ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Aug 16 2018

Contents
 
Introduction
 Release
 History
 Contact
 Overview
 Conventions
 Abbreviations
 Intro
 Scripting Tutorials
Reference Guide
Command Line User's Guide
References
Glossary
 
Index
PrevICM Language Reference
Release notes
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[ last-release ]

In this section we keep track of all the latest changes in different modules of ICM.

Version 3.8-7a Aug 16 2018

  • make reaction supports nProc
  • Added aromatic contact column in icmPocketFinder which contains percentage of the area exposed to aromatic rings
  • Added TLS v1.2 support for https connections
  • large file (>2.2GB) support for ICB (64 bit directory)
  • fixed bug in memory allocation of large matrices in buffer (e.g: when return from function)
  • Improvements in pKa model
  • atom-mapping number field is translated to R-groups when reading reactionfrom RXN
  • more robust connection to some SSL servers (e.g: uniprot) ("Remote host closed connection" problem)
  • Improvements in Enamine REAL DB online search. (Added interface from Chemical Search space)
  • Fixed online drugbank search
  • Fixed some issues with make reaction when product contains stereo centers.
  • Fixed wrong atom priority assignment for R/S detection in rare situations.
  • SALI analysis doesn't require N^2 memory and can work on very large files.
  • added 'Ligand Efficiency' calculation into 'Insert Column Dialog'
  • fixed bug in conversion of chiral compounds from smiles with coordinates.
  • added Srmsd( X_3D_chem ), Srmsd( X_3D_chem1, X_3D_chem2 ), Rmsd( X_3D_chem ) and Rmsd( X_3D_chem1, X_3D_chem2 ) for cross RMSD matrices.
  • Torsion customization ( 'totc' in mmff.tot ) now finds overlapped fragments.
  • Random Forest classifier supports multiple classes now. (97% accuracy on MNIST digit recognition test http://yann.lecun.com/exdb/mnist/)
  • Improvements in 2D depiction.
  • Fixed Score( X, X, field ) which return individual APF field components.
  • "Chemistry/Select Duplicates" allows to select by non-chemical columns.

Version 3.8-7

  • New functionality/Improvements
  • Standard way to install/update/remove ICM extensions. (File/Extensions)
  • added topological descriptors into Chemistry/Calculate Properties (http://molsoft.com/icm/icm-functions.html#Descriptor-numeric)
  • improved torsion rotation tool (changes cursor and shows angle on mouse-over)
  • Improved datesupport (GUI to convert, option to parse dates during import from SDF or CSV)
  • Added bioisostere replacement in Ligand Editor interface (Advanced/Find Bioisostere)
  • Updated bioisostere database
  • Self Organized Networks for chemical space visualisation
  • added options to ignore chirality and charges in joining by structure ('Edit/Table/Add External Columns' Dialog)
  • Added 'ECFP' option for fingerprints in clustering and PCA analysis.
  • Improvements in learn atom for pKa prediction
  • Added 'Tautomer Search' option into Chemical Substructure Search. (See also: find table find molcart )
  • New modern HTML template (no frames) for exporting to IcmJS html page.
  • Add ability to color plot using aggregate functions
  • read pdb automatically switches to MMTF (`read-pdb-mmtf) if the entry is not found in PDB format (usually large entries)
  • Added support for semi-chiral centers around flexible rings
  • Improvements in linker substitution in the ligand editor.
  • ability to specify low/high confidence intervals in Plot Options Dialog.
  • Added new options to 'Link Column Dialog' ('select matched' and 'show only matched')
  • New fonts on Linux in 3D (supports arbitrary sizes and anti-aliasing)
  • New functionality scripting
  • String( tree ) uses an exiting tree attached to the alignment.
  • added operation ( t.bit_column ~ bit_pattern )
  • added Nof( "maxFusedAromRings" )
  • Added Collection( chemical )
  • added charge option for build tautomer command to add charge state enumeration
  • added Index( as_ tautomer ) function to return current tautomer state. Takes two arguments: x : current count, y : chain length. E.g: function = "x**(0.5-0.5/y)"
  • added 'concat' aggregation function for group column command. Values with the same key will be stored in the array in each cell. (`split-column is opposite operation)
  • added new option for covalent docking project l_covMultiple which allows to try multiple covalent mechanisms for single compound.
  • Added function=| argument to learn and learn atom commands. Can be applied to counted fingerprints.
  • Bug fixes
  • fixed bug in "Docking/De-novo Tools/Scan Fragment" (Windows only)
  • fixed bug in aromaticity detection in certain ring systems
  • increased number of atom selections ("too many selections created already" error should be more rare)
  • fixed bug in Min( alig, seq )
  • fixed 2D to 3D conversion macro to avoid getting wrong chiral conformation
  • fixed incorrect zoom in the spreadsheet scaffold view.
  • Fixed freezing of 3D on Intel graphic cards. (GL_FEEDBACK mode)
  • Excel import (importExcel macro) improvements and fixes.
  • fixed hydrogen position in build hydrogen command for certain cases

Version 3.8-6a

  • Fixes and improvements in pKa models
  • Fixed freezing of 3D on Intel graphic cards. (GL_FEEDBACK mode)
  • fixed problem in read "https://...."
  • Insert/Calculate Column Dialog: 2DFrom_Smiles now correctly works with string column displayed as 2D.
  • Fixed freezing in range color dialog on Mac
  • Fixed bug in atom charging in Ligand Editor

Version 3.8-6

  • added inverse option to set chiral chemical. Inverts chiral centers.
  • added sequence accessibility information to alignment view
  • Selection propagation between 3D and 2D ligand diagram.
  • Table tools panel widgets can be arranged in two rows.
  • Advanced column coloring dialog
  • Added menu Chemistry.Superposition.Rigid Substructure Superposition to Template.
  • fixed issue with fork command. (child may hang in certain cases on exit)
  • Support for special values ( > ND, INF etc) in real arrays for Shuffle and show column added.
  • fixed bug in set charge formal auto so it does not clear positive charges which come from valency rules.
  • Chemical structures can be drawn as labels on plot axis. (smiles or chemical column can be provided)
  • Bioisostere search tool supports linker search and replacement
  • importExcel macro to import 'xlsx' file with embedded images.
  • 'minimize' option to find maximum common substructure command (used in MMP)
  • Chemical structures on plot axis labels.
  • Rich text support in axis and plot titles (Greek letters, bold, italic, superscript, etc.)
  • Pie chart style for both histogram and plot modes.
  • New chemical functions for Chemical Properties dialog:
    • pKa of Most basic or acidic group
    • MolCharge negative,positive or total at given pH
  • Chemical search dialog work with reaction tables.
  • Markush enumeration and filtering: auto completion for filter functions, ability to extract built-in R-groups
  • Options to keep header and grid in spreadsheet printing.
  • Move table column popup menu
  • Metabolic oxidation prediction model (Chemistry/MolScreen)
  • Improvements in SALI analysis (bug fixes and plot)
  • Improvements in chemical pair analysis (score and plot)
  • Find isostere by single atom replacement scan.
  • Find bioisostere groups and linkers (right-click chemistry)
  • reorder numerical columns by clustering
  • basic CDX format import support
  • added out-of-bag error estimate for Random Forest prediction model
  • improvements and bug fixes in 2D smiles depictions make flat
  • align by scaffold improved: make flat added pattern=X_scaffold argument
  • template (substucture and apf) support in the Ligand Editor
  • added charge option for build tautomer command to enumerate charge states (see also enumerate charge)
  • point label size control in plots
  • multiple curves in plots
  • matched pair analysis (chemMatchedPairs)
  • covalent docking hitlist: covalent residue is shown
  • Replace( , ) # efficient replace by dictionary
  • biomt support for MMTF (read pdb mmtf "4tvp")
  • option to show rainbow in chemical cells for color chemical command
  • background job finish dialog is non-modal now. (fixes the problem when multiple jobs finish in the same time)
* Table tools panel widgets can be arranged in two rows. * Advanced column coloring dialog

Version 3.8-5a

  • fixed bug in read table in CSV or TSV format when large integer numbers were truncated.
  • fixed crash in right click in table tools area
  • fixed crash when reading some PDB with small default buffer size
  • fixed PubChem services (http -> https)
  • fixed bug in Structure to Name conversion.

Version 3.8-5

  • Collection( ) collection with translation dictionary
  • Replace( [] ) translation operation
  • delete residue automatically adjusts internal alignment with construct sequence
  • Auto close mode for clustering tree (Right click: Preferences)
  • Fixes in assign residue (works with cyclic peptides and unusual amino acids)
  • residue field "_WORMRADIUS_" for variable thickness ribbon cylinder.
  • auto save dir is moved into $s_userDir/bak
  • fixed freezing in few places with modal file open dialog on Mac
  • selftethers: individual self tethers to a box defined by TOOLS.tsShapeData and Z-only mode
  • residue contributions from bonded MMFF terms
  • side display/undisplay individual buttons.
  • fixed bug in setting sequence type when load PFAM alignment
  • new maximum common substructure algorithm. ('sstructure' option for make tree to calculate common substructure for cluster nodes)
  • heatmap in plot area
  • Initial support for new pdb mmtf format (read pdb mmtf)
  • 2D ligand interactions diagrams
  • Entropy( R_frequences [ | R_energies r_RT ] ) is added.
  • Entropy( seq_ [simple|R_26res_prop] ) is added.
  • Added argument to InChi function. (InChI_API_Reference)
  • fixed bug in Map() function which may produces broken maps from crystallographic sources.
  • rotate and transform translate support linked meshes.
  • clustering make tree of very large data sets is possible. (fixed bug in make tree command)
  • Score(X_chem_n X_chem_m set ) and Distance( .. ) to calculated similarities and distances between chemical sets
  • read gui command to load user-defined menus
  • added HTTPS protocol support for read commands
  • format for label in the compressed chemical view TOOLS.chemicalGroupSubstFormat
  • Added "Edit/Auto Assign Charges" function in the molecular editor
  • Added "Modification History" table in the ligand editor
  • Control of Z-shift of residue labels (resLabelShift)
  • improved coloring by residue type
  • alignment panel: ability to select only visible blocks (and not select the hidden ones) with one swipe
  • alignment panel: ability to generate pseudo sequences from multiple alignment blocks (e.g. pocket)
  • Hetero and R-group scan in the Ligand Editor
  • binary read/write for profile objects
  • dynamic load of table cell from URL (image or HTML. 'set property load t.col')
  • few fixes in chemical depiction
  • retina support on Mac (no package yet)
  • svg export support for alignment and plots
  • read sequence swiss records the 1st res. position after signal peptide or 1 in i_2out
  • Cleaned drag'n'drop behavior. ( grob can be dropped on/from objects to link/unlink them )
  • 64 bit package for Windows
  • Distance( ~r_dist_0to2|M evolution ) returns Dayhoff corrected sequences
  • Color( M_Nx3_rgb [ name ] ) # changed to generate hex colors (e.g #ffaaff ), the old mode under the name function. also to support four hex formats for color ( #rgb, #argb, #rrggbb, and #aarrggbb ). formats #argb and #aarrggbb start from the alpha-channel (transparency) value.
  • Sequence( ali ) to return a parray of sequences from the alignment; Sequence ( ali group ) - an average sequence. Warning: the default changed. Previously Sequence ( ali ) returned an average sequence.
  • Sequence( S_seqNames name ) to return a parray of loaded to ICM sequences by name
  • Sequence( S_seqStrings S_seqNames ) create new seq. parray
  • Table( s_dot_svg plot ) # parsing an svg file with a graph of nodes and edges into table for resorting
  • makeSeqGraph : making 2D sequence maps. macro to generate input for network viewing.
  • realignBlock : improvements (allow empty sequences, improve parameters)
  • rotateView macro: generating standard view arrays

Version 3.8-4b

  • Non R/S chirality is preserved in reactions

Version 3.8-4a

  • Fixed memory leak in _dockScan (if ran with -s option)
  • Fixed crash in delete sequence from alignment
  • Fixed bug in binary write of objects with selftether
  • Corrected formal charge calculation for atoms with attachment points
  • Fixed bug in _protDesign script

Known bugs in 4a:

  • impossible to drop a sequence to an alignment with displayed tree (causes an infinite loop).

Version 3.8-4

  • Ligand Editor:
    • Close session function is added
    • Advanced/Export complex improvements
    • New distance and positional restraints
    • Added explicit flexible side-chain support in the Ligand Editor
    • Added an option to minimize ligand in full atom model inside the receptor. (in addition to soft grid minimization)
  • Mutation Design:
      Mutation.Protein Protein Binding Mutation.Protein Peptide Binding Mutation.Protein Stability Mutation.Protein Ligand Binding
  • GUI Misc
    • Added object popup "Tools.Move.Top/Bottom/Custom" to move objects in the workspace.
    • GUI.workspaceChainGroupStyle and GUI.workspaceChainGroupLimit are introduced to control the chain grouping in the workspace.
    • Feature view and annotation added to single sequences
  • New commands/methods
    • Collection( T_tab all ) and Table( k_collection ) functions are added to convert between collections and tables
    • Random Forest classifier and regression are added ( learn chemical )
    • color-molecule-chain(_MAINCOLOR_)
    • undo-store-slidecommand is introduced (push the current display state into undo stack)
    • enumerate-charge command is added to generate various protonation states
    • set-color-alignmentis added
  • Misc fixes and improvements:
    • "Docking/Export As Model" (export docking project as a single model icb file)
    • "Docking/Dock Chemical Table" supports models as a project input
    • _dockScan script supports model as project input
    • Several improvements in ECFP fingerprints for prediction models.
    • Fixed background job termination on Windows
    • added bar={ } to the montecarlo command to show the partial progress.
    • Easy molecular placement to a location with optimal distance-specified tethers added
    • Unique color added to molecule
    • Ability to split a pdb object by 'chain' added
    • original object type (XRAY,NMR,etc...) is preserved during the conversion and used in write pdb command
    • fixed bug in linker search when input file is SDF.
    • fixed bug in popup menu from sequence selection in the workspace
    • fixed bug in similarity search in MOLT files.
    • atoms radii are added to slides.
    • compress ali # remove gapped columns
    • Align ( ali dash ) # anneal frayed alignment ends
    • AlignSS ( seq1 seq2 0.1 ) # sequence structure alignment for homology modeling (eg GPCRs)
    • makeAlignmentFromSuper # structural alignment with superposition

Version 3.8-3

  • fixed crash in clustering certain large table under Windows (default stack size)
  • ND values are ignored in grouping by column (sum,mean,rmsd functions)
  • fixed crash in 'delete table' after sorting with distance matrix
  • Sort Column Dialog is added.
  • Multiple atom coloring schemes in icm.clr file (#COLOR_SCHEME)
  • Table copy/paste is improved (name preserved, allows to copy/paste row/column selection)
  • Fixed certain cases up/down bonds in 2D->3D conversion.
  • Transpose( [ ] ). (Tools/Table/Pivot Column)
  • "Test Covalent Mechanisms" is added into 'Chemistry' section of Insert Column Dialog
  • add align number chemical command
  • non-modal behavior for 2D editor in the 3D Ligand Editor
  • Linked meshes moved to the object folder in the workspace
  • Improvements in "grouped by column" view: sorting, coloring
  • Fixed crash when deleting singleton node in the cluster view
  • make-bond-chemicalis added
  • Index( connect ) returns iarray with atom numbers marked as attachment points.
  • 'Undo' support in protein sculpting mode.

Version 3.8-2

  • Fixed crash in certain combination of startup code and file contents
  • fixed sorting issues with table is dynamically grouped by a column.
  • Added HTTP.headers collection to send custom headers in http request
  • Added TCP listener mode to allow remote communications with ICM session.
  • Added GRAPHICS.atomRainbow (for cpk and xstick coloring)
  • Fixed some issues in http requests with authorization
  • Added "Flip Around Bond" operation into Molecule editor
  • Fold/unfold columns into array of collection and back
  • sort table by field from collection in the array
  • editable fields in collection in the table cell

Version 3.8-1

  • interactive collection view in tales cells.
  • configurable folders in molecular objects: "*so4*;sulfate-ion"
  • Score( [similarity|identity|.. [] ] ) extension to permit sequence identity normalized differently. The argument of 0 will divide the score/identity by the alignment length, rather than minimal sequence length. You may also specify a different number of positions.
  • calcSeqSimilarity macro for seq-in-alignment relative identities and similarities.
  • multiconf MOLT support in _chemSuper
  • Added "Stack->Movie" dialog
  • Support of multi line annotations in the alignment.
  • Added checking the availability of the newer ICM version
  • Improved "Edit/Restore Recent Backup" dialog.
  • Embedded custom models support.
  • Sequence drag'n'drop between sessions.
  • Fixed copy/paste reaction issues
  • Control of electrostatic calculation with TOOLS.rebelPatchSize (def. 1.) for find-grain calculation
  • Smooth electrostatic coloring with the heavy option in color grob potential command.
  • a table of 250 non-standard Amino Acids added and enabled for the mutation tool (make it visible with the Tools.AminoAcids menu)
  • Chemical dictionary extended for immediate.
  • Optimized dynamic group by column for large tables
  • Find chemical supports nProc
  • compress option for formatted output of real columns in tables
  • enumeration with ring formation (macrocycles) in make reaction
  • fixed bug in coloring plot by sarray columns
  • Added 'hash' option for text columns in plot
  • self containing model for APF QSAR
  • Added search in PubChem from the general search toolbar
  • sort column table is added
  • fixed repaint issue of the frozen column in the table.
  • _molScreen script and corresponding KNIME node is added. (interface to 2D fingerprint and 3D pharmacophore models)
  • SAR analysis command is added.
  • R-group decomposition supports R-groups with more than one heavy neighbor. (e.g: R1 in a ring)
  • Added MolMechanics/Try Mutation menu for protein binding and protein stability prediction.
  • Peptide builder from extended list of amino acids
  • Fixed crash on Linux when locale set to some non-English (e.g: de_LU.utf8)

Version 3.8-0

  • Export of chemical structures, alignments and plots to Windows Meta-file (WMF) now has anti-aliased fonts and smooth line connections.
  • Fixed crash on compress grob command
  • Anaglyph stereo mode is added.
  • added interface to BLAST search at NCBI (main Search bar in GUI)
  • added Extended Connectivity Fingerprints (ECFP)
  • Fixed bug with table selection in macros when table with the same name exists globally.
  • xstick transparency mask, atom and residue font size and family now are stored in slides.
  • Ctrl +/- in the table view resize the cell size (in addition to font size)
  • Chemical Search dialog allows to select an existing chemical table for Molcart or local search.
  • base html path is set correctly for commands like: read html "http://google.com"
  • Chemistry/Full Model Panel is added
  • Added macro and GUI to export object's stack as a movie. (Right click on the object: Tools/Export Stack")
  • Covalent docking in "batch" mode in the ligand editor.
  • "Find in alignment" supports wildcard patterns: N?[TS]
  • Added confidence interface visualisation in table plots. (see make plot command and GUI dialog)
  • InChI support. InChi( X_chemical [key] ), Chemical( S_inchi )
  • Name( user ) returns OS user name.
  • "copy off" option for set field command to prevent field from being copied with copy object command.
  • Added macro and GUI to export slides as a movie
  • added ToxScore function into Insert Column Dialog
  • fixed several issues with sugar molecules representation in the workspace
  • recursive SMARTS of more than one level are supported.
  • row heights are preserved in ICB file
  • added GUI interface to add image column and modify its contents
  • Fixed crash when deleting 2D label which was used in slides.
  • set type mmff on the converted object does not change aromatic bond type to pure aromatic
  • added GUI.font
  • added support for recursive SMARTS in R-group decomposition ( e.g: [R1;$(CCN)] )
  • Distance chemical supports nProc
  • Fixed a crash in 2D label edit dialog (image list)
  • Image column is exported to Excel.
  • Added the ability to add custom functions into 'Insert Column' dialog. (see gui programming for details)
  • Dynamic grouping by column
  • _chemSuper preserves original columns
  • Combined "Pretty" view from docking hit list and Ligand Editor.
  • set site alignment and delete site alignment are added
  • added simple=S_cols option for read table mol to prevent type guessing (keep column as sarray)
  • fixed some issues with HTTP.proxy
  • write image alignment and set property alignment commands
  • added support for STL mesh format (popular for 3D printing). Example: write grob g_mesh "mesh.stl"
  • PubChem CID lookup function and Insert column of pubchem CIDs into a chemical table

Version 3.7-3b

  • added search in POCKETOME option to the main search bar
  • added clusterTableApf 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 Kernel Regression 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 3.7-2f Aug 16 2018

  • "locked" objects can be copied
  • removed '*' from object/mol popup menus

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 date array
  • 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, also delete all compress
  • 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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