Re: [Jmol-users] bondOrder - what about 2.5 ? or 5.1 or 3.2....

[Bob H. <ha...@st...>]

OK, here is a total generalization of partial bonds. With this (11.3.28) 
you can draw any type of partial whatever up to 5 bonds. Works in 
bondOrder and connect, both:

  bondorder partial N.M
  connect (atomexpr1) (atomexpr2) partial N.M

where N is the number of bonds you want (1-5)
and M is a "bitmask" indicating which of those lines you want dotted.

You have to work in binary for this:

M   binary   meaning
0     00000  no lines dotted
1     00001  first line dotted
2     00010  second line dotted
3     00011  first and second line dotted
4     00100  third line dotted
....
31   11111 all (five) lines dotted

The following are equivalent IN APPEARANCE ONLY:

partial 1.0      single
partial 1.1      partial
partial 2.0      double
partial 2.1      aromatic
partial 2.2      partialDouble
partial 3.1      partialTriple
partial 3.4      partialTriple2

"Appearance only" in that if you create bonds of the type "partial 1.0" 
they look like single bonds, but they won't be found using

  x = connected("single")

Instead, for those you would have to use:

x = connected("partial 1.0")

Please do not ask for partial 6.1. We're out of bits.

:)

Bob


Angel Herraez wrote:

>Bob's and Nick's comments reminded me of a limitation I found out 
>this summer: 1,5 order bond order is not recognized from MDL MOL 
>files.
>To summarize current state (tested in 11.3.26):
>
>Bond order 0.5:
>	"partial" in connect and bondOrder commands
>	unavailable in MOL, but could be type 8 ("any"); Jmol already 
>renders 8 as partial.
>
>Bond order 1:
>	"single"
>	type 1 in MOL
>
>Bond order 1.25:
>	not implemented in Jmol
>	type 6 in MOL, "single/aromatic" [[ I don't think there is need to 
>support this ]]
>
>Bond order 1.5:
>	"partialDouble"
>	type 5 in MOL, but fails in Jmol, no bond is drawn [[ this must be 
>fixed, I see it as a bug ]]
>
>Bond order 1.5 also:
>	"aromatic"
>	type 4 in MOL
>
>Bond order 1.75:
>	not implemented in Jmol
>	type 7 in MOL, "double/aromatic" [[ I don't think there is need to 
>support this]]
>
>Bond order 2:
>	"double"
>	type 2 in MOL
>
>Bond order 2.5:
>	not implemented in Jmol, but requested
>	not available in MOL
>
>Bond order 3:
>	"triple"
>	type 3 in MOL
>
>Bond order 4:
>	"quadruple"
>	not available in MOL
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900