Acca
Version 0.931
Acca is a program which assists in conformation searching.
It takes an input file of structures in the MacroModel
format, and produces an output file of these structures
transformed in some way. The program is controlled by a
command file.
The program is invoked by typing:
acca COMFL
where COMFL is the name of the command file.
The first line of the command file is the name of the
input file. The second line is the name of the output
file. The rest of the file is a list of commands. Acca
keeps a log of its actions in COMFL.log.
The maximum number of commands is one hundred.
The commands that are currently available are:
- COMM: Comment line
- DEBG: Debug options
- FLIP: Flip a chiral centre
- CHNG: Change one group into another
- JOIN: Make a new bond
- INVT: Invert the whole structure
- ROTA: Rotate a sidechain
- DROT: Double rotation (Simple systematic search)
- WRIT: Write a structure
- DATM: Delete an atom
- DATT: Delete all atoms of a particular type
- DBND: Delete a bond
- CATM: Change an atom type
- HH2O: Turn isolated oxygen atoms into H2O
- FLTD: Filter structures, based on an atomic distance
- DBLE: Turn a CH2 into a ketone or C=CH2
- SBCF: Name of the Substructure Constraint File
- SROT: Set a torsion angle
- LROT: List torsion angles
- ADDA: Add atom to the end of the file
- BNDO: Change the order of an existing bond
The first two lines of COMFL are filenames, and all
the rest begin with a four letter code, followed by a space
followed by any data required, in a free format way. Only the first
eighty characters of each line are read.
For example:
INFILE
OUTFILE
COMM DEBG 1 write extra information about the FLIP
COMM process to COMFL.log
DEBG 1
COMM Do a flip
FLIP 1 2 3 4 5
COMM Now change some atoms
CHNG 6 7 4 0 1
SBCF SBCFIL
COMM Now join up a pair of atoms
JOIN 6 7 8 9 10 11 2.0
COMM A WRIT command is implicit at the end of every command file
More examples
FLIP, CHNG, JOIN commands can be put consecutively,
and will be executed in the right order. The atom numbers
must be correct for the molecule in its current state,
so, for example, if a FLIP is done after a CHNG, the atom
numbers correspond to the CHNGed structure.
Acca may create and delete temporary files,
called COMFL.tmpacca.*
Acca source code is not available, but the executable
may be downloaded. This documentation may not be copied
without the written permission of the author.
|
