Re: [Jmol-users] new feature: Z-matrix reader

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

More capabilities:

version=12.3.7_dev

# new feature: simple Z-Matrix reader
#  -- invoked by ZMATRIX:: or file starting with #ZMATRIX
#  -- lines starting with # are comments, which can contain jmolscript:
#  -- blank lines are ignored
#
#  #ZMATRIX -- methane
#  C
#  H   1 1.089000
#  H   1 1.089000  2  109.4710
#  H   1 1.089000  2  109.4710  3  120.0000
#  H   1 1.089000  2  109.4710  3 -120.0000
#
#  -- allows bond order specification
#
#  #ZMATRIX -- CO2
#  C
#  O   1 1.3000                 2
#  O   1 1.3000    2  180       2
#
#  -- any position number may be replaced by a unique atom name, with
number:
#
#  #ZMATRIX -- CO2
#  C1
#  O1   C1 1.3000                2
#  O2   C1 1.3000    O1  180     2
#
#  -- allows for dummy atoms Xn, allowing for positioning:
#
#  #ZMATRIX -- CO2
#  X1
#  X2   X1 1.0
#  C1   X1 1.0       X2 90
#  O1   C1 1.3000    X2 90   X1 0  2
#  O2   C1 1.3000    O1 180  X2 0  2
#
#  -- negative distance indicates that the second angle is a normal angle,
not a dihedral
#
#  #ZMATRIX -- NH3 (using simple angles only)
#  N1
#  H1 N1 1.0
#  H2 N1 1.0 H1 107
#  H3 N1 -1.0 H1 107 H2 107
#
#  -- negative distance and one negative angle reverses the chirality
#
#  #ZMATRIX -- NH3 (using simple angles only; reversed chirality)
#  N1
#  H1 N1 1.0
#  H2 N1 1.0 H1 107
#  H3 N1 -1.0 H1 -107 H2 107


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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