Section 2.4.7. Structural templates

In many chemical information systems, it is standard practice to build complete 2D molecular representations through the use of a library of commonly referenced structural templates, e.g. ligands, functional groups, amino-acid units etc.

In a MIF, molecular templates can be encapsulated as save frames, either within a data block for a specific molecule, or within a global block that is accessible to many data blocks. A simple application of a MIF template is shown in Fig. 2.4.7.1, where a 4-methylcyclohexyl ligand is used to encode the molecule tris(methylcyclohexyl)phosphine. In this example a molecular fragment is constructed in the save frame mechex, where the `atom' sites and `bond' connections appear in _atom_* and _bond_* loops. The molecule (2-methylcyclohexyl)(3-methyl­cyclohexyl)(4-methylcyclohexyl)phosphine is encoded by referencing the template fragment as the save frame $mechex. In the `atom' loop, the item _atom_environment identifies the components of the target molecule as an `atom' or `frag' (fragment). If the component is a fragment, the items _atom_frag_key and _atom_frag_id are used to specify the frame code and the ID of the attached atom in the fragment, respectively. In the `bond' loop, the connections from the atom P(1) to the template are encoded simply in terms of the _atom_id values. The necessary redefinition of the hydrogen and non-hydrogen counts of the template atoms is accomplished using the _atom_attach_h and _atom_attach_nh items, respectively. The external values override any values that are contained in, or derived from, the data in the template.

Figure 2.4.7.1 | top | pdf | MIF representation of (2-methylcyclohexyl)(3-methylcyclohexyl)(4-methylcyclohexyl)phosphine using a single global save frame that encapsulates the structure of methylcyclohexane, together with `external' referencing of save-frame atoms in _atom_ and _bond_ loops.

The same approach is used to construct the dipeptide alanyl­serine in Fig. 2.4.7.2. This employs the template peptide units described by the atoms and bonds in the save frames $alanyl and $seryl. The complete dipeptide is specified in its `atom' list as the template peptides (identified by their save-frame names) and an additional carboxylate O atom. Note that only the atom sites affected by molecule formation are identified explicitly in this list, which gives the values of _atom_attach_nh, _atom_attach_h and _atom_charge for the modified sites in the zwitterionic form of alanylserine.

Figure 2.4.7.2 | top | pdf | MIF representation of the dipeptide alanylserine constructed using alanyl and seryl templates encapsulated in global save frames.