[ last-release ]

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]