Figure 3 : Flowchart for the software package ALATIS.

From: Unique identifiers for small molecules enable rigorous labeling of their atoms

Figure 3

The webserver for ALATIS accepts a structure file for the compound as input (SDF or MDL Mol-V2000 file) along with optional atom labels. Three modules receive the data (dashed arrows). The InChI-1 program executes in the background to generate the standard InChI string for the input. The modules work in concert in order to assign unique labels to heavy atoms as well as to hydrogen atoms of the molecule (solid arrows). To label heavy atoms, two sub-modules are used to construct two graph representations for the molecule (using the input structure file and the generated standard InChI strings; see Supplementary Information 2 for the details of the graph representation). Another sub-module maps the graphs to a representation suitable for assigning unique labels to the heavy atoms. The module responsible for assigning unique labels to the hydrogen atoms imposes temporary chiral centers on the heavy atoms in order to distinguish between the hydrogens attached to each heavy atom. The idea of introducing temporary chiral centers is elaborated further to accommodate atom labeling of symmetric molecules. During this process the InChI-1 program is executed repeatedly and iteratively (solid arrows). In the cases where the input structure file contains multiple molecular structures (for example representing different tautomeric states), a separate module carries out the processing. ALATIS reports unique labels for molecules in the mixture and their constituent atoms. ALATIS outputs a standard InChI string for the compound, a structure file that contains the unique labels of the atoms, and a map between the atoms labels of the input and the generated unique atom labels.