tinkerxyz2sdf



tinkerxyz2sdf is able to update an existing SDF file with new coordinates taken from XYZ files which have been initially created by sdf2tinkerxyz, and then manipulated by TINKER. The original SDF file is read from standard input, while XYZ files by default are read from the current working directory; a different directory can be chosen with the -p command line option. If XYZ files were created by sdf2tinkerxyz with the -n command line option, this option must be used also with tinkerxyz2sdf. If several copies of the XYZ file are present, such as ligand.xyz, ligand.xyz_2, ligand.xyz_3, ligand.xyz_5 etc., the one with the highest number will be used, according to TINKER conventions. The updated SDF file is printed on the standard output, so that it can be easily piped into OpenBabel for conversion into a different format.


EXAMPLES

# Structures are read from the structures.sdf file, then converted to
XYZ and KEY files which are placed in the current working directory,
appending charge/bond keywowrds to the minimize.key KEY file. The
XYZ files are minimized and updated coordinates are written to the
structures_min.sdf file
sdf2tinkerxyz -k minimize.key < structures.sdf
for file in *.xyz; do
    base=`basename $file .xyz`
    minimize -k ${base}.key ${base}.xyz 0.001 > ${base}.out
done
tinkerxyz2sdf < structures.sdf > structures_min.sdf

# Structures are read from the ligands.mol2 file, then converted to
XYZ and KEY files which are placed in the xyz_ligands directory. The
XYZ files are minimized and updated coordinates are written to the
ligands_min.mol2 file
mkdir xyz_ligands
babel -imol2 ligands.mol2 -osdf \
    | sdf2tinkerxyz -p xyz_ligands -k minimize.key
for file in xyz_ligands/*.xyz; do
    base=`basename $file .xyz`
    minimize -k xyz_ligands/${base}.key \
        xyz_ligands/${base}.xyz 0.001 \
        > xyz_ligands/${base}.out
done
babel -imol2 ligands.mol2 -osdf \
    | tinkerxyz2sdf -p xyz_ligands \
    | babel -isdf -omol2 ligands_min.mol2

# the following command reads coordinates from the protein.pdb file
and outputs XYZ and KEY files in the current directory, appending
charge/bond keywords to the minimize.key KEY file. The protein
is then minimized and optimized coordinates are written to the
protein_min.pdb file
babel -ipdb protein.pdb -osdf \
| sdf2tinkerxyz -k minimize.key
minimize -k protein.pdb.key protein.pdb.xyz 0.01 > protein.pdb.out
babel -ipdb protein.pdb -osdf \
| tinkerxyz2sdf | babel -isdf -opdb protein_min.pdb

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Last update:
June 21. 2014 20:28:23

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