MN.CHECK - Structure Integrity Check and Normalization of Chemical State
CHECK performs structural state and integrity checking of chemical compounds.
Features & Functionality
| Features | Description |
|---|---|
| input file format | SDFile |
| output file format | SDFile |
| control ionization state | can produce a neutral form of the structure |
| hydrogen atoms | adds or strips away hydrogen atoms |
| nitro groups | controls ionization state of nitro groups (ionic or uncharged) |
| remove salt | removes smallest counterion or removes molecule identical to salt templates provided in a separate file |
| speed and reliability | processes a data set of 100,100 small to medium-sized molecules in 723 sec on a 1.0 GHz workstation (7 ms/cpd, 100% conversion rate) |
User Interface
- Command line interface supporting batch mode
- Component for Accelrys Pipeline Pilot
System Requirements
- Microsoft Windows NT/2000/XP
- SUSE Linux (Release 8/9/10, Kernel 2.4/2.6 for x86, 32/64bit)
- RedHat Linux (Release 8/9/Enterprise, Kernel 2.4/2.6 for x86, 32bit)
- Sun SPARC, Solaris 2.9 or higher
- Silicon Graphics, IRIX 6.5
Example
CHECK currently provides two methods for removing counterions from the input file based either on the size of the molecule or on the specification of given counterions.
Both methods are demonstrated here with three structures:
1. The default algorithm internally splits each input record into molecules and discards all but the largest molecule, as determined by the atom count, including hydrogen atoms.
2. Specified larger counterions can be removed by providing a salt file to the program. Molecules found in that file have precedence for deletion from the input record, even if they are larger than their counterparts. In this case, the salt file contains the pyridinium ion, which is removed from each structure.
Additional Info
Downloadable PDFs
Evaluation Version
A demo version is available on request free of charge. Please register yourself for our download area.