Mol file

The lUPAC International Chemical Identifier (InChl) [18] was invented in 2001. There are programs (World Wide Molecular Matrix) that can create an InChl from the molecular structure, e.g., via a MOL file [19]. For example, for benzene, the InChl is 

The MOL file belongs to the group of chemical table files. Molecular Design Limited did pioneering work in the development of such file formats [20]. Nowadays, many programs related to chemoinformatics are able to read this format. 

A MOL file contains information about a single connected structure. For example, the representation of ethane in a MOL file is shown in Table 14.6. 

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MDL mol file for acetic acid, in the hydrogen-suppressed form. 

Start ProPred from ICAS and draw the molecule (or import the mol-file of the molecular structure or specify the SMILES string)... 

In the case where MS analytical data has been contributed in the other formats, it is prepared into a NIST MS Database, using the NIST MS Search program. This program is used to create MS spectral files from the following electronic formats JCAMP, NIST ASCH, AMDIS, and NIST MS Database. If the analytical data contains no chemical structure, the structure is created in ISIS Draw and then imported into the database as an MOL file. The information associated with the MS analytical data is handled by the NIST program. 

The new versions of DfW are compatible with Microsoft Windows. For the prediction of toxicity the chemical structure of a compound is input into the system with the use of ISIS/Draw (from MDL Information Systems) or by importing a mol-file or sd-file (Figure 2a). After the system has the structure, pushing the process button starts the prediction. During processing, the system searches and identifies all known toxicophores in the structure from all the different toxicological endpoints within seconds. After completion of the analysis, the system opens a result window. The result window contains the imported structure, a list of toxicological endpoints that the system has made a prediction for, the number and name of... 

Integrate software using OLE including access to all formats provided by the sonrce application (e.g.. Molecule [MOL] files from ISIS/Draw, Rich Text Format (RTF) files from word processing applications, Comma Separated Valne (CSV) formats from worksheet applications). 

Upload the MOL file containing the structure of interest or sketch the molecule in Structure preview window (reeNote 3)... 

In the Data Analysis Wizard (MetaDrug ) window (step 1, Fig. 1) click In Browse under Upload CDX, SDF or MOL file and open an appropriate chemical structure file. If multiple structures are to be batch-uploaded from an SDF file, individual compound reports will be generated for each structure... 

This insert statement is a bit more complex than the one that inserted rows into the vla4.structure table. In that table, only one row was returned from the mol file mol function. The mol file properties function returns multiple rows for each molfile, when there are multiple properties for each molfile. The second select statement above (the one in parentheses and identified with the name atmp) selects all the rows for each molfile. The first select statement selects all the columns from each returned row from molfile properties. These are then inserted into the vla4. property table. 

Every one of these utilities will first require that a file of structures be loaded into a table in the database. Two methods are shown here importing a SMILES file and a mol file. Other file types could be added as needed, extending the core functions described earlier using mol file mol or molf ile to smiles as a model. OpenBabel is a good choice because of its support of many file formats. 

Chime A plug-in that allows chemical structures to be displayed within a web page. The structures, which are embedded as mol files, can be viewed Interactively l.e. they can be rotated, expanded, exported, and rendered In RasMol. The program Is the copyright of MDL Information Systems, Inc., and is available free (subject to a license agreement). 

We can also create the 3D MOL file as shown in the following figure. We need to type the following to get the desired result. 

Fig. 1.57 Search and results page for file upload (SD or MOL file, i.e., MDL format)...

One way to input molecular structure of the new component is to enter individual atoms and bonds. However, a simpler way is to import the molecular structure from other component databanks. A very useful resource is the NIST (National Institute of Standards and Technology) Chemistry WebBook. The information for this new component is shown in Figure 3.66. Click the molecular structure file, 2d Mol file, and save in a known directory with a given file name. The next step is to go to Molecular Structure of EMC under Properties and Click Import Structure to import this file into Aspen Plus (see Fig. 3.67). After this step, ask Aspen Plus to calculate bonds by clicking Calculate Bonds. The graphical structure of EMC is successfully imported into Aspen Plus as shown in Figure 3.68. 

Thli itruelure m also available at a 2d Mol file Dthar namaei Carbonic acid, adiyl-. methyl es earbenatt... 

Chemistry and Biochemistry. MOLCOORD, Ab Initio Coordinate Generation for Mol Files. The program is written in FORTRAN, runs under DOS, and requires merely 51 kilobytes. 

META takes advantage of the GUI (graphic user interface) technology and implements both graphic input and output along with traditional input such as SMILES code," KLN code," MOL file, and output such as text files. Figures 2 and 3 show the basic screens of META. Not having access to the other expert systems leaves us to conjecture about their user interface. We suspect that they also provide a choice of user friendly ways to input data and display results. 

The Mol file and associated formats, developed by MDL Information Systems, Inc., and maintained and supported by them as proprietary commercial products, but whose description is made freely available to other developers. 

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