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003 Helper Macros
Jordy Homing Lam edited this page Sep 25, 2022
·
16 revisions
Before we proceed to the research facilities of ICM, we need to introduce on some useful macros that make life easier. A list of macro can be found by ls
Alert s_message
AlignFromSuper &seq_1 &seq_2 r_stickiness
AlignSS &seq_1 &seq_2 r_stickiness
ArrayStats R )
BuildVariantList S_xxx s_Loop
CorrConfInt R_X R_Y
CorrPval R_X R_Y
CovalentMechanisms P_chem l_addChem
DihedralAngle as_plane1 as_plane2
Dweight r_dst )
EAlert s_message
Flexi_in_ali s_ali
GetScheduledICBIndex
Left_exp_noise R r_from (0.00) r_to (0.50)
Left_noise R )
Mqn_add T_table
OddsRatio i_a_DR i_b_Dr i_c_dR i_d_dr l_verbose (no)
OddsRatioTable S_name I_aDR i_acDsum I_bdR i_dbdsum
PopMessage s_message
PredictPIP S_seq l_pH r_pH
PredictSeq s_seq s_prop
PubchemName2Struct S_name
PubchemStruct2Name P_mol s_result ("cid")
RebuildLoop s_Loop r_rms
SSpredictBG s_inp l_allChains (no)
ScanLoops s_Loop_arg
SeqDesc P )
SetLoop s_Loop i_Candidate
SimDict S_X S_Y
TabUniqueRows T )
Table2collection T_tab )
ToxScore P_chem l_addpenal (yes) l_addname (no)
addModifierGroup s_Group
addSwiss
addToRecent s_ArrayName s_what
adjustLoopTables
aggregSeqBG s_seq l_curr (no) s_fout ("")
ali2seqid &ali_ i_ref_seq (0)
align2chemAPF as_mol1 as_mol2 l_static_m1 (no) l_rigid_m2 (no) l_super (no) r_thoroughness
align2seed s_seedSeq S_sequences (Name(sequence select)) s_aliName ("myali") s_alignFunction ("Align")
align2seqres auto as l_skip_seqres (no)
alignChem2DByPrev s_molCol
alignIsosterGroups s_smi1 s_smi2
alignSeqSel s_segrna ("")
alignTwoDnaSequences &seq_1 &seq_2 s_aliname ("dna_ali")
alignTwoSequences &seq_1 &seq_2 s_aliName ("NewAlignment") s_comp_matrix ("") s_alignmentAlgorithm ("ZEGA") r_GapOpen (2.4) r_GapExtension (0.15) i_maxPenalizedGap (99)
annotatemodels S_modelfullpath (Sarray(0)) s_modelexp ("") S_modeluniprot (Sarray(0)) auto
antiSuper os_template r_margin (2.)
apf3DqsarBG s_table s_activityColumn s_extraDesc ("") auto
appendMol ms_ s_objName ("")
append_image
aquaFlood auto R_6box i_nconf ( 1 ) i_nw ( 0 ) l_progress (no)
aquaFloodBG os_in (a_) R_6box (Box()) i_Nconf (100) l_density (no) l_mesh (no)
assignAbCDR s_seqNaLight s_seqNaHeavy l_setSite (yes)
assignCodes s_mol_tab_name s_patterns
assignSimpleCharges auto as_ (a_)
binaryToc s_file s_outName ("") auto
bindingScore ms_rec ( a_1 ) ms_lig ( a_2 ) r_ligVwhbtoFree (0.) s_covModRes ("") auto
bindingScoreMut ms_rec ( a_1 ) ms_lig ( a_2 ) l_ligInternalHBond (no)
branchScore as_
buildGlycan as_attach s_type ("MAN9") l_optimize (yes) l_display (yes)
buildMeshes l_show_wire (no) s_ch r_occ (0.) auto
buildModel auto as_ ( a_ ) I_params ({100,0,0,1}) s_modname ('hm') l_sample_side_chains (no) l_multiLoops (no) l_overwrite ( no)
buildModel1 auto &seq_hm ms_ ms_extra ( a_NONE. ) s_ali ("") i_max_looplen (100) i_Nterm_extension (0) i_Cterm_extension (0) i_Gap_extension (1) l_sample_side_chains (no) l_multiLoops (no) S_NCterms ({"",""})
buildModelCleanup
buildModelMulti s_seqNames s_aliNames ("") os_template
buildNuclModel s_sena s_alina ms_tmpl ( a_1 )
buildpep s_seq ("ala his")
buildwiki s_com
calc3Rocs R_scores I_labels l_keep_table (no) s_color ("navy") auto
calcAPFscore s_hitlist ("") r_apfratio (1.) auto
calcAPFsim s_tab1 ("") s_tab2 ("") l_replaceoriginal (yes) l_keepmatrix (yes) auto
calcApfScore as_site1 as_site2 s_option ("")
calcArea ms_
calcBBBScore P_mol
calcBindArea as_
calcBindScore &r_fisco r_unboundFF r_unboundEl r_unboundSf
calcBindingArea as_1 as_2
calcBindingEnergy ms_1 ( a_1 ) ms_2 ( a_2 ) s_terms ("el,sf,en")
calcBindingEnergyPep S_pept ({"a_1/10:20","a_1/12:17"}) S_nam ({"frag1","loopC"}) s_terms ("el,sf,en") s_output ("DE.tab")
calcContactAreas ms_ ( a_A )
calcDihedralAngle as_plane1 as_plane2
calcElectroProfile os_ os_ax
calcEllips &g_
calcEllipsoid auto M_xyz s_grobName ("g_ellipsoid")
calcEnergyStrain rs_ ( a_/A ) l_colorByEnergy (yes) r_max (7.)
calcEnsembleAver r_temperature (300.) s_parameter ("Value(v_/2/phi)")
calcHbResContacts as_
calcIntFingerprint as_rec_pocket as_lig
calcLigContactPairs ms_rec ms_lig
calcMCC I_1 I_2 l_silent (no) auto
calcMLR M_inputs R_outputs
calcMLRW M_inputs R_outputs R_weights ( Rarray(0))
calcMPOscore s_input s_MPO s_chartStyle ("vertical bars") auto
calcMaps s_receptorName ("rec") R_box r_gridSize (0.5)
calcNsa R_scores I_labels r_score_error (0.) l_linear_auc (no) l_keep_table (no) l_showresults (yes)
calcPIP s_seq ("") S_seq (Sarray(0)) l_pH (no) r_pH (7.4) auto
calcPValue r_tp i_nu
calcPepHelicity s_movieName r_temperature (300.)
calcProtUnfoldingEnergy ms_ ( a_1 ) i_mncalls (100)
calcProtUnfoldingEnergyW ms_ ( a_1 ) i_mncalls (100)
calcQMdeltaPKaBG s_table I_idx l_dontrun (no) s_options ("") s_gamessPath ("gms") auto
calcQMpocketBG as_ligand r_cutoff (5.) l_cleanup (no) l_dontrun (yes) s_gamessPath ("qsub -cwd /usr/local/bin/gms")
calcQMstrainsBG s_table I_idx l_dontrun (no) l_relative (yes) l_relax (no) l_minimize (yes) s_options ("") s_gamessPath ("rungms") auto
calcRMSD s_hitlist ("") auto
calcRMSE R_1 (Rarray(0)) R_2 (Rarray(0)) auto
calcRTCNN ms_rec ms_lig
calcResConservation rs_ l_color (no)
calcResContactAreas rs_1 (a_1) rs_2 (a_2) l_display (yes) i_xstick_zoom (100)
calcResContactPairs rs_1 (a_A/) rs_2 (a_A/)
calcResTable auto rs_ rs_env ( a_NULL./ )
calcRmsd rs_1 (a_1/*) rs_2 (a_2/*)
calcRoc R_scores I_labels l_keep_table (no)
calcSALI s_actCol s_actCol2 ("") l_useLogAct (no) r_distCutoff (0.15) auto
calcSeqContent S_sequenceNames
calcSeqIdent auto &ali_ l_sel (no)
calcSeqSimilarity auto &ali_ s_seqName ("") i_seq (0) l_sel (no)
calcSolvEnergy ms_ ( a_1 ) l_setCharge (yes)
calcSrmsd rs_1 (a_1/*) rs_2 (a_2/*)
calcTm as_ (a_A) s_Tenv
calcTp r_confidence i_nu
calc_noise_ab R
calc_short_distance_table auto as_ r_max_dist (0.9)
calcmsprofile s_tab ("msTargettxt") s_IDcol ("idxtmp") r_targetdistcutoff (0.) r_cmpddistcutoff (0.) l_targetonly (no) l_neato (no) auto
calcpPvalue R_score R_sortednoisescore l_probabilityscore (no) auto
calctaub R_1 R_2 l_silence (no) auto
calctaubM M_1 M_2
calctrainprofile S_models
calphaRebuild os_CalphaTrace ( a_ )
changeEntryAtom as_
chargeAtomOrGroup as_atom s_chargeInc
checkPredictionModels S_models
checkembeddata s_mod ("") i_row (0) auto
chem3dto2d ms_lig
chemAlignBG T_t I_idx i_mniter r_LipoWeight (1.) r_PolarWeight (1.) r_lambda (1.4) s_wtcol ("") i_nproc (1) auto
chemAssign2D s_tab s_col ("mol")
chemAssign3D s_tab
chemCalcIntFingerprint as_rec_pocket P_chem
chemCalcPKA s_molCol ("mol") l_setAtomLabels (yes) auto
chemClusterBySmarts s_tab s_structureCol ("mol") S_smarts ({"C(=O)[O;D1]"})
chemFreeWilsonAnalysis s_tab s_actColumn l_createRtables (no) auto
chemIUPACtoStructure S_iupac
chemImportSilcsBioPh4 s_file
chemLoadConfFromMolt s_moltFile i_molid (0) auto
chemLoadFilterSystemRgroupDB s_action ("") auto
chemLoadNicknameDict l_resetDefault (no) auto
chemMatchedPairs s_tab S_filterGroup (Sarray()) s_activityCol ("") r_splitDist (0.5) i_maxAtomsInGroup (12) l_allowRacemic (no) auto
chemPlotShape s_molCol l_moment (yes)
chemRIDEListDb s_url
chemRIDESuperBG as_template s_db r_APFcutoff (0.6) r_xweight (3.) r_excludeMargin (0.) as_exclude (a_NONE.) i_maxHits (10000) s_opt ("")
chemSuper3D os_in os_template l_flex (no) l_display (no) l_all (no) auto
chemSuperBG as_template s_table I_idx r_thoroughness (1.) l_sampleRings (no) l_sampleCisTrans (no) l_occupancy (no) l_score (no) l_tableOutput (no) l_mulipose (no) l_tautomer (no) l_envelope (no) l_strain (no) r_LipoWeight (1.) r_PolarWeight (1.) r_APFcutoff (0.) as_subtmpl (a_NONE.) i_nproc (1) s_optn ("") as_exclude (a_NONE.) r_Xweight (3.) auto
chemSuperSubstructure as_template s_tab
chemblapi s_query ("") s_source ("target") s_tabname ("") l_loadall (no) r_TaniSim (0.75) auto
chemblcompress s_origtab ("") l_combinemammal (yes) l_filterbysize (yes) l_removePubChem (yes) auto
chemblmol s_origtab ("") s_chemblid ("") s_molname ("") auto
chemicalBatchProcess s_inputFile s_outputFile S_options
cloudStandardizeChem P_mol
clusterChemObjFiles s_inObjects ("*.ob") s_outObject ("clustered.ob")
clusterTable3D s_tab s_labelCol ("none") s_sizeCol ("none") s_colorCol ("none") auto
clusterTableAPF s_tableName
clusterTableColumns S_cols l_reverse (no) auto
cluster_vars R_vars i_n r_vicinity (0.3)
colorConsensus l_resLabel (no)
colorGrobByProximity &g_ as_ (as_graph) s_rainbow ("#ffff00/#00aaaa") r_max (5.) i_NofSteps (10) l_colorPatchOnly (yes)
colorRebelGrob as_ (a_*) S_grobNames ({"g_pocket1"})
compSeqCross s_projCross ("cross1") s_proj1 ("sw1") s_proj2 ("pdb1") r_probability (0.01) l_appendProj (no)
compareSDFiles s_file1 s_file2 s_resultFile s_overlapType ("A")
compressModelcsv s_tab ("msLigandModel") s_uniquecol ("id") s_finaltab ("msLigandTarget") auto
compresstoTargetPair s_tabname ("")
confGenBG T_t I_idx i_mnconf (50) r_vicinity (30.) r_thoroughness (1.) l_sampleRings (yes) l_cisTrans (no) l_systematic (no) l_refine (no) l_warnings (no) l_keepHydrogens (no) l_pyramide (no) s_options ("") auto
confGenFileBG s_inputFile s_outputFile i_mnconf (50) r_vicinity (30.) r_thoroughness (1.) l_sampleRings (yes) l_cisTrans (no) l_systematic (no) l_refine (no) l_warnings (no) l_keepHydrogens (no) l_pyramide (no) auto
confGenMolCartBG s_table i_mnconf (30) r_vicinity (30.) r_thoroughness (1.) l_sampleRings (no) i_systematic (5) l_refine (no) i_from (1) i_to (0) l_Force (no) auto
consensusPh4byAPF ms_ligands R_5thresholds ( { 0.75 0.75 0.75 0.5 0.5 } ) l_blobsOnly (yes) l_display (yes) l_occupancy (no)
consensusligpocket
consensuspocket r_dist (1.0) auto
contourEDS s_mapName R_sigmas ({1.0, 2.5}) S_colors ({"yellow","blue"}) l_display (yes) l_trim (no) as_ (a_NONE.) auto
convert2Dto3D os_ l_build_hydrogens (yes) l_fixOmegas (yes) l_display (no) l_overwrite (yes)
convert3Dto3D os_ l_build_hydrogens (yes) l_display (no) l_overwrite (yes)
convertFile2Dto3D s_inputFile s_outputFile l_keep_hydrogens (yes) l_fix_omegas (yes)
convertObject ms_ (a_) l_delete_water (yes) l_optimize_hydrogens (no) l_replace_the_original (no) l_display (no) l_optimize_his (yes) l_maskMissing (no) l_assignHeteroCharges (yes) s_options ("") auto
convertObjectOld auto ms_ (a_) l_delete_water (yes) l_optimize_hydrogens (no) l_replace_the_original (no) l_display (no)
convertPepToHet ms_ l_reverse
convertTable2Dto3D s_tableName I_idx l_keep_hydrogens (yes) l_fix_omegas (yes) l_autoCharge (no) auto
convertXrayMap2Grid m_map r_gridSize (0.5) l_display
cool auto rs_ (a_) l_static (no)
copyMol ms_ s_objName ("") l_oneObj (yes) auto
copyResSel rs_ s_objName ("") i_bridgeGapsSmallerThan (3) auto
cursorBrowseLoopConfs i_confNum s_tabName
cursorBrowseLoopConfs_1loop i_confNum s_tabName
cursorBrowseLoops i_LoopNumber
cursorBrowseLoopsDoubleClick i_doubleClicked
cursorFindByPatternRes i_num l_showAlignment
cursorFindBySeqRes i_num l_showAlignment
cursorFindPDB i_num s_tableName
cutSignalPeptide &seq_ s_newSeqName
d3output S_output ({"HeatMap","Chord","Tree","Force","Neato"}) i_property (1) auto
dataObjAtomAction as_at
dataObjAtomActionTable s_objnam i_row
dec s_ipaddress ("" )
deleteExtraChainsGrafts auto ms_ ( a_ ) l_deleteNCSchains (no) l_gpcrGraftDelete (no)
deleteWeakWaters os_obj (a_) s_water ("")
designLoop rs_Nter rs_Cter i_minL (4) i_maxL (4)
diffPocketShape as_lig1 as_lig2 l_super (yes) s_tag ("")
displayModelPose s_posetab i_row
displayMolSummaryPose s_tab ("MolSummaryTab") i_row (0)
displayRECCONFlig as_lig (a_H) i_conf (1)
dock2SetupReceptor s_projName ("DOCK1") ms_receptor (a_*) as_bindPatch (a_/xxx) l_dockDisplay (yes) s_options ("none")
dock3DbScanPre s_projName ms_ s_newfilename
dock3DbScanSetup s_projName ("DOCK1") l_Ligand_from_ICM_Object (no) l_dockDisplay (yes) s_ligandname ("DOCK1_lig")
dock3IndexDb s_projname ("DOCK1") s_dbFile ("/data/acd/acd.mol2") s_dbIndex ("/data/icm/inx/ACD") s_dbType ("mol2") S_extraFields (Sarray(0))
dock4StatusEdit s_projName ("DOCK1") l_adjust_lig (no) l_adjust_box (no)
dock5CalcMaps s_projName ("DOCK1") r_gridSize (0.5) r_maxVW (4.0) l_occupancy (no)
dock6gridLig s_projName ("DOCK1") os_ligand l_calcRebelScore (no) l_useOneLigConfOnly (yes) l_externLig (no) r_mcLengthFactor (1.) l_dockDisplay (yes) l_writeTrajectory (no)
dock7stackSCARE s_projName ("DOCK1")
dock8refine s_projName ("DOCK1") s_objFileName ("DOCK1_answers1.ob") i_ligandRefine (1) i_nconf (5) s_runObj ("DOCK1_ref1") s_flexSel ("all") l_dockDisplay (no)
dock9eval s_projName ("DOCK1") s_objFileName ("DOCK1_ref1") s_evalName ("DOCK1_evref1")
dock9evalNov99 s_projName ("DOCK1") s_objFileName ("DOCK1_ref1")
dockBG P_chem S_dockPath r_thoroughness (1.) auto
dockBrowseScan s_projName ("DOCK1") s_objFileName ("DOCK1_answers*") l_dsPocket (no) l_dsHB (no)
dockBrowseStack s_projName ("DOCK1") s_objFileName ("") i_object (1) s_cnfFileName ("") l_dsPocket (no) l_dsHB (no)
dockCalcHB l_isItComplex i_currObjNumber r_radius r_lowLim r_uppLim
dockCalcPocket l_isItComplex i_currObjNumber s_grobtype r_radius
dockCheckObj s_objectName ("none") s_callingMacro ("none")
dockClearSession
dockColor as_ (a_//*) s_dsMode ("wire") s_colorBy ("atom")
dockDisplayBox s_projName ("DOCK1") l_display (yes)
dockDisplayHB s_projName ("DOCK1") s_objFileName ("DOCK1_ref1") r_lowlim (0.0) r_upplim (2.8) r_interfaceCutoffDist (-1.) l_dockDisplay (yes)
dockDisplayMol s_pname i_dsReceptor i_dsLigand
dockDsRecSkin s_projName ("DOCK1") r_margin ( 2. ) l_wire (no)
dockInit s_project s_prou
dockInputTable auto s_chemtable r_thoroughness ( 3. ) i_Nconf ( 3 ) l_double (no) l_racemic (no) l_tautomer (no) l_NN (no)
dockLogging s_pname s_header s_content s_macname s_tstart r_tstart
dockMakeInputTable s_projName s_chemtable
dockMakeModel s_modname ("") s_projname ("") s_fileName ("") l_keepModel (yes) auto
dockMenuDirect s_refmacro ("aa bb")
dockPrepExplicit s_projName ("DOCK1") rs_ l_hydroxyl
dockPrepRestraintTable s_projName
dockProcessAnswersFromInputTable s_chemtable
dockProjSummary s_projName
dockProt2SetupReceptor s_projName ("DOCK1") ms_receptor (a_*) l_dockDisplay (yes)
dockProt3LigandSetup s_projName ("DOCK1") ms_ligand (a_*) os_realObj (a_none.) r_startingPointSpacing (0.)
dockProt4SelInitPos s_projName ("DOCK1") l_ligand (no) l_receptor (yes)
dockProt5CalcMaps s_projName ("DOCK1") r_gridSize (0.7) r_gridMaxVW (1.0) l_occupancy (no)
dockProt6gridDock s_projName ("DOCK1") s_runObj ("DOCK1_f1") i_iniPosition (1) l_dockDisplay (no)
dockProt8refine s_projName ("DOCK1") s_recFile ("DOCK1_recOpt") s_ligFile ("DOCK1_ligOpt") s_cnfFile ("DOCK1_f1") i_confFrom (0) i_confTo (0) s_runObj ("DOCK1_ref1") l_dockDisplay (no)
dockProtCalcConfProperty s_conftab s_formula s_prpname
dockProtGlobCombVar s_projName ("DOCK1") s_baseName ("DOCK1_gd") s_stackName ("DOCK1_topgd") i_maxNofConf (400) l_solvScore (yes) l_gridShowResults (no)
dockProtGridRefine s_projName ("DOCK1") s_ligFile ("DOCK1_ligOpt") s_cnfFile ("DOCK1_f1") i_confFrom (0) i_confTo (0) s_runObj ("DOCK1_ref1") l_dockDisplay (no)
dockProtGridShowResults s_projName ("DOCK1") s_stackName ("DOCK1_topgd") i_nConf (0) l_display (no)
dockProtMakePBSglobDockFile s_projName ("DOCK1") s_globStack ("DOCK1_gd") s_queue ("") s_properties ("-l nodes=dual:ppn=1") l_submit (no)
dockProtMakePBSrefFile s_projname ("DOCK1") s_confTableToRefine ("DOCK1_gd") r_length (1.) i_confPerCycle (10) s_queue ("") s_properties ("")
dockProtMakePBSrefFileOld s_globProject ("D1ca01") s_stackToRefine ("D1ca01_glob") s_nameRun ("D1ca01_gr") s_queue ("none") s_properties ("long") l_gridRef (yes) i_confPerCycle (10)
dockProtMakeSGEglobDockFile s_projName ("DOCK1") s_globStack ("DOCK1_gd") s_queue ("") s_jobOptions ("") l_submit (no)
dockProtPrepFullStack s_projName ("DOCK1") s_tableName ("DOCK1_gd") I_confList ({1})
dockProtRef1Conf s_recMol ("1") s_ligMol ("2") r_length (1.) l_display (yes)
dockProtRefCombStack s_stackBase ("DOCK1_gr") s_stackName ("none")
dockProtRefStack s_projName s_stackName s_stackRefined i_first (1) i_last (0) r_length (1.) l_display (no)
dockSelFlexSChain s_projName ("DOCK1")
dockSetScorePreferences s_projName s_scoreVersion s_solElMethod l_strain
dockSetupCovalent s_projName as_modres T_rxn
dockSetupDisplay s_projName ("DOCK1") s_dspRec s_selRec s_clrRec s_dspSite s_selSite s_clrSite s_dspLig s_selLig s_clrLig
dockSetupGrid ms_ligand s_loadMapRootName ("none")
dockSetupInterRestraint s_projName as_dest s_group l_only
dockSetupTemplate s_projName s_tmplFileName as_Template s_scaffoldTbl
dockSetupXray s_projName m_density
dockTableValue s_projname s_varname s_vartype s_varvalue
dockUnpackProject P_proj
dockUpdateGlobals s_projname i_mode (1)
dockUpdateRestraintTable s_projName
ds3D auto M_dist S_names ({""}) S_comments ({""}) s_tabname ("")
dsCell os_ (a_) l_deleteRemoteNeighbors (yes) i_Ncells (4)
dsCellBox os_ (a_)
dsCellBoxMap m_
dsChem as_ ( a_ )
dsChemLock T_tab s_prefix i_row
dsChemLockDock s_hitlst s_prefix i_index l_dummy (yes) auto
dsChemLock_new auto s_tabName s_prefix i_row l_link (yes)
dsChemTemp T_tab i_row
dsChemTemp_new auto s_tabName i_row l_link (yes)
dsChemUnlockAll s_tab
dsChemUnlock_new s_tabName s_prefix i_row
dsChemical as_ s_style l_dsHydrogens
dsConsensus ali_ &seq_ l_dsLabels (yes) s_graphType ("skin")
dsCustom as_ (a_) s_dsMode ("wire") s_colorBy ("atom") l_color_only (no)
dsDistances i_mode r_min r_max
dsGoodSpace as_source (a_)
dsHit s_hitlist i_index l_dsCPK l_dsHbond l_dsSurf l_labelRes
dsIsoRebel auto as_regOfInterest r_margin (15.) R_5levels ({-5.,-1.,0.,1.,5.})
dsLigandComplex ms_rec ms_lig l_center
dsLigandComplex2 auto ms_lig ( a_H [1] ) ms_rec (a_none.) r_dist (1.25) l_center (no)
dsLocal as
dsLocalReliability ms_ (a_1) ali_ (alignment[0]) l_plot (no)
dsLocalwire as
dsLoops l_dsTemplate (yes)
dsModelReliability ms_ ( a_1 ) &seq_ r_probThreshold (0.0001)
dsMultiWindow os_ i_nWnd
dsPocket ms_lig (a_H [1]) s_GrobNa ("") l_overwr (yes) l_ds_xstick_hb (no) l_resLabels (yes) auto
dsPocketRec ms_ligand (a_H [1]) ms_receptor (a_!H ) r_margin ( 6.5 ) s_GrobName ("") l_overwrite (yes) l_dsXstickHb (no) l_resLabels (yes) auto
dsPocketVw ms_ligand (a_H [1])
dsPropertySkin as_sel (a_) l_wire (no) l_biggestBlobOnly (no)
dsPropertySurface as_sel (a_) l_wire (no)
dsPrositePdb ms_ (a_*) r_prositeScoreThreshold (0.7) l_reDisplay (no) l_dsResLabels (yes)
dsReadSel s
dsRebel as_ (a_*) l_assignSimpleCharges ( no ) l_display (no)
dsSelection auto s l_only (yes) l_water (no)
dsSeqPdbOutput s_projName ("brku") l_resort (no)
dsSkinLabel rs_ (a_/*) s_color ("magenta")
dsSkinPocket ms_ligand (a_2) ms_receptor (a_) r_radius (7.) l_biggestBlobOnly (yes)
dsSkinPocketIcm ms_ligand (a_H [1]) ms_receptor (a_!H) r_radius (7.) l_biggestBlobOnly (yes)
dsStackConf as_ (a_//n,ca,c) i_from (1) i_to (Nof(conf)) s_superimpRes ("*")
dsUnsatHbonds l_on (yes)
dsVarLabels
dsXyz M_3coor
e3dAddConstraint as_lig1 as_rec1 s_templ ("") auto
e3dAutoChargeLigand r_ph (7.0) l_updateDisplay (no)
e3dBindingScore ms_rec ms_lig r_ligVwhbtoFree (0.) l_set_nnInterMod (yes) auto
e3dCalcMaps l_force (no)
e3dCheckCovReaction s_rxn s_tab
e3dCreateLigandsTable s_name ("LIGANDS")
e3dCutRgroups
e3dDefaultDisplay
e3dDisplay i_mode (1) l_only (yes)
e3dDockTable s_tabName r_thoroughness (1.) i_numPoses (1) l_minOnly (no) s_rxn ("") l_use4D (no) auto
e3dDsChemLock s_tabName s_prefix i_row l_link
e3dDsiplayHbonds
e3dEval_nnInterMod as_lig
e3dExportComplex s_resObj l_display (no) l_newSession (no) s_pdbFile ("") auto
e3dExportPose i_row s_fileName ("") l_launchICM (yes)
e3dFindBioisostere i_maxHits (20) s_type ("2D") auto
e3dGenConfStack
e3dIcmPocketFinder os_rec r_threshold ( 4.6 )
e3dImposeContraints l_mute (no) l_calcRmsdOnly (no) auto
e3dInvalidateLigandScore ms_lig
e3dLoad4DRecConf i_conf l_rebuildMeshes (yes) auto
e3dMakeAPFMaps as_lig r_wAPF (3.) r_rAPF (1.2) r_wLipo (1.) r_wPolar (1.) s_occupancy ("") r_step (0.5) auto
e3dMakeDockingProject r_thor (1.) l_racemic (no) l_ct (no) i_rflex (0) l_neutralCarb (no) l_runNow (yes) auto
e3dMakeHref s_label s_dialogPath
e3dMakeInitalStack l_presample (yes) l_flip (yes) auto
e3dMinimizeTz as_tz l_mute (no) auto
e3dPrepExplicit l_displayOnly (yes) l_off (yes)
e3dProcessHitList s_projName
e3dRefinement i_mode rs_sel l_sampleLigand (no) l_redraw (no) auto
e3dRefreshDrestraintTable
e3dSetAPFReceptor as_tmpl r_wAPF r_rAPF r_wLipo r_wPolar r_step l_exvol as_exvol r_exwt
e3dSetFlexConf s_tab i_pos
e3dSetLigand ms_sel l_display (yes) l_autoAssignCharges (yes) r_pH (7.0) l_pep2chem (no) auto
e3dSetReceptor os_sel l_calcmaps i_keepWater (1) l_display (no) l_makeLigandPocket (no) s_edsMapName ("") l_optExistingHyd (no) l_optHis (yes) l_truncateRec (yes) l_maskMissing (yes) s_opt ("") auto
e3dSetTerms l_map (yes) auto
e3dSet_nnInterMod
e3dShowHideDrestraint s_tabName s_prefix i_row l_dummy l_rm (no) auto
e3dShowModificationHistory
e3dSubstLigand s_tab i_row
e3dSubstLigand0 s_tab i_row l_mute (no) auto
e3dTranslateToBox
e3dUpdateRSLabels l_on
e3dUpdateScoreComponents s_tab i_row
e3dVisualizeExvol
ePot auto r_height (1.4) r_dist (3.) r_trim (1.5)
ePotProtected auto ms_e (a_A,M) r_height (1.4) r_dist (2.)
editMoleculeTable3D s_tableName i_r
editSelection auto as_toedit l_display (yes) l_enumerateStereo (no) l_tableOutput (no) s_extraTerms ("") s_mol ("")
evalAPFdiversity os_in l_ds (no)
evalChemOdd s_chem
evalSidechainFlex rs_residues (a_) r_Temperature (600.) l_atomRmsd (yes) l_color (yes) l_bfactor (no) l_entropyBfactor (no)
expandMolSummary s_tab ("") s_MolSummarycol ("MolSummary") i_row (0)
expandMolSummaryTarget s_tab ("") s_MolSummarycol ("MolSummary") s_targetkey ("") l_appendcol (yes) S_appendcol ({"MolScore","MolpKd"}) auto
exportProjectForBrowsing s_tabName ("LIGANDS") auto
extractLigand ms_lig s_type l_append s_tabName l_opt2D (no) auto
fetchExperssionData auto s_colName l_logScale (no)
fftProtDockBG os_rec os_lig i_accuracy (0) os_refCmplx (a_none.) rs_focusRec (a_none.) rs_focusLig (a_none.) l_crossCont (no) r_contCutoff (10.) i_nproc (1)
fillGrobWithAtoms auto &g_ s_name ("") l_delete (no)
fill_box_with_water R_6box s_mol ("hoh") r_gridSize (3.1)
findAbTemplates s_seqNaLight s_seqNaHeavy
findBestRpairForSAR s_tab
findBioisoster s_groupSmi ("[C*](=O)O") r_dpkd (1.0) s_Attach ("") s_exactR2 ("") l_keepData (no) auto
findBioisoster3D s_groupSmi ("[C*](=O)[O-]") r_bur (0.5) s_Attach ("") s_exactR2 ("") l_keepData (no) auto
findChembl S_query ({""}) S_type ({""}) l_pkdonly (yes) s_version ("") l_quiet (yes) i_maxHits (1000) auto
findChemblBest s_table_name
findChemblObject os_1 s_uniprot l_mammalian (yes) l_keep (no) l_quiet (no) auto
findChemblSumm s_table_name
findChemblpkd s_uniprot ("") l_mammalian (no) s_version ("") l_removeinactive (yes) s_keyword ("") l_filterbysize (yes) l_drugbank (no) auto
findChemblpkdtxt s_txtfile ("") s_uniprot ("") l_removeinactive (yes) s_keyword ("") l_filterbysize (yes) l_drugbank (no) auto
findDecoy s_tab ("") r_multinof (10.) r_tight (1.) auto
findDrugbank S_query ({""}) s_where ("") l_append (no) l_quiet (no)
findDrugbankSumm s_table_name
findDrugbankTarget s_table_name ("") s_type ("all") I_row_index ({0}) auto
findEnamineRealBG s_what i_maxHits (1000) auto
findFuncMin s_Function_of_x ("Sin(x)*x-1.") r_xMin (-1.) r_xMax (2.) r_eps (0.00001)
findFuncZero s_Function_of_x ("Exp(-Exp(-x))-0.5") r_xMin (0.) r_xMax (1.) r_eps (0.00001)
findHomology s_what s_type l_split l_loadSequences (no) l_fast (no) l_append (no)
findICB s_what s_db ("") auto
findNextName s_def ("icm") s_ext (".png")
findPDB auto s_what ("") s_auth ("*") s_title ("") s_exp ("*") s_head ("*") r_res (9.9) s_het ("*") l_update_pdb_index (no) l_append (no) l_advSearch (no)
findPDB_db s_db s_what ("") s_het ("") l_oneHitDisplay (no) l_append (no) l_advancedSyntax (no) auto
findPharmacophore as_pharm s_file l_group (no) r_maxRmsd (0.5) i_maxHits (2000) auto
findPocketome s_what s_where ("proteinname") auto
findPubchem s_what l_append (no) l_3d (no) i_maxHits (100) auto
findSelHitDisplay s_hits i_row
findSequence s_what s_type l_split l_append (no)
findSequenceBlast s_what s_db ("nr") i_maxHits (1000) l_bg (no) auto
findSurechembl s_query ("") s_type ("") l_append (no) l_quiet (no)
findSwissNames S_seqNames
findSymNeighbors as_ ( as_graph ) r_radius (7.) l_append (no) i_extend_by (2) l_keepEntireChain (no) l_display (yes)
findSymNeighborsOld as_ ( as_graph ) r_radius (7.) l_makeObjects (yes) l_merge (no) l_display (yes)
findTCGACloudAliquot s_disease ("") auto
findTCGACloudAliquotLoad s_table_name ("") i_data_level (0) I_row_index ({0}) auto
findTCGACloudMaf s_disease ("") auto
findTCGACloudMafLoad s_table_name ("") I_row_index ({0}) auto
findTCGACloudMafStat s_table_name
find_related_sequences auto ms_ (a_*.A)
findpubmed s_searchterm ("") auto
fixBlastGiSeqNames
fixChirality l_deb (no)
fixQuotes s_str ("")
flexrec auto as_lig rs_rec i_mode
foldMolSummary s_tab ("") s_Pairwisetab ("msLigandModel") s_uniquecolumn ("") S_combinecol ({"MolScore","MolpKd","pPvalue","MolClass","MolSim"}) s_fileloc ("") l_keepall (yes) auto
funcChemCloudMap S_query s_fr s_to
funcChemCloudMapJson S_query s_fr s_to
funcChemCloudMapJsonTable T_tbl s_fr s_to
funcChemCloudMapMol P_query s_fr s_to
funcChemInfoByMol P_mol )
funcChemInfoByS S_nm )
funcChembl P_mol )
funcChemblJson S_query S_type l_pkdonly s_version
funcChemblJsonTable T_tbl
funcDrugbank P_mol )
funcDrugbankJsonTable T_tbl
funcLigStrain P_chem )
funcMolPSA as )
funcProtCloudMapJson S_query s_fr s_to s_org
funcProtCloudMapJsonTable T_tbl s_fr s_to s_org
funcProtCloudMapping S_query s_fr s_to s_org
funcPubchemCidLookup P_chem l_testedOnly )
funcPubchemLookup2 S_id s_typeFrom s_typeTo ("") s_lookupMolt ("")
genAltChargeStates T_chem I_idx r_pH (7.) r_delta (1.)
generalSearchFromGUI s_type s_searchWhat s_extra ("") l_append (no) i_maxHits (500) l_bg (no) l_advSearch (no) auto
generateBioisoster P_chem s_name ("") l_matchScaffoldAttachement (no) l_makeCompounds (yes) auto
getAtomProperties as_atom
getPharmProperties as_at
getTransformParams M_xyz
hbondPrepare os_objects
highlightLigandBySubstructure as_obj s_smiles
hitlist2ligedit s_hitlistfile
homModelBG os_in (a_) ms_hetero s_seqName s_aliName i_loopSampleLevel (0) I_indelExpand ({2,3}) r_effort (1.) s_opt ("")
homPrepAlignments ms_tplts s_seqLi
homodel ali_ l_quick (yes)
icmCavityFinder as_ ( a_A ) r_minVolume ( 3. )
icmFastAlignment s_seqName s_blast_file ("pdbseq") i_speed (5) i_mnhits (100) r_idUniqueSkip (0.1)
icmMacroShape auto as_ ( a_A,N ) i_complexity (8) r_gridStep (0.) r_contourLevel (0.) l_colorByDepth (yes) l_fast (no) l_display (no) s_rainbow ("")
icmPmfProfile os_ ( a_ ) l_accessibilityCorrection (yes) l_display ( no )
icmPocketFinder as_receptorMol r_threshold ( 4.6 ) l_displayPocket (yes) l_assignSites (no) l_link (yes) auto
icmPotential rs_ R_6box r_gridSize (1.) r_potStep (5.) s_term ("el") s_type ("wire")
icmProteinInterfaceOda ms_ (a_*) l_makeDotsObject (no) l_makeEnergyTables (yes) R_AbsoluteRangeODA ({0. 0.})
icmResidueProfile rs_ ( a_/A )
importExcel s_fileName s_opt ("") auto
installLoop auto rs_Nter rs_Cter rs_loop s_seq ("All ala") l_refine (no)
installOnlineExtension s_name l_on (yes) auto
krnnmol ms_ l_smooth
ligDiagCalcAccSurface ms_lig os_rec
ligDiagInteraction2D ms_lig os_rec (a_none.) P_chemTempl (Chemical()) r_hphobDist (4.5) r_hbStrength (0.8) i_labelStyle (1) l_assignSites (no) l_makeContactTable (no) auto
ligQSAR_apf P_chem
ligandAction as_sel1 s_what1 S_params1
ligandActionICM as_sel1 s_what1 S_params1
ligandBPMC
ligandProtonation ms_ligand
lighomBG os_tmpl (a_!*.) s_tmpl ("") os_ob (a_!*.) s_ob ("") s_ali ("") s_sdf ("") s_classcol ("") s_pkdcol ("") s_loop ("") s_anchor ("") r_nm (16.) l_forcestart (no) auto
linkUnlinkMeshes s_opt ("")
listOnlineExtensions
loadAlignmentBlast P_entry
loadBioisoster3Dpair s_tab i_ix l_display (yes)
loadEDS s_pdb ("1mui") l_diffmap (no) r_sigma (0.)
loadEDSweb auto s_pdb ("1mui") l_diffmap (no)
loadPDB s_code i_type l_deletewater (yes) l_delete_alternatives (yes)
loadPfamEntry auto s_find ("") l_all (no)
loadProtein s_proteinID s_proteinFileName
loadQMtorScanResult s_torProf
loadResources
loadSequenceBlast s_accession
loadSwissEntry ms_ l_load_sequence (yes) l_make_alignment (no) l_tranfer_sites_from_swiss (yes)
loadToxins
logPrebel ms_ (a_) l_resetCharges (no)
logPrebel1 ms_ (a_) l_resetCharges (no)
logPrebel2 ms_ (a_)
loopmodelBG rs_loop r_thoroughness (1.) l_sidechain (no) l_truncate (no) s_options ("")
makeAlignmentFromSuper auto ms ( a_*.A )
makeAllLoopTemplates as_
makeAxesObj auto R S ({"X"})
makeAxisArrow rs_ i_length (10) r_radius ( 0.12 ) r_head_width_ratio ( 2. )
makeBioMT os_pdb (a_) l_makeall (yes)
makeCaTrace os_
makeColorTable auto l_make3d (no)
makeContactMesh as_first (a_H) as_second (a_!H) l_apolar (yes)
makeDataObj R_X R_Y R_Z R_kr ({0.}) R_rad ({0.}) S ({""}) s_tabname ("") s_rainbow ("indigo/blue/green/yellow/orange/red") auto
makeDnaRna s_sequence ("ACTG") s_molName ("na") l_duplex (yes) l_min (yes) s_dna_rna ("dna")
makeGWmap as_site
makeGrobFromSel as_ s_color l_solid (no)
makeHtmlfromEdge s_tab ("") s_col1 ("") s_col2 ("") s_propertycol ("") s_distcol ("") S_nodesname (Sarray(0)) R_nodesproperty (Rarray(0)) S_d3type ({"all"}) auto
makeHtmlfromNode s_tab ("") s_col ("") s_distmat ("") s_propertymat ("") S_d3type ({"all"}) auto
makeIndexBlastPdb
makeIndexChemDb s_dbFile ("/data/acd/acd.mol") s_dbIndex ("/inx/ACD") s_dbType ("mol2") S_dbFields ({"ID"})
makeIndexPdb s_entriesFile ("http://ftp.wwpdb.org/pub/pdb/derived_data/index/entries.idx") l_updateLigands (no) auto
makeIndexSwiss s_swiss (s_swissprotDat) s_indexName (s_inxDir+"SWISS.inx")
makeLigandPocketSurface r_distance (3.5)
makeLigandPocketSurfaceLig ms_ligand r_distance (3.5)
makeLigandPocketSurfaceLigRec ms_lig os_rec R_box r_dist
makeLoopStackTable
makeLoopTemplate as_ l_loopDB (no) l_GAP (yes) l_context (yes) l_display (no)
makeMCSTreeBonds s_nk
makeMCStree s_tab s_label ("") l_optimize (no)
makeMini
makeModelPanel s_panel ("") s_modelname ("") s_keyword ("") s_origpanel ("") auto
makeModelPanelList s_panel ("CustomPanel") S_modelfullpath (Sarray(0)) s_modelexp ("") auto
makeMultiSuper as_
makeNewHtml s_name ("html1") l_pop (yes) s_text ("")
makeNewMPOscore s_name i_prefill l_assignColors (yes) auto
makePdbFromStereo R_xl R_xr R_yl R_yr r_stereoAngle ( 6. )
makePharma as_obj s_name ("pharm") l_points (yes) l_display (yes) as_exvol (a_NONE.) auto
makePharmaAtoms as_ i_type (1) r_radius (0.5) l_display (yes)
makePlotMatrix auto M s_rainbow ("white/pink/blue") s_title ("") s_I ("I") s_J ("J")
makePocketPh4 ms_rec R_box
makePocketomeAnnotation as_lig
makePocketomeFile as_lig s_pkfilename ("pk")
makeSSbridge auto rs_1 rs_2 ( a_NULL./ )
makeSeqClusters
makeSeqGraph auto P_seq (Parray(sequence)) s_tabname ("") I_fontsizes ({10,8}) R_3th ({0.8,0.6,0.3}) l_shortName (no) s_otype ("svg") l_progress (yes)
makeSideConf rs_
makeSimpleDockObj os_ s_newObjectName
makeSimpleModel &seq_ ali_ os_
makeTable s_tableName ("tbl") i_rows (20) i_Scols (2) i_Icols (1) i_Rcols (1) l_chemcol (no) l_rndS (no) l_rndI (no) l_rndR (no)
makeTagPocketFromLigand auto rs_lig os_ ( a_NONE. )
makeTrajectoryFromStack
make_axis_atoms auto i_fr (0) i_to (20) i_ax (3)
make_dfzBG s_target s_proj ("") os_obj (as_graph) l_addtomodel (yes) auto
make_globalkccBG s_target s_table ("LIG") s_activityColumn ("pkd") l_localtable (yes) s_unit ("pKd") l_charge (yes) auto
make_kcaBG s_target s_table ("LIG") s_activityColumn ("pkd") l_ChEMBLKdtopKd (yes)
make_localdfaBG s_target s_table ("LIG") s_activityColumn ("pkd") s_proj ("") os_obj (as_graph) l_localtable (yes) s_unit ("pKd") l_charge (yes) l_fromproject (yes) auto
make_localdpcBG s_target ("") s_table ("LIG") s_activityColumn ("pkd") s_proj ("") os_obj (as_graph) l_localtable (yes) s_unit ("pKd") l_charge (yes) l_fromproject (yes) auto
make_ssbonds_by_distance auto as_ ( a_ ) r_max_dist (2.4)
mcLigand i_mncallsMC (0)
mcMacro vs_ ( v_//x* ) as_tether
mcsImproveTriplet s_nk I_s I_b i_rd
mcsOnlyShowMajor s_nk I_s I_b i_rd
mergeMultipleSetsByRow S_tabs s_tres l_removeMerged (no) auto
mergeObj s_os ( "a_1,2." ) s_name ("merged")
mergePdb rs_source ( a_1.1/20:25 ) rs_graft ( a_2.1/20:25 ) s_combo ("combo")
mergeTwoSetsByRow s_t1 s_t2 s_tres
minimizeCartesian as_ i_nsteps (1400) l_ts (yes) r_weight (5.) auto
minimizeChemTable s_tab i_minCalls (2000) r_tsWeight (0.) auto
mkAtomsFromXyz M_xyz
mkLigContactTable rs_lig rs_pk r_di (1.4)
mkModPep s_se
mkMolSphere rs_ ( as_graph ) r_margin (0.) s_newObjName ("new")
mkNMstack as_ i_Nmodes (10) r_Amplitude (1.0) i_Steps (1) l_randomize (no) l_gap (no) l_local (no) l_singleMode (no)
mkSelectionObject rs_ ( as_graph ) s_newObjName ("") l_optExistingHyd (no) l_optHis (yes) l_maskMissing (no) auto
mkSeqQsarTable s_aliName
mkStackConf i_from (1) i_to (Nof(conf))
mkUniqPdbSequences auto i_identPercent ( 1 )
mkXpdbFileList
mk_model_tab
modifyGroup as_group s_Group l_reset_MMFF_types (yes) l_reassign_MMFF_charges (yes) l_optimize_geometry (no) i_Number_of_steps (600) auto
modifyGroupSmiles as_group s_Group l_reset_MMFF_types (yes) l_reassign_MMFF_charges (yes) l_optimize_geometry (no) auto
molEditBranch as_toedit
molEditBranch_load s_connectSel s_file
molcolors auto as_ (a_*.*) s_rainbow ("")
molskins auto as_ ( a_//!h* ) l_grob (yes) l_colorByContact (yes) s_rainbow ("")
morph2tz i_nIter rs_loop l_store_in_object (no) l_play_morph (yes) i_mncalls (1000)
morphFrames auto i_n (10) l_minimize (no) l_bb (no)
moveMol ms_ s_objName ("")
movie_delete_exported_files
movie_delete_scene
movie_delete_scenes
movie_edit_scene
movie_info
movie_init
movie_interpolate l_write i_steps
movie_load_scene i_num
movie_new s_dir
movie_open s_dir
movie_play_and_record l_export2file (no) s_mode ("")
movie_play_scene l_write_to_file i_scene
movie_record_scene
movie_rock l_write s_axis i_angle i_steps i_rocks
movie_rocking i_times i_angle_num i_nsteps s_rock_axis
movie_rotate l_write s_axis i_angle i_steps
movie_rotating i_angle_num i_nsteps s_rot_axis
movie_save_header
movie_scene_type_changed i_current_chioce
movie_set_first_view
movie_set_second_view
movie_still i_nsteps
movie_tween i_nsteps
mrcStack as_mainObj (a_) os_otherObjects (a_*.) l_super (no) l_optimizeH (yes)
msAPFpredict s_predict ("") s_train ("") s_activitycol ("pkd") l_cluster (yes) l_dockterms (yes) i_mintrainset (50) i_maxtrainset (500) auto
msAPFpredictcluster s_predict ("") s_train ("") s_activitycol ("pkd") l_cluster (yes) l_dockterms (yes) i_mintrainset (50) i_maxtrainset (500) i_mode (3) s_sshcommand ("ssh vls.molsoft.com") s_qsubarg ("-q all.q") auto
msAPFpredictresult s_predict ("") s_activitycol ("pkd") auto
msChEMBLcol s_col ("") I_entries (Iarray(0))
msChEMBLcpd P_mol (Chemical("")) S_smiles (Sarray(0)) r_tanisimilarity (0.75) auto
msChEMBLtarget s_target ("") S_target (Sarray(0)) r_pkdcutoff (0.) auto
msClusterHitRep s_tab ("") r_clusterdist (0.2) auto
msPanelCluster s_tab ("") l_calcmissing (no) I_selectedrows (Iarray(0)) s_plottype ("all") auto
msPocketoffset s_recligicb ("") os_rec (a_!*.) os_lig (a_!*. ) s_refrecligicb ("") r_effort (10.) auto
msReport s_tab ("") s_cpdnamecol ("") auto
msSelectPocket s_proj ("") s_sdf ("") l_optconf (no) l_ligpocket (yes) l_dock (no) l_RECCONF (yes) l_nocluster (yes) r_clustdist (1.0) i_maxsel (10) auto
msSelectPocketBG s_proj ("") s_sdf ("") l_dock (yes) i_mode (1) i_maxconf (10) auto
msSettings l_read (no) auto
msaddGO s_tab ("msLigandModel") auto
msdpcZScore s_modname ("") auto
msfilterGO s_tab ("msLigandModel") s_type ("") s_GOterm ("") auto
msnewMolScore s_tab ("") auto
msnnscore s_tab ("") auto
msorigtab s_tab ("") I_row (Iarray(0)) s_tabsource ("") s_column ("") auto
mstmpdockrun s_ligsdf ("") s_ligtmpl ("") I_conf (Iarray(0)) l_final (no) l_scare (no) r_effort (10.) auto
msunpackModels S_models s_modelsDir ("") auto
msunpackModelsncc s_tab ("") s_target ("") auto
msupdatetags s_tab ()
msupdatetoolspanel s_tab ("") auto
multiModels s_seqNames ms_templates
mutantCompStabilityBG auto as_ s_mutation ("ala") s_AAtable s_grp s_part1 s_part2 l_terms (no) i_batch (0)
mutantPeptCompStabilityBG s_inp s_mutation ("ala") s_AAtable s_grp s_part1 s_part2 l_scan1 (no) l_scan2 (no)
mutantProteinLigandBG s_inp s_mutation ("ala") ms_ligand l_scan (no) l_allChains (no)
mutantStabilityBG auto as_ s_mutation ("ala") s_AAtable s_grp l_allChains (no) l_daa (no) l_foreground (no) auto
mutateResidue rs_ s_res
mutateResidueExt rs_ s_res
name2Mol s_molname ("octanol") l_min (yes)
nice auto s_PdbSelection ("") l_invert (no) l_wormStyle (no) l_append (no) l_nodisplay (no)
normSubset s_tabname s_realColName r_mean r_std r_fract (0.1) l_normal (yes)
oniongroup s_tab ("") l_cluster (no) i_group (4) auto
openFile s_fls i_type (0) l_display (yes) l_rmothers (no) l_rmall (no) l_listOnly (no) s_extras ("") auto
optimize1His s_selection l_old (yes)
optimizeH_zeroOcc rs_ l_optimize_his l_dyn_prot
optimizeHbonds as_ l_rotatable_hydrogens (yes) l_optimizeHisAsnGln (yes)
optimizeHetTautomer auto ms_ r_dHcutoff ( 15. )
optimizeHeteroTautomer ms_hetero
optimizeHisProAsnGlnCys rs_HPNQCres
optimizeMCStree s_nk
optimizeProtonation rs_DEKHres
optoffset R_var &r_fff
orientXYZ l_vertical (yes)
parrayTo3D P_m l_autoCharge (no) l_fixOmegas (yes) auto
parrayToMol P_m
pcaBuildDescriptorWeights s_tab
pepSampleBG s_pepseq s_runName r_thoroughness (1.)
pkMakeChemTable
place2model ms_movable as_static as_pock r_effort (1.) l_display (no)
placeLigand auto ms_movable as_static r_effort (1.) l_display (no) l_debug (no)
placeLigand2Grob auto ms_movable &g_ l_flexible (no) r_effort (1.) l_delete (yes)
playObjectStack os_ r_from (10.) r_to (40.) s_options ("")
plot2DSeq ali_
plotBestEnergies s_McOutputFiles ("f1,f2") r_energyWindow (50.) s_extraPlotArgs ("display")
plotCluster M_distances S_names ({""}) s_plotArgs ("CIRCLE display {\"Title\" \"X\" \"Y\"}")
plotEnergy s_McOutputFiles ("f1.ou") r_energyWindow (50.) l_best (no)
plotFlexibility &seq_ i_windowSize (7)
plotLearningCurve s_NNlearningOutputFile ("a.ou")
plotMatrix M_data s_longXstring S_titles ({"Title","X","Y"}) s_fileName ("tm.eps") i_numPerLine (10) i_orientation (1)
plotRama rs_
plotRama2 auto rs_ (a_/A) l_mark_residue_label (yes) l_shaded_boundaries (no)
plotRamaEps auto rs_ (a_/A) l_mark_residue_label (yes) l_shaded_boundaries (no)
plotRose i_prime (13) r_radius (1.)
plotSeqDotMatrix &seq_1 &seq_2 s_seqName1 ("Sequence1") s_seqName2 ("Sequence2") i_mi (5) i_mx (20)
plotSeqDotMatrix2 &seq_1 &seq_2 s_seqName1 ("Sequence1") s_seqName2 ("Sequence2") i_mi (5) i_mx (20)
plotSeqProperty R_property s_seqString S_3titles ({"Title","Position","Y"}) s_fileName ("tm.eps") i_numPerLine (30) s_orientation ("portrait")
plotVwR6exp r_A r_B r_C r_A1 (0.) r_B1 (0.) r_C1 (0.)
predCov s_tab ("")
predCovfunc P_chem
pred_dfa P_mol
pred_dock P_mol
pred_eca P_mol
pred_kcc P_mol
pred_multidfz P_mol
pred_qsar P_mol
predictMetOx s_tab
predictModelPose s_tab ("") s_mod ("") l_keepOrigCol (yes) l_removeinactives (no)
predictModelPoseEmbed s_posetab ("msLigandModel")
predictModels s_tab ("") S_models l_color (yes) l_lookuponly (no) l_deleteEmptyCol (no) l_pose (yes) l_progress (yes) s_modelsDir ("") l_removeinactives (no) l_charge (yes) l_cluster (no) P_parameters (Collection()) i_start (0) i_end (0) auto
predictModelsBG s_tab ("") S_models i_processor (4) l_removeinactives (no) l_charge (yes) P_parameters (Collection()) i_start (0) i_end (0) auto
predictModelsCluster s_tab ("") S_models s_dir ("") s_sshcommand ("ssh vls.molsoft.com") s_qsubarg ("-q all.q") s_remotedir ("") s_remoteicmdir ("") s_remotemoddir ("") i_mode (2) l_removeinactives (no) l_charge (yes) i_ligperjob (1000) l_shortoutput (no) P_parameters (Collection()) i_start (0) i_end (0) i_queuemode (1) auto
predictModelsCol P_chem s_mod
predictModelsCompact s_tab ("") S_modelkey ({"kcc"}) S_combinecol ({"MolScore","MolpKd"})
predictModelsHit s_dir ("") s_sshcommand ("ssh vls.molsoft.com") s_remotedir ("") i_hit (1000) S_sortcol ({"MolScore","MolpKd"}) l_txtonly (no) i_start (0) i_end (0) auto
predictModelsResult s_dir ("") s_sshcommand ("ssh vls.molsoft.com") s_remotedir ("") i_start (0) i_end (0) auto
predictModelstxt2Hit s_tab ("msModeltxt")
predictProdrug s_tab ("") s_tag ("carboxylate") I_rxnrow (Iarray()) i_mode (2) auto
predictRxn s_tab ("") s_tag ("prodrug") I_rxnrow (Iarray()) i_mode (1) auto
predictSeq s_seq ("1crn_m") s_fileName ("plot") l_predictSstr (no) i_numPerLine (100)
predmcp s_tab ("")
prepSwiss s_IDpattern ("VPR_*") l_exclude (yes) s_file ("tm")
printMatrix s_format (" %4.1f") M_matrix (def)
printPostScript s_PrinterCommand ("lp") l_color (yes)
printTorsions rs_ (a_/A)
processAggreg1 s_tab1 ("results") s_tab2 ("t1") auto
processBlastResults s_url s_rid s_db s_scriptName
processLigand as_sel s_what S_params
processLigandICM as_sel s_action S_params l_bg (no) auto
processLigandSave s_tag ("") s_tab ("LIGANDS") auto
processProtD1 s_tab ("results") auto
processProtDSS
profilepair s_tab
rdAllObj s_obna
rdBlastOutput S_giArray
rdSeqTab s_dbase ("NCBI")
rdec s_inet_dec ("3488253803")
reactiveCys as_ (a_A) l_allChains (no)
readLargeSDF s_fileName
readModelIndication s_Indication ("") auto
readModelPanel l_updatefile (no) l_loadcustompanel (no) s_panelname ("") auto
readPredictionModels s_prefix l_checked
readSequenceTable s_file s_tab ("") s_format ("fasta") auto
readUniprot s_query ("")
readUniprot4pdb
readUniprotCloud S_query S_type l_quiet (no)
readUniprotCloudExtractSite s_table_name ("") s_type ("all") I_row_index ({0}) auto
readUniprotCloudInfoJson S_query S_type
readUniprotCloudInfoJsonTable T_tbl
readUniprotCloudLoadSeq s_table_name ("") I_row_index ({0}) auto
readUniprotCloudMakeAlign s_table_name ("") I_row_index ({0}) auto
readUniprotWeb auto s_query l_references (no) i_maxHits (200)
readUniprotlist S_ids
realignBlock s_aliName ("myali") i_start i_end r_stickiness (0.3) s_type ("align")
refineLigand ms_
refineLigandSphere auto rs_ligand r_effort (1.) r_sphere (6.) i_mode (2)
refineModel i_nRegIter (5) l_sideChainRefinement (no)
refineProtDockBG s_rigidResults ("dockedPoses") r_effort (1.)
regul rs_ (a_!W) s_ngroup ("nh3+") s_cgroup ("coo-") l_delete_water (yes) l_shortOutput (yes)
remarkObj
renumberBySeqres ms_
renumberResBySeq auto ms_ (a_1) &seq_ i_extraOffset (0)
reorderAlignmentSeq ali_
replaceBy1Het auto as_ s_name_comment ("")
resLinkFormatToggle rs_
ringBPMC
rotateView auto s_axis ("Y") r_angle (180.)
runDockScript s_prjName i_fromEntry i_toEntry s_outputFName r_thoroughness l_stack l_scoreStack
run_bg s_cmds s_inputVars s_outputVars
scan2Dto3Dconvert
scanAddExplicit
scanAppendHitList s_destList s_sourceList
scanCalcHitListProperty s_hitlist s_formula s_prpname
scanCalcIntFingerprint
scanCalcPartArea as_1
scanChargeGroups s_groups
scanCheckLipinski i_ix &l_bad
scanClusterHitList s_hitlist
scanClusterSolutions s_inObjects ("DOCK1_answers*.ob") s_outObject ("clustered.ob") R_box ( { 0. } )
scanConvertAnswer2SD s_inputFile s_outputFile
scanConvertAnswer2SDexact s_projName s_inputFile s_outputFile
scanCovModLig
scanCysBridges auto rs_1 rs_2 ( a_NULL./ )
scanDbMakeSubstLib s_dbIndex s_dbType ("mol") s_smileFile ("") s_smile ("Cc1ccccc1") i_in (2) i_out (1) l_add_hydrogens s_out_smiles_file l_interactive (yes) s_exclude_smiles ("") s_exclude_smiles_overlap ("") s_exclude_smiles_nonoverlap ("")
scanDsExtras s_hitlist s_mode
scanDsFragmentExamples s_projName s_hitlist s_pdbs
scanDsHit s_projName s_hitlist i_index l_dsHbond l_light (no)
scanEvalAPFsimil &r_diff
scanEvalAreaChange &r_diff
scanEvalHbondGraph &r_diff
scanEvalLigand
scanEvalNN &r_score
scanEvalReceptor
scanEvalRecognition s_hitlistwc ("") s_classcol ("") s_pKdcol ("") r_pKdcutoff (5.) s_DockScorecol ("Score") auto
scanEvalVolNoOverlap &r_diff
scanEvalVolumeChange &r_diff
scanFilterHitlist s_objFileName s_outPrefix ("top_") i_top (100) auto
scanInitStandalone s_projName s_hitlist
scanLoadStack s_stackFile s_recSpec l_complex
scanMakeHitList s_projName s_objFileName s_listName ("HITLIST") l_import2DfromDB (no) l_makeUnique (no) l_import3D (yes) i_topScored (0) auto
scanMcDock i_mncallsMC l_trajectory (no)
scanMutations rs_ S_mutations l_append (no)
scanOpenInLigedit s_hitlist i_row
scanOptLigand i_mncallsMC
scanOptRecProton
scanOutputFilter s_inObjects ("DOCK1_answers*.ob") s_suffix ("filtered") as_donors ( a_NONE ) as_acceptors ( a_NONE ) r_solubilityEnerCutoff ( 99. ) r_newScoreCutoff (0.) r_newMFScoreCutoff (0.) r_mmffStrainCutoff ( 999. )
scanParaCollect T_res
scanPrepConstraintOb
scanPrepLigPosStack
scanPrepMaps s_nameRoot l_smooth
scanRelaxCovComplex &r_dev
scanRelaxLigand s_projName s_hitlist i_index
scanSaveHitListICB s_hitlist
scanScoreExternal ms_receptor ( a_1 ) ms_ligand ( a_2 )
scanScoreInteractive s_projName ("DOCK1") os_ligand ( a_ )
scanSetConstraints
scanSortSolutions s_inObjects ("DOCK1_answers*.ob") s_outObject ("sorted.ob")
scanStandaloneHitList s_hitlist
scanStoreObject s_inputSDF
scanTemplateFilter as_template (a_) s_inObjFile ("DOCK1_answers1.ob") s_outObjFile ("DOCK1_answersFilters.ob") r_cutoff (2.)
searchObjSegment ms_ i_MinNofMatchingResidues (20) r_RMSD (5.)
searchPatternDb s_pattern ("?CCC?") s_dbase ("SWISS")
searchPatternPdb s_pattern ("[LIV][!P]AAAA$")
searchSeqDb s_projName ("sw1") S_seqNames ({""}) r_probability (0.00001) l_appendProj (no) s_dbase ("SWISS")
searchSeqFullPdb s_projName ("pdb1") r_probability (0.01) l_appendProj (no)
searchSeqPdb s_projName ("pdb1") r_probability (0.01) l_appendProj (no)
searchSeqProsite seq_
searchseqdb auto &seq_query s_blast_file ("/data/uniprot/spfas" )
selchain auto os_ ( a_ ) s_keep ("")
seq2chem s_seq l_2D (yes)
setApfTypes
setBPcnNA rs_1A rs_1B
setBondType i_type as_1 as_2
setChainOrphanHets ms_
setLigandBoxGrob s_g_pocket ms_lig os_rec l_orient r_margin
setLigandBoxSelection ms_lig os_rec l_orient r_margin
setPharmProperties as_at r_tolRadii i_type
setResLabel
setScheduledICBIndex S_dirs l_saveToCron (yes) l_runNow (no) s_password ("") auto
set_icmff auto r_vwSoftMaxEnergy (4.)
settz as_ M_xyz r_radius r_weight
settzparam as_ r_radius r_weight
shakeLoop as_loop s_args ("") l_keep (no)
shakeProtBG rs_2sample r_thoroughness (1.) r_vicinity (15.) r_temperature (600.) l_SCOnly (yes)
shiftResidueLabels2SidechainTips auto rs_ ( a_*.A )
siteScanBG as_site s_tag s_db ("") l_rapid (yes)
siteSuperAPF auto as_lig1 as_lig2 s_tag ("")
slide2view i_slide
slidesExportToMovie s_outputFile i_sillFrames (100) i_smooth (2000) i_blend (1000) i_rock (0) auto
smoothMaps s_na i_ini
solveCubicEquation r_a r_b r_c
sortSeqByLength
splitAlter as
splitByChain ms_ l_delete_source (no) l_fixOrphans (no) l_retainFirstOnly (no)
stackExportToMovie os_obj s_outputFile i_ncycle i_frames_before i_frames_after s_opt ("")
stackFilterConf os_ ( a_ ) r_rmsd (0.5)
standardizeTautomers &P_m l_pKa (yes)
substLigandBrowserMode s_tab i_row
superimposeSelection os_templateObj l_all
swapMaps s_na1 s_na2
switchChirality as_atom
symAxis os_in ( a_ ) i_nChain (1) l_display (yes) l_align (yes)
tTest R_sample1 R_sample2 r_mu0 (0.0) r_confidence (0.05) s_tail ("2sided") l_paired (no) l_varEqual (yes) auto
test_header
test_sdf ms_
torScan vs_1 r_step (5.) l_optPolar (no) l_reverse (yes)
torScanQM vs_1 r_step (10.) l_optPolar (no) l_reverse (yes) l_dontrun (yes) s_gamessPath ("/usr/local/gamess/rungms")
traverseTree s_nk s_fu l_sort (no) l_up (yes) i_root
treePointLayoutFractal s_nk I_s I_b i_rd
treePointLayoutWheel s_nk I_s I_b i_rd
treeWheelLayout s_nk i_root ( 0 )
trimMapSelection m_map as_
tryMut ms_rec (a_1) s_mutStr ("") l_optVic (no)
updateLigandEnv ms_lig l_set
updateLigandEnvDisplay ms_lig l_on
updateLigandInfo
updateLigandScore ms_lig r_score r_strain r_nn_score l_autoRecalc (yes)
updateLigandStrain l_keepStrainObj (no)
updatedfa s_dir ("") P_parameters (Collection()) auto
updatedpc s_dir ("") P_parameters (Collection()) auto
visualizeAPF l_display_box (yes) l_header (no) auto
visualizeAPFm l_display_box (yes) l_header (no) auto
visualizeNM as_ i_Nmodes (10)
visualizeQSARatomType s_atomKind r_level
viz_apf
waterDisplacement as_ligand s_tabName ("AQUASITES") r_distCutoff (1.9)
wrSeqAli ali_ s_file ("seq.fasta")
writeProject s_projName ("newProject1") l_force (no) l_system (no) s_args ("") i_ver (0) auto
Similar to DataFrames in Pandas Python, ICM can iterate on Table objects to facilitate control. Of course, they can be built from scratch assigning Parray,Sarray,Iarray, ... , some macros can avoid the tedious process. Usually, the tables were intended as a calculation of properties, but the structure/data of these tables can be reused in other calculations.
- Pairwise Distances
calc_short_distance_table a_//ca&a_/510:533 5.0
- Headers: [atom1, atom2, dist, res]
- This macro calculate all nC2 pairwise distances within atom selection and only record pairs that are within
5.0angstrom.- Facilitate assignment of
drestraintse.g. of a local helixcalc_short_distance_table a_//ca&a_SH/&a_/510:533 5.0
-
Residue Table
calcResTable Res( a_5w0pNoT506End.PTH1R ) a_NULL./ -
Internal coordinate
s_out = "IC_" + Name( a_ )[1]$s_out = Table( v_ & ! V_//V )add column $s_out Count( Nof( $s_out )) name="i" index=1group table append $s_out header Replace("#b_Apply (set object a_" + Name( a_ )[1] + ". ; set v_ & ! V_//V "+s_out+".Value[ "+s_out+".i ] )\n#b_Update ("+s_out+".Value[ "+s_out+".i ] = Value( v_ & ! V_//V ))" "#b" "# b") "cursor"set property $s_out header
- Chain Extension by Sequence
delete a_mdl. & a_*.//vt*if(String( aln_1 )=="align" )s_out = "align"if(String( aln_1 )!="align" )s_out = Name( aln_1 alignment )buildModel1 sp_Q03431_PTH1R_HUMAN a_5w0pNoT506End.b ( no )? Obj( a_5w0pNoT506End.b ) : a_NONE. s_out 100 1 6 1 no no { "" , "" }
- This is an extremely powerful ICM macro. Basically, what it does is that it takes
sp_Q03431_PTH1R_HUMANas template sequence,a_5w0pNoT506End.PTH1Ras template model,aln_1as alignment between model the sequence and output a model with padded N- and/or C- terminus extended by an assigned number of residues e.g. (0,5).- The output model topology is guaranteed valid. We may then optimise the model accordingly.
- It can also pair with other functionalities (e.g. EM density restraints) to extend model one residue per chain at a time. And of course, extended single chain models can be re-assembled and incorporate the rest of the multi-chain model.
- Note a few caveats
- All phosphorylations are lost after this step
- Residue number has to be corrected after this step
- Phosphorylation
mutateResidue Res( Res(as_graph) ) & a_A Trim( "sep" , all)
- One of the big kudos of ICM modelling is that it is packaged with all sorts of difficult decoration (peptide/nucleotide/sugar)
- Regularisation
- After optimisation under artificial constraints, regularisation is recommended to assure correct ramachandrans (and obviously omega angle). Note that even though the monte carlo of ICM carries regularisation procedure, if no conformation was accepted, then correction would not be saved in the resultant structure.
if no thens_out = "l_info=no\nregul " + String( Mol(as_graph) ) + " '" + "nter" + "' '" + "cooh" + "' " + String( yes ) + " yes\n"fixQuotes( s_out )run_bg s_strRes String( Obj( Mol(as_graph) )[1] ) "a_"elseregul Mol(as_graph) "nter" "cooh" yes yes
- Optimization of Rotamers, Tautomers, Hydrogens
- These are useful commands to optimize selected segment of structure
optimizeHisProAsnGlnCys a_/hi*,asn,gln,cysoptimizeH_zeroOcc rs_opt l_optimize_his l_dyn_protoptimizeHeteroTautomer a_H``
currentDockProj.S_projects=Unique(Sort(Replace( Name(Sarray( s_out + "/*_gc.map|*.dtb" directory sort simple )) "_gc*" "" )))scanMakeHitList project_name obj_file hit_file_name no yes yes 0