import  type={SDF <file=SDF filename>  \
    [y_var_name=<comma separated list | ALL>]  \
    | GRIDKONT [file=<.kont filename; defaults to grid.kont>]  \
    [replace_object_name={YES | NO; defaults to YES}]  \
    | MOE_GRID file=<file basename with regex>  \
    | MOLDEN file=<file basename with regex>  \
    | GRID_DX file=<file basename with regex>  \
    | FORMATTED_CUBE file=<file basename with regex>  [mo=<index number of MO to be imported | ALL; defaults to ALL>]  \
    | UNFORMATTED_CUBE file=<file basename with regex>  [mo=<index number of MO to be imported | ALL; defaults to ALL>]  \
    | GRID_ASCII file=<file basename with regex>  \
    | FREE_FORMAT file=<filename>  [skip_header=<number of values to be skipped>]  \
    [data_order=<coordinate variation speed from the fastest to the slowest; defaults to Z_COORD,Y_COORD,X_COORD,N_OBJECT,N_FIELD>];  \
    | DEPENDENT file=<text file with biological activities>  \
    [y_var_name=<comma separated list | ALL; defaults to ALL>]


The import keyword is used to import 3D molecular structures, molecular interaction fields or dependent variables from different sources identified by the type keyword.

In particular, 3D molecular structures can be imported from SDF (type=SDF) files, as generated by most molecular modelling packages. If the SDF file includes also fields with biological activity data, it is possible to import them through the y_var_name parameter, indicating the field names which should be imported. If multiple activity fields are to be imported, their names must be separated by commas. If, for instance, both pIC50 and pEC50 data fields are present, y_var_name=pIC50,pEC50 will import pIC50 as variable y1 and pEC50 as variable y2. Setting y_var_name to ALL will import all available data fields. If the y_var_name parameter is omitted, by default only structures are imported from the SDF file; to import activities, the y_var_name parameter must be specified.
If the PyMOL executable is in the path, it will be launched automatically to visualize the molecules if Open3DQSAR is running interactively; as a default, it will be invoked as pymol on Linux, Solaris, FreeBSD and Mac OS X, while on Windows pymol.bat will be searched. If the pymol executable is not in the path, full path to it (e.g., /usr/local/bin/pymol or C:\Program Files\PyMOL\bin\PyMOL.bat) can be assigned to the O3_PYMOL environment variable. The same effect can be obtained setting appropriately the pymol variable through the env keyword. Setting explicitly O3_PYMOL to a valid path or to "" respectively forces execution or non-execution of PyMOL no matter if Open3DQSAR is running interactively or not.

MIFs can be imported from:


# this command imports a SDF file and opens it in PyMOL, whose path is given
env  pymol=/usr/local/bin/pymol
import  type=SDF  file=my_dataset.sdf

# this command imports a GRIDKONT binary file as generated by the GRID program, then imports a series of 24 GAUSSIAN ESP cube files having as filenames g09_0001.cube, g09_0002.cube, ..., g09_0024.cube.
import  type=GRIDKONT  file=grid.kont
import  type=UNFORMATTED_CUBE  file=/path/to/g09_????.cube

#this command imports a series of 36 TURBOMOLE grid files having non-regular .dat filenames
import  type=FORMATTED_CUBE  file=/path/to/*.dat

# this command imports a series of 20 CoMFA files with steric and electrostatic fields extracted with the SPL script included in Open3DQSAR's distribution. These files are respectively named 1.efs.txt, 2.efs.txt, ..., 20.efs.txt (steric fields) and 1.efe.txt, 2.efe.txt, ..., 20.efe.txt (electrostatic fields)
import  type=GRID_ASCII  file=%d.efs.txt
import  type=GRID_ASCII  file=%d.efe.txt

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Last update:
May 31. 2015 20:39:42

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