MOE脚本命令简介_高级函数(3)？

准备材料

1.大骨洗净，用白开水烫30秒2.灯心草汤包打开洗净所有材料3.姜切片备用

将所有处理好的材料一起放进电饭锅里，放入适量的水

打开煮饭功能煮40分钟-1小时即可，我的是旧的人电饭锅，只有煮饭功能的那种，所以功率不大，慢慢煮很方便

煮好后加入适量盐就可以喝了

开吃啦～

<药效团筛选>moebatch-exec"run['ph4_search.svl',['dbfile.mdb','query.ph4',[out_dbfile:'ph4out01.mdb',abspos:0,action:0,descexpr:'',esel:0,maxconfhits:0,maxmolhits:1,molfield:'mol',o_molfield:'mol',o_mseqfield:'mseq',o_rmsdfield:'rmsd',o_rscore_colfield:'rscore[F#]',o_rscore_sumfield:'rscore',out_append:0,out_dbv:0,out_type_molecules:0,sortby:'RMSD',use_mseqfield:0,use_o_fileIdxField:0,use_o_fileNameField:0,use_o_hitmapfield:0,use_o_molfield:1,use_o_mseqfield:1,use_o_rmsdfield:1,use_o_rowfield:0,use_o_rscore_colfield:1,use_o_rscore_sumfield:1,use_o_rscore_vecfield:0,use_out_dbfile:1]]]"参数懒得翻译啦Thecompletelistofsearchparametersisasfollows:'dbfile.mdb'Theinputconformationaldatabaseofmolecularconformations.Theinputcanbespecifiedasasinglefilenameoralistoffilenames.Theconformationscanbestoredeitherinthemoleculefield,oneconformationperentry,orinaseparatefieldofallconformations,onemoleculeperentry.Ifstoredinthemoleculefield,conformationsofthesamemoleculemustbestoredinconsecutiveentries.'query.ph4'Thefilenameofthepharmacophorequerytobeusedtosearchtheinputdatabase.optionsVectorofoptionalattribute-valuecolon-separatedpairs:action:numThemethodofreportinghitsintheDatabaseVieweroftheinputdatabase.IftheinputdatabaseisnotopeninaDatabaseViewerorthevalueoftheargumentisnotspecified,noactionistaken.Otherwise,hitsarereportedasfollows:0-Noactiontaken[default]1-Hitentriesareselected2-Hitentriesareshown,missedentriesarehiddenmatchsize:numTheminimummatchsize.Ifspecified,thisnumberoverridestheminimummatchsizestoredwiththequery.Ifthevalueispositive,itspecifiestheminimumnumberoffeaturesthatmustbematched.Ifthevalueisnegative,itsabsolutevaluespecifiesthemaximumnumberoffeaturesthatmaybeunmatched.Ifthevalueiszero,allfeaturesmustbematched.Ifthevalueisnotspecifiedthenthequery'smatchsizeisused.esel:numArestrictionontheinputentries.IftheinputdatabaseisnotopeninaDatabaseViewerorthevalueoftheargumentisnotspecified,norestrictionapplies.Otherwise,theinputisrestrictedasfollows:0-Norestriction[default]1-Onlyselectedentrieswillbesearched2-Onlyvisibleentrieswillbesearchedmolfield:'fieldname'Thenameofthemolecule(ligand)field.Iftheemptytoken('')isgiventhenthefirstdatabasefieldoftypemoleculewillbeused.Thedefaultis''.mseqfield:'fieldname'use_mseqfield:flagThenameoftheinputfieldcontainingapre-calculatedmoleculesequencenumberandaflagindicatingwhetherornotthefieldistobeusedinthecalculation.Iftheflagisnonzero,thesearchwillusethemoleculesequencefieldspecified.Thedefaultfieldisname'mseq'andthedefaultflagis1.Iftheflagiszerothenthefieldisnotusedandthemoleculeswillbeindexedatruntime.out_dbfile:'filename'use_out_dbfile:flagThenameoftheoutputdatabase.Thedefaultnameis'ph4out.mdb'andthedefaultflagis1.out_dbv:flagIftheargumentisnon-zero,thesearchwillopentheoutputdatabaseinaDatabaseViewer.Thedefaultvalueis0.out_append:numThemodeinwhichtoopentheoutputdatabase.0-Overwrite;anypreviousdatawillbelost(default)1-Append;anynewdatawillbewrittentotheendofthedatabasereport_file:'filename'Thenameorthefilehandleofthereportfile.Ifthefilenameisnotspecifiedorsettotheemptyvectorthennoreportfilewillbewritten.firstentkey:entry_keyIfnon-zero,themdbentrykeyofthefirstentrytoprocessintheinputdatabase.Allpreviousentriesareskipped.Thedefaultvalueis0(i.e.don'tskipanyentries).firstent:numThefirstentrynumber(row)toprocessintheinputdatabase.Allpreviousentriesareskipped.Thedefaultvalueis1.Ifbothfirstentkeyandfirstentarespecified,thenthesearchstartsat(firstent-1)-stentryaftertheentryfirstentkey.lastent:numThelastentrynumber(row)toprocessintheinputdatabase.Allsubsequententriesareskipped.Thedefaultisthelastentryinthedatabase.Ifbothfirstentkeyandlastentarespecified,thenthesearchendsat(lastent-1)-stentryaftertheentryfirstentkey.skipmol:numThenumberofmoleculestobeskippedatthebeginningofthesearch.Ifeitherfirstentkeyorfirstentisspecified,thenthemoleculeswillbeskippedstartingfromthefirstentry.nmol:numThenumberofmoleculestobesearched.Iflastentisspecified,thenthesearchstopswheneitherlimitisreached.maxconfhits:numMaximumnumberofhitstocalculateandoutputperconformation.Allfurtherpossiblehitsonthesameconformationareskipped.Thedefaultvalueis1000.maxmolhits:numMaximumnumberofhitstocalculateandoutputpermolecule.Allfurtherpossiblehitsonthesamemoleculeareskipped.Thedefaultvalueis100000.out_maxent:numThemaximumnumberofentriestocreateintheoutputdatabase.Allfurtherpossiblehitsareskipped.Ifnotspecifiedthenthereisnomaximumnumberofentries.Thisattributeisleftunspecifiedbydefault.o_copyfields:['field1','field2',...]Vectoroftokensspecifyingthenamesoftheinputdatabasefieldsthatshouldbecopiedtotheoutputdatabase.Thedefaultvalueis[],nofieldsarecopied.o_mseqfield:'fieldname'use_o_mseqfield:flagThenameandusageflagofthemoleculesequencefield.Theusageflagindicateswhetherornotthefieldwillbegenerated.Themoleculesequencefieldcontainsanintegervaluethathasthepropertiesofamoleculesequence.Thevalueofthefieldstartsat1andisincrementedwitheverynewhitmolecule.Thedefaultfieldnameis'mseq'andthedefaultflagis1.o_molfield:'fieldname'use_o_molfield:flagThenameandusageflagofthemoleculefield.Theusageflagindicateswhetherornotthefieldwillbegenerated.Themoleculefieldcontainstheconformationfoundintheinputmoleculefield,rotatedandtranslatedtomatchthepharmacophorequery.Thedefaultfieldnameis'mol'andthedefaultflagis1.o_rmsdfield:'fieldname'use_o_rmsdfield:flagThenameandusageflagoftheRMSDfield.Theusageflagindicateswhetherornotthefieldwillbegenerated.TheRMSDfieldcontainstheroot-mean-squaredistancebetweenthequeryfeaturesandtheirmatchingligandtargetpoints.Thedefaultfieldnameis'rmsd'andthedefaultflagis1.o_rowfield:'fieldname'use_o_rowfield:flagThenameandusageflagoftherowfield.Theusageflagindicateswhetherornotthefieldwillbegenerated.Therowfieldcontainstheentrynumberofthematchedconformationinthesearchedinputdatabase.Thedefaultfieldnameis'row'andthedefaultflagis0.o_hitmapfield:'fieldname'use_o_hitmapfield:flagThenameandusageflagofthemapfield.Theusageflagindicateswhetherornotthefieldwillbegenerated.Themapfieldcontainsanumericalrepresentationofthemappingbetweenthequeryfeaturesandtheirmatchingligandannotationpoints.Foreachfeatureofthequery,thefieldstorestheindexofthematchedligandannotationpointor0ifthefeatureisnotmatched.Thedefaultfieldnameis'hitmap'andthedefaultflagis0.

<分子对接>对接一个分子，使用DockAtoms函数DockAtoms[recatoms,siteatoms,ligatoms,outfile,[outrmsd:1,csearch:1,sel_ent_only:0,maxpose:30,wall:['',0,[0,0,0],[1000000,1000000,1000000],0],placement:'TriangleMatcher',placement_opt:[timeout:300,nretpose:1000],scoring:firstscore,scoring_opt:scoreOpt,refine:refinemethod,refine_opt:refineOpt,rescoring:secondscore,rescoring_opt:rescoreOpt,remaxpose:30,dup_placement:1,dup_refine:1]];对接mdb数据库(包含多个分子)，使用DockFile函数DockFile[recatoms,siteatoms,ligatoms,outfile,[outrmsd:1,csearch:1,sel_ent_only:0,maxpose:30,wall:['',0,[0,0,0],[1000000,1000000,1000000],0],placement:'TriangleMatcher',placement_opt:[timeout:300,nretpose:1000],scoring:firstscore,scoring_opt:scoreOpt,refine:refinemethod,refine_opt:refineOpt,rescoring:secondscore,rescoring_opt:rescoreOpt,remaxpose:30,dup_placement:1,dup_refine:1]];这一部分看不懂不要紧，看看第4节的实战经验就懂了。

<加氢>moebatch-exec"runWashMDB['conf_out_0030.mdb','mol','../add_H_Charge/Enamine_conf_out_0030.mdb',[esel:0,opendbv:1,destfield:'mol',namefrom:'src',namefield:'',onecomp:1,salts:0,fragfield:'salt',depracids:1,protbases:1,neutralize:0,hydrogens:'add',tautotomers:1,enumsize:100,enumdup:0,seqfld:'pseq',depict:0,scale:0,verbose:1]];"<加电荷>moebatch-exec"runPartialChargeMDB['$mdbFile','MMFF94*','','',[esel:0,add_h:0]]"<能量最小化>moebatch-exec"rundb_Minimize['$mdbFile','mol',[esel:0,gCCCC:0.1,keep_chiality:0,rebuild:'Minimize',add_h:1,pot_charge:1]]"这一部分也看不懂？快看看第4节的实战经验吧。

<技巧(绝招)>要想了解更多函数，可以查看MOE手册。不过这里，我想教给大家一个技巧：先打开MOE图形界面进行常规操作，如药效团筛选等，执行完后，点击MOE窗口中的SVL菜单，来查看刚刚运行的命令吧。なに！SVL命令窗口中没有记录？大丈夫ですよ。你可以在常规操作一次，快速点击Cancel菜单看看正在执行那个函数吧。ちょっと待って，程序运行太快没看清？那就增大MOE的运算量吧，比如：我是怎么知道智能选择蛋白的函数是_SelectA['','$$receptor']的呢？导入一个200aa左右的蛋白，智能选择蛋白(右击|select|receptor)一下子就OK了，在Cancel中根本就看不到，那么你可以一次性导入30个蛋白试试看吧(100个看的更清楚哦，嘿嘿)。