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f2e9e3a031
* Start providing an update script for the cartridge * update readme * support enhanced stereo in cartridge * it makes more sense to bump the cartridge version to 4.0 * add MolToJSON to cartridge * add mol_from_json * docs update * changes in response to review
85 lines
3.6 KiB
Plaintext
85 lines
3.6 KiB
Plaintext
PgSQL/rdkit is a PostgreSQL contribution module, which implements
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*mol* datatype to describe molecules and *fp* datatype for fingerprints,
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basic comparison operations, similarity operation (tanimoto, dice) and index
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support (using GiST indexing framework).
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Compatibility: PostgreSQL 9.1+
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If using PostgreSQL packages from your linux distribution, be sure
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that you have the -devel package installed.
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Installation:
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Cartridge is build from the root RDKit level, i.e. you need to tell CMake to
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build it too by including the following switch:
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-D RDK_BUILD_PGSQL=ON
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if PostgreSQL is installed in a location where CMake is unable to find it,
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either set the environment variable PostgreSQL_ROOT or add a
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"-DPostgreSQL_ROOT" switch to the cmake command line, pointing to the
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PostgreSQL root directory, e.g. C:\Program Files\PostgreSQL\9.6
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Under Linux, if you install PostgreSQL using the RHEL/CentOS RPMs provided by
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the PostgreSQL RPM Building Project
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(http://yum.postgresql.org/repopackages.php),
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PostgreSQL lives under /usr/pgsql-9.x, and the
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include files are located under a path that the current FindPostgreSQL.cmake
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module is unable to find without a little help. Therefore, you will need to
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add a "-DPostgreSQL_TYPE_INCLUDE_DIR" switch pointing to the location of the
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"server" include directory. E.g., for PostgreSQL 9.6 the CMake PostgreSQL-
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related switches would be:
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-DPostgreSQL_ROOT=/usr/pgsql-9.6
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-DPostgreSQL_TYPE_INCLUDE_DIR=/usr/pgsql-9.6/include/server
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After building the RDKit, carry out the following steps:
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1) Open a shell (CMD under Windows) with administrator privileges
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2) Stop the PostgreSQL service:
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"C:\Program Files\PostgreSQL\9.6\bin\pg_ctl.exe" ^
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-N "postgresql-9.6" -D "C:\Program Files\PostgreSQL\9.6\data" ^
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-w stop (Windows)
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service postgresql stop (Linux)
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3) run the "pgsql_install" script (note that it is built by the root CMake):
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${CMAKE_BINARY_DIR}\Code\PgSQL\rdkit\pgsql_install.bat (Windows)
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sh ${CMAKE_BINARY_DIR}/Code/PgSQL/rdkit/pgsql_install.sh (Linux)
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which will install rdkit--3.5.sql, rdkit.control and rdkit.dll
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into PostgreSQL
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4) Under Windows, make sure that the Boost DLLs against which the RDKit
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is built are in the SYSTEM path, or PostgreSQL will fail to create the
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rdkit extension with a deceptive error message such as:
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ERROR: could not load library
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"C:/Program Files/PostgreSQL/9.6/lib/rdkit.dll":
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The specified module could not be found.
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Under Linux, make sure to add to the .bashrc of the postgres user
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an "export LD_LIBRARY_PATH" directive pointing to any dynamic
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libraries that the postgresql service may need (e.g., Boost or
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PostgreSQL libraries) which are not in the system ldconfig path.
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Alternatively, in some PostgreSQL distributions you may add a
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LD_LIBRARY_PATH = '/path/to/dynamic/libraries'
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line to /etc/postgresql/9.6/main/environment
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5) Start the PostgreSQL service, e.g.:
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"C:\Program Files\PostgreSQL\9.6\bin\pg_ctl.exe" ^
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-N "postgresql-9.6" -D "C:\Program Files\PostgreSQL\9.6\data" ^
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-w start (Windows)
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service postgresql start (Linux)
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Before running ctest, make sure that your current user has enough
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PostgreSQL privileges to carry out the database operations required by
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the tests. You might need to set the PGPASSWORD environment variable
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in your shell to avoid authentication issues.
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To install the rdkit cartridge into the database DB:
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psql -c 'CREATE EXTENSION rdkit' DB
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Uninstall cartridge from database DB:
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psql -c 'DROP EXTENSION rdkit CASCADE' DB
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Example:
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See sql/* and the cartridge tutorial for examples.
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Further Reading:
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Cartridge tutorial (https://rdkit.org/docs/Cartridge.html)
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