Knowledge Base

Article ID: 1439 - Last Modified: June 3, 2011

Can molecular descriptors be calculated with Schrödinger software, including topological and connectivity descriptors?

Yes. QikProp generates physically relevant descriptors, and uses them to perform ADME-tox predictions. The cheminformatics program Canvas has a Molecular Descriptors application, and there is a Script Center Script: Molecular Descriptors (molecular_descriptors.py). It computes a wide range of topological and connectivity descriptors. They are listed below.

Topological Descriptors

First Zagreb (ZM1)
First Zagreb index by valence vertex degrees (ZM1V)
Second Zagreb (ZM2)
Second Zagreb index by valence vertex degrees (ZM2V)
Polarity (Pol)
Narumi Simple Topological (NST)
Narumi Harmonic Topological (NHT)
Narumi Geometric Topological (NGT)
Total structure connectivity (TSC)
Wiener (W)
Mean Wiener (MW)
Xu (Xu)
Quadratic (QIndex)
Radial centric (RC)
Mean Square Distance Balaban (MSDB)
Superpendentic (SP)
Harary (Har)
Log of product of row sums (LPRS)
Pogliani (Pog)
Schultz Molecular Topological (SMT)
Schultz Molecular Topological by valence vertex degrees (SMTV)
Mean Distance Degree Deviation (MDDD)
Ramification (Ram)
Gutman Molecular Topological (GMT)
Gutman MTI by valence vertex degrees (GMTV)
Average vertex distance degree (AVDD)
Unipolarity (UP)
Centralization (CENT)
Variation (VAR)
Molecular electrotopological variation (MEV)
Maximal electrotopological positive variation (MEPV)
Maximal electrotopological negative variation (MENV)
Eccentric connectivity (ECCc)
Eccentricity (ECC)
Average eccentricity (AECC)
Eccentric (DECC)
Valence connectivity index chi-0 (vX0)
Valence connectivity index chi-1 (vX1)
Valence connectivity index chi-2 (vX2)
Valence connectivity index chi-3 (vX3)
Valence connectivity index chi-4 (vX4)
Valence connectivity index chi-5 (vX5)
Average valence connectivity index chi-0 (AvX0)
Average valence connectivity index chi-1 (AvX1)
Average valence connectivity index chi-2 (AvX2)
Average valence connectivity index chi-3 (AvX3)
Average valence connectivity index chi-4 (AvX4)
Average valence connectivity index chi-5 (AvX5)
Quasi Wiener (QW)
First Mohar (FM)
Second Mohar (SM)
Spanning tree number (STN)
Kier benzene-likeliness index (KBLI)
Topological charge index of order 1 (TCI1)
Topological charge index of order 2 (TCI2)
Topological charge index of order 3 (TCI3)
Topological charge index of order 4 (TCI4)
Topological charge index of order 5 (TCI5)
Topological charge index of order 6 (TCI6)
Topological charge index of order 7 (TCI7)
Topological charge index of order 8 (TCI8)
Topological charge index of order 9 (TCI9)
Topological charge index of order 10 (TCI10)
Mean topological charge index of order 1 (MTCI1)
Mean topological charge index of order 2 (MTCI2)
Mean topological charge index of order 3 (MTCI3)
Mean topological charge index of order 4 (MTCI4)
Mean topological charge index of order 5 (MTCI5)
Mean topological charge index of order 6 (MTCI6)
Mean topological charge index of order 7 (MTCI7)
Mean topological charge index of order 8 (MTCI8)
Mean topological charge index of order 9 (MTCI9)
Mean topological charge index of order 10 (MTCI10)
Global topological charge (GTC)
Hyper-distance-path index (HDPI)
Reciprocal hyper-distance-path index (RHDPI)
Square reciprocal distance sum (SRDS)
Modified Randic connectivity (MRC)
Balaban centric (BC)
Lopping centric (LC)
Kier Hall electronegativity (KHE)
Sum of topological distances between N..N (STD(N,N))
Sum of topological distances between N..O (STD(N,O))
Sum of topological distances between N..S (STD(N,S))
Sum of topological distances between N..P (STD(N,P))
Sum of topological distances between N..F (STD(N,F))
Sum of topological distances between N..Cl (STD(N,Cl))
Sum of topological distances between N..Br (STD(N,Br))
Sum of topological distances between N..I (STD(N,I))
Sum of topological distances between O..O (STD(O,O))
Sum of topological distances between O..S (STD(O,S))
Sum of topological distances between O..P (STD(O,P))
Sum of topological distances between O..F (STD(O,F))
Sum of topological distances between O..Cl (STD(O,Cl))
Sum of topological distances between O..Br (STD(O,Br))
Sum of topological distances between O..I (STD(O,I))
Sum of topological distances between S..S (STD(S,S))
Sum of topological distances between S..P (STD(S,P))
Sum of topological distances between S..F (STD(S,F))
Sum of topological distances between S..Cl (STD(S,Cl))
Sum of topological distances between S..Br (STD(S,Br))
Sum of topological distances between S..I (STD(S,I))
Sum of topological distances between P..P (STD(P,P))
Sum of topological distances between P..F (STD(P,F))
Sum of topological distances between P..Cl (STD(P,Cl))
Sum of topological distances between P..Br (STD(P,Br))
Sum of topological distances between P..I (STD(P,I))
Sum of topological distances between F..F (STD(F,F))
Sum of topological distances between F..Cl (STD(F,Cl))
Sum of topological distances between F..Br (STD(F,Br))
Sum of topological distances between F..I (STD(F,I))
Sum of topological distances between Cl..Cl (STD(Cl,Cl))
Sum of topological distances between Cl..Br (STD(Cl,Br))
Sum of topological distances between Cl..I (STD(Cl,I))
Sum of topological distances between Br..Br (STD(Br,Br))
Sum of topological distances between Br..I (STD(Br,I))
Sum of topological distances between I..I (STD(I,I))
Wiener-type index from Z weighted distance matrix - Barysz matrix (WhetZ)
Wiener-type index from electronegativity weighted distance matrix (Whete)
Wiener-type index from mass weighted distance matrix (Whetm)
Wiener-type index from van der waals weighted distance matrix (Whetv)
Wiener-type index from polarizability weighted distance matrix (Whetp)
Balaban-type index from Z weighted distance matrix - Barysz matrix (JhetZ)
Balaban-type index from electronegativity weighted distance matrix (Jhete)
Balaban-type index from mass weighted distance matrix (Jhetm)
Balaban-type index from van der waals weighted distance matrix (Jhetv)
Balaban-type index from polarizability weighted distance matrix (Jhetp)
Topological diameter (TD)
Topological radius (TR)
Petitjean 2D shape (PJ2DS)
Balaban distance connectivity index (J)
Solvation connectivity index chi-0 (SCIX0)
Solvation connectivity index chi-1 (SCIX1)
Solvation connectivity index chi-2 (SCIX2)
Solvation connectivity index chi-3 (SCIX3)
Solvation connectivity index chi-4 (SCIX4)
Solvation connectivity index chi-5 (SCIX5)
Connectivity index chi-0 (CIX0)
Connectivity chi-1 [Randic connectivity] (CIX1)
Connectivity index chi-2 (CIX2)
Connectivity index chi-3 (CIX3)
Connectivity index chi-4 (CIX4)
Connectivity index chi-5 (CIX5)
Average connectivity index chi-0 (ACIX0)
Average connectivity index chi-1 (ACIX1)
Average connectivity index chi-2 (ACIX2)
Average connectivity index chi-3 (ACIX3)
Average connectivity index chi-4 (ACIX4)
Average connectivity index chi-5 (ACIX5)
reciprocal distance Randic-type index (RDR)
reciprocal distance square Randic-type index (RDSR)
1-path Kier alpha-modified shape index (KAMS1)
2-path Kier alpha-modified shape index (KAMS2)
3-path Kier alpha-modified shape index (KAMS3)
Kier flexibility (KF)
path/walk 2 - Randic shape index (RSIpw2)
path/walk 3 - Randic shape index (RSIpw3)
path/walk 4 - Randic shape index (RSIpw4)
path/walk 5 - Randic shape index (RSIpw5)
E-state topological parameter (ETP)
Chirality count (CHRCOUNT)
Van der Waals surface area (VSA)


Mopac Descriptors

Final heat (KCal)
Final heat (KJ)
Total energy (Ev)
Electronic energy (Ev)
Point Group
Core-core repulsion (Ev)
Gradient norm
Ionization potential
No of filled levels
Dipole (Point Chg) - X
Dipole (Point Chg) - Y
Dipole (Point Chg) - Z
Dipole (Point Chg) - Total
Dipole (Hybrid) - X
Dipole (Hybrid) - Y
Dipole (Hybrid) - Z
Dipole (Hybrid) - Total
Dipole (sum) - X
Dipole (sum) - Y
Dipole (sum) - Z
Dipole (sum) - Total


Mopac Methods

RM1
AM1
PM3
MNDO
MNDOD


QikProp Descriptors

#stars
#amine
#amidine
#acid
#amide
#rotor
#rtvFG
CNS
mol_MW
SASA
FOSA
FISA
PISA
WPSA
volume
donorHB
accptHB
ACxDN^.5/SA
glob
QPpolrz
QPlogPC16
QPlogPoct
QPlogPw
QPlogPo/w
QPlogS
CIQPlogS
QPlogHERG
QPPCaco
QPlogBB
QPPMDCK
QPlogKp
#metab
QPlogKhsa
HumanOralAbsorption
PercentHumanOralAbsorption
SAfluorine
SAamideO
PSA
#NandO
RuleOfFive
RuleOfThree
#ringatoms
#in34
#in56
#noncon
#nonHatm

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