feat: Rdkit cart substructure search

Dockerfile.RDKit

@@ -0,0 +1,101 @@
+# https://github.com/rvianello/docker-postgres-rdkit/blob/master/Dockerfile
+ARG postgres_image_version=16 # changed from 16.2
+FROM docker.io/postgres:${postgres_image_version} AS builder
+ARG postgres_version=16
+ARG boost_dev_version=1.74
+ARG rdkit_git_url=https://github.com/rdkit/rdkit.git
+ARG rdkit_git_ref=Release_2024_03_1
+
+RUN apt-get update \
+    && apt-get install -yq --no-install-recommends \
+        ca-certificates \
+        curl \
+        gnupg \
+        lsb-release \
+    && curl https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - \
+    && echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list
+
+RUN apt-get update \
+    && apt-get install -yq --no-install-recommends \
+        build-essential \
+        cmake \
+        git \
+        coreutils \
+        libboost-iostreams${boost_dev_version}-dev \
+        libboost-regex${boost_dev_version}-dev \
+        libboost-serialization${boost_dev_version}-dev \
+        libboost-system${boost_dev_version}-dev \
+        libeigen3-dev \
+        libfreetype6-dev \
+        postgresql-server-dev-${postgres_version} \
+        zlib1g-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN mkdir -p /opt/RDKit-build \
+    && chown postgres:postgres /opt/RDKit-build
+
+USER postgres
+WORKDIR /opt/RDKit-build
+
+RUN git clone ${rdkit_git_url}
+WORKDIR /opt/RDKit-build/rdkit
+RUN git checkout ${rdkit_git_ref}
+
+RUN cmake \
+    -D RDK_BUILD_CAIRO_SUPPORT=OFF \
+    -D RDK_BUILD_INCHI_SUPPORT=ON \
+    -D RDK_BUILD_AVALON_SUPPORT=ON \
+    -D RDK_BUILD_PYTHON_WRAPPERS=OFF \
+    -D RDK_BUILD_DESCRIPTORS3D=OFF \
+    -D RDK_BUILD_FREESASA_SUPPORT=OFF \
+    -D RDK_BUILD_COORDGEN_SUPPORT=ON \
+    -D RDK_BUILD_MOLINTERCHANGE_SUPPORT=OFF \
+    -D RDK_BUILD_YAEHMOP_SUPPORT=OFF \
+    -D RDK_BUILD_STRUCTCHECKER_SUPPORT=OFF \
+    -D RDK_USE_URF=OFF \
+    -D RDK_BUILD_PGSQL=ON \
+    -D RDK_PGSQL_STATIC=ON \
+    -D PostgreSQL_CONFIG=pg_config \
+    -D PostgreSQL_INCLUDE_DIR=`pg_config --includedir` \
+    -D PostgreSQL_TYPE_INCLUDE_DIR=`pg_config --includedir-server` \
+    -D PostgreSQL_LIBRARY_DIR=`pg_config --libdir` \
+    -D RDK_INSTALL_INTREE=OFF \
+    -D CMAKE_INSTALL_PREFIX=/opt/RDKit \
+    -D CMAKE_BUILD_TYPE=Release \
+    . 
+RUN make -j$(nproc)
+
+USER root
+WORKDIR /opt/RDKit-build/rdkit
+
+RUN make install
+RUN /bin/bash /opt/RDKit-build/rdkit/Code/PgSQL/rdkit/pgsql_install.sh
+
+USER postgres
+WORKDIR /opt/RDKit-build/rdkit
+
+RUN initdb -D /opt/RDKit-build/pgdata \
+  && pg_ctl -D /opt/RDKit-build/pgdata -l /opt/RDKit-build/pgdata/log.txt start \
+  && RDBASE="$PWD" LD_LIBRARY_PATH="$PWD/lib" ctest -j4 --output-on-failure \
+  && pg_ctl -D /opt/RDKit-build/pgdata stop
+
+
+FROM docker.io/postgres:${postgres_image_version}
+ARG postgres_version=16
+ARG boost_version=1.74.0
+
+RUN apt-get update \
+    && apt-get install -yq --no-install-recommends \
+        libboost-iostreams${boost_version} \
+        libboost-regex${boost_version} \
+        libboost-serialization${boost_version} \
+        libboost-system${boost_version} \
+        libfreetype6 \
+        zlib1g \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /usr/share/postgresql/${postgres_version}/extension/*rdkit* /usr/share/postgresql/${postgres_version}/extension/
+COPY --from=builder /usr/lib/postgresql/${postgres_version}/lib/rdkit.so /usr/lib/postgresql/${postgres_version}/lib/rdkit.so
+

Dockerfile.chemotion-dev

@@ -10,9 +10,8 @@ ARG DEBIAN_FRONTEND=noninteractive
 RUN set -xe  && apt-get update -yqqq --fix-missing && apt-get upgrade -y
 RUN apt update && apt-get install -yqq --fix-missing bash ca-certificates wget apt-transport-https git gpg\
       imagemagick libmagic-dev libmagickcore-dev libmagickwand-dev curl gnupg2 \
-      build-essential sudo postgresql-client libappindicator1 swig \
-      gconf-service libasound2 libgconf-2-4 cmake \
-      libnspr4 libnss3 libpango1.0-0 libxss1 xdg-utils tzdata libpq-dev \
+      build-essential sudo postgresql-client swig cmake \
+      libnspr4 libnss3 libxss1 xdg-utils tzdata libpq-dev \
       gtk2-engines-pixbuf \
       libssl-dev libreadline-dev\
       unzip openssh-client \

app/api/chemotion/search_api.rb

@@ -27,7 +27,7 @@ class SearchAPI < Grape::API
             All Samples Reactions Wellplates Screens all samples reactions wellplates screens elements cell_lines by_ids advanced structure
           ]
           optional :molfile, type: String
-          optional :search_type, type: String, values: %w[similar sub]
+          optional :search_type, type: String, values: %w[similar sub subRDKit]
           optional :tanimoto_threshold, type: Float
           optional :page_size, type: Integer
           optional :structure_search, type: Boolean
@@ -97,10 +97,13 @@ def sample_structure_search(c_id = @c_id, not_permitted = @dl_s && @dl_s < 1)
 
         # TODO: implement this: http://pubs.acs.org/doi/abs/10.1021/ci600358f
         scope =
-          if params[:selection][:search_type] == 'similar'
+          case params[:selection][:search_type]
+          when 'similar'
             Sample.by_collection_id(c_id).search_by_fingerprint_sim(molfile, threshold)
-          else
+          when 'sub'
             Sample.by_collection_id(c_id).search_by_fingerprint_sub(molfile)
+          when 'subRDKit'
+            Sample.by_collection_id(c_id).search_by_rdkit_sub(molfile)
           end
         order_by_molecule(scope)
       end
@@ -519,12 +522,11 @@ def elements_by_scope(scope, collection_id = @c_id)
         end
 
         post do
-          Usecases::Search::StructureSearch.new(
-            collection_id: @c_id,
-            params: params,
-            user: current_user,
-            detail_levels: @dl,
-          ).perform!
+          samples = sample_structure_search
+          serialization_by_elements_and_page(
+            elements_by_scope(samples),
+            params[:page],
+          )
         end
       end
 

app/api/chemotion/ui_api.rb

@@ -30,6 +30,7 @@ class UiAPI < Grape::API
           has_radar: radar_config.present?,
           molecule_viewer: Matrice.molecule_viewer,
           collector_address: collector_address.presence,
+          pg_cartridge: Chemotion::Application.config.pg_cartridge,
           third_party_apps: Entities::ThirdPartyAppEntity.represent(ThirdPartyApp.all),
         }
       end

app/models/fingerprint.rb

@@ -70,6 +70,7 @@ class Fingerprint < ApplicationRecord
     fp_vector = Chemotion::OpenBabelService.bin_fingerprint_from_molfile(molfile) if molfile
     threshold = threshold.to_f
     query_num_set_bits = count_bits_set(fp_vector)
+    return none unless query_num_set_bits.positive?
 
     sim_query = sanitize_sql_for_conditions(
       [sql_query_similar, query_num_set_bits] + fp_vector + [