dc83d837a7824ef499d46401c4483158 *DESCRIPTION
784d7dc7357bd924e8d5642892bf1b6b *LICENSE
a0057ebdd98c02282ccde8e5106b3480 *NAMESPACE
90ecac75949618855d37c9257cd3f6ba *R/addAlgorithm.R
bbbe745099daaf0f38425ceb818192b9 *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
180728bfe376199f3c3cc243094d1d9f *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
ac449c1d936425aa7317a9f94209b874 *R/reactId_ExchClass.R
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
f1d2b505be834e29ec4af5b54dd9aa23 *README.md
c06bde718fecb3b7ee2418627670dc2c *build/vignette.rds
c3a4955df966f86bd01b43aef1f93ad8 *data/Ec_core.RData
dcb1bdb0b852efeed6c4633f10aa2fd0 *inst/CITATION
678947ff824467bbf47a01c8dc6eab53 *inst/NEWS.Rd
23d1433e302a9eba8ef18916b190c9d2 *inst/doc/sybil.R
24e6cf8fb9f47f6aa6c8b7bdf3957ca5 *inst/doc/sybil.Rnw
afb4d102d12b8b1af50b896645cc9be3 *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
c86e402632dcc2f03dcf70937352b20c *man/Ec_core.Rd
db4b540e8aedd32e4bec80d2c3fe8c4c *man/SYBIL_SETTINGS.Rd
4164ca5d202dd8247bafba72870504ef *man/addAlgorithm.Rd
ccbb1b64be579aeb71dd1522f3f10695 *man/addCols-methods.Rd
3d5869c25a747ea1953ce313a94a0820 *man/addColsToProb-methods.Rd
6a49b649205ddad8a8cefa7930f0943f *man/addExchReact.Rd
380aa459712d83ae234a211e3e6965f4 *man/addReact.Rd
4737b0148961738f3086198ac0386b83 *man/addRows-methods.Rd
9e7a78b98fd3b3ff331ec22eba507078 *man/addRowsCols-methods.Rd
7351ca459ef9b72a3460ae1ad8b3b34a *man/addRowsToProb-methods.Rd
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f93c8371c4efaa0625745a84abef0758 *man/applyChanges-methods.Rd
9c32cf1d270fb8fc18cd25cdf0548d92 *man/backupProb-methods.Rd
629e15843283c119fb45bd913c1f3bed *man/blockedReact.Rd
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1b733bc4fbe56b4f337e4e70ce12b4ec *man/changeColsBnds-methods.Rd
2680b6312f362ebba8a54d050ae29711 *man/changeColsBndsObjCoefs-methods.Rd
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a2fa38ed9e5faab8ab39624fa5b1780c *man/changeObjCoefs-methods.Rd
2b0046fae009e97e2bd6121345e44fa2 *man/changeObjFunc.Rd
65fd967772f69bbcf4f2bb63b631521a *man/changeRowsBnds-methods.Rd
9076aeb7d2c7e1bcd17407bf73dcbf47 *man/changeUptake-methods.Rd
83c2addad4c95cb4b7bfc162f51dfa77 *man/checkAkgorithm.Rd
2a37ec3eac03619cf5dad4ed5af92b78 *man/checkDefaultMethod.Rd
836cab880412c7ee3a1ac14cf755349b *man/checkOptSol-methods.Rd
75a794a7b610dc8ef645dcd74d0b7006 *man/checkReactId.Rd
54867eb71b870d2016c09d078851fd70 *man/checkVersion-methods.Rd
263e416c4114807b2958196c8fba5764 *man/checksol-class.Rd
e4868ce5d229f4fc7a8b5ceedcf71c54 *man/deadEndMetabolites-methods.Rd
ca45856a5b4fdd139adc100f732eaab1 *man/delProb-methods.Rd
313d52be143d03019bf3d674ee4a75c4 *man/deprecated.Rd
d744f62cc4c74fce1fe4b4d0b0c83cfd *man/doubleFluxDel.Rd
1dfc448de5761cf2b620ca77d329b39c *man/doubleGeneDel.Rd
f1632d4d423d8a96c203ffa7f80a09b2 *man/doubleReact.Rd
32aab6ff4a39b77c086d07b162e6cfc1 *man/editEnvir.Rd
ac79dd022ce0b3b0b1fe41b4dc722c95 *man/findExchReact.Rd
cc104c250303888f2e9501cdde4c23fc *man/fluxDistribution-class.Rd
a5c161561f082a02818fbe8995f81845 *man/fluxVar.Rd
ea280c0e0f9f50244e86448212845543 *man/geneDel.Rd
d01d83a4fb4c1e92812adb80d2d24487 *man/geneDeletion.Rd
a896cdcb99b4a5852d45ff5f19a7d3f5 *man/getColPrim-methods.Rd
a7b66d1823d9b4592e3a682fc7f1cdad *man/getColsLowBnds-methods.Rd
417cc38adbb6a57db510f0e0d710f4ea *man/getColsNames-methods.Rd
87317b916a7315e3ea1f5ab4f6021fec *man/getColsUppBnds-methods.Rd
4f37f934b4682cb4cc29f0e46ac7b533 *man/getFluxDist-methods.Rd
63e5368dbacdfdcc91d059775b3e297d *man/getNumCols-methods.Rd
02f5c9c796ed439c78d58bf64a0cd309 *man/getNumNnz-methods.Rd
d024b9f1b9d1e36acd01a055363dacfd *man/getNumRows-methods.Rd
3f5c799f5379f2753bf978d0bbf2b350 *man/getObjCoefs-methods.Rd
602d31181c1b79080c8db175ed747836 *man/getObjDir-methods.Rd
3566f7a4cd79ecdce7ec2a9e9af33a41 *man/getObjVal-methods.Rd
e7cf7a42cb3288efb8179d351d089c52 *man/getRedCosts-methods.Rd
a1493b612508bd30fc85efd7a62b34fd *man/getRowsLowBnds-methods.Rd
9f8f0fad881ed9ae40f80c2bac4423d4 *man/getRowsNames-methods.Rd
b809722b0e798279846d47b72e360fa3 *man/getRowsUppBnds-methods.Rd
20606bd44f717423a33314c9f149bad1 *man/getSolStat-methods.Rd
c738a32ab364dc573643fa6d8d1496e4 *man/getSolverParm-methods.Rd
697ae0fc7914329d0976b9aa73edee45 *man/getsybilenv.Rd
2cbc7543945ce53bf6e7d4cacc95f9df *man/initProb-methods.Rd
8819fbb3ace4a9c7b471485679ee30b4 *man/loadLPprob-methods.Rd
bb4b6f7548936663e667ff2cdc4aeb33 *man/loadQobj-methods.Rd
ab016e9888bcc22f937310730cee53c9 *man/makeOptsolMO.Rd
8b98b0302de494a5176d33ca59bf74ef *man/mergeReact2Modelorg.Rd
56def28382e1d48a3e05a389c741b530 *man/mod2irrev.Rd
a67c199110ba384e53f1a4482c2e6ca7 *man/modelorg-class.Rd
c33edf9c97fe4566183a250fb5ed7cc3 *man/modelorg2ExPA.Rd
b444bac723301fcd8fa2c99178a753a9 *man/modelorg2tsv.Rd
729d1469433621129707f70f4ae58c90 *man/modelorg_irrev-class.Rd
bdceb68d045dd2aa74889e4144d0323a *man/multiDel.Rd
972991fe9f65d23efb89c8764ab3f1d4 *man/netFlux-class.Rd
912f9506a873ab37e94d08e9f8fa0c47 *man/oneFluxDel.Rd
5883e3808898713121ce3d12b644eb00 *man/oneGeneDel.Rd
a7f0feaf4980038f5cca588d0d07fb16 *man/onlyChangeGPR.Rd
e6c788d2033089e98a086d9e87acabac *man/onlyCheckGPR.Rd
195b08d65de695d25261bcf3d3510607 *man/optObj-class.Rd
5a11f43cc2ec91af5d56cdd4e218cee1 *man/optObj.Rd
6efd30751fc5601ae24e43b29a7927a8 *man/optObj_clpAPI-class.Rd
9abd0afc80667e977922360d6ca2ca58 *man/optObj_cplexAPI-class.Rd
b710806ad01bdd7f4309c703c63c8e00 *man/optObj_glpkAPI-class.Rd
37630f320feb530f35651d23baed28ab *man/optObj_lpSolveAPI-class.Rd
1f3726f5df0b2d0e10e8e6c35207f8c9 *man/optimizeProb-methods.Rd
b66d9cecdd6b24cfa0a7b7beaa656b38 *man/optimizer.Rd
ba6b18efc63ccc4f2e5c17957a2b198e *man/optsol-class.Rd
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0e809c9ebe1516e3080448c5b458b20e *man/optsol_genedel-class.Rd
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b7ee6dbe8dcb010fa37d4c845164c99c *man/optsol_robAna-class.Rd
953e50ea0afa1819fa75a5ace6b0ac9e *man/phpp.Rd
9f2d803ca5a197b3deba968651ce07d5 *man/ppProc-class.Rd
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32034878a5b1a6d5fb0230fe88b2094e *man/printReaction-methods.Rd
99273db5ecc5314c01472be7b92c638a *man/promptSysBiolAlg.Rd
1bd59fc93f7161339f62741609ba6480 *man/reactId-class.Rd
e0dbe61f7c4a7c43d9edd9cd8032cdf5 *man/reactId_Exch-class.Rd
3c8748c15f05046a5f3fca6ffe990826 *man/readProb-methods.Rd
649947980df2a10ffe31616895e066cf *man/readTSVmod.Rd
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0a7f7b36b3eb6b65e64f35dfcb5a904e *man/rmReact.Rd
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7f00e44d2acfe74aa79a4686ccf8c54d *man/setRhsZero-methods.Rd
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eb85c0315e458422ef211479b03b61dd *man/setSolverParm-methods.Rd
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0b2e1ed5f4def3db82548b8b661eb92b *man/summaryOptsol-class.Rd
b10a64e2385e9b586625e98462a700e5 *man/summaryOptsol.Rd
7f7b5a4d8a297e2c5f175aedf805971d *man/sybil-internal.Rd
3ca8e3b47894e7361694b85427e71106 *man/sybil-package.Rd
0d6f4118f2fad152860602b3938707d6 *man/sybilError-class.Rd
4bebe17e9d02abf7b9f15fea5d72a118 *man/sybilLog-class.Rd
370014f7872fe7273fd97c947fe63872 *man/sybilStack.Rd
68e176fed208cde3be2b005285384b0f *man/sysBiolAlg-class.Rd
2f29363a5cdee45440f6b5fac447c861 *man/sysBiolAlg.Rd
5c1a6db862d57a1b7efb0c0aa9476948 *man/sysBiolAlg_fba-class.Rd
3e3d2925f0da5cbb9b5867445337dad0 *man/sysBiolAlg_fbaEasyConstraint-class.Rd
c28e3f57872ddd6b7e9ccea121e5cb10 *man/sysBiolAlg_fv-class.Rd
63f2dcf501360aa0cf7a73f22d113be3 *man/sysBiolAlg_lmoma-class.Rd
b3623f4b8e1e0b0712be68e17af1ec57 *man/sysBiolAlg_moma-class.Rd
f655910b3380507108d10d68c43984f7 *man/sysBiolAlg_mtf-class.Rd
c8117f98c6b668909cb7c9d88dd12bc7 *man/sysBiolAlg_room-class.Rd
82e7368bfd47dd3494afbe291d9209d8 *man/upgradeModelorg.Rd
48b214bb78de01423f03a9ad6754fb64 *man/writeProb-methods.Rd
180288d1be517a446f88dad48217f3be *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
