ec98efcf9f30900066aa62e653a3b325 *DESCRIPTION
6eacde726169b6ccd82ff93abe852e8d *NAMESPACE
0967d872ea73700b11a53f66d247d26d *R/addAlgorithm.R
6f2a3779b7a1eb44f6707429bffdd174 *R/addExchReact.R
91e1478240dfdc1d6b69acd54ab7e9b9 *R/addReact.R
7d24c8e88daa3beaa537fa02fb3e92fc *R/addSolver.R
111a4cd7342c967f778c9a912f3da42e *R/blockedReact.R
0d5b1d23d2330312bfed58c3f215d18b *R/bracket_pairs.R
23c59e0724cd3202e991a99e45c07add *R/ceilValues.R
49ccb19d034dc38f8026b0e2b73cd591 *R/changeBounds.R
8afc28a725d29cefd09bb3aacba96a5e *R/changeGPR.R
3c715951f6e999d72dae7562a89f507f *R/changeObjFunc.R
797676ba2454aa22b40d1105c8e5e1a3 *R/checkAlgorithm.R
0f2b9511c4c42106d7cca2581c49b720 *R/checkDefaultMethod.R
19aed637461dcf4f6603f24fc207e6cf *R/checkReactId.R
e8aa1e1cb278ee9cc537226cd4506af9 *R/check_brackets.R
bd222463b080a6ef88f62b30b75e5f2e *R/checksolClass.R
70f0ca7e482fc0c07efa04ca6cde26bf *R/createReactionString.R
e56395d6fe1b844d3904c4dfb12925af *R/deadEndMetabolite.R
1ab65bebbd5f78105552c6eb9d415cf8 *R/doInRound.R
0be60a8e748f4eb4bed1d8877b23e06e *R/doubleFluxDel.R
a42942cd9984225a015eabdae7b727ba *R/doubleGeneDel.R
18aa208a365ccc1d47bd8afe42ea8a20 *R/doubleReact.R
d1b3553b80648a20a356789167547835 *R/editEnvir.R
9626f3ab5f42192c009d32941a1b03ff *R/findExchReact.R
fc6835ab17729a630464d04030ffb3c1 *R/floorValues.R
4ddb28770bee6893680d979382cc536c *R/fluxDistributionClass.R
0de5689437a3aa4bdc04139dfe3317a4 *R/fluxVar.R
28fd13f64c83a054e2c740f8b8199f80 *R/geneDel.R
4638d8251a90935695c83ff3f68dce36 *R/geneDeletion.R
b35caf6cb0fbf678c0e84d974c6d6620 *R/generateFluxdels.R
b621643fb28ebdc9c9f5d86e8d6a06e0 *R/generateModKey.R
3aeb3fd21e59e4ae6b62f7c34e746306 *R/generateWT.R
030993a42715b33505cf22402f65291a *R/generics.R
0608bb9fe6382bfff5e21d495af44ded *R/getsybilenv.R
8dd2c676de508d643f6faae6dac8a55e *R/mod2irrev.R
d6a3bdf31d6ca8613e870e9787517c02 *R/modelorg2ExPA.R
5b9e4ec6797be7c99a0907b369b9a9d3 *R/modelorg2text.R
36f93f34542d3d78fd859acc8ae183ef *R/modelorg2tsv.R
c67cb39faec362c8a16f77c15b7b77e2 *R/modelorgClass.R
8666ea7d7a9020e8e8f8e3a3b95a581b *R/modelorg_irrevClass.R
a1f0fcbf88dd0a03a62ee718f057411c *R/multiDel.R
520c76986dbfdfb6cbd85f3163bba304 *R/netFluxClass.R
d577cf346016f883aa3e5c11d6433162 *R/oneFluxDel.R
8bb40392e25559ec14f37b73c0a59cf1 *R/oneGeneDel.R
e0474d4bb698404b8701bfb3c99eb54c *R/onlyChangeGPR.R
01665c9e695e92f9695c3be1d215895b *R/onlyCheckGPR.R
21cd3e1bebc6e9fb4b052ecf65fee105 *R/optObjClass.R
f6c0b0087ae066c01acbc9a5ef9ed317 *R/optObj_basicfunc.R
34b43c0f76ad685b28b8167248381350 *R/optObj_clpAPIClass.R
20b63eade7fbbed5edac01aa1414125e *R/optObj_cplexAPIClass.R
2852c0100dc11e2c5a285801b020f5e7 *R/optObj_glpkAPIClass.R
f9fe404e0eec3c77164c19958041c49c *R/optObj_lpSolveAPIClass.R
47f7acd2d5f1a8e595586d71ffbf5a70 *R/optObj_lpSolveAPIcompat.R
51884c0c66f8f90ee9dd968b5f8d31d6 *R/optObj_pointer.R
caf75481ae7cdb65a59bdde48f4c194c *R/optimizer.R
257e7955c7ee9f986ee93b1b2519ffa9 *R/optsolClass.R
c9d3be61374a93397da2bc37e665035b *R/optsol_blockedReactClass.R
5c8b0715b705f393f6625d8532539a1f *R/optsol_fluxVarClass.R
d6b34d3574ec4f51132d9017dd6a7073 *R/optsol_fluxdelClass.R
0d5d883276935a878fa2bd239474401c *R/optsol_genedelClass.R
586cec81f826b4524eef629f1abbe6f0 *R/optsol_optimizeProbClass.R
5305f8021b6a1f8c526da8d9c4425b91 *R/optsol_robAnaClass.R
156aa59c3ac90755ca1d0b842a9d3566 *R/parseBoolean.R
f3c5c82c6a0db68275f1a42c3f88e742 *R/ppProcClass.R
41d61e1c8899ba3870d0fb5000af1abd *R/ppProcessing.R
17ca61812480cf79679ff9a87ff1a555 *R/prepareSubSysMatrix.R
05a903c802c33b945aae2896ab24a027 *R/printLogComment.R
42468ab0d532dad34d781b9673dcb2fc *R/printNamedList.R
d209841319cfe9b6e5e7d88fba831459 *R/progress.R
e7d13a3ca57b9ba1cae6d76826fb8d9b *R/promptSysBiolAlg.R
dd2e72deb717a0002c4e5a0607130bdf *R/reactIdClass.R
a8804228dec5a994208a9e60cf0d0b61 *R/reactId_ExchClass.R
5b5f92ecc92e6b6ddbc95cb7271164fd *R/readTEXTmod.R
9539a1a333abd9ebdcaa28b607315744 *R/readTSVmod.R
62ceacf244dd9699eaaedab97c533002 *R/reassignFwBwMatch.R
0e4f4e09d2e7a3b09e2cd8144f7ec056 *R/recodeMatrix.R
241a88944e5f045b9fcd1a4590096674 *R/rmReact.R
00660531edfc77bea4dc89f3328151aa *R/robAna.R
81c45cc5943ccbec00a07b7b78481ffa *R/settings.R
aaac01575f9aab5af3ff26d9f4ded802 *R/singletonMetabolite.R
931197117f5cd72d7412e8e86d7fe607 *R/summaryOptsolClass.R
214950385daf5ffb4b9389cc65009753 *R/sybilErrorClass.R
d82025cc2159cc4571e0b719c5d648bd *R/sybilLogClass.R
5376c12aed3d9db5d2e3e758d91eaf69 *R/sybilStack.R
c7346766b4ee5fd5349ece613d61259a *R/sysBiolAlgClass.R
fb00ba257d87242e0af6317aa13eaaf7 *R/sysBiolAlg_fbaClass.R
2f7341d37a3be1a24dfbc212bc5ab753 *R/sysBiolAlg_fvClass.R
f067a97a4a23ff66e293ce4352168ee2 *R/sysBiolAlg_lmomaClass.R
79dcb749688b08a1ae2e9a982e384ab1 *R/sysBiolAlg_momaClass.R
cadd02e3f56b5e11b6a15d0f4df4f723 *R/sysBiolAlg_mtfClass.R
ecd3b402b1a0273e0927cb3297d320fb *R/sysBiolAlg_roomClass.R
bcb779c8c170d3a899b7f6b51dde871c *R/validmodelorg.R
2022edba44495fb8f9e64ec0d81c65f1 *R/validoptsol.R
daab3fbea6c5d401ba2eb997ca895a07 *R/validreactId.R
3e2a5e3f95aafa193a56408f0fa7d35a *R/validreactId_Exch.R
8353fdb16fdfb02b89ba52184d7396c4 *R/validsysBiolAlg.R
a5416627944b1048c2f82473a6299dbd *R/ypd.R
68c85bff6dccd62cb43f17b909429306 *R/zzz.R
42f22e08da875977b8b30a0ae23fd493 *data/Ec_core.RData
be0f5ed1e7712bded8b5afbda12e1530 *inst/NEWS.Rd
4c09bbdb0512ced8a39160b47040dd19 *inst/doc/sybil.Rnw
4f452e2d996803043c9bc99bcd4f8286 *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
8fc651939adb08a5b46e5997e026b434 *man/SYBIL_SETTINGS.Rd
91baf9c88ee095497d04e4de382810ed *man/addAlgorithm.Rd
6c27f136fede2f2b61d41e70a24b1105 *man/addCols-methods.Rd
edfc0fc9b04380722fb42b0a15630990 *man/addColsToProb-methods.Rd
244b2f7679e6f675d22c76c5b7f60f41 *man/addExchReact.Rd
85d5870f8953bff9355171ae1aae846b *man/addReact.Rd
2930a81a64927c46628367fe9ac6800d *man/addRows-methods.Rd
95fa7422e5bc69db2fa18b963e9e64bb *man/addRowsCols-methods.Rd
1df60bb03cc71f29e46406822623c577 *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
2a354e1c25f9c97b0645b52d54738ff2 *man/changeRowsBnds-methods.Rd
13c4d2e01b767d6e78b8a1bcfe1edcaa *man/checkAkgorithm.Rd
25d8d9f878a2e9874f559c9fdc95491e *man/checkDefaultMethod.Rd
3dccdca9ed6ab2f6f013c289d8f712c0 *man/checkOptSol-methods.Rd
acac8d48a4b7239229f9a448b346b41b *man/checkReactId.Rd
55fb3734c95a9b8e0d9e966c5625e95b *man/checksol-class.Rd
49fe53f837afa3374cf68289c101cb64 *man/delProb-methods.Rd
e1e2151d58adeccb57ce8306f9c5ba25 *man/deprecated.Rd
26e03d19e44f933776b94f920aeb7fdb *man/doubleFluxDel.Rd
70c72d6d9b52f4c43eba98bb483b4d14 *man/doubleGeneDel.Rd
af8281d26b5aac0f7e4abfb29d51aeb4 *man/doubleReact.Rd
095543ff853abb4bd81b939a8d69545e *man/editEnvir.Rd
f9686d540ae14b503dec5e5a71ef6ce2 *man/findExchReact.Rd
1b90ff80710e521af9be0b5bdd6e4141 *man/fluxDistribution-class.Rd
356f2ed5a86de97f6176c77aee129dc4 *man/fluxVar.Rd
3fdf6f10923cc06e74e7eb2095e56e48 *man/geneDel.Rd
f9b5d906701136829ae03c1080038636 *man/geneDeletion.Rd
e39d17224659711900b781a14423d549 *man/getColPrim-methods.Rd
e97b53805505e694a808a8da3daa2cb5 *man/getColsLowBnds-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
1e15f6c55acf4c7fd1c84aa8bee5b74c *man/getObjVal-methods.Rd
797a26ad768ff07f1446cb4ad8c14011 *man/getRedCosts-methods.Rd
3f01559adbe5dad23c0f2cb7e4b06a7d *man/getRowsLowBnds-methods.Rd
9a23c605c6ee8d9bfe62d9202638f405 *man/getRowsUppBnds-methods.Rd
33cbdfdde7c7f6aa8b4b1424012eaae4 *man/getSolStat-methods.Rd
69522b3c0c026fcda1b500c99e9f5580 *man/getSolverParm-methods.Rd
04d3531eb362b360bfc9b19dccc89fff *man/getsybilenv.Rd
4d8f5f90ce19b00a98c9c4cbc001a641 *man/initProb-methods.Rd
2af7395fcfc13244a61e9140e0886a08 *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
07bdacb5edb7f9a727186c0d0ca5e29f *man/optimizeProb-methods.Rd
7271968c5a9d1e9c157875479a43457d *man/optimizer.Rd
db5690cbd846128f0b1ec9e3ca684dae *man/optsol-class.Rd
da9a2166e7c46a6501b05951e15715d1 *man/optsol_blockedReact-class.Rd
fcafad5b1cc52ae6437de5b8a9ea9b25 *man/optsol_fluxVar-class.Rd
691f4bec13aae8b030697e3735c68cb4 *man/optsol_fluxdel-class.Rd
b8cd3ed4e9495338b78a402a7c88d92f *man/optsol_genedel-class.Rd
d1839b170e5e1e307e74f5a6e3ff15ff *man/optsol_optimizeProb-class.Rd
d554802bc52f4f63e107abd9b502d477 *man/optsol_robAna-class.Rd
90676f32ac5bf881e475ebb954bff92a *man/ppProc-class.Rd
d515ece15cc10d77b6e9a91b7d13f283 *man/printMetabolite-methods.Rd
0c77435cb8a535a26e8f514c6bb1c670 *man/printReaction-methods.Rd
2909dcd984b57c94ef700abadb7fe597 *man/promptSysBiolAlg.Rd
cee42fe979614dd859261da9cfa1035e *man/reactId-class.Rd
39b3bb7376c951031a12a277f7515bf6 *man/reactId_Exch-class.Rd
46195f55a18ff82d3643a05d861e7ae3 *man/readProb-methods.Rd
80dd92b05a5b0bbcf4bb6842695874b7 *man/readTSVmod.Rd
4e08c48d734ec15b9296492a8ac08a2d *man/resetChanges-methods.Rd
19291a1769e3d77264ce78815cb9836f *man/rmReact.Rd
7c9294493532a76a11c866146ac86591 *man/robAna.Rd
1232299eef2fc948a548fe398d899ec8 *man/scaleProb-methods.Rd
77e67dd4d631a7ff783b0684222da998 *man/sensitivityAnalysis-methods.Rd
242264cf73a7aed5c397c0ca651ce45a *man/setObjDir-methods.Rd
30ad21d37a2487c1616d8bf989cd672c *man/setRhsZero-methods.Rd
23c6a161dd7970aba95e7c72a05c151f *man/setSolverParm-methods.Rd
7c99f48a41b50df9d7db3c7ee816ba62 *man/shrinkMatrix-methods.Rd
1bf9996a6ddd326f83eab608865e2a85 *man/solveLp-methods.Rd
c607039da718d912578b68feb5f62607 *man/summaryOptsol-class.Rd
5e4642b4d3737311cd7043f9efb4a12c *man/summaryOptsol.Rd
7f7b5a4d8a297e2c5f175aedf805971d *man/sybil-internal.Rd
0870b9fa6e2d69b336b0a4998d11102e *man/sybil-package.Rd
f9c95cd1ef8f89d900e8562964d6d7ae *man/sybilError-class.Rd
cdc5cbb14d17ac4a70f03e815c3662fc *man/sybilLog-class.Rd
212e01a9b2d9de31110618004c438ec8 *man/sybilStack.Rd
c64bd0fb491c4962a2c48c4f1d571a53 *man/sysBiolAlg-class.Rd
aee7906c3689a7582bebfa5573abcdf4 *man/sysBiolAlg.Rd
0aa52d3e70b25ec29cc2bbcfce75d954 *man/sysBiolAlg_fba-class.Rd
7c86dc977110ec142bcd970448d9eaf5 *man/sysBiolAlg_fv-class.Rd
6bf54cf9238861e8ed5abacecf48ffc5 *man/sysBiolAlg_lmoma-class.Rd
a8a311e31d01aae9759cb561b4d5cab9 *man/sysBiolAlg_moma-class.Rd
4868d482c3fc8a16002495bcd214ea4a *man/sysBiolAlg_mtf-class.Rd
5350072dadd42f4a6929d1f9633d31be *man/sysBiolAlg_room-class.Rd
d5d581e9b1adc9eca6c1b9d455b95ef9 *man/writeProb-methods.Rd
cea331aefadefe7bd32f98a2180be635 *man/ypd.Rd
ceeeafbf54e3ec1ae03879b7fa70aef6 *vignettes/net-crop.pdf
a4dd95b5adf045c175e7028dae9f230f *vignettes/optObj-class.pdf
898aa3640f4a96f38f3c2d5d33743b33 *vignettes/optObj-const.pdf
19cb61396e63989e01ce0db167a2f80f *vignettes/optsol-class.pdf
4c09bbdb0512ced8a39160b47040dd19 *vignettes/sybil.Rnw
5fe9ba4104cbce4be936924bace1ddf4 *vignettes/sybil.bib
dea35836ec90ad8bc3702106ed5528d8 *vignettes/sysBiolAlg-class.pdf
c2182e6dd340a228aba67b0dd3a1cb19 *vignettes/sysBiolAlg-const.pdf
bc149984e431c983d88b6f1c2fbb3e80 *vignettes/sysBiolAlg-init.pdf
