ba4898b76ec3ae89651ff42e82d5f1cf *DESCRIPTION
6eacde726169b6ccd82ff93abe852e8d *NAMESPACE
e1132e2c6ce83e1edd4708e6a1a80afd *R/addAlgorithm.R
b5825162c602fc34a6ceb89db08ca34e *R/addExchReact.R
2d66c1002aa83bebaf48d5818ed8b03b *R/addReact.R
047b9ecd64368c0b64078d232b95d44b *R/addSolver.R
1749901f4975920478bdbde6b6545791 *R/blockedReact.R
4e6ef7cd8511ff1dfe6d4727982e3f1d *R/bracket_pairs.R
e4bc7ffcb4a7271c31b27a51ce7c02b2 *R/ceilValues.R
f478ce680889fa8505077fec957bb393 *R/changeBounds.R
55e3db25dbe49a039948d1d8c1e005b2 *R/changeGPR.R
013c7a44df120dcf59336cc15a996a36 *R/changeObjFunc.R
6cc18c49b99c10560d0e6924251cc9c5 *R/checkAlgorithm.R
5929811fd67cde2d25f802d715674939 *R/checkDefaultMethod.R
594fdb9cd108364205cd2aa0cef90320 *R/checkOptSol.R
e328fc7ee2dcc1d0fe131ef216e6842f *R/checkReactId.R
1ad3e09b77c4db9e8137dda4f3fb3d8b *R/check_brackets.R
13c830d2b2dc74f1dcac548d3fe0ed8b *R/checksolClass.R
46d9f929a3d5c7d820284f16bd6f4b6f *R/createReactionString.R
20980516b4f01a48c6c73d40c0511a74 *R/deadEndMetabolite.R
f2cb1c976e0d94d59895c2c1964ad141 *R/doInRound.R
6cc6fd0c47efa55d2a2c034d45ea2478 *R/doubleFluxDel.R
320c165986e5d2f024ffcf006667d401 *R/doubleGeneDel.R
eade225fa5a0708cb7f0868421f0071b *R/doubleReact.R
b3aaea90127bb74fa516b43f20f93b37 *R/findExchReact.R
0d729de1b03c2c61b07013498fd66b70 *R/floorValues.R
6cdefc2f6f438b7a401be770014ce845 *R/fluxDistributionClass.R
d2ed04c413393a6c2397f02e38d9e8f5 *R/fluxVar.R
2750733ff7ca429b2643d9c7de6a2e16 *R/geneDel.R
d217e624f4235ad55da1a8ce7cdb93a4 *R/geneDeletion.R
d8ebd0e5c43ad1e6d738a1226911494d *R/generateWT.R
4422619c434aeb4a4a537cfd5be4b442 *R/generics.R
c7d02a5d52849b0c87447d57bbeac2d5 *R/getsybilenv.R
b6322680e6cf98fe3a4e97cc881d03ad *R/mod2irrev.R
cb8701775b5f90838d3ddf447c1ea909 *R/modelorg2ExPA.R
3a20877ee01f900acab5bdc6b1fe531b *R/modelorg2text.R
932819e6aad38f427263fd9bad083f4c *R/modelorg2tsv.R
c7e9ef75452c59ebfe5dcdb877aa659c *R/modelorgClass.R
6e5ecbc1bd524a1daa92ac33f0cea021 *R/modelorg_irrevClass.R
289da8f75c1646fc9fccee46801ae4a6 *R/multiDel.R
04356115618f69c8834b0a5bcfc448fa *R/oneFluxDel.R
5cfbca7abb07883a6506592c7f52118b *R/oneGeneDel.R
2c7e639627beb40e5c9b5685f8470ae1 *R/onlyChangeGPR.R
569018ed4deb010849e139764069ced7 *R/onlyCheckGPR.R
8d802625c4c505863af80e6f179b9a31 *R/optObjClass.R
0077bf82d09dfa0e6cf53ef1490140b7 *R/optObj_basicfunc.R
d845069474b48114f1a7b7184e0537a8 *R/optObj_clpAPIClass.R
74fc2d5ace12596d898ef262277e9a42 *R/optObj_cplexAPIClass.R
62ae42056261b9a0aedaeae6b9d105eb *R/optObj_glpkAPIClass.R
c9e87f93b68c2206f77ff9ec2b7a6565 *R/optObj_lpSolveAPIClass.R
9209b656fd39c96d5d9876c57c346e4c *R/optObj_lpSolveAPIcompat.R
1784f87e473ba48a6cff443cb3ae5297 *R/optObj_pointer.R
3d9ac56725b3305dd8f918b07f6a228a *R/optimizer.R
baa7414604c496bd2c27e29a1e151217 *R/optsolClass.R
7b1832b54ed33814b880f88fc784bc35 *R/optsol_blockedReactClass.R
c169384831e9610caa3a799df8bc2fe0 *R/optsol_fluxVarClass.R
1a5835754fce503fd39446579df42e1a *R/optsol_fluxdelClass.R
0f0cbef7d75cfd591e8a6d9a1aee2690 *R/optsol_genedelClass.R
9b882731cb5de22dd3528e728a628d85 *R/optsol_optimizeProbClass.R
356b3186e392fd6988bce7982d7da10c *R/optsol_robAnaClass.R
ed7946ed505838ade1d0a70c1786cc8e *R/optsol_simpleFBAClass.R
53662012042be118e9753c1709af2748 *R/parseBoolean.R
e26e1acede5e920bf93c03381a5f2cbc *R/ppProcClass.R
4b5038d5a79a68e50b0565d876664462 *R/ppProcessing.R
8f13728735f1ab7c20e285c19ad8147e *R/prepProbObj.R
12311b8a094d9250b14952d17ecba01d *R/prepareSubSysMatrix.R
a0eaebaa4a163cedbe3a5f6d56a0c733 *R/printLogComment.R
02cb8704a3a92d065eb733698140568e *R/printNamedList.R
41832341f70a22bf7222c8f304711b32 *R/printObjFunc.R
94fa095012cb88b535943cd454ec6697 *R/progress.R
7fdd426110f630a7be8e4ec7ffc9230b *R/promptSysBiolAlg.R
0f9ea51037f0a3f36894d09a8fd4faa5 *R/reactIdClass.R
ea4324c982a2bd18a1bdd154a6975b6a *R/readTEXTmod.R
45b5930d37b74aaa193887b1c6abef91 *R/readTSVmod.R
d76347fc8c247063036b98a656ae2325 *R/reassignFwBwMatch.R
66aeab11946b3fd50d422f2f18a14272 *R/rmReact.R
8081c45431705c055bc26017b30a8b7b *R/robAna.R
0088c2757f91c0fbfc74456ea07cd7f1 *R/settings.R
325a40d8be445a22450fc9fd51a173ad *R/simpleFBA.R
623c0a4b4334ad3ce63e02737830c7ee *R/singletonMetabolite.R
e2ebab5d393c14adfa128baffb2d2425 *R/sybilErrorClass.R
875f429f5cd7523b07656672adadcecf *R/sybilLogClass.R
9db90f9129be62a5d60d8d1e174c97d2 *R/sybilStack.R
969ba864c2bc79006a9324d36cbfabcf *R/sysBiolAlgClass.R
747e46bb59ca8213e2593dad3a83a7ed *R/sysBiolAlg_fbaClass.R
ef74b368e673e0f4e9b521661898f26a *R/sysBiolAlg_fvClass.R
36d0d8c8a171a7914ab60f490b7e56b0 *R/sysBiolAlg_lmomaClass.R
9f60265defce306057ad0c819063a7d8 *R/sysBiolAlg_momaClass.R
fc6811e00368d67954c5ed21d9c3e141 *R/sysBiolAlg_mtfClass.R
ad603da7969bd78b9ede014aa02b4c49 *R/sysBiolAlg_roomClass.R
1d0a90a70a68efb599c76932934abbeb *R/validmodelorg.R
9c9511b961e495dfe6740dbb1327e316 *R/validoptsol.R
1eb7c645bf50b8ccf0cb040eb35db47c *R/validreactId.R
1125672b44edd4fde554643bc1e49a92 *R/validsysBiolAlg.R
594fceb256abf07dd0b6b8025e19ca4f *R/ypd.R
fdde38705f3e70b0b15b9c6084be9d75 *R/zzz.R
8447a040c5a7d2587ccb3e151cc3afcf *data/Ec_core.RData
800635704e85c9d91186ab9e19247ce7 *inst/NEWS.Rd
ea2b0cf494e2678661f03d37b510c9bc *inst/doc/sybil.Rnw
96c8f4dbb1e13ebccea4ac1bd05c6bf1 *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
df54ff6f79b5e17888e343012bf6edad *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
c62e1536db361c096f309229eb59f613 *man/optimizeProb-methods.Rd
f1bc9607b5299d3b96c0df12f4a4c279 *man/optimizer.Rd
080601b504639a09611e26e036226325 *man/optsol-class.Rd
4d895ac4612f77e1ddcf4993d4a2aa1c *man/optsol_blockedReact-class.Rd
8b46a6fc56578881f3d35b52b9886863 *man/optsol_fluxVar-class.Rd
5280f2f7601193d2264caadc73f54c62 *man/optsol_fluxdel-class.Rd
1a350675572789ffdf33d2fc9a331ac0 *man/optsol_genedel-class.Rd
1fe3ae140bf27d7e8bb67a49784380e6 *man/optsol_optimizeProb-class.Rd
d6e273cb9363d75fb0b1f935c0d2a99d *man/optsol_robAna-class.Rd
ac391f29c6f1b52febf07b914366c53e *man/optsol_simpleFBA-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
4dc3d1af00ef6beb6bfa0e4c154a6641 *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
2e982056223aa7713337cce3a7880e99 *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
a4dd95b5adf045c175e7028dae9f230f *vignettes/optObj-class.pdf
898aa3640f4a96f38f3c2d5d33743b33 *vignettes/optObj-const.pdf
9f0fc713476086a1122cf62076e8ce71 *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
