Most data are stacked in a large array, either bottom-up or top down, so that the stack size is
the limiting factor for the size of the problem that the program can handle. The program
reports on the maximum memory usage in the current run. The stack size is a program
implementation parameter.
The input list of atoms is checked on redundancy.
DATA and INSTRUCTION FILES
The order in which data are read is as follows:
- The primary datafile (e.g. sucrose.spf) is read. When an EOF or ENDS line is
encountered:
- A file named sucrose.def (when present) is read.
- Saved Instructions are read
−
Instructions from the keyboard or Mouse-clicks are processed
3.4 - Terms and Notions.
Connected sets of atoms are assembled in the following way. The procedure is started by
first fixing a suitable atom. Next symmetry operations are performed on all atoms in the
input set to find atoms that are connected to it. Atoms that are found to be connected are
fixed as well and used to fix yet other, possibly symmetry transformed, atoms bonded to
them as well. This procedure continues until no new bonded atoms are found. In the simple
case of one chemical unit per asymmetric unit this constitutes an object named a molecule
and is denoted with the identity code 1555. Symmetry related molecules are denoted by the
general code sklm, where s is the number of the symmetry operation of the space group and
k,l and m translation components. Chemical units may extend over more than one
asymmetric unit. They may have a symmetry element that coincides with the space group
symmetry such as an inversion centre or a screw axis. In such cases we will find atoms in
the above search for a connected set of atoms that are bonded to the connected set at a
position different from the one that was fixed in view of an earlier connection. Those atoms
are added to the connected set and marked as symmetry related. The symmetry operation of
this atom with respect to the primary one is coded and added to the molecule (aru) list. A
chemical unit around an inversion centre thus consists in the PLUTO78 terminology of two
molecules: 1555 and 2555. A further complication may be the presence of more than one
crystallographically independent chemical unit in the unit cell (including solvent molecules
and anions). In that case not all atoms will be fixed when the above procedure comes to an
end when no more connected atoms are found. In that case a new residue is started by again
arbitrarily fixing a suitable atom and expanding it to a connected set. A particular residue r
within a molecule is indicated with the code sklm.rr (e.g. 3564.03). It is understood that the
code without a fraction stands for the full collection of residues. Thus in the case of two
residues the molecule code 2562 is equivalent with the two residue codes 2562.01 and
2562.02. In order to be more precise two new terms have been introduced in PLUTON and
PLATON. The basic structural unit is the asymmetric residue unit ( = ARU) coded as
sklm.rr. A molecule (ion) will will be an assembly of at least one aru. The set of aru's
making up the asymmetric structural unit are called asu and encoded as sklm.
Disorder. Based on the supplied population parameters an attempt is made to suppress
bonds between disorder parts with unequal population parameter values.