Лаборатория изучения механизмов органических реакций

cfxyz

Usage: cfxyz files.xyz vs. FILES.xyz

  Compare spatial structures for each of files.xyz with each of FILES.xyz.
  Comparison is independent of order of atom's numeration.
  
'vs.' divides comparable molecules (from files.xyz) 
  and reference ones (from FILES.xyz)
  
  Another usage: cat files.xyz | cfxyz FILES.xyz
  f.e. xyz -n=1,-1 IRC.xyz | cfxyz *.O.xyz
  
  If file.xyz contains several molecules (concatenated xyz) 
  then each molecule is named as 'file_n'. Piped molecules is named as 'pipe_n'.
  
  -chiral  optical isomers are not identical
  -RMS=0.1  molecules are not identical if RMSD > 0.1
  -W  all atom weight to be equal 1 (default RMS is in sqrt(amu)*anstrom units).
      Don't take into account atom types for -dist.
  -H  don't take into account hydrogens
  -all  compare all files with each other: cfxyz -all FILES.xyz
  -pair compare 1st from files.xyz with 1st from FILES.xyz, 2nd with 2nd, etc
  -dih='i,j,k,l i1,j1,k1,l1, ...' compare by dihedrals, default -RMS=30 deg. 
  -dih=i,j,k,l,m,n,i,j,k  shorthand for sequential dihedrals (e.g. for cycles)
  -dihf=dihedrals  compare by dihedrals provided in 'dihedrals' file
     (dihedral per line, numbers of atoms through spaces)
     Automatic genaration of dihedrals: dih_list file.xyz > dihedrals
  -dist  use modified Grigoryan-Springborg algorithm (distance matrix) for 
         comparison. -chiral doesn’t affect
  -renum  cfxyz -renum *.xyz  OR  cat *.xyz | cfxyz -renum
          Renumbers the structures (each by the previous one) and 
          prints xyz to stdout.
  -verbose  more detailed output