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
• 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.