#1994 - Micro and macro structures connected through attachment point…

…s cannot be opened after save in CDX and Base 64CDX format in micro mode (#2024)

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

@@ -2,6 +2,7 @@
 enhanced_stereo1:success
 enhanced_stereo2:success
 enhanced_stereo3:success
+macro/sa-mono:success
 rgroup:success
 stereo_either-0020:success
 two_bn:success

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

@@ -1,2 +1,3 @@
 *** KET to CML ***
-1878-ket-to-cml.cml:SUCCEED
+1878-ket-to-cml.cml:SUCCEED
+macro/sa-mono.cml:SUCCEED

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

@@ -29,6 +29,7 @@ macro/modified/mod_rna_peptide.ket:SUCCEED
 macro/peptide-rna/peptide-rna.ket:SUCCEED
 macro/peptide-rna/peptide-rna-ac.ket:SUCCEED
 macro/polyphosphate/polyphosphate_rna.ket:SUCCEED
+macro/sa-mono.ket:SUCCEED
 macro/terminators/terms_peptide.ket:SUCCEED
 mon_long_id.ket:SUCCEED
 pepchem.ket:SUCCEED

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

@@ -1,3 +1,4 @@
 C1%82(C%83O%84%85)OC%86(C(O%87%88%89)C(O%90%91)C%921O%93%94%95)O%96%97%98.[*:1]%96.[*:2]%93.[*:3]%84.[*:4]%90.[*:5]%87.[*:6]%94%85.[*:7]%95%97.[*:8]%83.[*:9]%91%88.[*:10]%89%98.[*:11]%86.[*:12]%92.[*:13]%82 |$;;;;;;;;;;;;_R1;_R2;_R3;_R4;_R5;_R6;_R7;_R8;_R9;_R10;_R11;_R12;_R13$|
 [O-][N+](C1=NN=NN1CC1N=NNN=1)=O
 C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12,(25.51,-10.61,;25.51,-12.12,;24.22,-12.87,;26.82,-12.86,;26.82,-14.36,;25.51,-15.12,;25.52,-16.62,;26.82,-17.36,;26.82,-18.86,;28.12,-16.61,;28.12,-15.11,;29.18,-14.05,;28.11,-12.11,;29.41,-12.86,;28.11,-10.61,;26.82,-9.86,)|
+C1C=CC=CC=1*

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

@@ -730,16 +730,16 @@ CN_Bond-S-GRP.rxn
         </fragment>
         <fragment id="11">
             <n id="31" NodeType="Fragment">
-                <fragment id="32">
+                <fragment id="33">
                     <n id="14" p="444.486023 159.261002"/>
-                    <n id="33" NodeType="ExternalConnectionPoint"/>
-                    <b id="35" B="33" E="14"/>
+                    <n id="34" NodeType="ExternalConnectionPoint"/>
+                    <b id="36" B="34" E="14"/>
                 </fragment>
                 <t LabelJustification="Left" LabelAlignment="Above">
                     <s>R2</s>
                 </t>
             </n>
-            <n id="36" NodeType="Fragment">
+            <n id="32" NodeType="Fragment">
                 <fragment id="37">
                     <n id="12" p="413.790009 212.423996"/>
                     <n id="38" NodeType="ExternalConnectionPoint"/>
@@ -754,8 +754,8 @@ CN_Bond-S-GRP.rxn
                     <s font="3" size="10" face="96">NH</s>
                 </t>
             </n>
-            <b id="34" B="13" E="31"/>
-            <b id="39" B="13" E="36"/>
+            <b id="35" B="13" E="31"/>
+            <b id="39" B="13" E="32"/>
         </fragment>
         <t p="198.396011 175.387482" Justification="Center" InterpretChemically="no">
             <s font="3" size="10" face="96">+</s>
@@ -831,16 +831,16 @@ CN_Bond-S-GRP.rxn
         </fragment>
         <fragment id="11">
             <n id="31" NodeType="Fragment">
-                <fragment id="32">
+                <fragment id="33">
                     <n id="14" p="444.486023 159.261002"/>
-                    <n id="33" NodeType="ExternalConnectionPoint"/>
-                    <b id="35" B="33" E="14"/>
+                    <n id="34" NodeType="ExternalConnectionPoint"/>
+                    <b id="36" B="34" E="14"/>
                 </fragment>
                 <t LabelJustification="Left" LabelAlignment="Above">
                     <s>R2</s>
                 </t>
             </n>
-            <n id="36" NodeType="Fragment">
+            <n id="32" NodeType="Fragment">
                 <fragment id="37">
                     <n id="12" p="413.790009 212.423996"/>
                     <n id="38" NodeType="ExternalConnectionPoint"/>
@@ -855,8 +855,8 @@ CN_Bond-S-GRP.rxn
                     <s font="3" size="10" face="96">NH</s>
                 </t>
             </n>
-            <b id="34" B="13" E="31"/>
-            <b id="39" B="13" E="36"/>
+            <b id="35" B="13" E="31"/>
+            <b id="39" B="13" E="32"/>
         </fragment>
         <t p="198.396011 175.387482" Justification="Center" InterpretChemically="no">
             <s font="3" size="10" face="96">+</s>

api/tests/integration/tests/formats/cdx_export.py

@@ -27,6 +27,7 @@ def find_diff(a, b):
     "enhanced_stereo3",
     "two_bn",
     "rgroup",
+    "macro/sa-mono",
 ]
 
 ref_path = joinPathPy("ref/", __file__)
@@ -153,7 +154,7 @@ def test_file(filename, suffix=".mol"):
         )
         resb64 = rea.b64cdx()
         # with open(os.path.join(ref_path, filename + ".b64cdx"), "w") as file:
-        #    file.write(resb64)
+        #     file.write(resb64)
         with open(os.path.join(ref_path, filename + ".b64cdx"), "r") as file:
             refb64 = file.read()
         print(filename + (":success" if refb64 == resb64 else ":failed"))

api/tests/integration/tests/formats/ket_to_cml.py

@@ -23,15 +23,18 @@ def find_diff(a, b):
 root = joinPathPy("molecules/", __file__)
 ref_path = joinPathPy("ref/", __file__)
 
-files = ["1878-ket-to-cml"]
+files = ["1878-ket-to-cml", "macro/sa-mono"]
 
 files.sort()
 for filename in files:
     ket = indigo.loadMoleculeFromFile(os.path.join(root, filename + ".ket"))
 
+    cml = ket.cml()
+    # with open(os.path.join(ref_path, filename) + ".cml", "w") as file:
+    #     file.write(cml)
+
     with open(os.path.join(ref_path, filename) + ".cml", "r") as file:
         cml_ref = file.read()
-    cml = ket.cml()
     diff = find_diff(cml_ref, cml)
     if not diff:
         print(filename + ".cml:SUCCEED")

api/tests/integration/tests/formats/ket_to_mol.py

@@ -65,6 +65,7 @@ def find_diff(a, b):
     "macro/peptide-rna/peptide-rna-ac",
     "macro/polyphosphate/polyphosphate_rna",
     "macro/terminators/terms_peptide",
+    "macro/sa-mono",
 ]
 
 files.sort()

api/tests/integration/tests/formats/mol_to_smiles.py

@@ -26,3 +26,9 @@
         joinPathPy("molecules/atropisomer.mol", __file__)
     ).smiles()
 )
+
+print(
+    indigo.loadMoleculeFromFile(
+        joinPathPy("molecules/macro/sa-mono.mol", __file__)
+    ).smiles()
+)

api/tests/integration/tests/formats/molecules/macro/sa-mono.mol

@@ -0,0 +1,69 @@
+
+  -INDIGO-06262408322D
+
+  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 14.6598 -10.3251 0.0 0
+M  V30 2 C 16.3902 -10.3246 0.0 0
+M  V30 3 C 15.5266 -9.82497 0.0 0
+M  V30 4 C 16.3902 -11.3255 0.0 0
+M  V30 5 C 14.6598 -11.33 0.0 0
+M  V30 6 C 15.5288 -11.825 0.0 0
+M  V30 7 A 16.775 -7.75 0.0 0 CLASS=AA SEQID=1 ATTCHORD=(2 3 Al)
+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=(6 3 1 5 6 4 2) BRKXYZ=(9 0.000000 0.000000 0.000000 0.0-
+M  V30 00000 0.000000 0.000000 0.000000 0.000000 0.000000) BRKXYZ=(9 0.000000-
+M  V30  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.0000-
+M  V30 00) ESTATE=E SAP=(3 3 0 1)
+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 -0.980533 -0.306295 0.0 0
+M  V30 2 C -0.212531 0.205733 0.0 0 CFG=1
+M  V30 3 C -0.242457 1.35903 0.0 0
+M  V30 4 C 0.822229 -0.306295 0.0 0
+M  V30 5 O 0.846139 -1.22846 0.0 0
+M  V30 6 O 1.59031 0.205733 0.0 0
+M  V30 7 H -1.82323 0.0707134 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 0.421350 -0.188504 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 -0.384040 -0.256014 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 -0.421350 0.18850-
+M  V30 4 0.000000 0.384040 0.256014 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

api/tests/integration/tests/formats/ref/1878-ket-to-cml.cml

@@ -15,4 +15,4 @@
             <bond atomRefs2="a2 a0" order="1"/>
         </bondArray>
     </molecule>
-</cml>
+</cml>

api/tests/integration/tests/formats/ref/963-super.cdxml

@@ -19,9 +19,9 @@
     <page HeightPages="1" WidthPages="1">
         <fragment id="4">
             <n id="48" NodeType="Fragment">
-                <fragment id="49">
+                <fragment id="51">
                     <n id="11" p="59.835632 109.329903"/>
-                    <n id="50" NodeType="ExternalConnectionPoint"/>
+                    <n id="52" NodeType="ExternalConnectionPoint"/>
                     <n id="12" Element="8" NumHydrogens="0" p="30.202303 104.643272">
                         <t p="30.202303 104.643272" LabelJustification="Left">
                             <s font="3" size="10" face="96">O</s>
@@ -42,20 +42,20 @@
                     <b id="37" B="14" E="15"/>
                     <b id="38" B="14" E="16"/>
                     <b id="39" B="14" E="17"/>
-                    <b id="52" B="50" E="11"/>
+                    <b id="54" B="52" E="11"/>
                 </fragment>
                 <t LabelJustification="Left" LabelAlignment="Above">
                     <s>CO2tBu</s>
                 </t>
             </n>
-            <n id="53" NodeType="Fragment">
-                <fragment id="54">
+            <n id="49" NodeType="Fragment">
+                <fragment id="55">
                     <n id="18" Element="16" NumHydrogens="0" p="59.998569 229.331665">
                         <t p="59.998569 229.331665" LabelJustification="Left">
                             <s font="3" size="10" face="96">S</s>
                         </t>
                     </n>
-                    <n id="55" NodeType="ExternalConnectionPoint"/>
+                    <n id="56" NodeType="ExternalConnectionPoint"/>
                     <n id="19" p="60.107033 259.326599"/>
                     <n id="20" Element="8" NumHydrogens="0" p="30.000000 229.440125">
                         <t p="30.000000 229.440125" LabelJustification="Left">
@@ -70,13 +70,13 @@
                     <b id="41" B="19" E="18"/>
                     <b id="42" B="18" E="20" Order="2"/>
                     <b id="43" B="18" E="21" Order="2"/>
-                    <b id="57" B="55" E="18"/>
+                    <b id="58" B="56" E="18"/>
                 </fragment>
                 <t LabelJustification="Left" LabelAlignment="Above">
                     <s>Ms</s>
                 </t>
             </n>
-            <n id="58" NodeType="Fragment">
+            <n id="50" NodeType="Fragment">
                 <fragment id="59">
                     <n id="22" Element="16" NumHydrogens="0" p="168.518234 145.330887">
                         <t p="168.518234 145.330887" LabelJustification="Left">
@@ -120,8 +120,8 @@
             <b id="30" B="6" E="7"/>
             <b id="31" B="9" E="10" Order="2"/>
             <b id="32" B="10" E="8"/>
-            <b id="51" B="7" E="48"/>
-            <b id="56" B="10" E="53"/>
+            <b id="53" B="7" E="48"/>
+            <b id="57" B="10" E="49"/>
         </fragment>
     </page>
 </CDXML>