ICM Chemist

ICM Chemist is a standalone suite of programs for chemical drawing and editing, chemical database generation, chemical searching, clustering, and enumeration. ICM Chemist contains the features described below as well as all the tools contained within ICM Browser Pro. For additional chemistry features including a wider set of 3D chemical options, chemical superposition, 3D interactive ligand-receptor editing, and QSAR please see ICM Chemist Pro.

Chemical File Features

• Import SDF, mol, smiles, reaction, and csv format.
• Save SDF, mol, smiles, reaction, csv and export to Microsoft Excel.
• Save chemical images in PNG, SVG vector image files, and postscript format.
• Exchange files between ICM-Chemist and ISIS Draw.

ICM Molecular Editor

Draw and edit chemical compounds.

• Keyboard shortcuts for fast molecular sketching.
• A variety of fully-customizable templates to speed up chemical drawing including: bonds, atoms, amino acids, bases, bicyclics, dictionary of drug compounds, rings.
• Chemical properties are monitored on-the-fly as you sketch. Monitors are fully customizable but the default ones include: Formula, Smiles, IUPAC, Molecular Weight, Nof hydrogen bond acceptors and donors, Nof Rotatable bonds, DrugLikeness, MoldHf, MolLogP, MolLogS, MolPSA, Volume, bad groups.
• One click annotation, and highlighting of chemical groups, and bad groups.
• Assign stereocenters.
• Append molecules to chemical spreadsheets, edit chemical spreadsheets in molecular editor.
• Sketch 2D pharmacophores, Markush structures, and chemical reactions.
• Add text labels to chemicals.

Chemical Spreadsheets

Rich environment for display, manipulation and analysis of chemical datasets, from a few compounds to 100K. For more than 100K you can use our MOLT file format (see below) and /or MolCart.

• Display and manipulate multiple chemical spreadsheets.
• Custom view options e.g. table, grid, 'form'
• Find and replace in chemical spreadsheet. Chemical transformations such as charging/discharging basic or acidic groups.
• Add new entries, insert/delete column or row. Column calculators such as MolWeight() LogP() as well as arithmetics (ColumnZ = ColumnX/ColumnY)
• Copy, cut, and paste column(s) or row(s).
• Coloring by column values.
• Sorting and filtering data by column values. Label/select/show/hide rows.
• Support for columns of hyperlinks to connect to web pages (i.e. PubMed IDs, PDB etc).
• Align/color by 2D scaffold.
• Print table, individual entries, and grid view, copy/paste molecules as images. Copy/paste as SD for clipboard exchange with other programs
• Intelligent support for special cases of numeric data, e.g. "No Data", >10. , <5.
• Merge multiple spreadsheets.
• Compare multiple spreadsheets - overlap, only in first/second spreadsheet.
• Simple inline plots such as dose-response curves directly in a spreadsheet cell
• Import new data columns from other spreadsheets matched by a column (such as ID).
• Edit chemical and other data types.
• Chemical spreadsheet standardization: remove salts, remove explicit hydrogens, and standardize groups.

Chemical Searching

• Chemical similarity searching - substructure, atom and bond properties (Smiles and Smarts) search patterns , fingerprint similarity, similarity/substructure combo, and exact match.
• Search local tables (SDF, Mol files), local databases (Molt) or connect to a MolCart server.
• Tanimoto distance cutoffs, match salt, match stereo.
• Many customizable search rules: element, any aromatic, any aliphatic, any not carbon, any halogen, ring membership, ring size, charge, isotope, hybridization, aromaticity, connectivity, define attachment point.
• Various kinds of filters based upon the column content of the source file e.g. filter by chemical property such as molecular weight or string such as vendor name.
• Output search results to new chemical spreadsheet, select in the source or append to an existing one.

Chemical Clustering

Fast hierarchical clustering and trees.

• A selection of linkage types including: UPGMA, UPGMC, WPGMA, WPGMC, complete and single linkage, farthest first clustering.
• Chemical clustering by Tanimoto distance as well as clustering of other data types.
• Chemical spreadsheet can be colored by cluster.
• Open/close clusters, reorder branches by field, and reorder spreadsheet by field.
• Extract representative "center" structures from each node.
• Print, save and export image of cluster tree.
• Edit individual nodes of tree e.g. labels. colors, spacing...
• Interactive branch reordering and distance changing.

Chemical Enumeration, Decomposition by R-Group (Markush Structures)

• Generate focused compound libraries.
• Create or modify a Markush structure.
• Enumerate on-the-fly a new chemical database by adding chemical groups to defined R groups on a scaffold.
• Decompose a database into fragments.
• Enumerate by reaction.

Local Databases

Large database files optimized for fast search and other operations such as unique entry addition and diverse subset selection.

• Create database files from SDF, CSV/TSV, SMILES files and from ICM tables;
• Impose unique constraints on certain columns upon table creation to avoid redundancy;
• Store multiple tables in a single file; rename, delete tables in a database file;
• Search fast using advanced conditions, including advanced chemical search;
• Select diverse subsets from chemical database files;
• Browse database tables using flexible filtering and sorting conditions;
• Directly edit/delete/insert entries in the database;
• Export in popular formats, such as SDF (for chemistry) and CSV;
• Export and import tables to and from Molcart.

Apply Chemical and Mathematical Functions to Chemical Spreadsheets

Add the following functions to chemical spreadsheets:

• Chemical: Mol Weight, Mol Formula, IupacName, MolLogP, MolLogS, MolPSA, MolVolume, MoldHf, DrugLikeness, Smiles, BadGroups, FindChemPatterns,2D fromSmiles, Nof_Atoms, Nof_Molecules, Nof_Chirals, Nof_Rings, Max_Ring_Size, Min_Ring_Size, Max_Fused_Rings, Nof_RotB, Nof_H-bond Acceptor and Donors, Symmetry.
• Mathematical: Trigonometric, Abs, Ceil, Log, Sqrt...
• Arithmetical: +, - , * ...
• Transformations: ToInteger, ToReal, ToString ...
• Text: Length, LowerCase, FieldFind...
• Convert Units: Radian to Degree and Degree to Radian.

Plot Data

Plot chemical data in interactive plots and histograms.

• Histograms and X-Y scatter plots.
• Zoom in/out on one or both dimensions.
• Many plot customizing features including, mark size and shape, string labels, coloring, least square fitting line...
• Represent up to five dimensions of data using X-Y-color-size-shape.
• Selections made in plots are linked to the spreadsheet.
• Print plots.

QSAR

• Read in and use prediction models built in ICM-Chemist