Q2M(1OSC) OSC utilities Q2M(1OSC)
NAME
q2m - convert cartesian coordinate table to Sybyl MOL file
SYNOPSIS
q2m [ -i inpfile ] [ -o outfile ] [ -s string ] [ -f optfile
] [ -n molname ] [ -d length ] [ -m unit ] [ -l link-list ]
[ -u unlink-list ] [ -a maxatoms ] [ -b maxbonds ] [ inpfile
[ outfile ] ]
DESCRIPTION
The program q2m converts a table of cartesian coordinates of
atoms to a SYBYL MOL file format (SYBYL is a trademark of
Tripos Associates). It creates appropriate atom types and
bond types based on interatomic distances. The table of
cartesian coordinates has to contain one column which iden-
tifies element either by its chemical symbol, or atomic
mass, or atomic number. The MOL file so created can be read
into SYBYL for display or further manipulation.
OPTIONs
Option arguments contain characters which are frequently
conflicting with the shell interpretation. For safety, it is
advised that inclose them in single quotes.
-i inpfile
File inpfile contains cartesian coordinates. If inpfile
is not specified, standard input (stdin) is assumed.
inpfile can be also specified without -i option letter
as the first argument after all options.
-o outfile
File outfile will contain resulting MOL file. If out-
file is not specified standard output (stdout) is
assumed. outfile can be also specified without -o
option together with inpfile after all options as the
second argument.
-s string
The order and type of columns in the table is given by
string. Column is a series of nonblank characters fol-
lowed by one or more spaces or TABs. The following
colum types are recognized: M - atomic mass, A - atomic
number, C - chemical symbol (may be followed by digits
or other characters), S - column to discard, X - X
coordinate, Y - Y coordinate, Z - Z coordinate. Only
one M, A, or C column may be specified. The X, Y, or Z
columns cannot be repeated.
-f optfile
The options will be read from optfile. The optfile con-
tains options in the same format as if they appeared on
the command line.
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Q2M(1OSC) OSC utilities Q2M(1OSC)
-n molname
Using this option you can specify molecule name to be
included in the MOL file or otherwise it will be set to
"Unknown".
-d length
This is the length of longest possible bond [in
Angstroms] in the molecule. All atoms closer to each
other than length are considered bonded by a chemical
bond. Exception is used for hydrogen atoms. Two hydro-
gen atoms are considered bonded only if they are closer
than 0.8 Angstrom. If length is not specified 1.7
Angstrom is assumed.
-m unit
The coordinates in the input file may be specified in B
(bohrs, i.e. atomic units) N (nanometers) A
(Angstroms). If this option is not specified, Angstroms
are assumed.
-l link-list
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 link-list consist of entries of a
type ibj separated by commas or spaces. i is the number
of first atom, j is a number of second atom and b
specifies a type of bond between them. The bond type 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 com-
parisons. The link-list should be enclosed in single
quotes for safety.
-u unlink-list
Sometimes you want to remove some bonds which were
found by simple distance check. This option removes
bonds between atom pairs specified by unlink-list. Atom
numbers and their pairs can be separated by spaces or
any other nondigit characters.
-a maxatoms
If your coordinate table may contain more than 100
atoms, you need to specify larger limit for number of
atoms with this option.
-b maxbonds
If your molecule may contain more than 200 bonds, you
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Q2M(1OSC) OSC utilities Q2M(1OSC)
need to specify larger limit for number of bonds with
this option.
EXAMPLES
q2m -s SXYZM -m B -d 1.6 -l 1-4,1=2 -n propanal test.inp
requests that file test.inp is converted to MOL file and
sent to standard ouput. The coordinates are given origi-
nally 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.
FILES
The program resides in /loclib/q2m directory. Examples of
use are given in /loclib/q2m/test. The docs are in
/loclib/q2m/doc.
SEE ALSO
To familiarize yourself with MOL file format read appropri-
ate pages of SYBYL manual or use on-line help facility of
SYBYL.
DIAGNOSTICS
Most error messages are self-explanatory.
BUGS
Program does not find some atoms types and you have to enter
correct types by editing resulting 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.
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.
OSC Last change: 27 Mar 1991 3
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