Table 5 Comparison between the old software (TOMOCOMD) and the new one proposed in this report (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, \({\mathfrak{c}}\) = ±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

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