bd2225349c88 *man/mergeReact2Modelorg.Rd
9ee35d011ac095f088940edaefb1e6c9 *man/mod2irrev.Rd
80631bd50605a14d1b35d865bc7aaa5b *man/modelorg-class.Rd
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9639639a418f98f5055752005742de57 *man/modelorg2tsv.Rd
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3783494dda5616ccde027e5208340058 *man/oneGeneDel.Rd
b09443c6928d52f8c982deb5dccf42db *man/onlyChangeGPR.Rd
36394c12b65368cb5b60e0412739f347 *man/onlyCheckGPR.Rd
6958b875328aeee4fc7347947978b77d *man/optObj-class.Rd
6a0a84a5d221ca8d78e41dda6a9f1797 *man/optObj.Rd
edd7081ec5bd5a020ceb6df6a4b4aaab *man/optObj_clpAPI-class.Rd
5745e158940880620ba307090b32dee1 *man/optObj_cplexAPI-class.Rd
154354e20cf41ed81f512b028215640b *man/optObj_glpkAPI-class.Rd
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dbde8099a11f2f82d21d733d7a73d576 *man/optimizer.Rd
3a6bfe2f8992e368b78ee9df0d284864 *man/optsol-class.Rd
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1938c964a59711072f0063f7a10413b0 *man/reactId-class.Rd
99b253c8b5a4d9f7f0ee707008b02ac5 *man/reactId_Exch-class.Rd
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514a83fc5336bd51ed0f1311fe4e36e3 *man/readTSVmod.Rd
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8a42a208ff9cef2334fb7cb8749333bd *man/singletonMetabolites-methods.Rd
7c4d54ac3c37335066d64703b6d7ee2c *man/solveLp-methods.Rd
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7f7b5a4d8a297e2c5f175aedf805971d *man/sybil-internal.Rd
4c7ad078f6d50f55f0f081544be8af9a *man/sybil-package.Rd
7f30778ed4283b09f937b0be5cd68b6f *man/sybilError-class.Rd
c8ecb9260d9d0d8f5d786fd4e62e7595 *man/sybilLog-class.Rd
c69c80cd3c93a8bd543903a7baf66941 *man/sybilStack.Rd
91249ef7c6260d0575d24d5046832cfc *man/sysBiolAlg-class.Rd
2f052ecd118cdcc13039d59888d94b4a *man/sysBiolAlg.Rd
556088fea24b6d98e225f33ba171f78f *man/sysBiolAlg_fba-class.Rd
0915e690a98b59cc6674b1963e53f529 *man/sysBiolAlg_fbaEasyConstraint-class.Rd
5be2a6f5fcbb0aede2112bbb32df3363 *man/sysBiolAlg_fv-class.Rd
13df79590c229d6d08bb912088802810 *man/sysBiolAlg_lmoma-class.Rd
3582dc280c12bba765ec83623e2e008e *man/sysBiolAlg_moma-class.Rd
9991e8b05e83164ab5748341cbdf2887 *man/sysBiolAlg_mtf-class.Rd
6a53ae644d7fa977318c5627f432432c *man/sysBiolAlg_room-class.Rd
a036f16448d4018f119b828d3e8b3230 *man/upgradeModelorg.Rd
e758bd824a0b2985092a489b77b9e9ea *man/writeProb-methods.Rd
932a1a876bf6d10f4215b1bac95de6a3 *man/ypd.Rd
ceeeafbf54e3ec1ae03879b7fa70aef6 *vignettes/net-crop.pdf
dd206b0067ca7c1ee9142cc6c8d374c1 *vignettes/optObj-class.pdf
898aa3640f4a96f38f3c2d5d33743b33 *vignettes/optObj-const.pdf
b523ed39db8f4554bd02127af8e4b2a2 *vignettes/optsol-class.pdf
24e6cf8fb9f47f6aa6c8b7bdf3957ca5 *vignettes/sybil.Rnw
886fcb9c559cfa27bd841d8b5ecacd64 *vignettes/sybil.bib
341a4d54f6c30d3076500aff0dfc5212 *vignettes/sysBiolAlg-class.pdf
c2182e6dd340a228aba67b0dd3a1cb19 *vignettes/sysBiolAlg-const.pdf
bc149984e431c983d88b6f1c2fbb3e80 *vignettes/sysBiolAlg-init.pdf
