.TH Q2M 1OSC "27 Mar 1991" OSC "OSC utilities"
.SH NAME
q2m \- convert cartesian coordinate table to Sybyl MOL file
.SH SYNOPSIS
.B q2m 
[
.B -i
.I inpfile
]
[
.B -o
.I outfile
]
[
.B -s
.I string
]
[
.B -f
.I optfile
]
[
.B -n
.I molname
]
[
.B -d
.I length
]
[
.B -m
.I unit
]
[
.B -l
.I link-list
]
[
.B -u
.I unlink-list
]
[
.B -a
.I maxatoms
]
[
.B -b
.I maxbonds
]
[
.I inpfile
[
.I outfile
]
]
.br
.SH DESCRIPTION
The program
.B q2m
converts a table of cartesian coordinates of atoms to a
.I SYBYL
.B MOL
file format (\c
.I SYBYL
is a trademark of
.I Tripos Associates\c
). It creates appropriate atom types
and bond types based on interatomic distances. The table of cartesian
coordinates has to contain one column which identifies element either by
its chemical symbol, or atomic mass, or atomic number. The MOL file so created
can be read into
.I SYBYL
for display or further manipulation.
.SH OPTIONs
Option arguments contain characters which are frequently conflicting with
the shell interpretation. For safety, it is advised that inclose them in
single quotes.
.IP "\fB-i\fP \fIinpfile\fP"
File
.I inpfile
contains cartesian coordinates. If
.I inpfile
is not specified, standard input (stdin) is assumed.
.I inpfile
can be also specified without
.B -i
option letter as the first argument after all
options.
.IP "\fB-o\fP \fIoutfile\fP"
File
.I outfile
will contain resulting
.B MOL
file. If
.I outfile
is not specified standard output (stdout) is assumed.
.I outfile
can be also specified without
.B -o
option together with
.I inpfile
after all options as the second argument.
.IP "\fB-s\fP \fIstring\fP"
The order and type of columns in the table is given by
.I string.
Column is a series of nonblank characters followed by one or more spaces or
TABs. The following colum types are recognized: 
.B M
- atomic mass,
.B A
- atomic number,
.B C
- chemical symbol (may be followed by digits or other characters),
.B S
- column to discard,
.B X
- X coordinate,
.B Y
- Y coordinate,
.B Z
- Z coordinate. Only one 
.B M,
.B A,
or
.B C
column may be specified. The
.B X,
.B Y,
or 
.B Z
columns cannot be repeated.
.IP "\fB-f\fP \fIoptfile\fP"
The options will be read from
.I optfile.
The
.I optfile
contains options in the same format as if they appeared on the command line.
.IP "\fB-n\fP \fImolname\fP"
Using this option you can specify molecule name to be included in the
.B MOL
file or otherwise it will be set to "Unknown".
.IP "\fB-d\fP \fIlength\fP"
This is the
.I length
of longest possible bond [in Angstroms] in the molecule.
All atoms closer to each other than
.I length
are considered bonded by a chemical bond. Exception is used for hydrogen
atoms. Two hydrogen atoms are considered bonded only if they are closer than
0.8 Angstrom. If
.I length
is not specified 1.7 Angstrom is assumed.
.IP "\fB-m\fP \fIunit\fP"
The coordinates in the input file may be specified in
.I B
(bohrs, i.e. atomic units)
.I N
(nanometers)
.I A
(Angstroms). If this option is not specified, Angstroms are assumed.
.IP "\fB-l\fP \fIlink-list\fP"
Sometimes you want to include bonds which will not be found by a simple
distance checking. You may specify a list of bonded atom pairs and a type
of bond by which atoms are bonded. The
.I link-list
consist of entries of a type
.I ibj
separated by commas or spaces. 
.I i
is the number of first atom,
.I j
is a number of second atom and
.I b
specifies a type of bond between them. The bond type
.I b
may one of the following: : (unspecified - when bond type is not known),
- (single), = (double), # (triple), a (amide bond), r (aromatic), . (dummy -
not a true bond, but marker rather), u (unusual - nobody yet knows what it is).
This option may be used not only to add new bonds but also to specify
a correct bond type for bonds which are found from interactomic distance
comparisons. The
.I link-list
should be enclosed in single quotes for safety.
.IP "\fB-u\fP \fIunlink-list\fP"
Sometimes you want to remove some bonds which were found by simple distance
check. This option removes bonds between atom pairs specified by
.I unlink-list.
Atom numbers and their pairs can be separated by spaces or any other
nondigit characters.
.IP "\fB-a\fP \fImaxatoms\fP"
If your coordinate table may contain more than 100 atoms, you need to specify
larger limit for number of atoms with this option.
.IP "\fB-b\fP \fImaxbonds\fP"
If your molecule may contain more than 200 bonds, you need to specify
larger limit for number of bonds with this option.
.SH EXAMPLES
q2m -s SXYZM -m B -d 1.6 -l 1-4,1=2 -n propanal test.inp
requests that file
.B test.inp
is converted to MOL file and sent to standard ouput.
The coordinates are given originally in atomic units. The columns 2-4 contain
cartesian coordinates, while 5-th column contains atomic masses. Atoms are
considered bonded if they are closer than 1.6 Angstrom to each another.
The single bond is specified between atoms 1 and 4, and double bond between
atoms 1 and 2. 
.SH FILES
The program resides in /loclib/q2m directory. Examples of use are given in
/loclib/q2m/test. The docs are in /loclib/q2m/doc.
.SH SEE ALSO
To familiarize yourself with MOL file format read appropriate pages
of SYBYL manual or use on-line help facility of SYBYL.
.SH DIAGNOSTICS
Most error messages are self-explanatory.
.SH BUGS
Program does not find some atoms types and you have to enter correct
types by editing resulting
.B MOL
file. This program does not contain substructure searches necessary to match
some of the SYBYL atom types, however, most basic atom types are assigned
correctly. Report bugs to the author.
.SH AUTHOR
Jan Labanowski, Ohio Supercomputer Center,
1224 Kinnear Rd, Columbus, OH 43212-1163, ph. 614-292-9279, FAX: 614-292-7168,
e-mail: jkl@ccl.net, JKL@OHSTPY.BITNET.