0c77f9da1f664b6422ecb6c43cfdce0a *DESCRIPTION
9e67ef7613843de18475355ef889c4e2 *NAMESPACE
90ecac75949618855d37c9257cd3f6ba *R/addAlgorithm.R
8308e92d9fa5642ee9c53541989b0161 *R/addExchReact.R
c1f3bbb2aa4c9cfbad608c8698cc73b0 *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
a39db8a0d3043f200383baa7f49842eb *R/checksolClass.R
37cbc341d4ad73c05681b0d41960bf5e *R/createReactionString.R
ccdb865b09503162257aa1718fe48499 *R/deadEndMetabolite.R
563bed0f47351cf36e30310efb0f9a0c *R/doInRound.R
09fe429224ec77bc80848b4311fdd931 *R/doubleFluxDel.R
72590deb1656a9260198796b2d461d67 *R/doubleGeneDel.R
9aecec52feaa5637fbd465c4d1496c8d *R/doubleReact.R
e4cc6e7aaed353eae3ef9cff55baa72c *R/editEnvir.R
4a2d3a20fd392e13ebb6c738c9995f5b *R/findExchReact.R
6919dd17bfcfa206d62c6dc7008cb1fa *R/floorValues.R
104f2d92613e194c4d90a554ec75601b *R/fluxDistributionClass.R
47be7ca4522a71d3fc7a213215f0fc33 *R/fluxVar.R
1dddb5162ddd190387c3d8b1b4a6e116 *R/geneDel.R
54155cafbd020f506529f1d3b09712db *R/geneDeletion.R
0991ea1d270faf4fb8c17a95b3f9d696 *R/generateFluxdels.R
6a9ec13e76ac04adcee61d137c8e04c4 *R/generateModKey.R
6c52530b9364a4942163b56d04727739 *R/generateWT.R
6695f1aed10dd0884c47c47f4e67a2c9 *R/generics.R
78e77c1d83a0e64c470f83ed26f015f2 *R/getsybilenv.R
c9871521aa40b4ff5ef0366e25b99d14 *R/makeLPcompatible.R
b24905241f5563f655ed8f4e42a271d8 *R/mod2irrev.R
48057c793465f42492bfa86e38eca2de *R/modelorg2ExPA.R
ff95c8bba67c0872032c138e21917198 *R/modelorg2text.R
0008835ef92bd9dfc6cdfcb1c1e37a8d *R/modelorg2tsv.R
429cd503aef8feb246b97b264abbb9c3 *R/modelorgClass.R
8fe684fdc9b0ab7377f4d98aa0cd0791 *R/modelorg_irrevClass.R
a4b8a79f3c4db96bb62cf398e118c10d *R/multiDel.R
c8162b0edd7997141a9593e2b7e9b7de *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
5b5ab47d3a997f8ccc3fdc5760ff1df6 *R/optObj_cplexAPIClass.R
fd30bc55221d9366adb6b9b7319cfeff *R/optObj_glpkAPIClass.R
2ace750b30623a6517de62bf63c7652e *R/optObj_lpSolveAPIClass.R
6c54af969a8d735a0f2ab0efbb3847b6 *R/optObj_lpSolveAPIcompat.R
13d8595ffa2e6698dcbb24d7b1829ba1 *R/optObj_pointer.R
f93e8392e646cd6d2de35875fb314741 *R/optimizer.R
de4364012f1c8bf7cd102506e2dc9bd6 *R/optsolClass.R
d44617853b3fdaa5bcfc3970f5639658 *R/optsol_blockedReactClass.R
1305a4c4d7670148380769137faa0ab1 *R/optsol_fluxVarClass.R
4084b12497406ed203ee90c0d38a3974 *R/optsol_fluxdelClass.R
779410ed819ee7e293317d3166e4ec03 *R/optsol_genedelClass.R
ad77153623fb8016deacd79dddb92505 *R/optsol_optimizeProbClass.R
808e2febfbc830f8a675916093db1bd6 *R/optsol_phppClass.R
36484f89c9ae7b1d91e6ae2755211517 *R/optsol_robAnaClass.R
3b46ed30e1b95632e5a420554863fcfd *R/parseBoolean.R
4bcfa4434e025e5cf8acaf833aa544b9 *R/phpp.R
905d0f1ed5511a890d3d4c7f99c9b521 *R/ppProcClass.R
f121516c97606ece165c12fb90c40c8f *R/ppProcessing.R
824360522eddac0a8f23671af4115cca *R/prepareSubSysMatrix.R
75de08d58a12bfb6c75e3ee4640f611b *R/printLogComment.R
3cdeb4684cdde1ad915dc908de501c3a *R/printNamedList.R
725991084b78416f2909dce9f7f4bcfd *R/progress.R
b195ff2a50e46bf7fd7536dc6acb70b7 *R/promptSysBiolAlg.R
269041de08bc3dad5c9c716587408166 *R/reactIdClass.R
b51a65aacf11c0753e81f47402e484d6 *R/reactId_ExchClass.R
2e34eb29fd827974392ad2a369dd75e1 *R/readTEXTmod.R
9ae36b854ab4616e082ee1ebe2fe9984 *R/readTSVmod.R
2333f0e4415c6d759231f47091dbbf93 *R/reassignFwBwMatch.R
7be0d1c8f0aeb3ee77d934c87dfdb16e *R/recodeMatrix.R
48c5802eda19cb9954e68a3edd9b0e42 *R/rmReact.R
85ee480ef1164d83e4321ff56bac3aff *R/robAna.R
3a9e4c5e22775d5a36022717429ccf92 *R/settings.R
7021a4fdac1e26a687f3132087efc747 *R/singletonMetabolite.R
32671f31aeb7af2b401c2bf4f6fb1740 *R/summaryOptsolClass.R
474f5824d454b9e07b0828b7ef89a984 *R/sybilErrorClass.R
d9b5c25b4e3592096f8e8a55e2c2cc61 *R/sybilLogClass.R
d6d5eb8a09894326bb10f7132e757c2a *R/sybilStack.R
2166755221c7af433257e615f138b1fe *R/sysBiolAlgClass.R
2f995f47ac07359ba07824eb2e48ebcd *R/sysBiolAlg_fbaClass.R
6f9b45a4726bf832be14cc56118b2d28 *R/sysBiolAlg_fvClass.R
f910f8cc337b8cd369fe68588bed17fa *R/sysBiolAlg_lmomaClass.R
1e274ec357de9c6f3f660e91445e73d6 *R/sysBiolAlg_momaClass.R
086ed8679d6df46ea294beb9c4e88359 *R/sysBiolAlg_mtfClass.R
16080725438f60e6e181a063adf443da *R/sysBiolAlg_roomClass.R
0df4342509a6804d37e5c93df3e9ca71 *R/validmodelorg.R
581b6740b46f3230ea6b70225adb5baf *R/validoptsol.R
4bf1eb49479dde86718fc4257b3049d0 *R/validreactId.R
f9253acaee4e2dae34d57291e0471248 *R/validreactId_Exch.R
723c6b1fa7a331c280ca8b049396b6c8 *R/validsysBiolAlg.R
94eef6e16843a2cd6cf543132f24f8cd *R/ypd.R
33ac8ff1db54548242de00fad0a60f9c *R/zzz.R
f22e847ae803fbfa34fd13c8d1a4a936 *build/vignette.rds
42f22e08da875977b8b30a0ae23fd493 *data/Ec_core.RData
dcb1bdb0b852efeed6c4633f10aa2fd0 *inst/CITATION
8ca90b12e2702c33c0c048c85cbca0f3 *inst/NEWS.Rd
d870dc00e23f0705a112feb9816741f6 *inst/doc/sybil.R
6231205e5cfde61277bd95119ee6c7b4 *inst/doc/sybil.Rnw
149f6610bb1a7972513faaee47d11e59 *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
2b073b48a7b4f9ee8418ff1d7d389e26 *man/SYBIL_SETTINGS.Rd
91baf9c88ee095497d04e4de382810ed *man/addAlgorithm.Rd
6c27f136fede2f2b61d41e70a24b1105 *man/addCols-methods.Rd
edfc0fc9b04380722fb42b0a15630990 *man/addColsToProb-methods.Rd
244b2f7679e6f675d22c76c5b7f60f41 *man/addExchReact.Rd
7114fa7fcb96403ab01e7fb63d659911 *man/addReact.Rd
2930a81a64927c46628367fe9ac6800d *man/addRows-methods.Rd
95fa7422e5bc69db2fa18b963e9e64bb *man/addRowsCols-methods.Rd
3655d339c5642c23f049a4fe9c1033ff *man/addRowsToProb-methods.Rd
d70dc27609dd47f7821b311d19eb9886 *man/addSolver.Rd
4c614d9b111d14aca5f46cb75e7b6605 *man/applyChanges-methods.Rd
36d17c9513d8db37d54935848977adf0 *man/backupProb-methods.Rd
49ec69972b1b5569d8656e06e71fdbb7 *man/blockedReact.Rd
b24cef6df94a05630cc11b9b9e91b5d0 *man/changeBounds.Rd
f554e3c19b43421d9dcf4820c03cb9db *man/changeColsBnds-methods.Rd
e56395081a29587f2caa37b5e6ff441b *man/changeColsBndsObjCoefs-methods.Rd
6551752f734d7bb196af78620f33cc02 *man/changeGPR.Rd
9de2d484cfa89a32f61d3c285242a614 *man/changeMatrixRow-methods.Rd
3e0a1f3bf2a5d3f20ca5036ab5677af4 *man/changeObjCoefs-methods.Rd
606feb3d7fa9c67d54b5a33f60040ba0 *man/changeObjFunc.Rd
e7cebb3a438cc7c135fb568f82dec867 *man/changeRowsBnds-methods.Rd
869149a6e77f8ba6b12bee62566bf4c3 *man/changeUptake-methods.Rd
13c4d2e01b767d6e78b8a1bcfe1edcaa *man/checkAkgorithm.Rd
25d8d9f878a2e9874f559c9fdc95491e *man/checkDefaultMethod.Rd
3dccdca9ed6ab2f6f013c289d8f712c0 *man/checkOptSol-methods.Rd
acac8d48a4b7239229f9a448b346b41b *man/checkReactId.Rd
55fb3734c95a9b8e0d9e966c5625e95b *man/checksol-class.Rd
c3c7564fe9132effade29aff8201d7c8 *man/deadEndMetabolites-methods.Rd
49fe53f837afa3374cf68289c101cb64 *man/delProb-methods.Rd
e1e2151d58adeccb57ce8306f9c5ba25 *man/deprecated.Rd
26e03d19e44f933776b94f920aeb7fdb *man/doubleFluxDel.Rd
70c72d6d9b52f4c43eba98bb483b4d14 *man/doubleGeneDel.Rd
c5b57036c5c66ad363c13b0fc16d2690 *man/doubleReact.Rd
095543ff853abb4bd81b939a8d69545e *man/editEnvir.Rd
cd11f47f4b24abf967eacdd4ed272674 *man/findExchReact.Rd
1b90ff80710e521af9be0b5bdd6e4141 *man/fluxDistribution-class.Rd
cd1dfd507e666aba1c6da7c80ffcf8c7 *man/fluxVar.Rd
3fdf6f10923cc06e74e7eb2095e56e48 *man/geneDel.Rd
f9b5d906701136829ae03c1080038636 *man/geneDeletion.Rd
e39d17224659711900b781a14423d549 *man/getColPrim-methods.Rd
e97b53805505e694a808a8da3daa2cb5 *man/getColsLowBnds-methods.Rd
dc35e28afad03ba093a37af7c20510bf *man/getColsNames-methods.Rd
eec72ec44d3d009c376d281dc377bc81 *man/getColsUppBnds-methods.Rd
f3e4b056190ff33e057f8f6125d56e4f *man/getFluxDist-methods.Rd
c3f524ecea03dc5286fc543b801eb796 *man/getNumCols-methods.Rd
5fbfca8aebc9b58615973896fc60ee8e *man/getNumNnz-methods.Rd
fa2e65be94089dff5fbfb3ebfc87075c *man/getNumRows-methods.Rd
6608d0f4ad009a2af2f5cf0fb6ad83a5 *man/getObjCoefs-methods.Rd
220dde34fb5301cb9f4b6c046e1f1ddf *man/getObjDir-methods.Rd
ed9e6e88f7bf176417cc58ee28416174 *man/getObjVal-methods.Rd
797a26ad768ff07f1446cb4ad8c14011 *man/getRedCosts-methods.Rd
3f01559adbe5dad23c0f2cb7e4b06a7d *man/getRowsLowBnds-methods.Rd
776eaa3b68407306f03c06b2c29b5a6d *man/getRowsNames-methods.Rd
9a23c605c6ee8d9bfe62d9202638f405 *man/getRowsUppBnds-methods.Rd
33cbdfdde7c7f6aa8b4b1424012eaae4 *man/getSolStat-methods.Rd
69522b3c0c026fcda1b500c99e9f5580 *man/getSolverParm-methods.Rd
04d3531eb362b360bfc9b19dccc89fff *man/getsybilenv.Rd
009ad7b6b43a7212a631a4991e9f858c *man/initProb-methods.Rd
8287bebdb6eacd07fc5bb94d5cb04bbc *man/loadLPprob-methods.Rd
3b9a7508bf139135f5b8cd99410a29f9 *man/loadQobj-methods.Rd
283740d36591bf1f4a23719143e46ae0 *man/makeOptsolMO.Rd
d7d72105a9a70a5d70fd7b45254898a0 *man/mod2irrev.Rd
08bd0cbff01a8d4cdffc8907e229ea95 *man/modelorg-class.Rd
f37252c2e7f075433b3b5071160764a4 *man/modelorg2ExPA.Rd
a5b27dd9d2b71432d3c8353b231b4ab3 *man/modelorg2tsv.Rd
57f4ae694278958786a06910a9090639 *man/modelorg_irrev-class.Rd
0da7ced466288056cb59a0f569d40dc0 *man/multiDel.Rd
a832ff5aa34ee5beda8afe0f0401684d *man/netFlux-class.Rd
5c59c9f807e938041df958cf00cdf89c *man/oneFluxDel.Rd
dad2ddfce27fc8a7f98e445def429182 *man/oneGeneDel.Rd
36473471e1f8f96fc9e1b3aeb170f3b8 *man/onlyChangeGPR.Rd
d6ac7f0d2b36f8be8d30bdb6139e5435 *man/onlyCheckGPR.Rd
e2f9a3043c09db193aa8c4e16e6a7c98 *man/optObj-class.Rd
1eb5003db6bc1a2103b13cea10c84d92 *man/optObj.Rd
225142d09251677e6d24d100c35970cb *man/optObj_clpAPI-class.Rd
7630d226088079b00ff4bbc46957798f *man/optObj_cplexAPI-class.Rd
6119f2935b01530b34b3df2f463f44e8 *man/optObj_glpkAPI-class.Rd
c71584edec539cf8d805b2770ef178d8 *man/optObj_lpSolveAPI-class.Rd
2cb231ff9626c373503afe2726ea9bcd *man/optimizeProb-methods.Rd
e8ce00d44ab333dd24b19f32cc5afe6f *man/optimizer.Rd
3d70aab0c080c4ea61bc62c2755076a0 *man/optsol-class.Rd
da9a2166e7c46a6501b05951e15715d1 *man/optsol_blockedReact-class.Rd
fcafad5b1cc52ae6437de5b8a9ea9b25 *man/optsol_fluxVar-class.Rd
cf996ad3ea9b5dc9c1b4058f665a3997 *man/optsol_fluxdel-class.Rd
b8cd3ed4e9495338b78a402a7c88d92f *man/optsol_genedel-class.Rd
d1839b170e5e1e307e74f5a6e3ff15ff *man/optsol_optimizeProb-class.Rd
2ea1f1203a94c916810d416047deb525 *man/optsol_phpp-class.Rd
541ba04ae20f8303d506f1b5cd6c7e02 *man/optsol_robAna-class.Rd
0f701ee7607dd66d75cbfe6a59265865 *man/phpp.Rd
bed067ac63879752fa23b32ae340c4bd *man/ppProc-class.Rd
206b7c41b1dcf6fe1e758d14481f2305 *man/printMetabolite-methods.Rd
0c77435cb8a535a26e8f514c6bb1c670 *man/printReaction-methods.Rd
2909dcd984b57c94ef700abadb7fe597 *man/promptSysBiolAlg.Rd
b0e716e2bd895a05d656a4fe08690fd7 *man/reactId-class.Rd
0ad13c12ac52968cad7448c43b585b7a *man/reactId_Exch-class.Rd
46195f55a18ff82d3643a05d861e7ae3 *man/readProb-methods.Rd
247302f10cc3aa9350fba67ecb7c4e5c *man/readTSVmod.Rd
4e08c48d734ec15b9296492a8ac08a2d *man/resetChanges-methods.Rd
19291a1769e3d77264ce78815cb9836f *man/rmReact.Rd
132aa529e232cbef9f422f790d37334b *man/robAna.Rd
1232299eef2fc948a548fe398d899ec8 *man/scaleProb-methods.Rd
77e67dd4d631a7ff783b0684222da998 *man/sensitivityAnalysis-methods.Rd
46df754e7a07d61845526fcd21070cef *man/setColsNames-methods.Rd
242264cf73a7aed5c397c0ca651ce45a *man/setObjDir-methods.Rd
30ad21d37a2487c1616d8bf989cd672c *man/setRhsZero-methods.Rd
74a59cc83524ba96766147a9b8284635 *man/setRowsNames-methods.Rd
dd323d4b114cf1eda88d25427b8fa5a6 *man/setSolverParm-methods.Rd
a8607263718656d6d76219fa26006def *man/shrinkMatrix-methods.Rd
0e7f688b0d391d45a04badb714ed77b0 *man/singletonMetabolites-methods.Rd
1bf9996a6ddd326f83eab608865e2a85 *man/solveLp-methods.Rd
fb474c51c17ee98aff241f9de69e94d5 *man/summaryOptsol-class.Rd
5e4642b4d3737311cd7043f9efb4a12c *man/summaryOptsol.Rd
7f7b5a4d8a297e2c5f175aedf805971d *man/sybil-internal.Rd
73ef373546f4fb226d1a9930f008d33b *man/sybil-package.Rd
f9c95cd1ef8f89d900e8562964d6d7ae *man/sybilError-class.Rd
cdc5cbb14d17ac4a70f03e815c3662fc *man/sybilLog-class.Rd
212e01a9b2d9de31110618004c438ec8 *man/sybilStack.Rd
7f57072b98c250c4005ce4f42b147dc2 *man/sysBiolAlg-class.Rd
aee7906c3689a7582bebfa5573abcdf4 *man/sysBiolAlg.Rd
3310e1725c6a5312a32f39822dfc0991 *man/sysBiolAlg_fba-class.Rd
b7d48b9df18644e65d4314577e405d93 *man/sysBiolAlg_fv-class.Rd
47220b507338d3aedfcf03e5bf679987 *man/sysBiolAlg_lmoma-class.Rd
fed97c0b85071ed0fd23498109a23143 *man/sysBiolAlg_moma-class.Rd
0c8d1caedf8eef909fd7b57a46325e34 *man/sysBiolAlg_mtf-class.Rd
b7051f34a01fdf42a30c209568bfa1c0 *man/sysBiolAlg_room-class.Rd
d5d581e9b1adc9eca6c1b9d455b95ef9 *man/writeProb-methods.Rd
cea331aefadefe7bd32f98a2180be635 *man/ypd.Rd
ceeeafbf54e3ec1ae03879b7fa70aef6 *vignettes/net-crop.pdf
dd206b0067ca7c1ee9142cc6c8d374c1 *vignettes/optObj-class.pdf
898aa3640f4a96f38f3c2d5d33743b33 *vignettes/optObj-const.pdf
b523ed39db8f4554bd02127af8e4b2a2 *vignettes/optsol-class.pdf
6231205e5cfde61277bd95119ee6c7b4 *vignettes/sybil.Rnw
886fcb9c559cfa27bd841d8b5ecacd64 *vignettes/sybil.bib
341a4d54f6c30d3076500aff0dfc5212 *vignettes/sysBiolAlg-class.pdf
c2182e6dd340a228aba67b0dd3a1cb19 *vignettes/sysBiolAlg-const.pdf
bc149984e431c983d88b6f1c2fbb3e80 *vignettes/sysBiolAlg-init.pdf
