Changes in Dragon 5.5 blocks

The Dragon 5.5 block n.2 Topological descriptors was renamed as Topological indices and was divided into six sub-blocks:

Vertex degree-based indices
Distance-based indices
MTI indices
Path/walk indices
E-state indices
Centric indices

 

A few descriptors of the old block n. 2 Topological descriptors were moved elsewhere and, in almost all the cases, with a different label:

ID 5.5

Symbol 5.5

Symbol 6.0

Block 6.0

Sub-block 6.0

62

VDA

AVS_D

2D matrix-based descriptors

Topological distance matrix (D)

70

W

Wi_D

2D matrix-based descriptors

Topological distance matrix (D)

71

WA

WiA_D

2D matrix-based descriptors

Topological distance matrix (D)

72

Har

Wi_H2

2D matrix-based descriptors

Reciprocal squared distance matrix (H2)

73

Har2

H_D

2D matrix-based descriptors

Topological distance matrix (D)

74

QW

QW_L

2D matrix-based descriptors

Topological distance matrix (D)

75

TI1

TI1_L

2D matrix-based descriptors

Laplace matrix (L)

76

TI2

TI2_L

2D matrix-based descriptors

Laplace matrix (L)

77

STN

STN_L

2D matrix-based descriptors

Laplace matrix (L)

78

HyDp

HyWi_D

2D matrix-based descriptors

Topological distance matrix (D)

80

w

Wi_Dt

2D matrix-based descriptors

Detour matrix (Dt)

81

ww

HyWi_Dt

2D matrix-based descriptors

Detour matrix (Dt)

83

D/D

Wi_D/Dt

2D matrix-based descriptors

Distance / detour matrix (D/Dt)

85

WhetZ

Wi_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

86

Whetm

Wi_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

87

Whetv

Wi_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

88

Whete

Wi_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

89

Whetp

Wi_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

90

J

J_D

2D matrix-based descriptors

Topological distance matrix (D)

91

JhetZ

J_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

92

Jhetm

J_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

93

Jhetv

J_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

94

Jhete

J_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

95

Jhetp

J_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

100

S0K

S0K

Information indices

Basic descriptors

122 – 131

D\Dr03 – D\Dr12

D\Dtr03 – D\Dtr12

Ring descriptors

Basic descriptors

132 – 167

T(N..N) –  T(I..I)

T(N..N) –  T(I..I)

2D Atom Pairs

Weighted topological atom pairs

 

The block n. 3 Walk and path counts was divided into five different sub-blocks:

Walk counts
Self-returning walk counts
Path counts
Multiple path counts
ID numbers

These can be now calculated as integer numbers or by applying the transformation logarithmic (i.e., ln(1 + x)) depending on the specific setting chosen by the user. Dragon default is application of logarithmic transformation.

 

The block n. 4 Connectivity indices was divided into four sub-blocks and now includes a new set of molecular descriptors:

Kier-Hall molecular connectivity indices
Solvation connectivity indices
Randic-like indices (partly NEW)
Pseudo-connectivity indices (NEW)

 

The block n. 5 Information indices was divided into two sub-blocks:

Basic descriptors
Indices of neighborhood symmetry

 

The block n. 6 2D autocorrelations was divided into five sub-blocks and now includes a new set of molecular descriptors:

Broto-Mareau autocorrelations
Centred Broto-Moreau autocorrelations (NEW)
Moran autocorrelations
Geary autocorrelations
Topological charge autocorrelations (Old block n. 9 Topological charge indices)

 

The block n. 7 Edge adjacency indices was largely extended by introduction of indices from unsymmetrical weighted edge adjacency matrices in addition to indices from augmented edge adjacency matrices. Moreover, a basic set of spectral indices is now calculated from all the defined edge matrices. This block was divided into four sub-blocks:

Spectral indices (NEW)
Connectivity-like indices (Extended set)
Spectral moments (Extended set)
Eigenvalues (Extended set)

 

The block n. 8 Burden eigenvalues was extended by also including eigenvalues from Burden matrix based on ionization potential and topological intrinsic state as the atom weighting scheme. It was divided into two sub-blocks:

Largest eigenvalues
Smallest eigenvalues

 

The block n. 9 Topological charge indices no longer exists. It is now a sub-block of the block 2D Autocorrelations with the novel name Topological charge autocorrelations.

 

The block n. 10 Eigenvalue-based indices no longer exists. It was largely extended by application of basic spectral operators to a number of graph-theoretical matrices. The eigenvalue-based indices of Dragon 5.5 are now located in the block 2D matrix-based descriptors, most of them with a different label. The correspondence between Dragon 5.5 eigenvalue-based indices and those of Dragon 6.0 is reported below.

 

Dragon 5.5 eigenvalue-based indices in Dragon 6.0.

ID 5.5

Symbol 5.5

Symbol 6.0

Block 6.0

Sub-block 6.0

583

LP1

SpMax_A

2D matrix-based descriptors

Adjacency matrix (A)

584

Eig1Z

SpMax_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

585

Eig1m

SpMax_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

586

Eig1v

SpMax_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

587

Eig1e

SpMax_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

588

Eig1p

SpMax_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

589

SEigZ

SM1_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

590

SEigm

SM1_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

591

SEigv

SM1_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

592

SEige

SM1_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

594

AEigZ

SpAbs_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

595

AEigm

SpAbs_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

596

AEigv

SpAbs_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

597

AEige

SpAbs_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

598

AEigp

SpAbs_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

599

VEA1

VE1_A

2D matrix-based descriptors

Adjacency matrix (A)

600

VEA2

VE2_A

2D matrix-based descriptors

Adjacency matrix (A)

601

VRA1

VR1_A

2D matrix-based descriptors

Adjacency matrix (A)

602

VRA2

VR2_A

2D matrix-based descriptors

Adjacency matrix (A)

603

VED1

VE1_D

2D matrix-based descriptors

Topological distance matrix (D)

604

VED2

VE2_D

2D matrix-based descriptors

Topological distance matrix (D)

605

VRD1

VR1_D

2D matrix-based descriptors

Topological distance matrix (D)

606

VRD2

VR2_D

2D matrix-based descriptors

Topological distance matrix (D)

607

VEZ1

VE1_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

608

VEZ2

VE2_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

609

VRZ1

VR1_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

610

VRZ2

VR2_Dz(Z)

2D matrix-based descriptors

Barysz matrix weighted by atomic number (Dz(Z))

611

VEm1

VE1_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

612

VEm2

VE2_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

613

VRm1

VR1_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

614

VRm2

VR2_Dz(m)

2D matrix-based descriptors

Barysz matrix weighted by mass (Dz(m))

615

VEv1

VE1_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

616

VEv2

VE2_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

617

VRv1

VR1_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

618

VRv2

VR2_Dz(v)

2D matrix-based descriptors

Barysz matrix weighted by Van der Waals volume (Dz(v))

619

VEe1

VE1_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

620

VEe2

VE2_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

621

VRe1

VR1_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

622

VRe2

VR2_Dz(e)

2D matrix-based descriptors

Barysz matrix weighted by Sanderson electronegativity (Dz(e))

623

VEp1

VE1_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

624

VEp2

VE2_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

625

VRp1

VR1_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

626

VRp2

VR2_Dz(p)

2D matrix-based descriptors

Barysz matrix weighted by polarizability (Dz(p))

 

The block n. 11 Randic molecular profile was divided into two sub-blocks:

Molecular profiles
Shape profiles

 

The block n. 12 Geometrical descriptors was divided into four sub-blocks:

Size indices
Shape indices
Delocalization-degree indices
COMMA descriptors

Some of the indices originally included in this block are now located in the novel block of 3D Matrix-based descriptors, with a different label. They are listed in the table below.

Moreover, the set of substructure descriptors, which are defined as the sum of geometrical distances between pairs of atom types, are now located in the novel block of 3D Atom Pairs, with the name Weighted geometrical atom pairs

 

Dragon 5.5 geometrical descriptors that were placed in other blocks of Dragon 6.0.

ID 5.5

Symbol 5.5

Symbol

6.0

Block 6.0

Sub-block 6.0

668

W3D

Wi_G

3D matrix-based descriptors

Geometrical distance matrix (G)

669

J3D

J_G

3D matrix-based descriptors

Geometrical distance matrix (G)

670

H3D

H_G

3D matrix-based descriptors

Geometrical distance matrix (G)

671

AGDD

AVS_G

3D matrix-based descriptors

Geometrical distance matrix (G)

672

DDI

Wi_G/D

3D matrix-based descriptors

Distance/distance matrix (G/D)

673

ADDD

AVS_G/D

3D matrix-based descriptors

Distance/distance matrix (G/D)

682

FDI

SpMaxA_G/D

3D matrix-based descriptors

Distance/distance matrix (G/D)

685

SEig

SpAbs_G/D

3D matrix-based descriptors

Distance/distance matrix (G/D)

706 – 741

G(N..N) –

G(I..I)

G(N..N) –

G(I..I)

3D Atom Pairs

Weighted geometrical atom pairs

 

The block n. 13 RDF descriptors was extended from 150 to 210 indices and the block n. 14 3D-MoRSE descriptors from 160 to 224 indices, including also indices calculated on the basis of ionization potential and topological intrinsic state as the atom weighting scheme. These blocks were also divided into a number of sub-blocks according to the atom weighting scheme used for their calculation:

Unweighted
Weighted by mass
Weighted by van der Waals volume
Weighted by Sanderson electronegativity
Weighted by polarizability
Weighted by ionization potential (NEW)
Weighted by I-state (NEW)

 

In the block n. 15 WHIM descriptors, all the indices derived from the electrotopological state (s) as the atom weighting scheme were replaced with those calculated from the topological I-state (s) and indices based on the first ionization potential were added (i). This block was also divided into two sub-blocks:

Directional descriptors
Global descriptors

 

The block n. 16 GETAWAY descriptors was enlarged from 197 to 273 by introduction of the indices calculated from the ionization potential and the topological I-state as the atom weighting scheme. This block was also divided into three sub-blocks:

Basic descriptors
H-indices
R-indices

 

In the block n. 18 Atom-centred fragments five undefined molecular descriptors were deleted from the list.

 

The block n. 20 Molecular properties now includes some new molecular descriptors related to the total molecular volume and surface area of donor and acceptor atoms, a novel index of unsaturation and the packing density index. Moreover, some indices were moved to the novel block of Drug-like indices. These are listed below.

 

Dragon 5.5 descriptors of the block Molecular properties moved to the block Drug-like indices in Dragon 6.0.

ID 5.5

Symbol 5.5

Symbol 6.0

Block 6.0

Sub-block 6.0

1645

LAI

cRo5

Drug-like indices

Basic indices

1646

GVWAI-80

CMC-80

Drug-like indices

Basic indices

1647

GVWAI-50

CMC-50

Drug-like indices

Basic indices

1648

Inflammat-80

Inflammat-80

Drug-like indices

Basic indices

1649

Inflammat-50

Inflammat-50

Drug-like indices

Basic indices

1650

Depressant-80

Depressant-80

Drug-like indices

Basic indices

1651

Depressant-50

Depressant-50

Drug-like indices

Basic indices

1652

Psychotic-80

Psychotic-80

Drug-like indices

Basic indices

1653

Psychotic-50

Psychotic-50

Drug-like indices

Basic indices

1654

Hypertens-80

Hypertens-80

Drug-like indices

Basic indices

1655

Hypertens-50

Hypertens-50

Drug-like indices

Basic indices

1656

Hypnotic-80

Hypnotic-80

Drug-like indices

Basic indices

1657

Hypnotic-50

Hypnotic-50

Drug-like indices

Basic indices

1658

Neoplastic-80

Neoplastic-80

Drug-like indices

Basic indices

1659

Neoplastic-50

Neoplastic-50

Drug-like indices

Basic indices

1660

Infective-80

Infective-80

Drug-like indices

Basic indices

1661

Infective-50

Infective-50

Drug-like indices

Basic indices

 

The blocks n. 21 2D Binary fingerprints and n. 22 2D Frequency fingerprints no longer exist, they being now the sub-blocks Binary Atom Pairs and Frequency Atom Pairs, respectively, into the novel block 2D Atom Pairs.