Table 5.
Comparison between the old software (TOMOCOMD) and the new one proposed in this report (QuBiLS-MAS)
| Features | Computer program | |
|---|---|---|
| TOMOCOMD | QuBiLS-MAS | |
| Description level | ||
| Theoretical | ||
| Algebraic form maps | 3 (quadratic, bilinear and linear) | |
| Atom and Bond level | Yes | Yes |
| Matrices | 2 (NS, SS) | 4 (NS, SS, DS, MP) |
| Atom Weightings | 4 (M, V, P, E) | 10 (M, V, P, E, A, C, PSA, R, H, S) |
| Local-fragments | 3 (D, G, X) | 7 (A, C, D, G, M, P, X) |
| Chirality | YES, = ±1 | YES, extended to = ±0.25 to ±3 with a 0.25 step |
| Lone-pair electrons | – | Yes |
| Topological constraints | – | Yes, three cut-off types (SRW, NSRW, Lag P) |
| H-atoms consideration | – | Yes, permits inclusion or removal |
| Invariants or aggregation operators | – | Yes, 21 aggregation operators classified in four major groups |
| Computational | ||
| Open source | – | Yes, under LGPL |
| Availability | Shareware | Freeware |
| Programming language | Borland Delphi | Java |
| Clear Object-oriented source code design | – | Yes |
| Canonical namespace packages structure | – | Yes, under com.tomocomd.qublis. |
| Target operating system(OS) | Microsoft Windows | Platform-independent |
| Graphical user interface | Yes | Yes |
| Command line | – | Yes |
| Portable MDs library | – | Yes, as pre-compiled Java JAR file |
| Supported input format | In-house file format | mol/sdf MDL |
| Output format | Text File (TSV) | Text File (TSV, SSV, CSV), Weka (ARFF) |
| Structure curation and cleaning | – | Yes, available under Structure menu item (with 10 check/cleaning tasks, H-atoms handling, and function for chemical formats conversion) |
| Built-in example data | – | Yes, six chemical datasets |
| Unique MD header | – | Yes, identifying the codification scheme |
| Batch Processing mode | – | Yes |
| Parallelized computing | – | Yes, using the Fork/Join framework |
| Configurable projects | – | Yes |
| Import/export configuration | – | Yes, using a XML file format |
| Calculation progress | – | Yes, for descriptors and molecules |
| Real-time memory monitor | – | Yes, with garbage collection option when desired |
| Events logging | – | Yes, accessible through the History Tab |
| Calculation report | – | Yes |
| Runtime help accessibility | – | Yes |
| User owner’s manual | – | Yes |
| Online webpage | – | Yes http://www.tomocomd.com/qubils |
Matrices Non-stochastic (NS), simple stochastic (SS), double stochastic (DS) and mutual probability (MP). Atom weightings (atomic properties) (1) atomic mass (M), (2) the Van der Waals volume (V), (3) the atomic polarizability (P), (4) atomic electronegativity according to Pauling scale (E), (5) atomic Ghose–Crippen LogP (A), (6) atomic Gasteiger–Marsili charge (C), (7) atomic polar surface area (PSA), (8) atomic refractivity (R), (9) atomic hardness (H), and (10) atomic softness (S). Local-fragments (atom-type and/or group-type) H-bond acceptors (A), carbon atoms in aliphatic chains (C), H-bond donors (D), halogens (G), terminal methyl groups (M), carbon atoms in an aromatic portion (P) and heteroatoms (X). Chirality trigonometric 3D-chirality correction factor (). Topological constraints (cut-offs) (1) keeping only the diagonal elements of the matrix, denoted as “Self-Returning Walks” (SRW), (2) keeping only the offdiagonal elements of the matrix, denoted as “Non-Self-Returning Walks” (NSRW), and (3) keeping only the elements within a given interval, based on the topological distance for a path cut-off, denoted as Lag p