Molfile format

Parallel to that the MDL Molfile format (see the Tutorial in Section 2.4.6) developed at Molecular Design Limited (now MDL Information Systems, Inc.) became a de facto standard file format [50]. 

In order to understand the Molfile format let us look at a sample file and recognize its fundamental structure. For simplicity, some less important details will be omitted in the discussion. For a complete description, users are referred to MDL s CTfile format specification [50],... 

To demonstrate the use of binary substructure descriptors and Tanimoto indices for cluster analysis of chemical structures we consider the 20 standard amino acids (Figure 6.3) and characterize each molecular structure by eight binary variables describing presence/absence of eight substructures (Figure 6.4). Note that in most practical applications—for instance, evaluation of results from searches in structure databases—more diverse molecular structures have to be handled and usually several hundred different substructures are considered. Table 6.1 contains the binary substructure descriptors (variables) with value 0 if the substructure is absent and 1 if the substructure is present in the amino acid these numbers form the A-matrix. Binary substructure descriptors have been calculated by the software SubMat (Scsibrany and Varmuza 2004), which requires as input the molecular structures in one file and the substructures in another file, all structures are in Molfile format (Gasteiger and Engel 2003) output is an ASCII file with the binary descriptors. 

II... some calculation logic specific to molfile format return molweight ... 

Imports data in SD file format, MDL molfile format, SMILES text strings, Daylight Chemical Information Systems Inc. s Thor Data Tree (TDT) format, and Tripos Inc. s Sybyl Line Notation (SLN) format. 

The MolFile format is proprietary to Molecular Design Limited. 

Tel. 412-279-6700, fax 412-279-2118, e-mail info gaussian.com Gaussian 92 for ab initio molecular orbital calculations (Hartree-Fock, direct HF, Moller-Plesset, Cl, reaction field theory, electrostatic-potential-derived charges, vibrational frequencies, etc.). Gaussian 92/DFT for density functional theory calculations. Browse for archival storage of computed results. Processing on parallel machines. NEWZMAT to interconvert molfile formats. Inter-... 

Tel. 612-337-0200, fax 612-337-3400, e-mail xmol msc.edu Molecular graphics from existing molfiles. Formats supported include Alchemy, CHEMLAB-II, Gaussian, MOLSIM, MOPAC, Brookhaven PDB, and MSCI s XYZ. DECstation, Silicon Graphics, and Sun. Available by anonymous from ftp.msc.edu. 

A common way of distributing structural and chemical data is in the form of an SDF file. An SDF file is a collection of compounds stored in molfile format and separated with a record containing the string. Many compound vendors make their libraries available this way. Many research publications include SDF files of structures and data. In the following... 

Generic or Markush structures are a form of structural representation that can be used to encompass many individual molecules having common structural features. Figure 6.5 shows a simple example. They are particularly associated with chemical patents,but may also be used (often with a table of values for the R-groups) to represent sets of related molecules involved in structure - activity relationship studies, or large combinatorial libraries. The RGfile variant of the Molfile format can represent restricted forms of Markush structure, as can Sybyl line notation,and a variety of vendors have implemented ad hoc extensions (which have some Markush capabilities) to SMILES. 

Tel. 612-626-1888, e-mail x-mol msc.edu Molecular display for structures in various molfile formats. DEC, Silicon Graphics, and Sun workstations. 

The SDF structure file is used for delivery to hosts and in-house customers of the Beilstein structure file. Other delivery formats produced by the registry software include Tel6systemes-DARC and MDL MOLfile formats. Large DARC and MOLfile structure files have been created at the Beilstein Institute for the purpose of benchmarking the DARC-SMS and MDL MACCS-II substructure search systems against the S4 substructure search system developed jointly by the Beilstein Institute and the software house Softron GmbH . 

D coordinates for a small set of molecules are defined using standard modeling techniques, saved in one of the chemical MIME formats, associated with the appropriate MIME type (e.g., chemical/x-mdl-molfile, chemical/x-pdb, chemical/x-xyz) and placed on a Web server. The molfile format in particular carries an atom connection table, which will allow structures encoded in this format to serve as a substructure search query in an appropriate database if necessary. 

A new project on electronic publishing, financially supported by the German Ministry of Research, and worked out by Wiley-VCH/Chemical Concepts, uses JCAMP and MDL standards (Figure 1). Spectroscopic data acquired directly from the spectrometer site are converted to the JCAMP format. The software TranSpec allows structure input or import in Molfile format. Quality control modules check the reliability of the information. The files in JCAMP and MDL formats are sent to the data server by email. Special software extracts the data from the email automatically and handles the entry into the database. 

The Standard Molecular Data (SMD) format is designed to provide such an integration tool on the basis of a file format. It has been developed in the course of the CASP project (Computer Assisted Synthesis Planning) which is run by a consortium of seven German and Swiss Chemical Companies (BASF, Bayer, Ciba-Geigy, Hoechst, E Merck, Hoffmann La Roche and Sandoz). The basis of this development was the Molfile format of the earlier SECS program (4) (Simulation and Evaluation of Chemical Synthesis). 

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