1ed86f2ad9181da3e826fa0d2008f2ba *DESCRIPTION
6eacde726169b6ccd82ff93abe852e8d *NAMESPACE
07fe7b6b2febba60ced25d3bf5972076 *R/addAlgorithm.R
cca9cf97e38ff91be391a34b5482f4aa *R/addExchReact.R
098d6f6ad76d518c5c819b838505e825 *R/addReact.R
72b4288596730e88ed84cf6d4ed3290b *R/addSolver.R
9dac1f10f0a334eee47889c483556c12 *R/blockedReact.R
f453d787da16ce394b94a74972925456 *R/bracket_pairs.R
aa686be4358ba5ffaf9b7618725fe0c6 *R/ceilValues.R
9bde657f3b3921f003523c5a15776d68 *R/changeBounds.R
c6a59115a1ead78e06284206926a2d7f *R/changeGPR.R
f1c4329e1b03975f4400e1f0d18d6c81 *R/changeObjFunc.R
7a03e7dd0fd878323720f8e1728f71c2 *R/checkAlgorithm.R
0ad9e469e8aa116b620b297f1332188a *R/checkDefaultMethod.R
f16c04cf3eea4697441dd2a6c833d75e *R/checkOptSol.R
ba3e02e0a0cba2dd67971bda848e7aef *R/checkReactId.R
946e2ddef956bfc34e3cc75db3b19bfe *R/check_brackets.R
cbebd4837e278199236f183b63b647b9 *R/checksolClass.R
d5c4ef27e2c88ac2a5d2106acbbbcabe *R/createReactionString.R
dea706ed7f0232193aca2c33ef0deb9c *R/deadEndMetabolite.R
ae72e9202a03682541adb2e2afdcb47f *R/doInRound.R
b26e183e7cd61ceee074d6bc54127e37 *R/doubleFluxDel.R
6bae0d34128b47ba33c7a86befdd3c1c *R/doubleGeneDel.R
afa32f293ac7f740bd8018d83a7f5c8a *R/doubleReact.R
b6cf997a30f6a6d26a39ecbca1345dbb *R/findExchReact.R
2bcaa251030f0fcc770d4a00843bb28f *R/floorValues.R
43aa0da3735c354cf63ec02649272826 *R/fluxDistributionClass.R
bc1af7f7c941b1b073da4332ed16fe1c *R/fluxVar.R
1ef6130e919599603ce30f815127b1be *R/geneDel.R
309cfa08f5ea95ba2a476296fc20ff7c *R/geneDeletion.R
cf7fa22ec3ef4c5f5e398c456e54a8f6 *R/generateWT.R
f7921d632d0f45dd24b1ccb27bd3c749 *R/generics.R
e35b8cb50af8689e2a830e3d53ba1e48 *R/getsybilenv.R
ac272cca577b2510baad7f48f144cf3e *R/mod2irrev.R
448e3748757c743ef808c1f097988d26 *R/modelorg2ExPA.R
e5b6db566b81dbe23ea9e2ee6253d2a0 *R/modelorg2text.R
ef98a9a51e74c4aadc70acc0c6ad59e9 *R/modelorg2tsv.R
9ce6dce10da732124c1ae7de98e1fdce *R/modelorgClass.R
e13dcbfe98b29db8f6dd2dfa6393357f *R/modelorg_irrevClass.R
1a16bd5159c5baa3c7ecc5b5b330339d *R/multiDel.R
9ca9a56e1cf4d52bebbf2fa3bdeaf91c *R/oneFluxDel.R
5d457491691e994cd6df854b5f990597 *R/oneGeneDel.R
b69459a621b003e5e95318ef84be1795 *R/onlyChangeGPR.R
4294d9fc2998d6bcfddd29956d2b22a0 *R/onlyCheckGPR.R
32c3bdac1f8d8d12410b5838ded7c8e7 *R/optObjClass.R
5a54d555e97cb8e8ad4ed7867296780d *R/optObj_basicfunc.R
be5a45ad40a5c1a2dbc75a3adc6c707e *R/optObj_clpAPIClass.R
315ce5a2a13b8ac94e8431ab7386b435 *R/optObj_cplexAPIClass.R
a716b4912a3376424294666bf374de38 *R/optObj_glpkAPIClass.R
1cf64d794e6b010e111ec6253277d691 *R/optObj_lpSolveAPIClass.R
cc591205dd59843589f1b41b8ce4c092 *R/optObj_lpSolveAPIcompat.R
0b967c11a79d6df85a157b28cc1169c0 *R/optObj_pointer.R
da3340fc5bde58ea27bd97755c5b50b7 *R/optimizer.R
d7384daab4ce0bb83933d7796b76d3e8 *R/optsolClass.R
d7b46fa265f3e28e138e2555da90f986 *R/optsol_blockedReactClass.R
ceda5b01d5dcfb65b7d15f8a4b7b06ae *R/optsol_fluxVarClass.R
689d4688fe022809c2111a7d20fbf5a8 *R/optsol_fluxdelClass.R
3522f607430088a080ed6374a3f7e3e0 *R/optsol_genedelClass.R
da3505068207422aa29b8992f3de0356 *R/optsol_optimizeProbClass.R
29ba40ad85e87fcb25b2bcb1e2a6186c *R/optsol_robAnaClass.R
5cab814731b4957a3aa5671749e97911 *R/parseBoolean.R
21d74ecdc011c0d9f628a0d4ca89c693 *R/ppProcClass.R
e26c54c9290a8b57b9775bd19541d7fb *R/ppProcessing.R
eb43084e823d40d4890e92f61b9b2c94 *R/prepProbObj.R
d69a92cd956ad3fd58fda2a0dea996f1 *R/prepareSubSysMatrix.R
6a6428615f149938c6db6b9242a03e16 *R/printLogComment.R
534e53514126277c6e758edaf594a6cc *R/printNamedList.R
dedefa71791862af5d8beb884239038b *R/printObjFunc.R
4d2d9953a29e0fa114f33a82b630e49e *R/progress.R
717401e4a0419af2cd107eb39bc5d2ab *R/promptSysBiolAlg.R
99634c444c4913f98986720c527cdf0f *R/reactIdClass.R
b47a4e1ea2579db3cca555f0eaa084e1 *R/readTEXTmod.R
3daa00e12c4ef74e42b4d0fd61bab326 *R/readTSVmod.R
b44d4edce2777a7d383c83621117352e *R/reassignFwBwMatch.R
23bf2a548c3278ce268cfd4be5833afb *R/rmReact.R
13d1a8b585f59981cc10d412959095d5 *R/robAna.R
3bebd25a41cf8362c9415f36a9ce68fc *R/settings.R
45b26dac363f12ac163a30b9fdf4bf39 *R/simpleFBA.R
70d7455a64c6c6b310fd1ad5e0cfab31 *R/singletonMetabolite.R
782004168cf861ac31a10590ade0c5f9 *R/sybilErrorClass.R
11009cb8043522e15984d19204420d66 *R/sybilLogClass.R
ed2a5010964343a44b3ca789cfd1ac28 *R/sybilStack.R
ea24cd179daf6273686695b0c32fde11 *R/sysBiolAlgClass.R
2194804110eb8514e82e6937cd23d37e *R/sysBiolAlg_fbaClass.R
5a73de05be2e56397925511194bd0593 *R/sysBiolAlg_fvClass.R
5c5fa2cfbee90f3230d87994bc365d24 *R/sysBiolAlg_lmomaClass.R
13ff1ec30a58f80ff99e6e79caaa1572 *R/sysBiolAlg_momaClass.R
964fc89f4e623083a11b78abc4d72b62 *R/sysBiolAlg_mtfClass.R
3d4594672d0177681fa47b5060f7651f *R/sysBiolAlg_roomClass.R
ec7802f04a92e0a632f756d8546447d2 *R/validmodelorg.R
2620f43db18b7a058127dd85ad9bcc96 *R/validoptsol.R
0c8d38da18b68775a7a96ae1498d919e *R/validreactId.R
23979f6620a47e39edba8ca6c35eca63 *R/validsysBiolAlg.R
974720ad3d5258d31e00d968d676ae89 *R/ypd.R
8cccbcfca033c4dee9111bafbd03e874 *R/zzz.R
8447a040c5a7d2587ccb3e151cc3afcf *data/Ec_core.RData
45b819717e9accbe45b16433e0cf7a88 *inst/NEWS.Rd
ea2b0cf494e2678661f03d37b510c9bc *inst/doc/sybil.Rnw
6c9065518d1cb18bd75920f428e9e6fd *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
85212a39318ffd14ec23b85429f02540 *inst/extdata/rbc.tsv
c94a9ca15e74ec5de8c7be9976faeaed *man/Ec_core.Rd
8cf9248fb55a469b2ae0fb16e99cc344 *man/SYBIL_SETTINGS.Rd
286b85ff7bf37eee125edc73e792c2cd *man/addAlgorithm.Rd
5132481a94ddf1e5cb604f38afdd7c83 *man/addCols-methods.Rd
1ca80fa4418fcd8cb51078ad9d0e3e57 *man/addColsToProb-methods.Rd
244b2f7679e6f675d22c76c5b7f60f41 *man/addExchReact.Rd
201f60898b84a173b5408a1876c8fdb4 *man/addReact.Rd
6a377d9b45f66b1f63e1e39a8eccf52c *man/addRows-methods.Rd
9e538091f327960674825f366414d585 *man/addRowsCols-methods.Rd
5c9433789ce3cc5af509739005c1defa *man/addRowsToProb-methods.Rd
d70dc27609dd47f7821b311d19eb9886 *man/addSolver.Rd
b0a88d4f50b4956617a008ac3611e608 *man/backupProb-methods.Rd
8674d1fb222551c4b956683cfa39e07c *man/blockedReact.Rd
ebca3e643e05683d7bd505d601916c24 *man/changeBounds.Rd
c6e3aaee366964c308abebe12039d2fd *man/changeColsBnds-methods.Rd
4796ad715c8d70e5b49a1fcef426ff31 *man/changeColsBndsObjCoefs-methods.Rd
a2890084575f596d8f4b3269c8a9cd49 *man/changeGPR.Rd
63cea8e2b279c8580a17ea7a81f675d1 *man/changeMatrixRow-methods.Rd
03cdeb9fe2f7de81cbb4faab143f6dd6 *man/changeObjCoefs-methods.Rd
dd9539764bc24f7e01b535ca482553c4 *man/changeObjFunc.Rd
55ea462d99bbb597202e38258eef078c *man/changeRowsBnds-methods.Rd
ee7b9f960de7d15f5e557243e1764941 *man/checkAlgorithm.Rd
f9ad3d4755a3ea1c6272e0ed5e8ada29 *man/checkDefaultMethod.Rd
34c38dcb1b686eaaee9dab71c26bed10 *man/checkOptSol.Rd
19975268780fd3a564c518c8e2e15cac *man/checkReactId.Rd
6e1521ad618bd9701069b04a3e4e780c *man/checksol-class.Rd
f0621a773ddac44a8ba831684c6a7151 *man/delProb-methods.Rd
9e4ab63ef0edd330bcdcd9522e3c6e0e *man/deprecated.Rd
879735cbbc68bdd9dee310cd964825dc *man/doubleFluxDel.Rd
dacd2eca5c606166ba19154249352d96 *man/doubleGeneDel.Rd
500a45045d381ccdb9af80e4e6911ae1 *man/doubleReact.Rd
04620f86f6d5d83e44716e98f4f84baa *man/findExchReact.Rd
f939904f1825f257cebcbbe6a380cd3b *man/fluxDistribution-class.Rd
aeb21fde725b3eb4f2f71b3be2b69eae *man/fluxVar.Rd
7638606495f83199f47364c54cb22176 *man/geneDel.Rd
0a1cb5a0216c092546c42d7045f7a614 *man/geneDeletion.Rd
84d593d2cc2571796c6926502844b5cb *man/getColPrim-methods.Rd
4d1393f44a78660b2686fd051030f975 *man/getColsLowBnds-methods.Rd
e79e4b4d421edbb8c8e8deef3624550b *man/getColsUppBnds-methods.Rd
228f8d68ec6c5bc5d55cc29e1126c691 *man/getFluxDist-methods.Rd
5239fe081d8f78e95f242156fbb0d44d *man/getNumCols-methods.Rd
08ad141e0595204ccc3dea1c4a4dab72 *man/getNumNnz-methods.Rd
35c1c74b0318713efc6aaa1d98b02ba5 *man/getNumRows-methods.Rd
2f180daa4688c15abe69c1a57ad62f4a *man/getObjCoefs-methods.Rd
d2c7364b7e946b8fb252d609d1c97943 *man/getObjDir-methods.Rd
8b661a2193effb49d8b53fefeac948b3 *man/getObjVal-methods.Rd
2e5bd057ad5e58d72460170898b5c035 *man/getRedCosts-methods.Rd
644b27e68b4e772fde3600017c6c1c15 *man/getRowsLowBnds-methods.Rd
09b69a449896c37052f4ceff11639f4e *man/getRowsUppBnds-methods.Rd
cb9b3213bcf36487daa18f126e38b798 *man/getSolStat-methods.Rd
b03abed0742f37cc40736401aea86ccd *man/getSolverParm-methods.Rd
6246cfcb4ef080be72c8f4c4c93c921a *man/getsybilenv.Rd
102ff5f2b78ef636aae59d033d24783b *man/initProb-methods.Rd
3b901f8e58503339b495c508a911cdbf *man/loadLPprob-methods.Rd
ca3dc6996c28cfa0f099bff276d54962 *man/loadQobj-methods.Rd
1739bb6798a683fa6f333e963cd1ef76 *man/mod2irrev.Rd
5ae8270163f7786c5ac7e3023d2286b6 *man/modelorg-class.Rd
36c6fcc829cfbf709696b64e7f76c084 *man/modelorg2ExPA.Rd
46daece363cd93add9b7dd8beb28794f *man/modelorg2tsv.Rd
57f4ae694278958786a06910a9090639 *man/modelorg_irrev-class.Rd
b537d74ba9b7cb923a7cb50c8f28e9e9 *man/multiDel.Rd
c84b983045aa2f1d0d68379347676c0b *man/oneFluxDel.Rd
6da9a75964da68f745354fff076d87cc *man/oneGeneDel.Rd
36473471e1f8f96fc9e1b3aeb170f3b8 *man/onlyChangeGPR.Rd
d6ac7f0d2b36f8be8d30bdb6139e5435 *man/onlyCheckGPR.Rd
c72fc3a0723381d87b4bdf108aac78f6 *man/optObj-class.Rd
1586c0d6d98bf7957b85655fa4bfe255 *man/optObj.Rd
cf4fc5a4b902e9ebf6816b95df0ce380 *man/optObj_clpAPI-class.Rd
438fee846eb7a6c64006e65732263bbc *man/optObj_cplexAPI-class.Rd
067a97ac6e80c712d997f171829c2219 *man/optObj_glpkAPI-class.Rd
a22221338969d528290a28fe24ea3d72 *man/optObj_lpSolveAPI-class.Rd
bd8c1d459a40e1c9b19623f823c04ed0 *man/optimizeProb-methods.Rd
f1bc9607b5299d3b96c0df12f4a4c279 *man/optimizer.Rd
335e7f5e671515401b7dc779a24f5491 *man/optsol-class.Rd
5fc2a3629d9cc275ad6b3d2fde540160 *man/optsol_blockedReact-class.Rd
59764221e57bdca89d7f1d014b36f75c *man/optsol_fluxVar-class.Rd
a7598030d79483a9923bee76d60e2ea1 *man/optsol_fluxdel-class.Rd
385511cd8b163a548b13de91e88e865a *man/optsol_genedel-class.Rd
34b707899f9981c6bc55cb8f00e7f874 *man/optsol_optimizeProb-class.Rd
70160bd91b8a4d3c36ebe8ffe1713f7e *man/optsol_robAna-class.Rd
17f10ed78379598396f6bf3b4bfd6f2b *man/ppProc-class.Rd
104a8276925aa41fbc2171944f5a9d79 *man/prepProbObj.Rd
1548fceea593ad19fea89155b68fd988 *man/printObjFunc.Rd
c70345f9871bd303c0aa9dec400948e1 *man/promptSysBiolAlg.Rd
714428d10704b17877c174953976f37e *man/reactId-class.Rd
f969029dba01f30985507e072d0d5080 *man/readTSVmod.Rd
19291a1769e3d77264ce78815cb9836f *man/rmReact.Rd
602ff04fdb1b4905a5a7734eff371afc *man/robAna.Rd
d6afb302bc204d2a9b47eba51b7084ff *man/scaleProb-methods.Rd
3c64ae4c5d2349d1aa532440167e8ddd *man/sensitivityAnalysis-methods.Rd
503e638aba77c13a23e09df720520b39 *man/setObjDir-methods.Rd
6f46e103d8695d62afdb5425db4969e5 *man/setRhsZero-methods.Rd
ecaaf8f5748620f171dec5d067bc402b *man/setSolverParm-methods.Rd
595586a2483e1007170f57212d417218 *man/simpleFBA.Rd
75410ee9eb28b94abd09a0dd49e66f44 *man/solveLp-methods.Rd
701e646815d3d50fb88ca66df1a04dfb *man/sybil-internal.Rd
8e0f6a6257b7c74093c33bf6e85dd6e1 *man/sybil-package.Rd
f9c95cd1ef8f89d900e8562964d6d7ae *man/sybilError-class.Rd
452a705945fdecc23f585e8b9d60e645 *man/sybilLog-class.Rd
212e01a9b2d9de31110618004c438ec8 *man/sybilStack.Rd
16feb11b0304d6eacb0004023df4a6cb *man/sysBiolAlg-class.Rd
a6bbcd52f14ae37010c771c05bf4e8c8 *man/sysBiolAlg.Rd
70768dc76596c44231d2f38de356135a *man/sysBiolAlg_fba-class.Rd
e08e0ff5c5db45827e0b21cca51f641f *man/sysBiolAlg_fv-class.Rd
f0c0e955083074b3bf815dbac3cd1155 *man/sysBiolAlg_lmoma-class.Rd
a29a459c1884f60a15408d77690e6850 *man/sysBiolAlg_moma-class.Rd
9b6dc5325af5ed754e28059d7252c095 *man/sysBiolAlg_mtf-class.Rd
783102267ecc2478b4d8144ec6995afb *man/sysBiolAlg_room-class.Rd
aa9e54b9f5a83f2c8eb5bdb0ffdf68b4 *man/writeProb-methods.Rd
cea331aefadefe7bd32f98a2180be635 *man/ypd.Rd
ceeeafbf54e3ec1ae03879b7fa70aef6 *vignettes/net-crop.pdf
fca7ac4d7e22f561ee136977ee2e5121 *vignettes/optObj-class.pdf
898aa3640f4a96f38f3c2d5d33743b33 *vignettes/optObj-const.pdf
26a603385d7001d4eec60b48d9e30ff7 *vignettes/optsol-class.pdf
ea2b0cf494e2678661f03d37b510c9bc *vignettes/sybil.Rnw
5fe9ba4104cbce4be936924bace1ddf4 *vignettes/sybil.bib
1cb0866fe10c1f5c2cd0319ccb71c528 *vignettes/sysBiolAlg-class.pdf
c2182e6dd340a228aba67b0dd3a1cb19 *vignettes/sysBiolAlg-const.pdf
bc149984e431c983d88b6f1c2fbb3e80 *vignettes/sysBiolAlg-init.pdf
