#1412 Nucleotide splitting for V3000 molfile SCSR

.ci/docker/buildpack-arm64/Dockerfile

@@ -1,11 +1,11 @@
-FROM ubuntu:16.04
-
+FROM ubuntu:20.04
 RUN apt update && \
     apt upgrade -y && \
     apt install -y --no-install-recommends \
         apt-transport-https \
         curl \
         software-properties-common \
+        gpg-agent \
         lsb-release \
         && \
     export UBUNTU_VERSION=$(lsb_release -cs) && \
@@ -21,23 +21,23 @@ RUN apt update && \
     # Install tools required for building Indigo
     apt install -y --no-install-recommends \
         cmake \
-        g++-5-aarch64-linux-gnu \
+        g++-10-aarch64-linux-gnu \
         git \
         libfontconfig1-dev:arm64 \
         libfreetype6-dev:arm64 \
         make \
         qemu-user-static
 
-ENV CC=aarch64-linux-gnu-gcc-5
-ENV CXX=aarch64-linux-gnu-g++-5
+ENV CC=aarch64-linux-gnu-gcc-10
+ENV CXX=aarch64-linux-gnu-g++-10
 ENV INDIGO_QEMU_BINARY=qemu-aarch64-static
 ENV ASAN_OPTIONS=alloc_dealloc_mismatch=0
 RUN echo $'leak:libfontconfig\nleak:libc\n' >> /opt/external.supp
 ENV LSAN_OPTIONS=suppressions=/opt/external.supp
 
 RUN cmake --version && \
-    aarch64-linux-gnu-gcc-5 --version && \
-    aarch64-linux-gnu-g++-5 --version && \
+    aarch64-linux-gnu-gcc-10 --version && \
+    aarch64-linux-gnu-g++-10 --version && \
     git --version && \
     make --version
 

.ci/docker/indigo-tester/Dockerfile

@@ -64,8 +64,8 @@ RUN set -eux && \
     ln -fs /opt/ironpython/net${DOTNET_VERSION}/ipy.sh /opt/ironpython/ipy && \
     rm IronPython.${IRONPYTHON_VERSION}.zip && \
     # Python 3 packages
-    python3 -m pip install --upgrade pip && \
-    python3 -m pip install --upgrade setuptools wheel twine && \
+    python3 -m pip install wheel && \
+    apt install -y python3-pip python3-setuptools twine && \
     apt autoremove -y
 
 COPY ./ /indigo
@@ -74,22 +74,22 @@ RUN cd /indigo && \
     cd build && \
     cmake .. && \
     cmake --build . --target indigo-python --config Release -- -j $(nproc) && \
-    python3 -m pip install ../dist/*.whl
+    python3 -m pip install ../dist/*.whl --break-system-packages
 
-COPY /api/http/requirements.txt ./api_requirements.txt
-COPY /api/http/requirements_dev.txt ./api_requirements_dev.txt
-COPY /utils/indigo-service/backend/service/requirements.txt ./service_requirements.txt
-COPY /utils/indigo-service/backend/service/requirements.dev.txt ./service_requirements_dev.txt
+COPY ./api/http/requirements.txt ./api_requirements.txt
+COPY ./api/http/requirements_dev.txt ./api_requirements_dev.txt
+COPY ./utils/indigo-service/backend/service/requirements.txt ./service_requirements.txt
+COPY ./utils/indigo-service/backend/service/requirements.dev.txt ./service_requirements_dev.txt
 
 RUN python3 -m pip install  \
       -r api_requirements.txt  \
       -r api_requirements_dev.txt  \
       -r service_requirements.txt  \
-      -r service_requirements_dev.txt && \
+      -r service_requirements_dev.txt --break-system-packages && \
     rm ./api_requirements.txt ./api_requirements_dev.txt ./service_requirements.txt ./service_requirements_dev.txt
 
-COPY /bingo/bingo-elastic/python/ ./bingo-elastic
-RUN cd ./bingo-elastic && python3 -m pip install -e . && cd .. && rm -rf ./bingo-elastic
+COPY ./bingo/bingo-elastic/python/ ./bingo-elastic
+RUN cd ./bingo-elastic && python3 -m pip install -e . --break-system-packages && cd .. && rm -rf ./bingo-elastic
 
 ENV JAVA_HOME=/opt/jdk
 ENV PATH=${PATH}:${JAVA_HOME}/bin:/opt/jython/bin:/opt/maven/bin:/opt/ironpython

api/c/tests/unit/tests/formats.cpp

@@ -179,7 +179,7 @@ TEST_F(IndigoApiFormatsTest, loadAssert)
 
 TEST_F(IndigoApiFormatsTest, fromBuffer)
 {
-    const byte mStr[] = "[CX4H3][#6]";
+    const uint8_t mStr[] = "[CX4H3][#6]";
     const int buffSize = sizeof(mStr);
 
     try
@@ -190,11 +190,11 @@ TEST_F(IndigoApiFormatsTest, fromBuffer)
         EXPECT_EQ(2, indigoCountAtoms(obj));
         EXPECT_EQ(1, indigoCountBonds(obj));
 
-        const byte react2[] = "C1CC[NH:2]CC1.C1CC[S:1]CC1>>C1CC2CC[S:2]CC2C[NH:1]1";
+        const uint8_t react2[] = "C1CC[NH:2]CC1.C1CC[S:1]CC1>>C1CC2CC[S:2]CC2C[NH:1]1";
         obj = indigoLoadStructureFromBuffer(react2, sizeof(react2), "");
         EXPECT_EQ(3, indigoCountMolecules(obj));
 
-        const byte react[] = "C[12CH2:1]C(CCCC)[CH]CCCCCCC>>C[13CH2:1]C(CCCC)[C]CCCCCCCC |^1:7,^4:22|";
+        const uint8_t react[] = "C[12CH2:1]C(CCCC)[CH]CCCCCCC>>C[13CH2:1]C(CCCC)[C]CCCCCCCC |^1:7,^4:22|";
         obj = indigoLoadStructureFromBuffer(react, sizeof(react), "query");
         EXPECT_EQ(2, indigoCountMolecules(obj));
     }

api/tests/integration/tests/formats/ref/anacyclamide.ket

@@ -146,28 +146,28 @@
         ],
         "templates": [
             {
-                "$ref": "monomerTemplate-Gln_0"
+                "$ref": "monomerTemplate-Gln_1"
             },
             {
-                "$ref": "monomerTemplate-Ser_1"
+                "$ref": "monomerTemplate-Ser_2"
             },
             {
-                "$ref": "monomerTemplate-Thr_2"
+                "$ref": "monomerTemplate-Thr_3"
             },
             {
-                "$ref": "monomerTemplate-Pro_3"
+                "$ref": "monomerTemplate-Pro_4"
             },
             {
-                "$ref": "monomerTemplate-Val_4"
+                "$ref": "monomerTemplate-Val_5"
             },
             {
-                "$ref": "monomerTemplate-Gly_5"
+                "$ref": "monomerTemplate-Gly_6"
             },
             {
-                "$ref": "monomerTemplate-Trp_6"
+                "$ref": "monomerTemplate-Trp_7"
             },
             {
-                "$ref": "monomerTemplate-Ile_7"
+                "$ref": "monomerTemplate-Ile_8"
             }
         ]
     },
@@ -180,7 +180,7 @@
             "y": -5.031300067901611
         },
         "alias": "Gln",
-        "templateId": "Gln_0"
+        "templateId": "Gln_1"
     },
     "monomer1": {
         "type": "monomer",
@@ -191,7 +191,7 @@
             "y": -5.031300067901611
         },
         "alias": "Ser",
-        "templateId": "Ser_1"
+        "templateId": "Ser_2"
     },
     "monomer2": {
         "type": "monomer",
@@ -202,7 +202,7 @@
             "y": -5.031300067901611
         },
         "alias": "Thr",
-        "templateId": "Thr_2"
+        "templateId": "Thr_3"
     },
     "monomer3": {
         "type": "monomer",
@@ -213,7 +213,7 @@
             "y": -5.031300067901611
         },
         "alias": "Pro",
-        "templateId": "Pro_3"
+        "templateId": "Pro_4"
     },
     "monomer4": {
         "type": "monomer",
@@ -224,7 +224,7 @@
             "y": -5.031300067901611
         },
         "alias": "Val",
-        "templateId": "Val_4"
+        "templateId": "Val_5"
     },
     "monomer5": {
         "type": "monomer",
@@ -235,7 +235,7 @@
             "y": -5.031300067901611
         },
         "alias": "Pro",
-        "templateId": "Pro_3"
+        "templateId": "Pro_4"
     },
     "monomer6": {
         "type": "monomer",
@@ -246,7 +246,7 @@
             "y": -5.031300067901611
         },
         "alias": "Ser",
-        "templateId": "Ser_1"
+        "templateId": "Ser_2"
     },
     "monomer7": {
         "type": "monomer",
@@ -257,7 +257,7 @@
             "y": -5.031300067901611
         },
         "alias": "Gly",
-        "templateId": "Gly_5"
+        "templateId": "Gly_6"
     },
     "monomer8": {
         "type": "monomer",
@@ -268,7 +268,7 @@
             "y": -5.031300067901611
         },
         "alias": "Trp",
-        "templateId": "Trp_6"
+        "templateId": "Trp_7"
     },
     "monomer9": {
         "type": "monomer",
@@ -279,11 +279,11 @@
             "y": -5.031300067901611
         },
         "alias": "Ile",
-        "templateId": "Ile_7"
+        "templateId": "Ile_8"
     },
-    "monomerTemplate-Gln_0": {
+    "monomerTemplate-Gln_1": {
         "type": "monomerTemplate",
-        "id": "Gln_0",
+        "id": "Gln_1",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "Q",
@@ -493,9 +493,9 @@
             }
         ]
     },
-    "monomerTemplate-Ser_1": {
+    "monomerTemplate-Ser_2": {
         "type": "monomerTemplate",
-        "id": "Ser_1",
+        "id": "Ser_2",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "S",
@@ -660,9 +660,9 @@
             }
         ]
     },
-    "monomerTemplate-Thr_2": {
+    "monomerTemplate-Thr_3": {
         "type": "monomerTemplate",
-        "id": "Thr_2",
+        "id": "Thr_3",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "T",
@@ -844,9 +844,9 @@
             }
         ]
     },
-    "monomerTemplate-Pro_3": {
+    "monomerTemplate-Pro_4": {
         "type": "monomerTemplate",
-        "id": "Pro_3",
+        "id": "Pro_4",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "P",
@@ -1010,9 +1010,9 @@
             }
         ]
     },
-    "monomerTemplate-Val_4": {
+    "monomerTemplate-Val_5": {
         "type": "monomerTemplate",
-        "id": "Val_4",
+        "id": "Val_5",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "V",
@@ -1169,9 +1169,9 @@
             }
         ]
     },
-    "monomerTemplate-Gly_5": {
+    "monomerTemplate-Gly_6": {
         "type": "monomerTemplate",
-        "id": "Gly_5",
+        "id": "Gly_6",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "G",
@@ -1281,9 +1281,9 @@
             }
         ]
     },
-    "monomerTemplate-Trp_6": {
+    "monomerTemplate-Trp_7": {
         "type": "monomerTemplate",
-        "id": "Trp_6",
+        "id": "Trp_7",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "W",
@@ -1582,9 +1582,9 @@
             }
         ]
     },
-    "monomerTemplate-Ile_7": {
+    "monomerTemplate-Ile_8": {
         "type": "monomerTemplate",
-        "id": "Ile_7",
+        "id": "Ile_8",
         "class": "AminoAcid",
         "classHELM": "PEPTIDE",
         "alias": "I",

api/tests/integration/tests/formats/ref/chem.ket

@@ -4,13 +4,13 @@
         "connections": [],
         "templates": [
             {
-                "$ref": "monomerTemplate-cch_2"
+                "$ref": "monomerTemplate-cch_3"
             }
         ]
     },
-    "monomerTemplate-cch_2": {
+    "monomerTemplate-cch_3": {
         "type": "monomerTemplate",
-        "id": "cch_2",
+        "id": "cch_3",
         "class": "Chem",
         "classHELM": "CHEM",
         "alias": "cch",

api/tests/integration/tests/formats/ref/conj_no_class.mol

@@ -660,7 +660,7 @@ M  V30 0 0.000000 0.000000 0.000000) LABEL=K CLASS=AA SAP=(3 1 11 Al) SAP=(3 -
 M  V30 4 12 Br) SAP=(3 9 10 Cx)
 M  V30 END SGROUP
 M  V30 END CTAB
-M  V30 TEMPLATE 11 AA/Sec/U
+M  V30 TEMPLATE 11 AA/U/U
 M  V30 BEGIN CTAB
 M  V30 COUNTS 9 8 4 0 0
 M  V30 BEGIN ATOM