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Table 5 Comparison between the old software (TOMOCOMD) and the new one proposed in this report (QuBiLS-MAS)

From: QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

Features Computer program
Description level
 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, \({\mathfrak{c}}\) = ±1 YES, extended to \({\mathfrak{c}}\) = ±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
 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
  1. 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 (\({\mathfrak{c}}\)). 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