import  type={SDF <file=SDF filename>  \
    [y_var_name=<comma separated list | ALL>]  \
    | 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 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 Open3DALIGN 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 Open3DALIGN is running interactively or not.


# 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

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Last update:
May 31. 2015 20:39:55

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