Molconn-Z 3.50 Manual: Appendix II

Appendix II

The List of Variables in the .S File

The S file consists of 11 (or more) records for each molecule. The list of all variables output to the .S file is given below. An experienced-based rank of usefulness for QSAR for the parameters is given below:

** very useful
* sometimes useful
- not useful

It is possible, with all versions of Molconn-Z, to eliminate non-useful structure descriptors from the output by deselecting the appropriate records for output to the .s file.

Record(s) variable use
rank description comments

1 id n/a molecule ID from the .B file

nvx * number of nonhydrogen atoms in molecule

nrings * number of rings (nxp1 - (nvx - 1)) in graph

ncirc - number of circuits in graph

nelem - number of elements in molecule

fw * molecular weight

name n/a molecule name from the .B file

2 x0 - xp10 * connectivity simple path indices examine pairwise correlations of chi indices and retain set in which r < 0.80

3 xv0 - xvp10 ** connectivity valence path indices

4 xc3, xc4 * connectivity simple cluster indices

xpc4 * connectivity simple path/cluster-4 index

xch3 - xch10 * connectivity simple chain indices

5 xvc3,xvc4 ** connectivity valence cluster indices

xvpc4 ** connectivity simple path/cluster-4 index

xvch3 - xvch10 ** connectivity valence chain indices

6 dx0 - dxp10 * difference connectivity: simple path indices not to be used when the direct chi indices (above) are used; examine pairwise correlations of difference chi indices and retain set in which r < 0.80

7 dxv0 - dxvp10 * difference connectivity valence path indices

8 k0 - Kappa zero

k1 - k3 - Kappa simple indices

ka1 - ka3 ** Kappa alpha indices

si - Shannon information index

totop * Total Topological Index t

sumI ** sum of the intrinsic state values I

sumdelI ** sum of delta-I values

tets2 * total topological state index based on electrotopological state indices

phia ** flexibility index (k1*k2/nvx)

9 S1-S15 n/a Electrotopological state index values for atoms 1-15 these sets of atom-level indices can be used in QSAR, but are dependent upon constant atom numbering in a common core

10 S16 - S30 n/a Electrotopological state index values for atoms 16-30

11 S31 - S45 n/a Electrotopological state index values for atoms 31-45

12 S46 - S60 n/a Electrotopological state index values for atoms 46-60

13 S61 - S75 n/a Electrotopological state index values for atoms 61-75

14 S76 - S90 n/a Electrotopological state index values for atoms 76-90

15-21 SHsOH, SHdNH, SHsSH, SHsNH2, SHssNH, SHtCH, SHother, SHCHnX ** Atom Type Electrotopological state index values for atom types in general, keep any non-zero variance decriptors

Hmax, Gmax, Hmin, Gmin **

Hmaxpos, Hminneg - duplicates of Hmax and Hmin

SsLi, SssBe, SssssBem, SssBH, SsssB, SssssBm -

SsCH3, SdCH2, SssCH2, StCH, SdsCH, SaaCH, SsssCH, SddC, StsC, SdssC, SaasC, SaaaC, SssssC **

SsNH3p, SsNH2, SssNH2p, SdNH, SssNH, SaaNH, StN, SsssNHp, SdsN, SaaN, SsssN, SddsN, SaasN, SssssNp **

SsOH, SdO, SssO, SaaO **

SsF **

SsSiH3, SssSiH2, SsssSiH, SssssSi -

SsPH2, SssPH, SsssP * not likely non-zero

SdsssP, SsssssP **

SsSH, SdS, SssS, SaaS, SdssS, SddssS, SssssssS **

SsCl **

SsGeH3, SssGeH2, SsssGeH, SssssGe -

SsAsH2, SssAsH, SsssAs, SdsssAs, SsssssAs -

SsSeH, SdSe, SssSe, SaaSe, SdssSe, SddssSe -

SsBr **

SsSnH3, SssSnH2, SsssSnH, SssssSn -

SsI **

SsPbH3, SssPbH2, SsssPbH, SssssPb -

22-28 CHsOH - CssssPb n/a Atom Type Counts for atom types in records 15-21 average atom-type E-State, i.e., records 15-21 divided by records 22-28, may be useful

29 HES1 - HES15 n/a Hydrogen Electrotopological state index values for atoms 1-15 these sets of atom-level indices can be used in QSAR, but are dependent upon constant atom numbering in a common core

30 HES16 - HES30 n/a Hydrogen Electrotopological state index values for atoms 16-30

31 HES31 - HES45 n/a Hydrogen Electrotopological state index values for atoms 31-45

32 HES46 - HES60 n/a Hydrogen Electrotopological state index values for atoms 46-60

33 HES61 - HES75 n/a Hydrogen Electrotopological state index values for atoms 61-75

34 HES76 - HES90 n/a Hydrogen Electrotopological state index values for atoms 76-90

35 IdW - IdC - Bonchev-Trinajstic information indices

W - Wiener number

Wp - Wienerp

Pf - Plattf

Wt - total Wiener number

knotp - difference of chi-cluster-3 and path/cluster-4

knotpv - valence difference of chi-cluster-3 and path/cluster-4

nclasss * number of classes of topologically (symmetry) equivalent graph vertices

numHBd * number of hydrogen bond donors

numwHBd * number of hydrogen bond donors

numHBa * number of hydrogen bond acceptors

36 nxp1 - nxp10 n/a counts of path subgraphs indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis

nxc3,nxc4 n/a counts of cluster subgraphs

nxpc4 n/a count of path/cluster-4 subgraphs

nxch3 - nxch10 n/a counts of chain subgraphs

ntpath n/a total number of paths

diam n/a graph diameter

muldiam n/a multiplicity of diameter

rad n/a graph radius

mulrad n/a multiplicity of radius

ishape n/a (diam - rad)/rad

37 nasH n/a number of atoms of element Hydrogen indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis

... n/a ...

nasZn n/a number of atoms of element Zinc

38 nasGa n/a number of atoms of element Gallium

... n/a ...

nasW n/a number of atoms of element Tungsten

39 nasRe n/a number of atoms of element Rhenium

... n/a ...

nasRn n/a number of atoms of element Radon

40 nd1 n/a number of vertexes for which delta d = 1 indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis

... n/a ...

nd6 n/a number of vertexes for which delta = 6

ne11 n/a number of edges between d=1 and d=1

... n/a ...

ne16 n/a number of edges between d=1 and d=6

ne22 n/a number of edges between d=2 and d=2

... n/a ...

ne26 n/a number of edges between d=2 and d=6

... n/a ...

ne66 n/a number of edges between d=6 and d=6

tg - tg3 n/a terminal groups/ tg separated by 3 edges

tm - tm3 n/a terminal methyls/ tm separated by 3 edges

41 n2pe11 n/a number of vertices with d=1 and d=1 separated by 2 edges indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis

... n/a ...

n2pe66 n/a number of vertices with d=6 and d=6 separated by 2 edges

42 n3pe11 n/a number of vertices with d=1 and d=1 separated by 3 edges

... n/a ...

n3pe66 n/a number of vertices with d=6 and d=6 separated by 3 edges

43 n4pe11 n/a number of vertices with d=1 and d=1 separated by 4 edges

... n/a ...

n4pe66 n/a number of vertices with d=6 and d=6 separated by 4 edges

44 ec1 - ec30 n/a vertex eccentricities for vertices 1 to 30

45 ec31 - ec60 n/a vertex eccentricities for vertices 31 to 60

46 ec61 - ec90 n/a vertex eccentricities for vertices 61 to 90

47 SHCsats ** E-State of C sp³ bonded to other saturated C atoms

SHCsatu ** E-State of C sp³ bonded to unsaturated C atoms

SHvin ** E-State of C atoms in the vinyl group, =CH-

SHtvin ** E-State of C atoms in the terminal vinyl group, =CH₂

SHavin ** E-State of C atoms in the vinyl group, =CH-, bonded to an aromatic C

SHarom ** E-State of C sp² which are part of an aromatic system

SHHBd ** hydrogen bond donor index, sum of Hydrogen E-State values for -OH, =NH, -NH2, -NH-, -SH, and #CH

SHwHBd ** weak hydrogen bond donor index, sum of C-H Hydrogen E-State values for hydrogen atoms on a C to which a F and/or Cl are also bonded

SHHBa ** hydrogen bond acceptor index, sum of the E-State values for -OH, =NH,- NH2, -NH-, >N-, -O-, =O, -S- along with -F, and -Cl

Qv ** General Polarity descriptor

48 NHBint2 * count of potential internal hydrogen bonders

... * ...

NHBint10 * count of potential internal hydrogen bonders

SHBint2 * E-State descriptors of potential internal hydrogen bond strength

SHBint3 - SHBint6 ** E-State descriptors of potential internal hydrogen bond strength

SHBint7 - SHBint10 * E-State descriptors of potential internal hydrogen bond strength

49 elem1 - elem7 * elements in structures molecular formula

50 count1 - count7 * count of atoms for elements in structures molecular formula

Record(s)	variable	use rank	description	comments
1	id	n/a	molecule ID from the .B file
	nvx	*	number of nonhydrogen atoms in molecule
	nrings	*	number of rings (nxp1 - (nvx - 1)) in graph
	ncirc	-	number of circuits in graph
	nelem	-	number of elements in molecule
	fw	*	molecular weight
	name	n/a	molecule name from the .B file
2	x0 - xp10	*	connectivity simple path indices	examine pairwise correlations of chi indices and retain set in which r < 0.80
3	xv0 - xvp10	**	connectivity valence path indices
4	xc3, xc4	*	connectivity simple cluster indices
	xpc4	*	connectivity simple path/cluster-4 index
	xch3 - xch10	*	connectivity simple chain indices
5	xvc3,xvc4	**	connectivity valence cluster indices
	xvpc4	**	connectivity simple path/cluster-4 index
	xvch3 - xvch10	**	connectivity valence chain indices
6	dx0 - dxp10	*	difference connectivity: simple path indices	not to be used when the direct chi indices (above) are used; examine pairwise correlations of difference chi indices and retain set in which r < 0.80
7	dxv0 - dxvp10	*	difference connectivity valence path indices
8	k0	-	Kappa zero
	k1 - k3	-	Kappa simple indices
	ka1 - ka3	**	Kappa alpha indices
	si	-	Shannon information index
	totop	*	Total Topological Index t
	sumI	**	sum of the intrinsic state values I
	sumdelI	**	sum of delta-I values
	tets2	*	total topological state index based on electrotopological state indices
	phia	**	flexibility index (k1*k2/nvx)
9	S1-S15	n/a	Electrotopological state index values for atoms 1-15	these sets of atom-level indices can be used in QSAR, but are dependent upon constant atom numbering in a common core
10	S16 - S30	n/a	Electrotopological state index values for atoms 16-30
11	S31 - S45	n/a	Electrotopological state index values for atoms 31-45
12	S46 - S60	n/a	Electrotopological state index values for atoms 46-60
13	S61 - S75	n/a	Electrotopological state index values for atoms 61-75
14	S76 - S90	n/a	Electrotopological state index values for atoms 76-90
15-21	SHsOH, SHdNH, SHsSH, SHsNH2, SHssNH, SHtCH, SHother, SHCHnX	**	Atom Type Electrotopological state index values for atom types	in general, keep any non-zero variance decriptors
	Hmax, Gmax, Hmin, Gmin	**
	Hmaxpos, Hminneg	-		duplicates of Hmax and Hmin
	SsLi, SssBe, SssssBem, SssBH, SsssB, SssssBm	-
	SsCH3, SdCH2, SssCH2, StCH, SdsCH, SaaCH, SsssCH, SddC, StsC, SdssC, SaasC, SaaaC, SssssC	**
	SsNH3p, SsNH2, SssNH2p, SdNH, SssNH, SaaNH, StN, SsssNHp, SdsN, SaaN, SsssN, SddsN, SaasN, SssssNp	**
	SsOH, SdO, SssO, SaaO	**
	SsF	**
	SsSiH3, SssSiH2, SsssSiH, SssssSi	-
	SsPH2, SssPH, SsssP	*		not likely non-zero
	SdsssP, SsssssP	**
	SsSH, SdS, SssS, SaaS, SdssS, SddssS, SssssssS	**
	SsCl	**
	SsGeH3, SssGeH2, SsssGeH, SssssGe	-
	SsAsH2, SssAsH, SsssAs, SdsssAs, SsssssAs	-
	SsSeH, SdSe, SssSe, SaaSe, SdssSe, SddssSe	-
	SsBr	**
	SsSnH3, SssSnH2, SsssSnH, SssssSn	-
	SsI	**
	SsPbH3, SssPbH2, SsssPbH, SssssPb	-
22-28	CHsOH - CssssPb	n/a	Atom Type Counts for atom types in records 15-21	average atom-type E-State, i.e., records 15-21 divided by records 22-28, may be useful
29	HES1 - HES15	n/a	Hydrogen Electrotopological state index values for atoms 1-15	these sets of atom-level indices can be used in QSAR, but are dependent upon constant atom numbering in a common core
30	HES16 - HES30	n/a	Hydrogen Electrotopological state index values for atoms 16-30
31	HES31 - HES45	n/a	Hydrogen Electrotopological state index values for atoms 31-45
32	HES46 - HES60	n/a	Hydrogen Electrotopological state index values for atoms 46-60
33	HES61 - HES75	n/a	Hydrogen Electrotopological state index values for atoms 61-75
34	HES76 - HES90	n/a	Hydrogen Electrotopological state index values for atoms 76-90
35	IdW - IdC	-	Bonchev-Trinajstic information indices
	W	-	Wiener number
	Wp	-	Wienerp
	Pf	-	Plattf
	Wt	-	total Wiener number
	knotp	-	difference of chi-cluster-3 and path/cluster-4
	knotpv	-	valence difference of chi-cluster-3 and path/cluster-4
	nclasss	*	number of classes of topologically (symmetry) equivalent graph vertices
	numHBd	*	number of hydrogen bond donors
	numwHBd	*	number of hydrogen bond donors
	numHBa	*	number of hydrogen bond acceptors
36	nxp1 - nxp10	n/a	counts of path subgraphs	indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis
	nxc3,nxc4	n/a	counts of cluster subgraphs
	nxpc4	n/a	count of path/cluster-4 subgraphs
	nxch3 - nxch10	n/a	counts of chain subgraphs
	ntpath	n/a	total number of paths
	diam	n/a	graph diameter
	muldiam	n/a	multiplicity of diameter
	rad	n/a	graph radius
	mulrad	n/a	multiplicity of radius
	ishape	n/a	(diam - rad)/rad
37	nasH	n/a	number of atoms of element Hydrogen	indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis
	...	n/a	...
	nasZn	n/a	number of atoms of element Zinc
38	nasGa	n/a	number of atoms of element Gallium
	...	n/a	...
	nasW	n/a	number of atoms of element Tungsten
39	nasRe	n/a	number of atoms of element Rhenium
	...	n/a	...
	nasRn	n/a	number of atoms of element Radon
40	nd1	n/a	number of vertexes for which delta d = 1	indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis
	...	n/a	...
	nd6	n/a	number of vertexes for which delta = 6
	ne11	n/a	number of edges between d=1 and d=1
	...	n/a	...
	ne16	n/a	number of edges between d=1 and d=6
	ne22	n/a	number of edges between d=2 and d=2
	...	n/a	...
	ne26	n/a	number of edges between d=2 and d=6
	...	n/a	...
	ne66	n/a	number of edges between d=6 and d=6
	tg - tg3	n/a	terminal groups/ tg separated by 3 edges
	tm - tm3	n/a	terminal methyls/ tm separated by 3 edges
41	n2pe11	n/a	number of vertices with d=1 and d=1 separated by 2 edges	indices computed by Molconn-Z which are not used for QSAR analysis but are used for other kinds of structure analysis
	...	n/a	...
	n2pe66	n/a	number of vertices with d=6 and d=6 separated by 2 edges
42	n3pe11	n/a	number of vertices with d=1 and d=1 separated by 3 edges
	...	n/a	...
	n3pe66	n/a	number of vertices with d=6 and d=6 separated by 3 edges
43	n4pe11	n/a	number of vertices with d=1 and d=1 separated by 4 edges
	...	n/a	...
	n4pe66	n/a	number of vertices with d=6 and d=6 separated by 4 edges
44	ec1 - ec30	n/a	vertex eccentricities for vertices 1 to 30
45	ec31 - ec60	n/a	vertex eccentricities for vertices 31 to 60
46	ec61 - ec90	n/a	vertex eccentricities for vertices 61 to 90
47	SHCsats	**	E-State of C sp³ bonded to other saturated C atoms
	SHCsatu	**	E-State of C sp³ bonded to unsaturated C atoms
	SHvin	**	E-State of C atoms in the vinyl group, =CH-
	SHtvin	**	E-State of C atoms in the terminal vinyl group, =CH₂
	SHavin	**	E-State of C atoms in the vinyl group, =CH-, bonded to an aromatic C
	SHarom	**	E-State of C sp² which are part of an aromatic system
	SHHBd	**	hydrogen bond donor index, sum of Hydrogen E-State values for -OH, =NH, -NH2, -NH-, -SH, and #CH
	SHwHBd	**	weak hydrogen bond donor index, sum of C-H Hydrogen E-State values for hydrogen atoms on a C to which a F and/or Cl are also bonded
	SHHBa	**	hydrogen bond acceptor index, sum of the E-State values for -OH, =NH,- NH2, -NH-, >N-, -O-, =O, -S- along with -F, and -Cl
	Qv	**	General Polarity descriptor
48	NHBint2	*	count of potential internal hydrogen bonders
	...	*	...
	NHBint10	*	count of potential internal hydrogen bonders
	SHBint2	*	E-State descriptors of potential internal hydrogen bond strength
	SHBint3 - SHBint6	**	E-State descriptors of potential internal hydrogen bond strength
	SHBint7 - SHBint10	*	E-State descriptors of potential internal hydrogen bond strength
49	elem1 - elem7	*	elements in structures molecular formula
50	count1 - count7	*	count of atoms for elements in structures molecular formula