#1800 only one of the R groups is saved to CDX format

.ci/version.txt

@@ -1,5 +1,5 @@
 1.21.0
 dev
-3
+6
 
-06abd97c62e7e31f12c5c13d4772cbfc7f0e9154fbe2ffc657902f2ca084e561
+e09af5d158c0b3735c76498fb07c11836ca7f74bf6e49a071c3f92486fbe4c40

.github/workflows/indigo-ci.yaml

@@ -785,7 +785,7 @@ jobs:
   build_indigo_ketcher:
     runs-on: ubuntu-latest
     needs: static_analysis
-    container: emscripten/emsdk:1.40.1
+    container: emscripten/emsdk:3.1.60
     steps:
       - name: Checkout
         uses: actions/checkout@v3
@@ -817,7 +817,7 @@ jobs:
   build_indigo_ketcher_cjk:
     runs-on: ubuntu-latest
     needs: static_analysis
-    container: emscripten/emsdk:1.40.1
+    container: emscripten/emsdk:3.1.60
     steps:
       - name: Checkout
         uses: actions/checkout@v3

api/c/indigo-inchi/CMakeLists.txt

@@ -16,6 +16,11 @@ if (NOT EMSCRIPTEN)
     target_include_directories(${PROJECT_NAME}
             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/)
 
+    if(MSVC)
+        target_link_options(${PROJECT_NAME}
+            PRIVATE -force:multiple)
+    endif()
+
     if(UNIX AND NOT APPLE)
         target_link_options(${PROJECT_NAME} PRIVATE -Wl,--version-script=${CMAKE_CURRENT_SOURCE_DIR}/src/libindigo-inchi.sym)
     endif()

api/dotnet/src/Indigo.Net.csproj

@@ -2,7 +2,7 @@
 
 	<PropertyGroup>
 		<TargetFrameworks>netstandard2.0</TargetFrameworks>
-		<Version>1.21.0-dev.3</Version>
+		<Version>1.21.0-dev.6</Version>
 		<Authors>EPAM Systems Life Science Department</Authors>
 		<Company>EPAM Systems</Company>
 		<Description>Universal cheminformatics toolkit</Description>

api/http/requirements.txt

@@ -1,7 +1,7 @@
 anyio==3.7.0
 asgiref==3.7.1
 click==8.1.3
-epam.indigo==1.21.0.dev3
+epam.indigo==1.21.0.dev6
 fastapi==0.95.2
 h11==0.14.0
 idna==3.4

api/http/setup.py

@@ -20,7 +20,7 @@
 
 setup_kwargs = {
     "name": "indigo-service",
-    "version": "1.21.0.dev3",
+    "version": "1.21.0.dev6",
     "description": "",
     "long_description": None,
     "author": "Ruslan Khyurri",

api/indigo-version.cmake

@@ -1,4 +1,4 @@
-set(INDIGO_DEFAULT_VERSION "1.21.0-dev.3")
+set(INDIGO_DEFAULT_VERSION "1.21.0-dev.6")
 set(INDIGO_MAX_REVISION 1000)
 find_package(Git)
 if(GIT_EXECUTABLE)

api/java/pom.xml

@@ -17,7 +17,7 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>${maven.compiler.source}</maven.compiler.target>
-        <revision>1.21.0-dev.3</revision>
+        <revision>1.21.0-dev.6</revision>
     </properties>
 
     <licenses>

api/python/indigo/__init__.py

@@ -3,4 +3,4 @@
 from .indigo.indigo_exception import IndigoException  # noqa
 from .indigo.indigo_object import IndigoObject  # noqa
 
-__version__ = "1.21.0.dev3"
+__version__ = "1.21.0.dev6"

api/python/setup.py

@@ -98,7 +98,7 @@
 
 setup(
     name="epam.indigo",
-    version="1.21.0.dev3",
+    version="1.21.0.dev6",
     description="Indigo universal cheminformatics toolkit",
     author="EPAM Systems Life Science Department",
     author_email="[email protected]",

api/r/DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rindigo
-Version: 1.21.0-dev.3
+Version: 1.21.0-dev.6
 Date: 2020-12-10
 Title: R Package for Indigo Toolkit
 Authors@R: c(person(given = "Mikhail", family = "Kviatkovskii", role = c("cre"),

api/tests/integration/ref/formats/fasta_to_ket.py.out

@@ -4,6 +4,6 @@ test_rna.ket:SUCCEED
 test_dna.ket:SUCCEED
 multiseq.ket:SUCCEED
 break_peptide.ket:SUCCEED
-break_rna.fasta:SEQUENCE loader: SequenceLoader::loadFasta(), Invalid symbols in the sequence: *
+break_rna.fasta:SEQUENCE loader: Invalid symbols in the sequence: *
 comment.ket:SUCCEED
 test_1881.ket:SUCCEED

api/tests/integration/ref/formats/idt_to_ket.py.out

@@ -9,8 +9,8 @@ idt_prefix_suffix.ket:SUCCEED
 idt_singe_32moera_nucleoside.ket:SUCCEED
 idt_single_nucleoside.ket:SUCCEED
 idt_std_phosphates.ket:SUCCEED
-Test '!+-$#12w12r23e32e33': got expected error 'SequenceLoader::loadIdt(), Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3'
-Test '+/5Phos/A': got expected error 'Sugar prefix could not be used with '/5Phos/''
+Test '!+A-$#12w12r23e32e33': got expected error 'Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3'
+Test '+/5Phos/A': got expected error 'Sugar prefix could not be used with modified monomer.'
 Test '/': got expected error 'Unexpected end of data'
 Test '//': got expected error 'Invalid modification: empty string.'
 Test '/32MOErA/T': got expected error 'IDT alias 32MOErA not found at five-prime end position.'
@@ -21,11 +21,13 @@ Test '/a/': got expected error 'Invalid modification: a.'
 Test '/i2MOErA/': got expected error 'IDT alias i2MOErA not found at three-prime end position.'
 Test '/i2MOErA/T': got expected error 'IDT alias i2MOErA not found at five-prime end position.'
 Test 'A*': got expected error 'Invalid IDT sequence: '*' couldn't be the last symbol.'
-Test 'A+/3Phos/': got expected error 'Sugar prefix could not be used with '/3Phos/''
-Test 'Am/3Phos/': got expected error 'Sugar prefix could not be used with '/3Phos/''
-Test 'Ar/3Phos/': got expected error 'Sugar prefix could not be used with '/3Phos/''
+Test 'A*/3Phos/': got expected error 'Phosphor /3Phos/ cannod be modified with '*'.'
+Test 'A+/3Phos/': got expected error 'Sugar prefix could not be used with modified monomer.'
+Test 'Am/3Phos/': got expected error 'Sugar prefix could not be used with modified monomer.'
+Test 'Ar/3Phos/': got expected error 'Sugar prefix could not be used with modified monomer.'
 Test 'T/52MOErA/': got expected error 'IDT alias 52MOErA not found at three-prime end position.'
 Test 'T/5Phos/': got expected error 'IDT alias 5Phos not found at three-prime end position.'
 Test 'T/i2MOErA/': got expected error 'IDT alias i2MOErA not found at three-prime end position.'
-Test 'm/5Phos/A': got expected error 'Sugar prefix could not be used with '/5Phos/''
-Test 'r/5Phos/A': got expected error 'Sugar prefix could not be used with '/5Phos/''
+Test 'm/5Phos/A': got expected error 'Sugar prefix could not be used with modified monomer.'
+Test 'r+A': got expected error 'Sugar prefix 'r' whithout base.'
+Test 'r/5Phos/A': got expected error 'Sugar prefix could not be used with modified monomer.'

api/tests/integration/ref/formats/ket_cdxml.py.out

@@ -11,3 +11,4 @@ multi_overlap.cdxml:SUCCEED
 multi_overlap.ket:SUCCEED
 *** KET to CDXML ***
 963-super.cdxml:SUCCEED
+R3R4R5.cdxml:SUCCEED

api/tests/integration/ref/formats/ket_to_idt.py.out

@@ -9,12 +9,12 @@ idt_prefix_suffix.ket:SUCCEED
 idt_singe_32moera_nucleoside.ket:SUCCEED
 idt_single_nucleoside.ket:SUCCEED
 idt_std_phosphates.ket:SUCCEED
-Test ket-to-idt-invalid-last-phosphate: got expected error 'Canot save molecule in IDT format - phosphate sP cannot be last monomer in sequence.'
+Test ket-to-idt-invalid-last-phosphate: got expected error 'Cannot save molecule in IDT format - phosphate sP cannot be last monomer in sequence.'
 Test ket-to-idt-invalid-nucleotide: got expected error 'IDT alias for group sugar:m2e2r base:z8c3G phosphate:mepo2 not found.'
-Test ket-to-idt-invalid-posphates: got expected error 'Canot save molecule in IDT format - sugar R with too much phosphates connected P and P.'
+Test ket-to-idt-invalid-posphates: got expected error 'Cannot save molecule in IDT format - sugar R with too much phosphates connected P and P.'
 Test ket-to-idt-invalid-sugar: got expected error 'IDT alias for sugar:m2e2r not found.'
 Test ket-to-idt-invalid-sugar-base: got expected error 'IDT alias for group sugar:m2e2r base:z8c3G not found.'
 Test ket-to-idt-invalid-sugar-phosphate: got expected error 'IDT alias for group sugar:m2e2r phosphate:mepo2 not found.'
-Test ket-to-idt-peptide: got expected error 'Canot save molecule in IDT format - AA monomer DPhe4C cannot be first.'
-Test ket-to-idt-r1r1connection: got expected error 'Canot save molecule in IDT format - sugar MOE connected to monomer MOE with class SUGAR (only base or phosphate expected).'
-Test ket-to-idt-two-bases: got expected error 'Canot save molecule in IDT format - sugar R with two base connected A and C.'
+Test ket-to-idt-peptide: got expected error 'Cannot save molecule in IDT format - AA monomer DPhe4C cannot be first.'
+Test ket-to-idt-r1r1connection: got expected error 'Cannot save molecule in IDT format - sugar MOE connected to monomer MOE with class SUGAR (only base or phosphate expected).'
+Test ket-to-idt-two-bases: got expected error 'Cannot save molecule in IDT format - sugar R with two base connected A and C.'

api/tests/integration/ref/formats/mol_to_ket.py.out

@@ -2,6 +2,8 @@
 1032-quadra.ket:SUCCEED
 1046-imp_hydrogen.ket:SUCCEED
 1465-lr_sugar.ket:SUCCEED
+1972-case1.ket:SUCCEED
+1972-case2.ket:SUCCEED
 SgroupDifferent.ket:SUCCEED
 acgt_1412.ket:SUCCEED
 anacyclamide.ket:SUCCEED

api/tests/integration/tests/formats/idt_to_ket.py

@@ -29,9 +29,9 @@ def find_diff(a, b):
 ref_path = joinPathPy("ref/", __file__)
 
 idt_data = {
-    "idt_single_nucleoside": "A",
-    "idt_bases": "ATCGUI",
-    "idt_prefix_suffix": "mA*rT*+C*G*+UrImA",
+    "idt_single_nucleoside": "  A  ",
+    "idt_bases": "  ATCGUI  ",
+    "idt_prefix_suffix": "  mA*rT*+C*G*+UrImA  ",
     "idt_modifications": "/52MOErA/*/i2MOErA//32MOErA/",
     "idt_52moera_with_3phos": "/52MOErA//3Phos/",
     "idt_singe_32moera_nucleoside": "/32MOErA/",
@@ -60,10 +60,11 @@ def find_diff(a, b):
         print(diff)
 
 idt_errors = {
-    "!+-$#12w12r23e32e33": "SequenceLoader::loadIdt(), Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3",
+    "!+A-$#12w12r23e32e33": "Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3",
     "/": "Unexpected end of data",
     "//": "Invalid modification: empty string.",
     "/a/": "Invalid modification: a.",
+    "r+A": "Sugar prefix 'r' whithout base.",
     "A*": "Invalid IDT sequence: '*' couldn't be the last symbol.",
     "/i2MOErA/": "IDT alias i2MOErA not found at three-prime end position.",
     "/i2MOErA/T": "IDT alias i2MOErA not found at five-prime end position.",
@@ -74,12 +75,13 @@ def find_diff(a, b):
     "/3Phos/T": "IDT alias 3Phos not found at three-prime end position.",
     "T/5Phos/": "IDT alias 5Phos not found at three-prime end position.",
     "/5Phos/*A": "/5Phos/ cannot be modified to 'sP'",
-    "r/5Phos/A": "Sugar prefix could not be used with '/5Phos/'",
-    "+/5Phos/A": "Sugar prefix could not be used with '/5Phos/'",
-    "m/5Phos/A": "Sugar prefix could not be used with '/5Phos/'",
-    "Ar/3Phos/": "Sugar prefix could not be used with '/3Phos/'",
-    "A+/3Phos/": "Sugar prefix could not be used with '/3Phos/'",
-    "Am/3Phos/": "Sugar prefix could not be used with '/3Phos/'",
+    "r/5Phos/A": "Sugar prefix could not be used with modified monomer.",
+    "+/5Phos/A": "Sugar prefix could not be used with modified monomer.",
+    "m/5Phos/A": "Sugar prefix could not be used with modified monomer.",
+    "Ar/3Phos/": "Sugar prefix could not be used with modified monomer.",
+    "A+/3Phos/": "Sugar prefix could not be used with modified monomer.",
+    "Am/3Phos/": "Sugar prefix could not be used with modified monomer.",
+    "A*/3Phos/": "Phosphor /3Phos/ cannod be modified with '*'.",
 }
 for idt_seq in sorted(idt_errors.keys()):
     error = idt_errors[idt_seq]

api/tests/integration/tests/formats/ket_cdxml.py

@@ -84,6 +84,7 @@ def find_diff(a, b):
 root_m = joinPathPy("molecules/", __file__)
 files = [
     "963-super",
+    "R3R4R5",
 ]
 
 files.sort()

api/tests/integration/tests/formats/ket_to_idt.py

@@ -56,11 +56,11 @@ def find_diff(a, b):
         )
 
 idt_errors = {
-    "ket-to-idt-r1r1connection": "Canot save molecule in IDT format - sugar MOE connected to monomer MOE with class SUGAR (only base or phosphate expected).",
-    "ket-to-idt-peptide": "Canot save molecule in IDT format - AA monomer DPhe4C cannot be first.",
-    "ket-to-idt-two-bases": "Canot save molecule in IDT format - sugar R with two base connected A and C.",
-    "ket-to-idt-invalid-posphates": "Canot save molecule in IDT format - sugar R with too much phosphates connected P and P.",
-    "ket-to-idt-invalid-last-phosphate": "Canot save molecule in IDT format - phosphate sP cannot be last monomer in sequence.",
+    "ket-to-idt-r1r1connection": "Cannot save molecule in IDT format - sugar MOE connected to monomer MOE with class SUGAR (only base or phosphate expected).",
+    "ket-to-idt-peptide": "Cannot save molecule in IDT format - AA monomer DPhe4C cannot be first.",
+    "ket-to-idt-two-bases": "Cannot save molecule in IDT format - sugar R with two base connected A and C.",
+    "ket-to-idt-invalid-posphates": "Cannot save molecule in IDT format - sugar R with too much phosphates connected P and P.",
+    "ket-to-idt-invalid-last-phosphate": "Cannot save molecule in IDT format - phosphate sP cannot be last monomer in sequence.",
     "ket-to-idt-invalid-nucleotide": "IDT alias for group sugar:m2e2r base:z8c3G phosphate:mepo2 not found.",
     "ket-to-idt-invalid-sugar-phosphate": "IDT alias for group sugar:m2e2r phosphate:mepo2 not found.",
     "ket-to-idt-invalid-sugar": "IDT alias for sugar:m2e2r not found.",

api/tests/integration/tests/formats/mol_to_ket.py

@@ -47,6 +47,8 @@ def find_diff(a, b):
     "1465-lr_sugar",
     "removed_phosphate",
     "taspoglutide",
+    "1972-case1",
+    "1972-case2",
 ]
 
 files.sort()

api/tests/integration/tests/formats/molecules/1972-case1.mol

@@ -0,0 +1,32 @@
+
+  -INDIGO-05282400262D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 7 7 1 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 3.48485 -6.77507 0.0 0
+M  V30 2 C 5.21515 -6.77459 0.0 0
+M  V30 3 C 4.35164 -6.27497 0.0 0
+M  V30 4 C 5.21515 -7.77553 0.0 0
+M  V30 5 C 3.48485 -7.78002 0.0 0
+M  V30 6 C 4.35382 -8.27503 0.0 0
+M  V30 7 H 4.35225 -5.27497 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 3 1
+M  V30 2 1 1 5
+M  V30 3 2 5 6
+M  V30 4 1 6 4
+M  V30 5 2 4 2
+M  V30 6 1 2 3
+M  V30 7 1 3 7
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(7 3 1 5 6 4 2 7) BRKXYZ=(9 0.000000 0.000000 0.000000 0-
+M  V30 .000000 0.000000 0.000000 0.000000 0.000000 0.000000) BRKXYZ=(9 0.0000-
+M  V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00-
+M  V30 0000) ESTATE=E SAP=(3 3 7 )
+M  V30 END SGROUP
+M  V30 END CTAB
+M  END

api/tests/integration/tests/formats/molecules/1972-case2.mol

@@ -0,0 +1,70 @@
+
+  -INDIGO-05282400262D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 8 7 1 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 5.90985 -7.05007 0.0 0
+M  V30 2 C 7.64015 -7.04959 0.0 0
+M  V30 3 C 6.77664 -6.54997 0.0 0
+M  V30 4 C 7.64015 -8.05053 0.0 0
+M  V30 5 C 5.90985 -8.05502 0.0 0
+M  V30 6 C 6.77882 -8.55003 0.0 0
+M  V30 7 H 6.77725 -5.54997 0.0 0
+M  V30 8 A 11.425 -6.975 0.0 0 CLASS=AA SEQID=1
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 3 1
+M  V30 2 1 1 5
+M  V30 3 2 5 6
+M  V30 4 1 6 4
+M  V30 5 2 4 2
+M  V30 6 1 2 3
+M  V30 7 1 3 7
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(7 3 1 5 6 4 2 7) BRKXYZ=(9 0.000000 0.000000 0.000000 0-
+M  V30 .000000 0.000000 0.000000 0.000000 0.000000 0.000000) BRKXYZ=(9 0.0000-
+M  V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00-
+M  V30 0000) ESTATE=E SAP=(3 3 7 )
+M  V30 END SGROUP
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 1 AA/Ala/A/ NATREPLACE=AA/A
+M  V30 BEGIN CTAB
+M  V30 COUNTS 7 6 3 0 0
+M  V30 BEGIN ATOM
+M  V30 1 N -1.2549 -0.392 0.0 0
+M  V30 2 C -0.272 0.2633 0.0 0 CFG=1
+M  V30 3 C -0.3103 1.7393 0.0 0
+M  V30 4 C 1.0523 -0.392 0.0 0
+M  V30 5 O 1.0829 -1.5722 0.0 0
+M  V30 6 O 2.0353 0.2633 0.0 0
+M  V30 7 H -2.3334 0.0905 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 2 1
+M  V30 2 1 2 3 CFG=1
+M  V30 3 1 2 4
+M  V30 4 2 4 5
+M  V30 5 1 4 6
+M  V30 6 1 1 7
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(1 2)
+M  V30 END COLLECTION
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(1 7) XBONDS=(1 6) BRKXYZ=(9 0.539250 -0.241250 0.000000-
+M  V30  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=-
+M  V30 LGRP
+M  V30 2 SUP 2 ATOMS=(1 6) XBONDS=(1 5) BRKXYZ=(9 -0.491500 -0.327650 0.00000-
+M  V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLAS-
+M  V30 S=LGRP
+M  V30 3 SUP 3 ATOMS=(5 1 2 3 4 5) XBONDS=(2 6 5) BRKXYZ=(9 -0.539250 0.24125-
+M  V30 0 0.000000 0.491500 0.327650 0.000000 0.000000 0.000000 0.000000) LABE-
+M  V30 L=A CLASS=AA SAP=(3 1 7 Al) SAP=(3 4 6 Br) NATREPLACE=AA/A
+M  V30 END SGROUP
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END