ac38dbcf3c52b5cde373635d15a5839b *DESCRIPTION
6eacde726169b6ccd82ff93abe852e8d *NAMESPACE
59bb4aef6a14515abe423ebd9d2f4320 *NEWS.Rd
e1132e2c6ce83e1edd4708e6a1a80afd *R/addAlgorithm.R
b5825162c602fc34a6ceb89db08ca34e *R/addExchReact.R
05a46ba817e2d56ec6920e66afbaeea8 *R/addReact.R
047b9ecd64368c0b64078d232b95d44b *R/addSolver.R
0af1242a113033b3c373dfbf9d669adb *R/blockedReact.R
4e6ef7cd8511ff1dfe6d4727982e3f1d *R/bracket_pairs.R
e4bc7ffcb4a7271c31b27a51ce7c02b2 *R/ceilValues.R
313f97300d16f6134eb15739dbbb849c *R/changeBounds.R
55e3db25dbe49a039948d1d8c1e005b2 *R/changeGPR.R
f1ca2fc7a7965d75f5c3539bc62f6e8c *R/changeObjFunc.R
6cc18c49b99c10560d0e6924251cc9c5 *R/checkAlgorithm.R
e0123d7d78b6730407548754c238d2da *R/checkDefaultMethod.R
149607031be4516090f5c527797e2a2d *R/checkReactId.R
1ad3e09b77c4db9e8137dda4f3fb3d8b *R/check_brackets.R
a6ec2392d72c3a20c9aee3d6c701b5eb *R/checksolClass.R
46d9f929a3d5c7d820284f16bd6f4b6f *R/createReactionString.R
20980516b4f01a48c6c73d40c0511a74 *R/deadEndMetabolite.R
f569f724fba0a6ca9fa50215d8bfed88 *R/doInRound.R
97e9d8b1c4f594ce78ef295cfea40505 *R/doubleFluxDel.R
9e3c0b5ea7246b0c3878d58d06c65540 *R/doubleGeneDel.R
eade225fa5a0708cb7f0868421f0071b *R/doubleReact.R
4eaf1ae34b03c2d95d6e041513a9b4bb *R/findExchReact.R
0d729de1b03c2c61b07013498fd66b70 *R/floorValues.R
e778a56568403bfbbc136ab82be7a283 *R/fluxDistributionClass.R
34879ee7376d99a81245ab06e5f25f3e *R/fluxVar.R
1addf790d1fd825666ef26addc159eaf *R/geneDel.R
d217e624f4235ad55da1a8ce7cdb93a4 *R/geneDeletion.R
47f1e5f6f41a2faaf96aa5d852acc91a *R/generateWT.R
5ff3dd05307764091a5c913e44d860cf *R/generics.R
c7d02a5d52849b0c87447d57bbeac2d5 *R/getsybilenv.R
fb6fc7e61e76059302dbf95ae4555403 *R/mod2irrev.R
7eb15ab0efb9f2120f1998e46f8a0eb9 *R/modelorg2ExPA.R
3a20877ee01f900acab5bdc6b1fe531b *R/modelorg2text.R
932819e6aad38f427263fd9bad083f4c *R/modelorg2tsv.R
75aa97c63d02015d801e19814b715a18 *R/modelorgClass.R
281cb3286e380968e7b0f746b4bcb89a *R/modelorg_irrevClass.R
289da8f75c1646fc9fccee46801ae4a6 *R/multiDel.R
e52598554234ceb111e8aad23dfcc31f *R/oneFluxDel.R
5cfbca7abb07883a6506592c7f52118b *R/oneGeneDel.R
2c7e639627beb40e5c9b5685f8470ae1 *R/onlyChangeGPR.R
569018ed4deb010849e139764069ced7 *R/onlyCheckGPR.R
0e009d049e1437d95c7e76151679a09c *R/optObjClass.R
edfbd88afddaa3795f5662be16741196 *R/optObj_basicfunc.R
1f73e50365593014336e55e006142cad *R/optObj_clpAPIClass.R
2750831170ad3ead57217101edde31b1 *R/optObj_cplexAPIClass.R
30c3e05131e4c6254074907fe835f29f *R/optObj_glpkAPIClass.R
474849f3799a30f2b8f3f9f51626d4a0 *R/optObj_lpSolveAPIClass.R
9209b656fd39c96d5d9876c57c346e4c *R/optObj_lpSolveAPIcompat.R
1784f87e473ba48a6cff443cb3ae5297 *R/optObj_pointer.R
628dafcd40e0421a2f84a181607f4401 *R/optimizer.R
ad3af2506d17d2a3b0202e00aef2bd42 *R/optsolClass.R
7b1832b54ed33814b880f88fc784bc35 *R/optsol_blockedReactClass.R
781b868008027aea726e4fa7cc9d0378 *R/optsol_fluxVarClass.R
e1beda7ecd0da7e82af81047cf0272fb *R/optsol_fluxdelClass.R
0f0cbef7d75cfd591e8a6d9a1aee2690 *R/optsol_genedelClass.R
9b882731cb5de22dd3528e728a628d85 *R/optsol_optimizeProbClass.R
e021ada69f3cf13efd3a091c66659eb1 *R/optsol_robAnaClass.R
53662012042be118e9753c1709af2748 *R/parseBoolean.R
a735882cf82723d64dd061007b86888c *R/ppProcClass.R
4b5038d5a79a68e50b0565d876664462 *R/ppProcessing.R
12311b8a094d9250b14952d17ecba01d *R/prepareSubSysMatrix.R
a0eaebaa4a163cedbe3a5f6d56a0c733 *R/printLogComment.R
02cb8704a3a92d065eb733698140568e *R/printNamedList.R
94fa095012cb88b535943cd454ec6697 *R/progress.R
bd5c7041d0938f36e7f40e305899455b *R/promptSysBiolAlg.R
66dfa4cae4b03107e164b6b709154a22 *R/reactIdClass.R
7adebbf80b2e44caa58248fa9c4cee20 *R/reactId_ExchClass.R
41ebc0f2d4f14f659faf38866990d2dd *R/readTEXTmod.R
30524b03b6ac81994fe163365687f323 *R/readTSVmod.R
d76347fc8c247063036b98a656ae2325 *R/reassignFwBwMatch.R
05f8cbaf6c116a15ec346658af6244a5 *R/recodeMatrix.R
46bd4dc040fe02270418a0caca1d45b7 *R/rmReact.R
70c57c60911d862289d86f7b12ce285c *R/robAna.R
0088c2757f91c0fbfc74456ea07cd7f1 *R/settings.R
623c0a4b4334ad3ce63e02737830c7ee *R/singletonMetabolite.R
2d03454defc780b0859abc1fe7e2ca72 *R/summaryOptsolClass.R
e2ebab5d393c14adfa128baffb2d2425 *R/sybilErrorClass.R
875f429f5cd7523b07656672adadcecf *R/sybilLogClass.R
9db90f9129be62a5d60d8d1e174c97d2 *R/sybilStack.R
8ce4c143e78d366b1020e06d6949778b *R/sysBiolAlgClass.R
fd6775ef6393ecb91df68e7085f09023 *R/sysBiolAlg_fbaClass.R
9663adec8e2ab5ad5c47f40aee076b07 *R/sysBiolAlg_fvClass.R
92194d93bfd5fd6aef12f0c71c4e6c51 *R/sysBiolAlg_lmomaClass.R
ee7c6ca459058388dd8e9a3dcdad065e *R/sysBiolAlg_momaClass.R
1cc2fbc52bc32801b5f360f058afb832 *R/sysBiolAlg_mtfClass.R
9e5631c5c542b977c083a8de8b392304 *R/sysBiolAlg_roomClass.R
8cfefd9db07e298b52a1e38747ac288e *R/validmodelorg.R
9c9511b961e495dfe6740dbb1327e316 *R/validoptsol.R
45fcea1f767e2f24a7ad4b775dd0bd08 *R/validreactId.R
3a3dafa9f9527c6635a888dc83330939 *R/validreactId_Exch.R
1125672b44edd4fde554643bc1e49a92 *R/validsysBiolAlg.R
8e90c86c3d8255e36a168ad920aa7163 *R/ypd.R
fdde38705f3e70b0b15b9c6084be9d75 *R/zzz.R
42f22e08da875977b8b30a0ae23fd493 *data/Ec_core.RData
5e39c2adfa1fe5e2d81da0291b341815 *inst/NEWS.Rd
95913ac72d07c8922fa4acbc1e1bcaaa *inst/doc/sybil.Rnw
016d66f237ff2c296a79d3ff1b2f02b2 *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
286b85ff7bf37eee125edc73e792c2cd *man/addAlgorithm.Rd
6c27f136fede2f2b61d41e70a24b1105 *man/addCols-methods.Rd
edfc0fc9b04380722fb42b0a15630990 *man/addColsToProb-methods.Rd
244b2f7679e6f675d22c76c5b7f60f41 *man/addExchReact.Rd
201f60898b84a173b5408a1876c8fdb4 *man/addReact.Rd
2930a81a64927c46628367fe9ac6800d *man/addRows-methods.Rd
95fa7422e5bc69db2fa18b963e9e64bb *man/addRowsCols-methods.Rd
1df60bb03cc71f29e46406822623c577 *man/addRowsToProb-methods.Rd
d70dc27609dd47f7821b311d19eb9886 *man/addSolver.Rd
36d17c9513d8db37d54935848977adf0 *man/backupProb-methods.Rd
49ec69972b1b5569d8656e06e71fdbb7 *man/blockedReact.Rd
b24cef6df94a05630cc11b9b9e91b5d0 *man/changeBounds.Rd
f554e3c19b43421d9dcf4820c03cb9db *man/changeColsBnds-methods.Rd
e56395081a29587f2caa37b5e6ff441b *man/changeColsBndsObjCoefs-methods.Rd
a2890084575f596d8f4b3269c8a9cd49 *man/changeGPR.Rd
9de2d484cfa89a32f61d3c285242a614 *man/changeMatrixRow-methods.Rd
3e0a1f3bf2a5d3f20ca5036ab5677af4 *man/changeObjCoefs-methods.Rd
606feb3d7fa9c67d54b5a33f60040ba0 *man/changeObjFunc.Rd
2a354e1c25f9c97b0645b52d54738ff2 *man/changeRowsBnds-methods.Rd
ee7b9f960de7d15f5e557243e1764941 *man/checkAlgorithm.Rd
3d0a22ec4b8513e72394fdaf1ea4ac1f *man/checkDefaultMethod.Rd
5a3f1da422f51e3110bc303ae9d888f1 *man/checkOptSol-methods.Rd
3c2b1497f8189825285f3ab10d12f66c *man/checkReactId.Rd
6e1521ad618bd9701069b04a3e4e780c *man/checksol-class.Rd
5b021ec4f7a6543b4e8b912e02b8a1a4 *man/delProb-methods.Rd
e1e2151d58adeccb57ce8306f9c5ba25 *man/deprecated.Rd
14a3362d120e1d7ec218cef8e21d4dad *man/doubleFluxDel.Rd
1c4d7e0ebd8ae95e74490d86e24cffbe *man/doubleGeneDel.Rd
af8281d26b5aac0f7e4abfb29d51aeb4 *man/doubleReact.Rd
f9686d540ae14b503dec5e5a71ef6ce2 *man/findExchReact.Rd
ca7a7229ccb57d5ae21cab07d603015d *man/fluxDistribution-class.Rd
ed8203a403f14c757e9d85959628d8ca *man/fluxVar.Rd
bb35ec8d5954d7ae1671c4fc0579c5da *man/geneDel.Rd
68065aa34b05b19583a315369c334918 *man/geneDeletion.Rd
e39d17224659711900b781a14423d549 *man/getColPrim-methods.Rd
e97b53805505e694a808a8da3daa2cb5 *man/getColsLowBnds-methods.Rd
eec72ec44d3d009c376d281dc377bc81 *man/getColsUppBnds-methods.Rd
33be75be708b84b20979b99cc6795833 *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
ec3df22fc8c8a38500dec6bc88c77601 *man/getRowsLowBnds-methods.Rd
96c5185df557a661298ee89601296d3c *man/getRowsUppBnds-methods.Rd
33cbdfdde7c7f6aa8b4b1424012eaae4 *man/getSolStat-methods.Rd
06f7a6852074294f22e9a6d94fb6e5d2 *man/getSolverParm-methods.Rd
6246cfcb4ef080be72c8f4c4c93c921a *man/getsybilenv.Rd
4d8f5f90ce19b00a98c9c4cbc001a641 *man/initProb-methods.Rd
69e7be20d4d2bca83abd40ba4d63afd9 *man/loadLPprob-methods.Rd
89d43efb63116034793f2c5f6cd60f63 *man/loadQobj-methods.Rd
1739bb6798a683fa6f333e963cd1ef76 *man/mod2irrev.Rd
c271d8c8e11b09b7803ea4a1e636d12a *man/modelorg-class.Rd
248b364e7013f28b348b62cb1ac591c0 *man/modelorg2ExPA.Rd
46daece363cd93add9b7dd8beb28794f *man/modelorg2tsv.Rd
57f4ae694278958786a06910a9090639 *man/modelorg_irrev-class.Rd
b537d74ba9b7cb923a7cb50c8f28e9e9 *man/multiDel.Rd
e5ebf374188bf03a976a14944d823852 *man/oneFluxDel.Rd
5564207416b48f432286b743b28ab16e *man/oneGeneDel.Rd
36473471e1f8f96fc9e1b3aeb170f3b8 *man/onlyChangeGPR.Rd
d6ac7f0d2b36f8be8d30bdb6139e5435 *man/onlyCheckGPR.Rd
e2f9a3043c09db193aa8c4e16e6a7c98 *man/optObj-class.Rd
a086d42d5074eba4b68ddae80d6920fe *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
99c51b05d066af40cc89b2f70504d610 *man/optimizeProb-methods.Rd
80aec000f8c662c3fd105f79ab2a2d8f *man/optimizer.Rd
78578654f5337f452db268e79f317ca0 *man/optsol-class.Rd
8eee2bd977bd248a61f52914e6e46030 *man/optsol_blockedReact-class.Rd
d86d76f7c46436005bfdea152090facd *man/optsol_fluxVar-class.Rd
4720bdd17a5f893bf48214989b99481e *man/optsol_fluxdel-class.Rd
73a0335030e736ba33479083904a3af9 *man/optsol_genedel-class.Rd
7b43add2b0a9ad203b23aacd7ad52de9 *man/optsol_optimizeProb-class.Rd
469f882016030efd0c0eaeecccc06a03 *man/optsol_robAna-class.Rd
90676f32ac5bf881e475ebb954bff92a *man/ppProc-class.Rd
9982f4bfd02b05200e3adf15d92196db *man/printMetabolite-methods.Rd
3bdb93cd2fcda0d815177f235ef8af06 *man/printReaction-methods.Rd
0cf2723dae7006c3130d6067970d78de *man/promptSysBiolAlg.Rd
beea2dab039f04f87c024541aa4e0a9c *man/reactId-class.Rd
c99c5d738ea5c62b7e77784500ced747 *man/reactId_Exch-class.Rd
46195f55a18ff82d3643a05d861e7ae3 *man/readProb-methods.Rd
f969029dba01f30985507e072d0d5080 *man/readTSVmod.Rd
19291a1769e3d77264ce78815cb9836f *man/rmReact.Rd
b986fb3655258a190cde360018d14fa6 *man/robAna.Rd
1232299eef2fc948a548fe398d899ec8 *man/scaleProb-methods.Rd
77e67dd4d631a7ff783b0684222da998 *man/sensitivityAnalysis-methods.Rd
242264cf73a7aed5c397c0ca651ce45a *man/setObjDir-methods.Rd
30ad21d37a2487c1616d8bf989cd672c *man/setRhsZero-methods.Rd
26b0e649bc6077af62389ad317aba758 *man/setSolverParm-methods.Rd
7c99f48a41b50df9d7db3c7ee816ba62 *man/shrinkMatrix-methods.Rd
1bf9996a6ddd326f83eab608865e2a85 *man/solveLp-methods.Rd
d8323d4b20bff977c77b76964d1e8115 *man/summaryOptsol-class.Rd
62277743259c4c64192f33cd030f22f4 *man/summaryOptsol.Rd
7f7b5a4d8a297e2c5f175aedf805971d *man/sybil-internal.Rd
0870b9fa6e2d69b336b0a4998d11102e *man/sybil-package.Rd
f9c95cd1ef8f89d900e8562964d6d7ae *man/sybilError-class.Rd
452a705945fdecc23f585e8b9d60e645 *man/sybilLog-class.Rd
212e01a9b2d9de31110618004c438ec8 *man/sybilStack.Rd
be7c95c060ee88100650a4e4d03e58d2 *man/sysBiolAlg-class.Rd
917b465e5d626640b761ea07938411b8 *man/sysBiolAlg.Rd
f7e6d6eb3c591f2a3f9e96f46931050f *man/sysBiolAlg_fba-class.Rd
91f2a1e181c897e3ed79047708034728 *man/sysBiolAlg_fv-class.Rd
8be53065895da6d89a1ea5b6c81c4351 *man/sysBiolAlg_lmoma-class.Rd
7dc13a3094984722874bec7e09238bfe *man/sysBiolAlg_moma-class.Rd
5e46d6f08e10bca7cd9d7ad2f75c6d69 *man/sysBiolAlg_mtf-class.Rd
674b7632a6063ddc3eb1012b1db7c77f *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
beec0d947701ef0f5a9790f759ca4849 *vignettes/optsol-class.pdf
95913ac72d07c8922fa4acbc1e1bcaaa *vignettes/sybil.Rnw
5fe9ba4104cbce4be936924bace1ddf4 *vignettes/sybil.bib
1cb0866fe10c1f5c2cd0319ccb71c528 *vignettes/sysBiolAlg-class.pdf
c2182e6dd340a228aba67b0dd3a1cb19 *vignettes/sysBiolAlg-const.pdf
bc149984e431c983d88b6f1c2fbb3e80 *vignettes/sysBiolAlg-init.pdf
