cht(1) [debian man page]

CHT(1)								   User commands							    CHT(1)

NAME

       cht - chemtool drawings analyzer

SYNOPSIS

       cht [options] filename.cht

DESCRIPTION

       cht  is	a  commandline	tool to derive the sum formula and molecular mass of the molecule depicted in a chemtool drawing file.	It is also
       available from within chemtool to calculate these data for the current structure or a marked fragment of it.

       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.

       It can handle two levels of parentheses; e.g. P[OCH(CH_3)_2]_3.

       When  cht  detects any duplicate (overlapping) bonds in the drawing file, it will prepend an exclamation mark to the calculated (and likely
       wrong) sum formula.

OPTIONS

       cht understands the following options:

       -h, --help
	      Displays brief help and list of options.

       -e, --exact
	      Calculate exact mass for MS.

       -v, --verbose
	      Be verbose.

       -d, --debug
	      Be extremely verbose.

BUGS

       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
       cht.

       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.

       In general, one should check the plausibility of the generated sum formula wherever possible.

SEE ALSO

       chemtool(1)

AUTHOR

       Radek Liboska

1.6.13								   June 17, 2001							    CHT(1)

trjorder(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       trjorder(1)

NAME

       trjorder - orders molecules according to their distance to a group

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       trjorder  -f  traj.xtc  -s  topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -[no]version -nice int -b time -e time -dt time
       -xvg enum -na int -da int -[no]com -r real -[no]z

DESCRIPTION

	trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate  (with  option   -z).   With
       distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected mole-
       cules will be reordered according to the shortest distance between atom number  -da in the molecule and all  the  atoms	in  the  reference
       group.  The  center of mass of the molecules can be used instead of a reference atom by setting	-da to 0.  All atoms in the trajectory are
       written to the output trajectory.

	trjorder can be useful for e.g. analyzing the n waters closest to a protein.  In that case the reference group would be  the  protein  and
       the  group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can
       be used with any Gromacs program to analyze the n closest waters.

       If the output file is a	.pdb file, the distance to the reference target will be stored in the B-factor field in order to color	with  e.g.
       Rasmol.

       With option  -nshell the number of molecules within a shell of radius  -r around the reference group are printed.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -o ordered.xtc Output, Opt.
	Trajectory: xtc trr trj gro g96 pdb

       -nshell nshell.xvg Output, Opt.
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -na int 3
	Number of atoms in a molecule

       -da int 1
	Atom used for the distance calculation, 0 is COM

       -[no]comno
	Use the distance to the center of mass of the reference group

       -r real 0
	Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein

       -[no]zno
	Order molecules on z-coordinate

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       trjorder(1)