ACD/ChemFolder
List of Features
ACD/ChemFolder includes:
ACD/ChemFolder includes the ACD/ChemSketch report and structure editor, and ACD/ChemCoder. The ACD/ChemSketch module further includes ACD/Dictionary, ACD/Tautotomers, ACD/3D Viewer, ACD/Name (Restricted Freeware Version), ACD/Labs Extensions for ChemDraw, ACD/I-Lab Add-on for ChemSketch, and ACD/ChemBasic and Goodies Package.
Manage Structural and Chemical Information a Flexible Database
- Create your own structure, reaction and property databases. The size of an ACD/ChemFolder database is limited to 512,000 records or a maximum 2 GB database file size. Each record can be provided with:
- Chemical structures, reactions, or graphics from ACD/ChemSketch.
- User defined data fields.
- Free-form text notes.
- Complex multi-step reaction schemes (maps).
- Import data from the foremost chemical drawing, cheminformatic system, generic, and standard data interchange formats. (see Input/Output page for details):
- Flexible import options for SDfiles and molfiles can be set to control content update.
- Import databases in SMILES notation to ACD/ChemFolder to obtain a fully structure-searchable database.
- Define up to 16,000 data fields for one record and easily browse through all of them in a scrollable list.
- Create new calculated User Data fields in a record with mathematical and logical operations with values of other fields. Special calculated data fields which values are a result of scripts that you wrote. Such fields may be useful for automatic calculation of specific data or to control the validity of other values in the record.
- Include links (URL) to any external documents:
- Include links to text file, Microsoft Word document, or Excel spreadsheet containing notes, plots, assay results, or reaction conditions.
- Create links to spectral or plot files.
- Establish links to image files such as well plate or microscopy images.
- Link to WAV and AVI files.
- Insert links to other ACD/ChemFolder databases.
- Add a representative picture to the textual information provided in the "About Database" dialog box. For example, you may add a logo of the database producer.
- Standardize data entry forms with obligatory fields including text boxes, drop-down lists, or check boxes that are set to your specifications.
- The integrated Database Forms Manager will allow you to quickly and easily design an input dialog box so that whenever an entry is made to the database, certain database values are requested or filled automatically.
- You can merge, intersect, or compare your ACD/ChemFolder databases. Merge options prevent or allow data and structure duplication. You can:
- Merge to and Merge from any other database.
- Define multiple database lists for merging.
- Specify what information will be used for comparison of databases.
- Choose an action for duplicated data.
- Keep a log file with information about each added, skipped, or updated record.
- Customize and extend the functionality of your database with the add-on organizer:
- De-salt a ChemFolder database with an add-on to prevent missing relevant chemicals in a search. Removal of the counter-ions from salts drawn as covalent bonds or in ionic form and minimizing the charge can substantially increase the number of relevant hits where the exact nature of the counter-ion is not intended to be part of your search criteria.
ACD/ChemFolder can assist you in managing reactions and mapping complex chemical pathways:
- Store single and multi-step chemical reactions:
- Manage and map complex metabolic biotransformation data or degradation pathways.
- Map out observed mass fragmentation pathways from your MS, MS /MS, and MS(n) experiments.
- And more...
- Define structures with special Markush fragments with mass or formula difference values to describe partially known chemical and metabolic transformations.
- Manually or automatically create reaction maps for complex chemical processes and multi-step reactions.
- Keep complete notes and information for the overall synthesis and each component in a single record.
- Automatically calculate and store quantities of reactant, product, solvent, and catalyst:
- All the data you need to perform a synthesis can be calculated and stored within a ChemFolder database.
- Create lists of common solvents, catalysts, and reagents with their molecular formulae, formula weights, names, densities, and concentrations.
- Highlight created, broken, and changed bonds in different colors. Customize the presentation of the reaction mechanism.
ACD/ChemFolder includes the following powerful structure and reaction search capabilities:
- Easily find information on chemically similar compounds:
- Search by molecular structure, substructure, and Markush structure using query atoms and bonds.
- Find different relevant tautomeric forms for a structure or target specific stereoisomers.
- Search by chemical Formula or Formula Weight.
- View the query fragment within the retrieved structure after a substructure search:
- Highlight up to eight found fragments.
- Set different user defined colors for fragments.
- Mark intersecting fragments with separate colors.
- Search for reactions and subreactions, as well as reactants and products.
- Limit structure searches to Parent (Reactants) or Metabolites (Products) compounds.
- Perform structure similarity searches by the Tanimoto, Cosine, Dice, Hamming Distance, and Euclidean Distance algorithms to find exact and related structure matches.
- Easily find text or numerical values in user data fields or structural parameters.
- Search by empirical chemical formula. Allowed specific atom count, ranges, or exclusions can be specified to narrow or extend the search.
- Search by specific Formula Weight or range.
- Flexible stereo search options allow you to selectively search compounds while taking into account configuration of chiral centers and double bonds.
- Perform more specific mass searches according to the structures' molecular weight, nominal, or monoisotopic mass values to facilitate mass-spectral data queries.
ACD/ChemFolder also includes a flexible set of data query and management tools for properties and other non-structural information:
- Find specific information by searching multiple data fields simultaneously. Create more narrow queries using logical (AND, OR, NOT, AND NOT), comparison (exact, exists, include, =, <, ≤, ≥, >, ≠), and containment (in range, contains) operators to narrow your search.
- Save complex search query for applying the same search in other databases. The search query is expressed in plain command-line ready text.
- Interactively select database records in Tile or Table view using convenient checkboxes to pick items of interest. Set or save lists from your selections, invert selections to pick the complementary set, or load previous lists.
- Use your database screen layout as a search form to specify new or existing search parameters.
- Store your Search History, and set Search history files as Macro buttons on the toolbar and commands in Search menu. The audit trail (Search History) for complex searches keeps information about performed searches and is used to perform similar searches in other database ChemFolder databases.
- Execute case-sensitive searches of text within User Notes and User Data Fields.
- Query multiple databases at the same time.
- Manipulate sets of search results as lists, which correspond to a subset of the database matching the search criteria. ACD/ChemFolder permits set operation between an active lists and a secondary list that are labeled List A and B, respectively. Available list commands follow:
- Save List A for later reuse.
- Duplicate List A in B.
- Switch List A with List B.
- Merge, intersect, subtract, and ‘subtract+duplicate' the two lists to restrict or expand search results.
- Subtract current IDs.
- Create a custom lists by with a text list of IDs, or use the list checkboxes to create a new lists.
You can calculate and update the following properties for chemical structures directly from your ChemFolder database:
- InChI structure identifiers
- Predict macroscopic properties of organic compounds through ACD/ChemSketch (See Calculation of Liquid Properties):
- Molar Refractivity
- Molar Volume
- Parachor
- Index of refraction
- Surface tension
- Density
- Dielectric Constant (for hydrocarbons)
- Polarizability
- Optional properties, if a corresponding ACD/Labs package is installed:
- IUPAC and Index Name
- LogP , BCF, and KOC for neutral species
- LogD , BCF, and KOC for partially ionized species at a given pH
- Solubility
- pKa
- Boiling point
- User Data fields in any new record can be populated automatically with properties calculated if the appropriate ACD/Labs prediction and nomenclature software is also installed. (See Integration)
Group and analyze your data using advanced graphic presentation and statistical analysis.
- Choose different ways of representing your data graphically:
- Use the Bar Chart or 2D view.
- View several graphs or histograms at a time.
- Click a point on a graph to view the structure and data associated with this point.
- View data from the search list in addition to the whole database.
- Customize colors and data sources.
- Zoom on any graph regions.
- Attach annotations, values, and structures to the selected points of the graph.
- Perform simple regression analysis:
- View regression lines, the table of regression parameters, and ANOVA table.
- Convenient reports:
- Insert Graphs with regression data and annotations into an ACD/ChemSketch report, copy it to the clipboard, or save it as an Adobe PDF file.
You can view and browse data from different perspective in the ACD/ChemFolder database:
- Review records one by one in single record view (for structure, reaction, or graphic records).
- Display single record of reactions in a dedicated Reaction Table (for reaction records only) that facilitates reaction management manipulations: calculate, add, and store synthesis data for each reaction component.
- Browse through multiple database records in Table view and sort by columns to reveal hidden trends.
- Scan through records in Tile view to highlight characteristic chemical structure information and selected names and properties.
- Create custom data layouts for the database window to present selected information in way that allows you to complete specific task quickly.
- The Screen Forms Manager lets you intuitively create forms in seconds using a similar interface to the Data Forms Manager.
- Format text and set font style in User Notes. Copy, paste, drag-and-drop text, save and load notes as plain or formatted text.
- Customize structure display style by setting its structure drawing properties, like coloration, to highlight specific functional groups. Custom structure display options can be set for the atom font and color as well as bond length, bond width, and bond color.
- Print reports according to the currently selected ACD/ChemFolder database screen form:
- The database screen form can also be used as a template for creating high-quality Adobe PDF or *.sk2 reports using the ACD/ChemSketch editor.
- Draft quick reports using the Database/Print command.
- Manage all associated documents through a single application. The ACD/ChemFolder database supports full "drag-and-drop" capability to place text contents into a searchable field.
ACD/ChemFolder can now directly open, search, and view SDfiles. The new module—ACD/SDF Viewer—allows you to:
- Navigate SDfile records.
- Copy data to ACD/ChemSketch, or print records directly from the SDF Viewer window.
- Search by structure, substructure, and user data.
- Create and manage lists.
- Display data in a variety of view modes, including graphs.
- Export records to a new SDfile.
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