背景
PolarDB 的云原生存算分离架构, 具备低廉的数据存储、高效扩展弹性、高速多机并行计算能力、高速数据搜索和处理; PolarDB与计算算法结合, 将实现双剑合璧, 推动业务数据的价值产出, 将数据变成生产力.
本文将介绍PolarDB 开源版 通过rdkit 支撑生物、化学分子结构数据存储与计算、分析
测试环境为macOS+docker, PolarDB部署请参考如何用 PolarDB 证明巴菲特的投资理念 - 包括PolarDB简单部署。
rdkit 介绍
分子具有连接、分形、图、组合的特征, 低级生命组成高级生命, 众多高级生命组成社会, 众多低维生物通过分形组成高维生物.
https://www.rdkit.org/docs/Overview.html
Business-friendly BSD license
Core data structures and algorithms in C++
Python 3.x wrappers generated using Boost.Python
Java and C# wrappers generated with SWIG
2D and 3D molecular operations
Descriptor generation for machine learning
Molecular database cartridge for PostgreSQL
Cheminformatics nodes for KNIME (distributed from the KNIME community site: https://www.knime.com/rdkit)
PolarDB 通过rdkit插件实现生物、化学分子结构数据存储与计算、分析. (相似搜索、子结构或精确匹配搜索、分子比较等)
https://www.rdkit.org/docs/Cartridge.html
数据类型
postgres=# \dT
List of data types
Schema | Name | Description
--------+-----------+-------------
public | bfp | a bit vector fingerprint
public | _internal |
public | mol | an rdkit molecule.
public | qmol | an rdkit molecule containing query features
public | reaction |
public | sfp | a sparse count vector fingerprint
(6 rows) 操作符
postgres=# \do+
List of operators
Schema | Name | Left arg type | Right arg type | Result type | Function | Description
--------+------+---------------+----------------+------------------+------------------------+-------------
public | # | bfp | bfp | boolean | public.dice_sml_op |
public | # | sfp | sfp | boolean | public.dice_sml_op |
public | % | bfp | bfp | boolean | public.tanimoto_sml_op |
public | % | sfp | sfp | boolean | public.tanimoto_sml_op |
public | < | bfp | bfp | boolean | bfp_lt |
public | < | mol | mol | boolean | mol_lt |
public | < | sfp | sfp | boolean | sfp_lt |
public | <#> | bfp | bfp | double precision | dice_dist |
public | <%> | bfp | bfp | double precision | tanimoto_dist |
public | <= | bfp | bfp | boolean | bfp_le |
public | <= | mol | mol | boolean | mol_le |
public | <= | sfp | sfp | boolean | sfp_le |
public | <> | bfp | bfp | boolean | bfp_ne |
public | <> | mol | mol | boolean | mol_ne |
public | <> | reaction | reaction | boolean | reaction_ne |
public | <> | sfp | sfp | boolean | sfp_ne |
public | <@ | mol | mol | boolean | public.rsubstruct |
public | <@ | qmol | mol | boolean | public.rsubstruct |
public | <@ | reaction | reaction | boolean | public.rsubstruct |
public | = | bfp | bfp | boolean | bfp_eq |
public | = | mol | mol | boolean | mol_eq |
public | = | reaction | reaction | - | - |
public | = | sfp | sfp | boolean | sfp_eq |
public | > | bfp | bfp | boolean | bfp_gt |
public | > | mol | mol | boolean | mol_gt |
public | > | sfp | sfp | boolean | sfp_gt |
public | >= | bfp | bfp | boolean | bfp_ge |
public | >= | mol | mol | boolean | mol_ge |
public | >= | sfp | sfp | boolean | sfp_ge |
public | ?< | reaction | reaction | boolean | rsubstructfp |
public | ?> | reaction | reaction | boolean | substructfp |
public | @= | mol | mol | boolean | mol_eq |
public | @= | reaction | reaction | boolean | reaction_eq |
public | @> | mol | mol | boolean | public.substruct |
public | @> | mol | qmol | boolean | public.substruct |
public | @> | reaction | reaction | boolean | public.substruct |
(36 rows) 函数
postgres=# \df
List of functions
Schema | Name | Result data type | Argument data types | Type
--------+------------------------------+------------------+----------------------------------------------------------------------------------------------------------+------
public | add | sfp | sfp, sfp | func
public | all_values_gt | boolean | sfp, integer | func
public | all_values_lt | boolean | sfp, integer | func
public | atompair_fp | sfp | mol | func
public | atompairbv_fp | bfp | mol | func
public | avalon_fp | bfp | mol, boolean DEFAULT false, integer DEFAULT 15761407 | func
public | bfp_cmp | integer | bfp, bfp | func
public | bfp_eq | boolean | bfp, bfp | func
public | bfp_from_binary_text | bfp | bytea | func
public | bfp_ge | boolean | bfp, bfp | func
public | bfp_gt | boolean | bfp, bfp | func
public | bfp_in | bfp | cstring | func
public | bfp_le | boolean | bfp, bfp | func
public | bfp_lt | boolean | bfp, bfp | func
public | bfp_ne | boolean | bfp, bfp | func
public | bfp_out | cstring | bfp | func
public | bfp_to_binary_text | bytea | bfp | func
public | dice_dist | double precision | bfp, bfp | func
public | dice_sml | double precision | bfp, bfp | func
public | dice_sml | double precision | sfp, sfp | func
public | dice_sml_op | boolean | bfp, bfp | func
public | dice_sml_op | boolean | sfp, sfp | func
public | featmorgan_fp | sfp | mol, integer DEFAULT 2 | func
public | featmorganbv_fp | bfp | mol, integer DEFAULT 2 | func
public | fmcs | text | mol | agg
public | fmcs | text | text | agg
public | fmcs_mol_transition | internal | internal, mol | func
public | fmcs_mols | text | internal | func
public | fmcs_smiles | cstring | cstring, cstring | func
public | fmcs_smiles | text | text | func
public | fmcs_smiles | text | text, text | func
public | fmcs_smiles_transition | text | text, text | func
public | gbfp_compress | internal | internal | func
public | gbfp_consistent | boolean | internal, bytea, smallint, oid, internal | func
public | gbfp_decompress | internal | internal | func
public | gbfp_distance | double precision | internal, bytea, smallint, oid | func
public | gbfp_fetch | internal | internal | func
public | gbfp_penalty | internal | internal, internal, internal | func
public | gbfp_picksplit | internal | internal, internal | func
public | gbfp_same | internal | internal, internal, internal | func
public | gbfp_union | _internal | internal, internal | func
public | gen_arr | integer[] | normal integer, hot integer | func
public | gin_bfp_consistent | boolean | internal, smallint, bfp, integer, internal, internal, internal, internal | func
public | gin_bfp_extract_query | internal | bfp, internal, smallint, internal, internal, internal, internal | func
public | gin_bfp_extract_value | internal | bfp, internal | func
public | gin_bfp_triconsistent | boolean | internal, smallint, bfp, integer, internal, internal, internal | func
public | gmol_compress | internal | internal | func
public | gmol_consistent | boolean | bytea, internal, integer | func
public | gmol_decompress | internal | internal | func
public | gmol_penalty | internal | internal, internal, internal | func
public | gmol_picksplit | internal | internal, internal | func
public | gmol_same | internal | bytea, bytea, internal | func
public | gmol_union | integer[] | bytea, internal | func
public | greaction_compress | internal | internal | func
public | greaction_consistent | boolean | bytea, internal, integer | func
public | gsfp_compress | internal | internal | func
public | gsfp_consistent | boolean | bytea, internal, integer | func
public | gslfp_compress | internal | internal | func
public | gslfp_consistent | boolean | bytea, internal, integer | func
public | gslfp_decompress | internal | internal | func
public | gslfp_penalty | internal | internal, internal, internal | func
public | gslfp_picksplit | internal | internal, internal | func
public | gslfp_same | internal | bytea, bytea, internal | func
public | gslfp_union | integer[] | bytea, internal | func
public | has_reaction_substructmatch | SETOF reaction | queryreaction character, tablename regclass, columnname text | func
public | is_valid_ctab | boolean | cstring | func
public | is_valid_mol_pkl | boolean | bytea | func
public | is_valid_smarts | boolean | cstring | func
public | is_valid_smiles | boolean | cstring | func
public | layered_fp | bfp | mol | func
public | maccs_fp | bfp | mol | func
public | mol_adjust_query_properties | mol | mol, cstring DEFAULT ''::cstring | func
public | mol_adjust_query_properties | qmol | qmol, cstring DEFAULT ''::cstring | func
public | mol_amw | real | mol | func
public | mol_chi0n | real | mol | func
public | mol_chi0v | real | mol | func
public | mol_chi1n | real | mol | func
public | mol_chi1v | real | mol | func
public | mol_chi2n | real | mol | func
public | mol_chi2v | real | mol | func
public | mol_chi3n | real | mol | func
public | mol_chi3v | real | mol | func
public | mol_chi4n | real | mol | func
public | mol_chi4v | real | mol | func
public | mol_cmp | integer | mol, mol | func
public | mol_eq | boolean | mol, mol | func
public | mol_exactmw | real | mol | func
public | mol_formula | cstring | mol, boolean DEFAULT false, boolean DEFAULT true | func
public | mol_fractioncsp3 | real | mol | func
public | mol_from_ctab | mol | cstring, boolean DEFAULT false | func
public | mol_from_json | mol | cstring | func
public | mol_from_pkl | mol | bytea | func
public | mol_from_smiles | mol | cstring | func
public | mol_from_smiles | mol | text | func
public | mol_ge | boolean | mol, mol | func
public | mol_gt | boolean | mol, mol | func
public | mol_hallkieralpha | real | mol | func
public | mol_hba | integer | mol | func
public | mol_hbd | integer | mol | func
public | mol_in | mol | cstring | func
public | mol_inchi | cstring | mol, cstring DEFAULT ''::cstring | func
public | mol_inchikey | cstring | mol, cstring DEFAULT ''::cstring | func
public | mol_kappa1 | real | mol | func
public | mol_kappa2 | real | mol | func
public | mol_kappa3 | real | mol | func
public | mol_labuteasa | real | mol | func
public | mol_le | boolean | mol, mol | func
public | mol_logp | real | mol | func
public | mol_lt | boolean | mol, mol | func
public | mol_murckoscaffold | mol | mol | func
public | mol_ne | boolean | mol, mol | func
public | mol_nm_hash | cstring | mol, cstring DEFAULT 'AnonymousGraph'::cstring | func
public | mol_numaliphaticcarbocycles | integer | mol | func
public | mol_numaliphaticheterocycles | integer | mol | func
public | mol_numaliphaticrings | integer | mol | func
public | mol_numamidebonds | integer | mol | func
public | mol_numaromaticcarbocycles | integer | mol | func
public | mol_numaromaticheterocycles | integer | mol | func
public | mol_numaromaticrings | integer | mol | func
public | mol_numatoms | integer | mol | func
public | mol_numbridgeheadatoms | integer | mol | func
public | mol_numheavyatoms | integer | mol | func
public | mol_numheteroatoms | integer | mol | func
public | mol_numheterocycles | integer | mol | func
public | mol_numrings | integer | mol | func
public | mol_numrotatablebonds | integer | mol | func
public | mol_numsaturatedcarbocycles | integer | mol | func
public | mol_numsaturatedheterocycles | integer | mol | func
public | mol_numsaturatedrings | integer | mol | func
public | mol_numspiroatoms | integer | mol | func
public | mol_out | cstring | mol | func
public | mol_phi | real | mol | func
public | mol_recv | mol | internal | func
public | mol_send | bytea | mol | func
public | mol_to_ctab | cstring | mol, boolean DEFAULT true, boolean DEFAULT false | func
public | mol_to_cxsmarts | cstring | mol | func
public | mol_to_cxsmarts | cstring | qmol | func
public | mol_to_cxsmiles | cstring | mol | func
public | mol_to_json | cstring | mol | func
public | mol_to_json | cstring | qmol | func
public | mol_to_pkl | bytea | mol | func
public | mol_to_smarts | cstring | mol | func
public | mol_to_smarts | cstring | qmol | func
public | mol_to_smiles | cstring | mol | func
public | mol_to_smiles | cstring | qmol | func
public | mol_to_svg | cstring | mol, cstring DEFAULT ''::cstring, integer DEFAULT 250, integer DEFAULT 200, cstring DEFAULT ''::cstring | func
public | mol_to_svg | cstring | qmol, cstring DEFAULT ''::cstring, integer DEFAULT 250, integer DEFAULT 200, cstring DEFAULT ''::cstring | func
public | mol_to_v3kctab | cstring | mol, boolean DEFAULT true | func
public | mol_tpsa | real | mol | func
public | morgan_fp | sfp | mol, integer DEFAULT 2 | func
public | morganbv_fp | bfp | mol, integer DEFAULT 2 | func
public | qmol_from_ctab | qmol | cstring, boolean DEFAULT false | func
public | qmol_from_json | qmol | cstring | func
public | qmol_from_smarts | qmol | cstring | func
public | qmol_from_smiles | qmol | cstring | func
public | qmol_in | qmol | cstring | func
public | qmol_out | cstring | qmol | func
public | qmol_recv | qmol | internal | func
public | qmol_send | bytea | qmol | func
public | rdkit_fp | bfp | mol | func
public | rdkit_toolkit_version | text | | func
public | rdkit_version | text | | func
public | reaction_difference_fp | sfp | reaction, integer DEFAULT 1 | func
public | reaction_eq | boolean | reaction, reaction | func
public | reaction_from_ctab | reaction | cstring | func
public | reaction_from_smarts | reaction | cstring | func
public | reaction_from_smiles | reaction | cstring | func
public | reaction_in | reaction | cstring | func
public | reaction_ne | boolean | reaction, reaction | func
public | reaction_numagents | integer | reaction | func
public | reaction_numproducts | integer | reaction | func
public | reaction_numreactants | integer | reaction | func
public | reaction_out | cstring | reaction | func
public | reaction_recv | reaction | internal | func
public | reaction_send | bytea | reaction | func
public | reaction_structural_bfp | bfp | reaction, integer DEFAULT 5 | func
public | reaction_to_ctab | cstring | reaction | func
public | reaction_to_smarts | cstring | reaction | func
public | reaction_to_smiles | cstring | reaction | func
public | reaction_to_svg | cstring | reaction, boolean DEFAULT false, integer DEFAULT 400, integer DEFAULT 200, cstring DEFAULT ''::cstring | func
public | rsubstruct | boolean | mol, mol | func
public | rsubstruct | boolean | qmol, mol | func
public | rsubstruct | boolean | reaction, reaction | func
public | rsubstruct_chiral | boolean | mol, mol | func
public | rsubstructfp | boolean | reaction, reaction | func
public | sfp_cmp | integer | sfp, sfp | func
public | sfp_eq | boolean | sfp, sfp | func
public | sfp_ge | boolean | sfp, sfp | func
public | sfp_gt | boolean | sfp, sfp | func
public | sfp_in | sfp | cstring | func
public | sfp_le | boolean | sfp, sfp | func
public | sfp_lt | boolean | sfp, sfp | func
public | sfp_ne | boolean | sfp, sfp | func
public | sfp_out | cstring | sfp | func
public | size | integer | bfp | func
public | substruct | boolean | mol, mol | func
public | substruct | boolean | mol, qmol | func
public | substruct | boolean | reaction, reaction | func
public | substruct_chiral | boolean | mol, mol | func
public | substruct_count | integer | mol, mol, boolean DEFAULT true | func
public | substruct_count | integer | mol, qmol, boolean DEFAULT true | func
public | substruct_count_chiral | integer | mol, mol, boolean DEFAULT true | func
public | substruct_count_chiral | integer | mol, qmol, boolean DEFAULT true | func
public | substructfp | boolean | reaction, reaction | func
public | subtract | sfp | sfp, sfp | func
public | tanimoto_dist | double precision | bfp, bfp | func
public | tanimoto_sml | double precision | bfp, bfp | func
public | tanimoto_sml | double precision | sfp, sfp | func
public | tanimoto_sml_op | boolean | bfp, bfp | func
public | tanimoto_sml_op | boolean | sfp, sfp | func
public | torsion_fp | sfp | mol | func
public | torsionbv_fp | bfp | mol | func
public | tversky_sml | double precision | bfp, bfp, real, real | func
(213 rows) 索引
403 | btree_mol_ops
403 | btree_bfp_ops
403 | btree_sfp_ops
405 | hash_mol_ops
405 | hash_bfp_ops
405 | hash_sfp_ops
783 | gist_mol_ops
783 | gist_qmol_ops
783 | gist_bfp_ops
783 | gist_sfp_ops
783 | gist_sfp_low_ops
783 | gist_reaction_ops
2742 | gin_bfp_ops 部署rdkit on PolarDB
boost依赖
wget https://boostorg.jfrog.io/artifactory/main/release/1.69.0/source/boost_1_69_0.tar.bz2
tar -jxvf boost_1_69_0.tar.bz2
cd boost_1_69_0
./bootstrap.sh --with-libraries=serialization
sudo ./b2 --prefix=/usr/local/boost -a install cairo依赖
sudo yum install -y cairo-devel cairo reetype依赖
wget https://download.savannah.gnu.org/releases/freetype/freetype-2.12.1.tar.gz
tar -zxvf freetype-2.12.1.tar.gz
cd freetype-2.12.1
./autogen.sh
./configure --prefix=/usr/local/freettype
make -j 6
sudo make install
sudo vi /etc/ld.so.conf
# add
/usr/local/freettype/lib
sudo ldconfig rdkit
wget https://github.com/rdkit/rdkit/archive/refs/tags/Release_2022_09_3.tar.gz
tar -zxvf Release_2022_09_3.tar.gz 4.1 Comic_Neue 依赖
## in macOS
https://fonts.google.com/download?family=Comic%20Neue
cp Comic_Neue.zip /home/postgres/rdkit-Release_2022_09_3/Code/GraphMol/MolDraw2D
## in docker
sudo chown postgres:postgres /home/postgres/rdkit-Release_2022_09_3/Code/GraphMol/MolDraw2D/Comic_Neue.zip 4.2 rdkit
cd rdkit-Release_2022_09_3
mkdir build
cd build
cmake -DBOOST_ROOT=/usr/local/boost -DBoost_INCLUDE_DIR=/usr/local/boost/include -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="/home/postgres/tmp_basedir_polardb_pg_1100_bld" -DFREETYPE_LIBRARY=/usr/local/freettype/lib/libfreetype.so.6 -DFREETYPE_INCLUDE_DIRS=/usr/local/freettype/include/freetype2 -DRDK_TEST_MULTITHREADED=OFF -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/local/rdkit -Wno-dev ..
// OR
// cmake -DBOOST_ROOT=/usr/local/boost -DBoost_INCLUDE_DIR=/usr/local/boost/include -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="/home/postgres/tmp_basedir_polardb_pg_1100_bld" -DFREETYPE_LIBRARY=/usr/local/freettype/lib/libfreetype.so.6 -DFREETYPE_INCLUDE_DIRS=/usr/local/freettype/include/freetype2 -DRDK_TEST_MULTITHREADED=OFF -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/local/rdkit -DRDK_BUILD_MOLINTERCHANGE_SUPPORT=OFF -Wno-dev ..
// 编译时需要联网, cmake的时候需要git clone代码, 期间会下载几个依赖的软件, 如果没有下载成功就多试几次
// ...
make -j 6
// 编译时需要联网, make的时候也需要git clone代码
sudo make install 安装rdkit插件到polardb.
psql
postgres=# create extension rdkit ;
CREATE EXTENSION rdkit 编译选项:
rdkit-Release_2022_09_3/CMakeLists.txt
option(RDK_BUILD_SWIG_WRAPPERS "build the SWIG wrappers" OFF )
option(RDK_BUILD_PYTHON_WRAPPERS "build the standard python wrappers" ON )
option(RDK_BUILD_COMPRESSED_SUPPLIERS "build in support for compressed MolSuppliers" OFF )
option(RDK_BUILD_INCHI_SUPPORT "build the rdkit inchi wrapper" OFF )
option(RDK_BUILD_AVALON_SUPPORT "install support for the avalon toolkit. Use the variable AVALONTOOLS_DIR to set the location of the source." OFF )
option(RDK_BUILD_PGSQL "build the PostgreSQL cartridge" OFF )
option(RDK_BUILD_RPATH_SUPPORT "build shared libraries using rpath" OFF)
option(RDK_PGSQL_STATIC "statically link rdkit libraries into the PostgreSQL cartridge" ON )
option(RDK_BUILD_CONTRIB "build the Contrib directory" OFF )
option(RDK_INSTALL_INTREE "install the rdkit in the source tree (former behavior)" ON )
option(RDK_INSTALL_DLLS_MSVC "install the rdkit DLLs when using MSVC" OFF)
option(RDK_INSTALL_STATIC_LIBS "install the rdkit static libraries" ON )
option(RDK_INSTALL_PYTHON_TESTS "install the rdkit Python tests with the wrappers" OFF )
option(RDK_BUILD_THREADSAFE_SSS "enable thread-safe substructure searching" ON )
option(RDK_BUILD_SLN_SUPPORT "include support for the SLN format" ON )
option(RDK_TEST_MULTITHREADED "run some tests of multithreading" ON )
option(RDK_BUILD_SWIG_JAVA_WRAPPER "build the SWIG JAVA wrappers (does nothing if RDK_BUILD_SWIG_WRAPPERS is not set)" ON )
option(RDK_BUILD_SWIG_CSHARP_WRAPPER "build the experimental SWIG C# wrappers (does nothing if RDK_BUILD_SWIG_WRAPPERS is not set)" OFF )
option(RDK_SWIG_STATIC "statically link rdkit libraries into the SWIG wrappers" ON )
option(RDK_TEST_MMFF_COMPLIANCE "run MMFF compliance tests (requires tar/gzip)" ON )
option(RDK_BUILD_CPP_TESTS "build the c++ tests (disabing can speed up builds" ON)
option(RDK_USE_FLEXBISON "use flex/bison, if available, to build the SMILES/SMARTS/SLN parsers" OFF)
option(RDK_TEST_COVERAGE "Use G(L)COV to compute test coverage" OFF)
option(RDK_USE_BOOST_SERIALIZATION "Use the boost serialization library if available" ON)
option(RDK_USE_BOOST_STACKTRACE "use boost::stacktrace to do more verbose invariant output (linux only)" ON)
option(RDK_BUILD_TEST_GZIP "Build the gzip'd stream test" OFF)
option(RDK_OPTIMIZE_POPCNT "Use SSE4.2 popcount instruction while compiling." ON)
option(RDK_USE_STRICT_ROTOR_DEFINITION "Use the most strict rotatable bond definition" ON)
option(RDK_BUILD_DESCRIPTORS3D "Build the 3D descriptors calculators, requires Eigen3 to be installed" ON)
option(RDK_BUILD_FREESASA_SUPPORT "build the rdkit freesasa wrapper" OFF )
option(RDK_BUILD_COORDGEN_SUPPORT "build the rdkit coordgen wrapper" ON )
option(RDK_BUILD_MAEPARSER_SUPPORT "build the rdkit MAE parser wrapper" ON )
option(RDK_BUILD_MOLINTERCHANGE_SUPPORT "build in support for CommonChem molecule interchange" ON )
option(RDK_BUILD_YAEHMOP_SUPPORT "build support for the YAeHMOP wrapper" OFF)
option(RDK_BUILD_XYZ2MOL_SUPPORT "build in support for the RDKit's implementation of xyz2mol (in the DetermineBonds library)" OFF )
option(RDK_BUILD_STRUCTCHECKER_SUPPORT "build in support for the StructChecker alpha (not recommended, use the MolVS integration instead)" OFF )
option(RDK_USE_URF "Build support for Florian Flachsenberg's URF library" ON)
option(RDK_INSTALL_DEV_COMPONENT "install libraries and headers" ON)
option(RDK_USE_BOOST_REGEX "use boost::regex instead of std::regex (needed for systems with g++-4.8)" OFF)
option(RDK_USE_BOOST_IOSTREAMS "use boost::iostreams" ON)
option(RDK_BUILD_MINIMAL_LIB "build the minimal RDKit wrapper (for the JS bindings)" OFF)
option(RDK_BUILD_CFFI_LIB "build the CFFI wrapper (for use in other programming languges)" OFF)
option(RDK_BUILD_FUZZ_TARGETS "build the fuzz targets" OFF) make installcheck
cd rdkit-Release_2022_09_3/Code/PgSQL/rdkit
[postgres@aa25c5be9681 rdkit]$ USE_PGXS=1 make installcheck
/home/postgres/tmp_basedir_polardb_pg_1100_bld/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=./ --bindir='/home/postgres/tmp_basedir_polardb_pg_1100_bld/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 bfpgin sfpgist slfpgist fps reaction
(using postmaster on 127.0.0.1, default port)
============== dropping database "contrib_regression" ==============
DROP DATABASE
============== creating database "contrib_regression" ==============
CREATE DATABASE
ALTER DATABASE
============== running regression test queries ==============
test rdkit-91 ... ok
test props ... ok
test btree ... ok
test molgist ... ok
test bfpgist-91 ... ok
test bfpgin ... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
test reaction ... ok
===========================================================
All 10 tests passed.
POLARDB:
All 10 tests, 0 tests in ignore, 0 tests in polar ignore.
===========================================================
