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PSCI 6670 CADD I

posted Oct 1, 2018, 1:21 PM by Dong Xu

For oddt environment, installed oddt,  openbabel 2.4.0 from oddt channel, rdkit/chemfp from bioconda channel

For rotatable bonds in Openbabel, I need to modify plugindefine.txt in this dir:  /home/xudong/apps/anaconda2/envs/oddt/share/openbabel/2.4.0

At the end of file, add

SmartsDescriptor

rotors

[!$(*#*)&!D1]-!@[!$(*#*)&!D1]

Number of rotatable bonds\n

http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#ROTATE

See

 https://sourceforge.net/p/openbabel/mailman/message/30659149/

and

 https://sourceforge.net/p/openbabel/mailman/message/35262691/

oddt conda installation is missing  '/home/xudong/apps/anaconda2/envs/oddt/lib/python2.7/site-packages/oddt/filter/pains.smarts'

Need to create the filter folder and download raw file from https://github.com/oddt/oddt/blob/master/oddt/filter/pains.smarts

Compiler filter-it:

Need to edit cmake/modules/FindOpenBabel2.cmake

With anaconda, the following lines need to be added

        find_path (

                OPENBABEL2_INCLUDE_DIRS

                NAMES

                        openbabel/obconversion.h

                        openbabel-2.0/openbabel/obconversion.h

                PATHS

                        /usr/

                        /usr/local/

                        /usr/local/include/

                        /usr/local/openbabel/

                        ENV

                        BABEL_INCLUDEDIR

                        ~/apps/anaconda2/envs/molfp/include/

                )

        find_library (

                OPENBABEL2_LIBRARIES

                NAMES

                        openbabel

                PATHS

                        /usr/

                        /usr/local/

                        /usr/local/lib/

                        /usr/lib/local/

                        /usr/local/openbabel/

                        /usr/lib/openbabel/

                        /usr/local/openbabel/lib/

                        ~/apps/anaconda2/envs/molfp/lib/

                        ENV

                        BABEL_LIBDIR

 

Note conda install mgltools BREAK other apps, oddt, rdkit etc.!!!

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