.TH "CHT" "1" "June 17, 2001" "1.6.13" "User commands"

.SH NAME
cht \- chemtool drawings analyzer

.SH SYNOPSIS
.B cht
.RB [ options ]
.I filename.cht

.SH DESCRIPTION
.B cht
is a commandline tool to derive the sum formula and molecular
mass of the molecule depicted in a
.B chemtool 
drawing file.
It is also available from within \fBchemtool\fR to calculate these data for
the current structure or a marked fragment of it. 
.PP
.B cht
currently recognizes the element symbols  C, H, O, N, P, S, Si, B, Br, Cl, F,
I, Al, As, Ba, Be, Bi, Ca, Cd, Co, Cr, Cs, Cu, Fe, Ga, Ge, In, K, Li, Mg, Mn,
Na, Ni, Pb, Rb, Sb, Sc, Se, Sn, Sr, Te, Ti, Tl, V, Zn (that is, all main group 
elements except the noble gases, and the first row of transition metals) 
and the abbreviations Ac, Ade, Bn, Bu, iBu, tBu, Bz, BOC, Cyt, CE, DBAM, 
DMAM, DMTr, Et, Gua, Me, Ms, MOC, MOM, MMTr, Ph, Pr, iPr, Tf, Thy, Tol,
Tr, Ts, TBDMS, TBDPS, TMS, TMTr, Ura, Z.
.PP
It can handle two levels of parentheses; e.g. P[OCH(CH_3)_2]_3.
.PP
When 
.B cht
detects any duplicate (overlapping) bonds in the drawing file, it will 
prepend an exclamation mark to the calculated (and likely wrong) sum
formula.

.SH OPTIONS
.B cht
understands the following options:
.TP
.B \-h, \-\-help
Displays brief help and list of options.
.TP
.B \-e, \-\-exact
Calculate exact mass for MS.
.TP
.B \-v, \-\-verbose
Be verbose.
.TP
.B \-d, \-\-debug
Be extremely verbose.

.SH BUGS
.B cht
can misinterpret molecules that contain the 'aromatic ring' symbol, as it
uses a fixed search radius to identify the aromatic system that it denotes.
It also does not handle the 'partial double bond', so you should avoid these
two in drawings that you intend to use with \fBcht\fR.
.PP
A label that is offset from the corresponding bond end by
more than five pixels is not recognized, so that the default CH2 or CH3 
group enters the calculation in its place.
.PP
In general, one should check 
the plausibility of the generated sum formula wherever possible.

.SH SEE ALSO
.BR chemtool (1)

.SH AUTHOR
\fBRadek Liboska\fR