Q2M(1OSC) OSC utilities Q2M(1OSC)
NAME
q2m - convert cartesian coordinate table to Sybyl MOL file
SYNOPSIS
q2m [ -i _i_n_p_f_i_l_e ] [ -o _o_u_t_f_i_l_e ] [ -s _s_t_r_i_n_g ] [ -f _o_p_t_f_i_l_e
] [ -n _m_o_l_n_a_m_e ] [ -d _l_e_n_g_t_h ] [ -m _u_n_i_t ] [ -l _l_i_n_k-_l_i_s_t ]
[ -u _u_n_l_i_n_k-_l_i_s_t ] [ -a _m_a_x_a_t_o_m_s ] [ -b _m_a_x_b_o_n_d_s ] [ _i_n_p_f_i_l_e
[ _o_u_t_f_i_l_e ] ]
DESCRIPTION
The program q2m converts a table of cartesian coordinates of
atoms to a _S_Y_B_Y_L MOL file format (_S_Y_B_Y_L is a trademark of
_T_r_i_p_o_s _A_s_s_o_c_i_a_t_e_s). 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 _S_Y_B_Y_L 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 _i_n_p_f_i_l_e
File _i_n_p_f_i_l_e contains cartesian coordinates. If _i_n_p_f_i_l_e
is not specified, standard input (stdin) is assumed.
_i_n_p_f_i_l_e can be also specified without -i option letter
as the first argument after all options.
-o _o_u_t_f_i_l_e
File _o_u_t_f_i_l_e will contain resulting MOL file. If _o_u_t_-
_f_i_l_e is not specified standard output (stdout) is
assumed. _o_u_t_f_i_l_e can be also specified without -o
option together with _i_n_p_f_i_l_e after all options as the
second argument.
-s _s_t_r_i_n_g
The order and type of columns in the table is given by
_s_t_r_i_n_g. 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 _o_p_t_f_i_l_e
The options will be read from _o_p_t_f_i_l_e. The _o_p_t_f_i_l_e 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 _m_o_l_n_a_m_e
Using this option you can specify molecule name to be
included in the MOL file or otherwise it will be set to
"Unknown".
-d _l_e_n_g_t_h
This is the _l_e_n_g_t_h of longest possible bond [in
Angstroms] in the molecule. All atoms closer to each
other than _l_e_n_g_t_h 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 _l_e_n_g_t_h is not specified 1.7
Angstrom is assumed.
-m _u_n_i_t
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 _l_i_n_k-_l_i_s_t
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 _l_i_n_k-_l_i_s_t consist of entries of a
type _i_b_j 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 _l_i_n_k-_l_i_s_t should be enclosed in single
quotes for safety.
-u _u_n_l_i_n_k-_l_i_s_t
Sometimes you want to remove some bonds which were
found by simple distance check. This option removes
bonds between atom pairs specified by _u_n_l_i_n_k-_l_i_s_t. Atom
numbers and their pairs can be separated by spaces or
any other nondigit characters.
-a _m_a_x_a_t_o_m_s
If your coordinate table may contain more than 100
atoms, you need to specify larger limit for number of
atoms with this option.
-b _m_a_x_b_o_n_d_s
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.
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