Quelltext der Seite Xyz2cane.exe

=== Synopsis ===

* Bestimmung von CANE-Zahlen
* Bestimmung von strukturellen Aromatizitästkriterien
* liest die von [[seqlog2xyz.exe]] zusammentragenen diversen Aromatizitästkriterien aus verschiedenen xyz-Quellen in den xyz-Kommentarzeilen.
* Position von ghost-atoms berechnen.
* ISE/FISE Substitution
* Eier legen, Milch geben, Wolle produzieren.

Nützlich für:

* conformational search
* Annulene

=== Installation ===
* alle acid-Rechner
* [http://scholle.oc.uni-kiel.de/herges/download/arbeiten/koehler_dissertation_2008_install.zip Download ]
* Gitrepo: '''sftp://acid8/home/koehler/gitmaster/cpp_thesis'''

=== Usage ===
Kommandozeile. Beispiel:
 xyz2cane -s sel/c12ringtors.sel -i cs/c12_mmp_csearch.xyz -o c12_mmp_csearch.cane.xyz -v > c12_mmp_csearch.cane.csv

=== Longhelp ===
 xyz2cane 1.0.4
       (c) 2006, 2007 Felix Koehler
 Synopsis:
    Writes a (CANE) Canonical Enumeration nomenclature string list 
    for all structures in xyzfile.
 Usage:  xyz2cane <Options>
 Options:
   -s <selectionname> name of the selection file
   -d : don't delete double cane values with same energy
   -i <xyzname>  name of the xyz input file
   -n <nicsname> name of the xyz file with nics positions as ghost atoms
                 (Bq)
   -o <cleanxyzname>  name of the xyz outputfile, doublettes cleaned out
   -m <mutatealgorithm>: Produce xyzfiles with inden and isoinden derivates
                         into structure. 8 is standard algorithm.
                         1:  substitute preferably at outer atoms
                         ....
                         8:  substitute preferably at most planar section
 
                         1: ~ centerdistance
                         2: ~ planarity * centerdistance
                         3: ~ planarity * scaled centerdistance
                         4: ~ planarity^2 * centerdistance
                         5: ~ planarity^2 * scaled centerdistance
                         6: ~ planarity^3 * centerdistance
                         7: ~ planarity^3 * scaled centerdistance
                         8: ~ planarity
   -x <maxbondlength> : only in combination with -m option. Maximum
                        allowed bondlength for substitution. Default is 
                        1.40, which is larger than the aromatic bond in benzene
                        Use this to make sure isoinden/indene substitutiuon is
                        never at single bonds.
   -v : verbose output
   -V : output version and exit
   -vv : very verbose output, prints distances and dieders
   -c : comments contain alternate number for structure
   -e <energy> :  energy difference where structures still are considered
                  to be of same energy, default = 0.05 kcal/mol.