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Vector Menu .v2.0.8.rar

The impulse response of a system is the change in an evolving variable in response to a change in the value of a shock term k periods earlier, as a function of k. Since the AR model is a special case of the vector autoregressive model, the computation of the impulse response in vector autoregression#impulse response applies here.

Vector Menu .v2.0.8.rar

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[ add alias align Append command assign break build call center clear color Color chemical Color accessibility Compare compress connect continue convert copy crypt Date array Delete display edit elseif endfor endif endmacro Enumerate charge Enumerate chiral Enumerate tautomer Enumerate library endwhile exit find fix for fork fprintf function Global goto group Gui help history if info keep join tables Learn Learn ann Link group Link variables Link ms2ali list List binary List database list directory list molcart load Macro make minimize menu modify Modify rotate Modify chem montecarlo move pause plot Plot area predict print Print bar printf print image Query molcart quit randomize read rename return rotate select Set show sort split sprintf store ssearch strip superimpose Superimpose minimize Sys test then transform translate undisplay undisplay window unfix wait web while write ]

ICM commands have a certain structure:they use command words from this list: align assign build clear compare connect convert copy compress cryptdelete display edit enumerate exit exclude filter find fix fork fprintf group gui keep learn loadmake menu minimize modify montecarlo movepause plot predict print printf quit query randomize read redo refresh rename restore rotateselect set show sort split sprintf ssearch store strip superimposetest transform translate undisplay undo unfix unselect unix wait writealias antialias center color help history link list macro model sql webaccessibility alignment amber angle area aselection atom axisbackground ball base bar bfactor bond born boundary boxcatalog cavity cell chain charge cmyk column command comment comp_matrix conf cpk csd cursor chemical cistransdatabase distance directory disulfide dot drestraintenergy error evolution factor field filename font foreground frame functiongamess genome gradient grid grob hbond header html hydrogeniarray icmdb idb image index info input integer intensity inverse iupac json kernel key label library logical loop limitmargin material map matrix memory merit mol mol2 moldb molcart molecule movie molsarname nucleotideobject occupancy oracle origin outputpage parray pattern peptide pipe pdb plane postscript potential preference preview problem profile project property prosite protein pharmacophorerarray reaction real regression reflection residue resolution ring rgb ribbon regexp rainbowsarray segment selection selftether separator sequence session site size skin slide salt solution stack stdin stdout sticksstructure string surface symmetry system svariabletable term tether texture topology torsion trajectory transparent tree type unknown uservariable vector version view virtual volume vrestraint vselection water weight window wire xstickadd all append auto auxiliary binary bold bw cartesian clash chiral dash exact joinfast fasta flat formal format full gcg gif global graphic heavy identity italic jpeg lastleft local mmcif mmff msf mute new none nosort number off on only pca pir pmf png pseudo povreverse right similarity simple sln smiles smooth solid static stereo swiss targa tautomer underline unique wavefront xplor the they arguments consisting of constants, named shell variables or expressions including functions, e.g. display ribbon Res(Sphere( a_H a_A 7.6 ))the order of arguments of different data type is arbitraryat the end of the command one may have a list of additional shell variables that will be redefined temporarily only for the duration of this command, e.g. montecarlo v_//x* mncalls=200 mncallsMC=20000 temperature=1000. several commands in one line can be separated by a semicoloncommands can return certain shell variables, like i_out , i_2out, r_out , l_out , s_out , R_out , as_out .. with useful outputto suppress command output redefine those shell variables: l_info=no or l_warn=no (for some commands there is also a mute option ) add[ Add column Add matrix Add slide Add table ]

Adding a single column/header you may add a column (or columns) to an existing table T or create a new one if the specified name does not exist. add column T IRSPirs [name= s [appenddelete] ] [index= i_pos] [mute] [local] add header T IRSPirsMetc [name= s [appenddelete] ] [mute] [local](to add a row see add table args )Adding multiple column/headers add column T IRSPirs IRSPirs .. [name= S [appenddelete]] [index= i_pos ] [mute] [local] add header T IRSPirsMetc IRSPirsMetc .. [name= S .. ] [index= i_pos ] [mute] [local]this command adds one or several columns to an existing table in the i_pos column(in other words if you want you column to be in the 2nd position, specify 2 as an argument). The columns are append to the end of the table by default.If the table does not exist the command will create a new table. It an integer, string, or real are specified as an argument instead of a column-array, this value is multipled to create a column of the appropriate size.Options:append: if the name option is specified prevents overwriting the column with the same name, instead modifies the provided name (e.g. 'A' -> 'A_1' )delete: if the name option is specified overwrites the column with the same name. Without delete (default) it will be overwritten only if the data type is the same.mute : The mute option suppresses the info (equivalent to temporarily setting l_info=no ).local : for use in macros ans shell functions: allows for local tables independent from tables with the same name at higher levels.Examples:add column t 1 2 3 # create a new tableadd header t "A new table" name="title" # add a string to the header sectionadd column t "a","b","c" name="AA" # column AA is appendedadd column t "x","y","z" index = 2 # adding a chemical arrayadd column t Parray("CC","CC(O)=O","CCO" smiles) name = "mol" index = 1# adding multiple arraysadd column t 1 2 3 3 2 1 "a","b","c" Parray("CC","CC(O)=O","CCO" smiles) name="A","B","C","mol"t #>T t #>-A-----------B-----------C-----------mol-------- 1 3 a "CC" 2 2 b "CC(O)=O" 3 1 c "CCO"The columns can also be functions, e.g.add column t 1. 2. 3. 2 3 4add column t function="A+B" name="AplusB"add column t function="Log(A,10)" name="log10A"Use add column inside a macro:macro ResAreas rs_sel rs_sel = Res( rs_sel & a_*.!W ) show surface area Mol(rs_sel) Mol(rs_sel) add column t Name(Res(rs_sel) full) Area(Res(rs_sel)) Area( a_1.A/A )/Area( a_1.A/A type) local name="sel","area","rel_area" set format t.sel "%1" if(Type(resAreas)!="unknown") delete resAreas rename t "resAreas" keep resAreasendmacroSee also: move column , add column functionAdd columns using internal functions in dynamic or static manner add column T function=s_expression [static] [name=s] [index= i_pos]By default the column is added in a dynamic manner so that it can be recalculated from other columns. Option static adds the new column as a value and will not allow for the recalculation.Adds a column a string that contains an expression or a reference to one of three sources of functions: one of a few fast-access internal functions listed below, e.g. function="Sqrt"one of a thousand built-in ICM-shell functions (described in this manual), e.g. function="Icm::Min(COL)"an arbitrary user-defined ICM-shell function loaded from a file or .icm/user_startup.icm file. E.g. function="myfunc(A)" which may contain operations with other columns in the same table.The generating expression information is attached to the column,which allows one to recalculate the values in the column using the same expression. The following functions are supported:Basic arithmetical operations on columns are supported, examples: add column t 1. 2. 3. 1. 2. 3.add column t function="A+B" name="C"add column t function="A-B" name="D"add column t function="A*B" name="E"add column t function="A/B" name="F"add column t function="A**0.5 + B**0.5" name="G"build column tshow tThe following mathematical and data conversion functions are supported: Ceil, Floor, Log, Sqrt, Sign, String, PowerExamples:add column t 1. 2. 3. 1. 2. 3.add column t function="Sqrt(A)" name="C"Chemical functionsThe following internal functions (not ICM-shell functions) are allowed in function=".." expressions (eg add column t function="MolPSA(mol)":Examples of chemical functions usage:add column t Chemical("CCO"//"CCCCO"//"CCCC#N")add column t function="Nof_Atoms(mol,'*')" name="nof1" # all atomsadd column t function="Nof_Atoms(mol,'[!H]')" name="nof2" add column t function="Nof_Atoms(mol,'[C,O]')" name="nof3" add column t function="Nof_Atoms(mol,'[H]')" name="nof4" add column t function="MolWeight(mol)" name="molWeight"add column t function="MolLogP(mol)" name="molLogP"add column t function="MolLogS(mol)" name="molLogS"add column t function="MolPSA(mol)" name="molPSA"add column t function="MolVolume(mol)" name="molVolume"add column t function="MoldHf(mol)" name="moldHf"add column t function="calcBBBScore(mol)" index=2 name="bbbScore" append vector add column t function="MolSynth(mol)" index=2 name="molSynth" append vector User-defined functionsA user can defined custom function to be used in column formula expression directly : function="userFunctionName(columnArgument)"Example:function ligStrain( P_chem ) # returns strain for a given 3D chemical vwMethod = "exact" dielConst = 2. read mol P_chem name="LIGSTRAIN" build hydrogen set type charge mmff convert auto minimize cartesian "mmff" mncalls=1 newE = Energy("ener") minimize cartesian "mmff" 5000 baseE = Energy("ener") r_ligandStrain = newE - baseE delete a_ return r_ligandStrainendfunction# assumes that t_3D exists and contains 3D chemicals in the mol columnadd column t_3D function="ligStrain(mol)" name="strain" # strain for every row in the tableICM built-in shell functions.ICM build-in functions can also be used in the expression with "Icm::" prefix.Example:add column drugs function = "Icm::Sum(Icm::Unique(Icm::Sort(Icm::Sarray(A.dosages.dosage:route))),',')" name="route"Recalculating.To recalculate use the build column column_name command.Examples:add column T Chemical( "c1(c(nc(N)nc1O)O)N", "c1c[nH]c2C(N=C(N)Nc12)=O" ) name="mol"add column T function="MolWeight(mol)" name="MW"add T # add new rowT.mol[3] = Chemical("CC")#build column T.MW # recalculate mol. weights, setting the value for the new rowadd column T2 1 2 3 4 5 6add column T2 function= "A+B" # sum of two columnsSee also: build column to update values, Parray ( X [ s_func ] ) to add a fixed columnAdding real arrays as matrix rows add matrix [ M ] RM2adds a matching row R or a matrix with the matching number of columns to matrix M, by stacking extra rows at the bottom. If the matrix does not exist it is createdwith the default name (the name is returned in s_out )Example:add matrix M 1. 2. # creates new matrix Madd matrix M 3. 3. # adds a rowshow M #>M M 1. 2. 3. 3.add matrix M Matrix(2) # adds two rows Note that to extend the matrix horizontally (adding columns) can be done with the double-slash operator ( M1 // M2 ).add slide to a slideshow. add slide [i_posInCurrentSlideshow] [s_slideTitle] [comment = s_slideComment] [ display= "-option-option2" ]adds a slide to the slideshow table. This table contains one parray, called slideshow.slides . If the slide position is not specified the slide will be added to the end.Alternatively, it will be inserted after the specified i_posInCurrentSlideshowNormally the slide is saved with window layout, and graphical parameters. Those can be ignored if you add the display="-option" flag (all listed properties are 'on' by default). "-layout" # ignores the window/panel layout "-smooth" # ignores smooth view transitions between slides "-add" # do not overwrite the previous slide views, just add to it "-gf" # ignore graphical representations, inherit them "-color" # ignore colors , inherit them "-labeloffs" # do not display labels "-viewpoint" # ignore viewpoint changes "-graphopt" # "-mol" # do not display the chem-table window "-grob" # do not display grobs "-map" # do not display maps "-all" # switches off all the above propertiesExample:build string "ala ala ala"display ribbon a_ display xstick a_/12,13 magentaadd slide "My View" comment = "Two magenta residues" display="-layout" undisplay # hide all# wait..display slide "My View" # bring it backSee also: display slide , SlideAdd / insert table rows. Append tables. add T_1 [ i_RowNumber ] [ T_2 row_selection number=i_nofRows ] [ simple ] add/insert rows (or another table with the same coloumns) to table T_1 at the target row position i_RowNumber . Use 1 (one) if you need to insert the first line. If the second table or selection is not provided, the command adds an empty row. In this case you can add number option to specify the number of rows to add/insert.The row_selection can contain rows from the same table or from a different table with a matching column structure. In the latter case, the columns may be matched by their names regardless of column order. Default values are inserted for all absent columns.The defaults for an empty line are empty string or zero value for strings or numbers, respectively. The target position will thencorrespond to the index of the first inserted row.simple option toggle column matching order 'by position' instead of default 'by name'.From version 3.6-1e the add tableName command also returns the current row as i_out . Examples: group table t 1 2 3 "a" "b","d","e" "b" show t #>T t #>-a-----------b---------- 1 b 2 d 3 e add t 1 # insert empty line before 1st show t #>T t #>-a-----------b---------- 0 "" 1 b 2 d 3 e group table t 1 2 3 "a" "b","d","e" "b" # recreate the table add t 3 t[1] # insert a duplicate of 1st row after the 2nd show t #>T t #>-a-----------b---------- 1 b 2 d 1 b 3 e group table t 1 2 3 "a" "b","d","e" "b" # recreate the table group table tt 1 2 3 "c" "b","d","e" "b" 4 5 6 "a" # another table # order is diffferent, extra column present add t 3 tt[1:2] # or add t 3 tt.aaT t #>-a-----------b---------- 1 b 2 d 4 b 5 d 3 e alias alias abbreviation word1 word2 ... create alias alias delete abbreviation delete alias It is important that the abbreviation is not used in the ICM-shell. The same names can not be given later to ICM-shell objects. Alias may contain arguments $0, $1, $2, etc. ICM-shell will pick space-separated words following the alias name and substitute $1, $2, etc. arguments by the specified argument. $0 stands for all the arguments after the alias name. Examples: alias seq sequence # seq will invoke sequence alias delete seq # delete alias name seq alias dsb display a_//ca,c,n # abbreviate several words to # reduce typing efforts # aliases with arguments alias NORM ($1-Mean($1))/Rmsd($1) show NORM 6,7,8,4,6,5,6,7,5,6 # make sure there is no space align[ Align number chemical Align res numbers Align sequence Align fragments Align 3D Align 3D heavy ] 041b061a72


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