I have tried a lot to convert pharmacophore created by ligandscout in hypoedit format into query file.chm
I used piplinepilot component pharmacophore generator hypoedit and checked true to intermediate files and here is the error page
I would like to point out that there is a dictionary.chm file which is distributed by the company and I should edit the hypoedit file to point to the location of the dictionary
..............................................
FILE: cannot open file: C:\Windows\system32\config\systemprofile\.Catalyst: No such file or directory
Successfully opened file hypoedit_input.txt (C:\ligandscout/hypoedit_input.txt).
Need to specify
Usage: hypoedit -desc file (file contains command line parameters) or
Usage: hypoedit [OPTIONS] []
where options are:
-desc parameters are read from , not command line
-blobtodist replace blobs with dists
-sdtoshape converts the MDL SD to a shape query
and writes shape query to
Note: Parameters (e.g. Similarity Min, Max) are read
from [Install Directory]/share/Catalyst/conf/shapeConstraints
file. To change
these, copy constraints file locally and edit
-fittoand replace all FIT operators with ANDs
-xvolfactor replace all excluded volume xfactors with
-scaletol scales all blob tolerances by
-scaledist scales all distance tolerances by
-dilate dilate blob locations by factor
-mirror mirror images hypo
-dict dictionary file
-feat add feature of specified definition.
-blob add blob on -th point in query
-blobn add blob on next point in query
-dist add distance between points and
-angle add angle for points , , and
angles are radian values. range: 0 to PI
-torsion add torsion for points , ,,
angles are radian values. valid range: -PI to PI
-xvol add excluded volume sphere
-setFeatCoords set feature coordinates based on blob coordinates
-dbin make query for dist bin. E.g.: = AHH223121
-cpddir
-moldir
-spst
-xgen generate excluded volumes according to
-xsur generate excluded volumes surrounding mols in
................................................
the file which i want to convert
\$CATALYST_BIN/hypoedit \
-dict \$CATALYST_DICTIONARY/Dictionary.chm \
-feat "HBA-F" \
-feat "HYDROPHOBIC" \
-feat "HYDROPHOBIC" \
-feat "HBA-F" \
-feat "HBA-F" \
-feat "HYDROPHOBIC" \
-feat "HBA-F" \
-blob -834.79993 4272.10010 -1039.20007 100.00000 1 \
-blob -1086.40002 4052.10010 -906.40002 150.00000 2 \
-blob -1106.38330 4466.43896 -1460.73889 150.00000 3 \
-blob -543.29999 4316.43311 -1295.86670 150.00000 4 \
-blob -1019.40002 4725.79980 -652.59998 100.00000 5 \
-blob -955.00000 4807.60010 -417.99997 150.00000 6 \
-blob -1152.09998 4626.10010 -1096.50000 100.00000 7 \
-blob -1312.69995 4778.79980 -990.20007 150.00000 8 \
-blob -921.94165 4313.88037 -514.29669 150.00000 9 \
-blob -1219.59998 4589.30029 -694.70001 100.00000 10 \
-blob -1312.69995 4778.79980 -990.20007 150.00000 11 \
-xvol -902.29999 4671.39990 -1667.30005 150.00000 \
-xvol -671.60004 4357.30029 -99.40000 100.00000 \
-xvol -595.69446 4787.33887 -1044.54993 150.00000 \
-xvol -1321.19995 4459.40039 -1936.40002 100.00000 \
-xvol -935.09998 4904.00000 -910.59998 100.00000 \
-xvol -633.40002 3852.69995 -313.89999 100.00000 \
-xvol -933.13330 4081.41089 -1804.96118 150.00000 \
-xvol -1383.90002 4806.50000 -1794.89990 100.00000 \
-xvol -352.62039 4559.04102 -1712.16467 150.00000 \
-xvol -361.86667 3958.83325 -1594.63342 150.00000 \
-xvol -720.40002 4662.50000 -1460.09998 150.00000 \
-xvol -595.20831 4679.90576 -542.15277 150.00000 \
-xvol -1246.50000 5027.39990 -734.29999 100.00000 \
out.chm
I used piplinepilot component pharmacophore generator hypoedit and checked true to intermediate files and here is the error page
I would like to point out that there is a dictionary.chm file which is distributed by the company and I should edit the hypoedit file to point to the location of the dictionary
..............................................
FILE: cannot open file: C:\Windows\system32\config\systemprofile\.Catalyst: No such file or directory
Successfully opened file hypoedit_input.txt (C:\ligandscout/hypoedit_input.txt).
Need to specify
Usage: hypoedit -desc file (file contains command line parameters) or
Usage: hypoedit [OPTIONS] [
where options are:
-desc
-blobtodist replace blobs with dists
-sdtoshape
and writes shape query to
Note: Parameters (e.g. Similarity Min, Max) are read
from [Install Directory]/share/Catalyst/conf/shapeConstraints
file. To change
these, copy constraints file locally and edit
-fittoand replace all FIT operators with ANDs
-xvolfactor
-scaletol
-scaledist
-dilate
-mirror mirror images hypo
-dict
-feat
-blob
-blobn
-dist
-angle
angles are radian values. range: 0 to PI
-torsion
angles are radian values. valid range: -PI to PI
-xvol
-setFeatCoords set feature coordinates based on blob coordinates
-dbin
-cpddir
-moldir
-spst
-xgen
-xsur
................................................
the file which i want to convert
\$CATALYST_BIN/hypoedit \
-dict \$CATALYST_DICTIONARY/Dictionary.chm \
-feat "HBA-F" \
-feat "HYDROPHOBIC" \
-feat "HYDROPHOBIC" \
-feat "HBA-F" \
-feat "HBA-F" \
-feat "HYDROPHOBIC" \
-feat "HBA-F" \
-blob -834.79993 4272.10010 -1039.20007 100.00000 1 \
-blob -1086.40002 4052.10010 -906.40002 150.00000 2 \
-blob -1106.38330 4466.43896 -1460.73889 150.00000 3 \
-blob -543.29999 4316.43311 -1295.86670 150.00000 4 \
-blob -1019.40002 4725.79980 -652.59998 100.00000 5 \
-blob -955.00000 4807.60010 -417.99997 150.00000 6 \
-blob -1152.09998 4626.10010 -1096.50000 100.00000 7 \
-blob -1312.69995 4778.79980 -990.20007 150.00000 8 \
-blob -921.94165 4313.88037 -514.29669 150.00000 9 \
-blob -1219.59998 4589.30029 -694.70001 100.00000 10 \
-blob -1312.69995 4778.79980 -990.20007 150.00000 11 \
-xvol -902.29999 4671.39990 -1667.30005 150.00000 \
-xvol -671.60004 4357.30029 -99.40000 100.00000 \
-xvol -595.69446 4787.33887 -1044.54993 150.00000 \
-xvol -1321.19995 4459.40039 -1936.40002 100.00000 \
-xvol -935.09998 4904.00000 -910.59998 100.00000 \
-xvol -633.40002 3852.69995 -313.89999 100.00000 \
-xvol -933.13330 4081.41089 -1804.96118 150.00000 \
-xvol -1383.90002 4806.50000 -1794.89990 100.00000 \
-xvol -352.62039 4559.04102 -1712.16467 150.00000 \
-xvol -361.86667 3958.83325 -1594.63342 150.00000 \
-xvol -720.40002 4662.50000 -1460.09998 150.00000 \
-xvol -595.20831 4679.90576 -542.15277 150.00000 \
-xvol -1246.50000 5027.39990 -734.29999 100.00000 \
out.chm