ICM Manual v.3.7
by Ruben Abagyan,Eugene Raush and Max Totrov Copyright © 2013, Molsoft LLC May 16 2013
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[ last-release ]
In this section we keep track of all the latest changes in different modules of ICM.
Version 3.7-3b May 16 2013
- added search in POCKETOME option to the main search bar
- added clsuterTableApf macro
- Wire color is not saved in ICB file. FIXED
- Wire thickness is not saved in ICB file. FIXED
- Fixed inability to drag distance labels after changing font.
- added R/S labels display in the 3D ligand editor
- added optional normal vector argument to Grob( "ELLIPSOID"|"TORUS"|"CYLINDER" ...)
- plot labels now support '\n'
- fixed bug in title label for histogram plot with multiple series.
- icm.gui 'REQUIRED' checks for empty selection
- KNIME nodes v1.01 (Ligand selection in MolDockPrep module, new options in the MolDock module )
- Added Nearest Neighbor model. (`learn{ lean type="nn" })
- added support for MOL V3000 extension format.
- optimized core replacement search speed
- added blob support in the shell
- UTF8 encoding support in the terminal
- Column format dialog works with column selection.
- OpenMP support nProc variable to toggle internal parallelization of ICM commands.
- Fixed bug in read grob from URL
- Fixed bug in write matrix into ICB file (if rows were reordered)
- Collection( table ) and Table( collection ) were added
- Added the ability to use ICM built-in functions in the function section of the add column function command
- makeIndexPdb macro also builds PDB ligand table which can be search by substructure from the PDB search bar (just paste smiles or use molecular editor)
- Added COLOR preferences (accessible through GUI Preferences dialog)
- Detachable tabs with tables, alignments and other objects. (Drag the tab outside and it will become a separate window).
- Index( alig as_ )
- alig[ I_index ] non-continuous sub-alignment
- added support for optional ph4 features and constraints
- added 'onSelectionChange' object named field to assign actions for selection changes in 3D
- added ability to link mesh to the object for simultaneous rotation, superimpose and display.
- added scanFilterHitlist macro to quickly filter large docking hit lists for top scored hits. (Integrated into main scanMakeHitList macro and corresponding GUI dialog)
- optimized read object for big files.
- added $ support in index expression. (refer to the last element of the array)
- Fixed bug in Date to String conversion. (week of the day and related fields are OK now)
- Added conditional expression support a?b:c
- Added 'delete query' option to modify chemical command to clear SMARTS search attributes.
- logical expression shortcuts: if ( Nof(A)>=5 & A[5] == 1 ) ...
- added 'term' option in macro declaration: saves and restores energy terms after return from the macro
- balloon tooltip for cluster nodes (Right Click/Change Record Labels to specify list of columns in the dialog)
- better docking convergence in the Ligand Editor
- LIGAND.displayDockingMoves is set to 'no' by default
- new Area/Volume distribution for icmPocketFinder plot
- comments for stack conformations. ( set comment store conf Name conf )
- Initial stack of ligand positions before docking in the ligand editor
- 'MolArea' model is added to calculate accessible surface are for 2D chemical. Predict( Chemical("CCCCO") "MolArea" )
- File.ICM Session.New/Clone added.
- JavaScript errors are printed to the terminal
- added Image( X_Chemical )
- covalent ligand support in the ligand editor.
- added triple-quote string constants (arbitrary length and content text can be easily used as string constants)
- make tree object fills "ORDER" atom field which corresponds to the original atom order. (can be used to assign various properties)
- added Chemical( R_react ) and Chemical( X_chem, reaction ) to convert reaction to chemical and back
- write image chemical supports HTML5 canvas export and does not require X11 connection on Linux anymore (can be used in various batch scripts, CGIs, etc. )
- added Info model function to return prediction model properties.
- added Split( [i_minSize] [i_maxSize] bond ) to split molecule into a various fragments
- speed improvements in enumerate tautomer command
- Added String( macro all ) to return macro source and all dependent macros.
- Added String( X_chem html ) String( w_img html ) to export chemicals and images into in-line html representation
- HTML5 canvas support for 2D drawing. (chemicals,plots,alignments,etc. ...)
- read json now accepts entries with multiple roots. (array on the top level)
- XML parser treat comments and CDATA correctly.
- added Select by alignment function
- fixed bug in select-alignment
- allow to use ICM user-defined functions in add column function
- _dockScan script is KNIME compatible. Added _dockProjPrep script to prepare docking project in the KNIME work-flow.
- new sugar view in the workspace.
- assign residue command
- Easy selection finder in the alignment ('Highlight Selection' checkbox in the tools panel)
- Balloon popup over plot elements. ('tooltip' option in the command line + GUI element in the dialog). See make plot
- LIGAND.displayDockingMoves option to control display of montecarlo moves in Ligand Editor docking.
Version 3.7-2e
- fixed rendering of down bond for scaled down compounds
- fixed false interpretation of '$' in single quoted strings
- quotes are processed properly in dialog input elements
- JSON parser accepts array as a top element: Collection( "['a','b']" )
- fixed atom naming in llp residue according to PDB convention
- Interrupt button cancels read from url
- grob clipping works with wire and dot representation.
- Fixed read pdb with 'non-standard' hydrogen names
- Optimized speed of the write map command
- Fixed inverted stereo in problem after "Extract ligand" in some cases.
- Mouse wheel in the workspace scrolls again.
- Fixed display of the variables in the Ligand Editor: Display Strain
- Fixed bug in copy/paste of single table column with empty rows.
- HTML tags from column format are not exported into SDF file
Version 3.7-2d
- Added docking hitlist filtering macro to get N top scored poses. scanFilterHitlist. (The option is also available in the GUI "Make hit list" dialog)
- fixed bug in Formula for structures with no hydrogen.
- Removed unnecessary ligand surface rebuilds in the Ligand Editor
- Fixed bug in display slide when skin representation wasn't preserved.
- Index( X, X atom map function is added to find atom number correspondence between two chemicals
- fixed nested index access to collection
- Fixed crash in make map potential
- Unix and Mac: "Save project As" works if path contains spaces.
- Windows only: -R option sets stdin/stdout to binary mode which makes possible to use pipe-able scripts in KNIME nodes
- fixed numerical instability in minimize
- fixed bug in make reaction
- _confGen and _chemSuper can be used in unix pipes and KNIME nodes
- Min/`Max functions work with datearrays
- Fixed bug recently introduced in IcmSequence function
Version 3.7-2c
Major new Features:
- New linker and core replacement tool in the 3D ligand editor
- Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm).
- Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe\*.icm)
- copy/paste and drag'n'drop between icm sessions ( images, molecular objects, meshes, tables )
New Features:
- Added Collection( t|t.column format ) to get the various column properties as a collection object.
- Added Table( model chem [inverse] ) function.
- reading large file by chunks ( read file by chunk ) now supports zipped file.
- Score( X_3Dn [ X_3Dm ] [similarity|distance] ) → M_nxm apf_scores normalization of apf cross-scores.
- added option=s_filename argument for make plot command which allows one to generate plot images in the batch mode.
- added PDF/EPS format for saving plot as an image.
- rename of the object/mesh/map keeps slides and distances in consistent state.
- switching the receptor conformation in the ligand editor rebuild ligand and pocket surface if they are present
- Nof( fork ) is added to get the number of available processors
- pipe options is added for fork command
- a_SLIDE. selection is added. Returns list of objects used in slides.
- learn remembers columns calculated with add column function to automatically recalculated in 'predict and Predict
- _chemSuper supports input from pipe.
- Slides now remember the conformation from the object's stack
- Added stack option for read mol command.
- read mol can read directly from chemical array
- Score( as_ as_ field ) and Score( chem_array field ) are added for APF clustering
- Added stack option for read mol command to read SD file with multiple conformations as an object with a stack.
- Added export alignment to PDF or EPS. (Right click "Save/Export To Image/Save Image")
- Added support of the APF ligand based project in the 3D ligand editor.
- Srmsd( .. .. [weight|chemical] matrix ) returns sarray of static RMSDs or, with option weight, superposition errors computed according to the TOOLS.superimposeMaxDeviation (consistent with r3_out of superimpose minimize )
- Volume( R6 box )
- Table(residue) now returns residues from the icm.res and usr.res libraries. New residues added for
CME, CSD, CSO, HYP, KCX, LLP, PTR, SEP, TPO, TYS, and CIR modified amino acids.
- read binary pdb s_4letter_code to read .icb files in pdb-style subdirectories according to the s_xpdbDir root (also extended to allow http , e.g.
s_xpdbDir = "http://xablab.ucsd.edu/xpdb/"
- term ts , TOOLS.tsShape and TOOLS.tsShapeData to allow soft penalties for atoms moving outside certain shapes (sphere, box).
- String( s [16|32] key ) (hash function generating 8-character long keys) fixed; String( s hash ) added to generate stronger keys of length 26 or 32
- added coloring for cluster nodes (heat maps)
- added Index compare function to compare different arrays
- parray supported as collection elements
- plot rendering speed is optimized significantly.
- added 'add exact' combination for make grob map command to allow absolute increment
- delete command works directly with index expression in collection (delete c["aaa","bbb"])
- individual atom ball&stick radius.
- added ability to read large portions of data by chunks ( see: read file by chunk )
- added ND word. (for non-defined )
- Added HTTP.cookies collection to allow easier control over http cookies.
- GUI access to molecular named fields (see set field)
- added image rendering for 2D labels
Bug fixes:
- fixed bond removal in cyclopeptides in convert command.
- fixed crash in build tautomer command
- Fixed bug in map contouring with large buffer size values.
- Fixed bug in skin rendering in display stack
- Fixed bug in readUniprotWeb macro when l_references is 'yes'
- Fixed bug in "Filter Graphical Selection" dialog
- Fixed bug in S_ ~ s_ and S_ == s_
- Fixed rare crash in mc
- fixed bug in cis/trans smiles generation ( when cis or trans bond is a ring closure bond )
Version 3.7-2b
- Fixed permission issue in Molcart on MySQL 5.5
- added output= argument for all show commands which allows one to grab the output for further processing.
- Improved rendering speed of xstick representation
- Fixed cis/trans depiction for R-group substituents in enumerate library
- Fixed memory few memory leaks when working with tables in macros.
- Fixed chemical formula generation for isotopes.
- copy/paste multiple cells from Excel into ICM spreadsheet.
- Fixed crash "Changing the final row in a filtered column crashes ICM" bugzilla: #697
- Fixed crash in pasting a column in the table with plot.
- XML parsing functionality. read xml, Collection, xml drugbank example
- fixed incorrect cis/trans bond interpretation in smiles. ( (\R)C=C → R/C=C )
- new attachment point rendering style
- fixed parsing bug in cell hyper links ( set format )
- fixed "interrupted system call" error in read http.
- chiral centers with an R-group attached are correctly treated (stereo is preserved by parity) in make reaction.
- smiles property for sarray columns in a table. Toggles on-the-fly 2D chemical depiction.
- Fixed bug with non-preserving center of rotation in slides after clipping planes were moved. (also fixed in activeICM 1.1-5)
- Multi-receptor support in the 3D editor
- make reaction allows arbitrary R-group numbering
- multiple drag-able resize-able images in set background image command
- added 'Unlock ICB' function which clears read-only or password protection from ICB without reopening it.
- fixed few bugs in with password protected ICB files
- removing salts with modify chem delete salt
- preview for ICB files (Windows browser + ActiveICM)
Version 3.7-2a
- single quote string constant support.
- reader.icm script
- Logical(r|i|s)
- GRAPHICS.cpkClipCaps preference (1,2,3)
- SolveCubic( a,b,c,d | R_3|4 [all] ) → R, SolveQuadratic( a,b,c | R2|3 )
- fixed overlapping shaded and bordered boxes in alignment view. All view preferences now stored in ICB.
- WebKit integration is added
- other types of occlusion shading added ( TOOLS.occlusionColorStyle = "dark outside" or "light outside")
- fixed bug with opposite rotation of connected molecules/objects or grobs
- delete sequence nucleotide|protein|peptide
- fixed rdpdb for consecutive atoms with identical coordinates, e.g. 1a69, ds skin molecule,
- Nof( bond [error]) Nof( selftether [error] ), Select( selftether [error] ), Select( bond [error] )
- selftether treatment: set selftether , delete selftether , Srmsd( as selftether ), minimize "ts" , replaced tether= by selftether= in minimize montecarlo ; convert to set selftether
- improved convertObject (protonation of a_/U, minimize "ts" for the convert deviants)
- added output option for Rmsd and Srmsd function to store individual deviations into R_2out
- grouping by table column works with ND values correctly in aggregation operations.
- write gamess to write correct Z-matrix, memory limits.
- TOOLS.membrane, update icm.hdt, surfaceMethod="membrane" supported in Area( energy) and energy evaluations.
- bug with residue names for residue names starting from a leading blank after reading some pdbs fixed. (previously was breaking 1ytw,2i42,3f9a,2i4e,1kpe)
- CubicRoot(|)
- bug with crashes in find database fixed
- improving find database results (prioritize SC for HUMAN, ECOLI, BOVIN etc. in case of identical scores)
- a_J selection to filter short peptides.
- Name(sequences) returns an empty array (not error) when there are no sequences
- set column format supports internal ICM links.
- exclude and number options for learn atom command.
- set atom named fields is added
- anti-aliased and scalable fonts (atom/residue labels,etc) in 3D for windows and MAC
- Pattern( rs ), selections a_/Bbarcode_like_A12L2L and a_/Qbarcode
- translation to a destination point for a molecular and object selections (see translate )
- new 2D compound rendering option: color rectangles on hetero atoms instead of atom labels. See set property chemical view
- fixed crash in Askg
- new Iarray( a_// topology ) function
- new align sequence command (align number .. )
- new Select_by_sequence function
- find molecule sstructure drestraint ms1_inIcmObj ms2_inTheSameIcmObj added to set drestraints by chemical similarity
- delete link alignment ; link ms_ rewritten, many options added. autoLink action improved.
- join by structure column ignores hydrogens (3D can now be joined with 2D structures). stereo off option is added to ignore chirality.
- copy/paste and drag'n'drop between icm sessions ( images, molecular objects, meshes)
- build tautomer and set tautomer can be applied to HIS residues
- ND support for individual real values
- large 64 bit integer support for integer variables
- Grob( "cylinder", r_ra r_H )
- arbitrary length atom labels and ball radius (`set-label-atom and set atom ball command)
- search functionality in preference dialog.
- restore preference command is added (allows one to set system preferences and variables to default values)
- date type is introduced
- new annotation style for alignments
- Charge/protonation state prediction using pKa model
- pKa predictions for bases and acids (`set-charge-auto command )
- GUI parser patched and icm.gui cleaned from in-line argument declarations to allow natural command syntax (the percent symbol, like %i_out , is no long needed ) in dialog descriptions
- option to avoid sampling His, Gln, Asn, etc. and hydrogens upon convertObject added (allows one to keep atoms as is)
- concurrent multiple level contouring (with multiple colors) of distant density added
- read pdb improved to recognize unusual amino acids
- mmff treatment of two nitrogens in a fused aromatic ring improved
- set field can be used with alignments
- set color alignment is added
- Header(grob)
- make distance append behavior corrected (tool first order). Option make distance append P_atompairs .. added.
- superimpose P_atompairs os_movable command added
- set tether P_atompairs os_movable command added
- Area( grob error ) returns the percentage of unclosed area (to detect surfaces that are not fully closed)
- Volume( grob ) returns the percentage of unclosed area in r_2out
- copyMol, moveMol and jumping molecules
- not properly recognized chemical templates in 2D chem drawing
- unusual amino acids are not recognized ( 2jge )
- mmff treatment of two nitrogens in a fused aromatic ring problematic
- adding ligand (without receptor) to the table causes icm/C5H5N> processLigandSave Error> [2191] index 1 of array out of range [1:0]
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