Support for bond orders

Jmol supports bond orders (i.e., different from single bonds).

File formats that specify bond order --and Jmol recognizes as such:

• MOL specifies bond order natively, using certain numeric codes (see table below)
• MOL2 specifies bond order natively, using certain alphanumeric codes (see table below)
• PDB can do it using a trick: specify twice each CONECT record for a double bond.

Jmol commands that assign bond order:

• connect accepts parameters (see table below)
• bondOrder (new in Jmol 11.3.x) accepts parameters (see table below)

Visualization of non-single bonds can be supressed (all will show as single) if set showMultipleBonds off is issued.

bond order	Jmol syntax	bond code in MOL file	bond code in MOL2 file
0.5	hBond	n/a	n/a
0.5	partial	8	n/a
1	single	1	1
1.5	partialDouble	5	n/a
1.5	aromatic	4	ar
2	double	2	2
2.5	partialTriple	n/a	n/a
3	triple	3	3
4	quadruple	n/a	n/a

Note :

Contributors

AngelHerraez, NicolasVervelle