cip bonds fix

epam · Sep 27, 2024 · 3a54755 · 3a54755
1 parent 5ac50b2
commit 3a54755
Show file tree

Hide file tree

Showing 2 changed files with 125 additions and 6 deletions.
diff --git a/api/tests/integration/ref/basic/molfile_stereo_desc.py.out b/api/tests/integration/ref/basic/molfile_stereo_desc.py.out
@@ -1326,6 +1326,126 @@ M  SDD   3     0.0000    0.0000    DR    ALL  1       1
 M  SED   3 (E)
 M  END
 
+cip_high_load
+
+  -INDIGO-01000000002D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 36 35 15 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 7.8 -7.025 0.0 0
+M  V30 2 C 8.666 -7.525 0.0 0 CFG=1
+M  V30 3 C 9.5321 -7.025 0.0 0 CFG=2
+M  V30 4 C 10.3981 -7.525 0.0 0 CFG=1
+M  V30 5 C 11.2641 -7.025 0.0 0 CFG=2
+M  V30 6 C 12.1301 -7.525 0.0 0 CFG=2
+M  V30 7 C 12.9962 -8.025 0.0 0 CFG=1
+M  V30 8 C 13.8622 -7.525 0.0 0 CFG=2
+M  V30 9 C 14.7282 -8.025 0.0 0 CFG=1
+M  V30 10 C 15.5942 -7.525 0.0 0 CFG=2
+M  V30 11 C 16.4603 -8.025 0.0 0 CFG=2
+M  V30 12 C 17.3264 -8.525 0.0 0 CFG=1
+M  V30 13 C 18.1924 -8.025 0.0 0 CFG=2
+M  V30 14 C 19.0584 -8.525 0.0 0 CFG=1
+M  V30 15 C 19.9245 -8.025 0.0 0 CFG=2
+M  V30 16 C 20.7905 -8.525 0.0 0 CFG=2
+M  V30 17 C 8.666 -8.525 0.0 0
+M  V30 18 C 9.5321 -6.025 0.0 0
+M  V30 19 C 10.3981 -8.525 0.0 0
+M  V30 20 C 11.2641 -6.025 0.0 0
+M  V30 21 C 12.9962 -9.025 0.0 0
+M  V30 22 C 13.8622 -6.525 0.0 0
+M  V30 23 C 14.7282 -9.025 0.0 0
+M  V30 24 C 15.5942 -6.525 0.0 0
+M  V30 25 C 17.3264 -9.525 0.0 0
+M  V30 26 C 18.1924 -7.025 0.0 0
+M  V30 27 C 19.0584 -9.525 0.0 0
+M  V30 28 C 21.4976 -9.2321 0.0 0 CFG=1
+M  V30 29 C 22.4635 -8.9733 0.0 0 CFG=2
+M  V30 30 C 23.1706 -9.6804 0.0 0
+M  V30 31 C 19.9245 -7.025 0.0 0
+M  V30 32 C 22.7223 -8.0074 0.0 0
+M  V30 33 C 21.2388 -10.198 0.0 0
+M  V30 34 C 21.2905 -7.659 0.0 0
+M  V30 35 C 12.6301 -6.659 0.0 0
+M  V30 36 C 16.9603 -7.159 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 3 4
+M  V30 4 1 4 5
+M  V30 5 1 5 6
+M  V30 6 1 6 7
+M  V30 7 1 7 8
+M  V30 8 1 8 9
+M  V30 9 1 9 10
+M  V30 10 1 10 11
+M  V30 11 1 11 12
+M  V30 12 1 12 13
+M  V30 13 1 13 14
+M  V30 14 1 14 15
+M  V30 15 1 15 16
+M  V30 16 1 2 17 CFG=1
+M  V30 17 1 3 18 CFG=1
+M  V30 18 1 4 19 CFG=1
+M  V30 19 1 5 20 CFG=1
+M  V30 20 1 7 21 CFG=1
+M  V30 21 1 8 22 CFG=1
+M  V30 22 1 9 23 CFG=1
+M  V30 23 1 10 24 CFG=1
+M  V30 24 1 12 25 CFG=1
+M  V30 25 1 13 26 CFG=1
+M  V30 26 1 14 27 CFG=1
+M  V30 27 1 16 28
+M  V30 28 1 28 29
+M  V30 29 1 29 30
+M  V30 30 1 15 31 CFG=1
+M  V30 31 1 29 32 CFG=1
+M  V30 32 1 28 33 CFG=1
+M  V30 33 1 16 34 CFG=1
+M  V30 34 1 6 35 CFG=1
+M  V30 35 1 11 36 CFG=1
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STERAC1 ATOMS=(17 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 28 29)
+M  V30 END COLLECTION
+M  V30 BEGIN SGROUP
+M  V30 1 DAT 1 ATOMS=(1 3) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000   -
+M  V30  0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 2 DAT 2 ATOMS=(1 4) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000   -
+M  V30  0.0000    DR    ALL  1       1  " FIELDDATA="(S)"
+M  V30 3 DAT 3 ATOMS=(1 5) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000   -
+M  V30  0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 4 DAT 4 ATOMS=(1 6) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000   -
+M  V30  0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 5 DAT 5 ATOMS=(1 7) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000   -
+M  V30  0.0000    DR    ALL  1       1  " FIELDDATA="(S)"
+M  V30 6 DAT 6 ATOMS=(1 8) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000   -
+M  V30  0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 7 DAT 7 ATOMS=(1 9) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000   -
+M  V30  0.0000    DR    ALL  1       1  " FIELDDATA="(S)"
+M  V30 8 DAT 8 ATOMS=(1 10) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000  -
+M  V30   0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 9 DAT 9 ATOMS=(1 11) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000  -
+M  V30   0.0000    DR    ALL  1       1  " FIELDDATA="(S)"
+M  V30 10 DAT 10 ATOMS=(1 12) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000-
+M  V30     0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 11 DAT 11 ATOMS=(1 13) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000-
+M  V30     0.0000    DR    ALL  1       1  " FIELDDATA="(S)"
+M  V30 12 DAT 12 ATOMS=(1 14) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000-
+M  V30     0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 13 DAT 13 ATOMS=(1 15) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000-
+M  V30     0.0000    DR    ALL  1       1  " FIELDDATA="(S)"
+M  V30 14 DAT 14 ATOMS=(1 16) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000-
+M  V30     0.0000    DR    ALL  1       1  " FIELDDATA="(S)"
+M  V30 15 DAT 15 ATOMS=(1 28) FIELDNAME=INDIGO_CIP_DESC FIELDDISP="    0.0000-
+M  V30     0.0000    DR    ALL  1       1  " FIELDDATA="(R)"
+M  V30 END SGROUP
+M  V30 END CTAB
+M  END
+
 cis
 
   -INDIGO-01000000002D

diff --git a/api/tests/integration/tests/basic/molfile_stereo_desc.py b/api/tests/integration/tests/basic/molfile_stereo_desc.py
@@ -17,12 +17,11 @@ def stereo_desc_test(py_file, out_queue):
     indigo.setOption("molfile-saving-add-stereo-desc", "1")
     str_res = "This test checks correct determination and saving of CIP stereo descriptors\n"
     for filename in sorted(os.listdir(joinPathPy("molecules/CIP", py_file))):
-        if filename != "cip_high_load.mol":
-            mol = indigo.loadMoleculeFromFile(
-                joinPathPy("molecules/CIP/" + filename, py_file)
-            )
-            str_res = str_res + "%s" % filename[:-4] + "\n"
-            str_res = str_res + mol.molfile() + "\n"
+        mol = indigo.loadMoleculeFromFile(
+            joinPathPy("molecules/CIP/" + filename, py_file)
+        )
+        str_res = str_res + "%s" % filename[:-4] + "\n"
+        str_res = str_res + mol.molfile() + "\n"
 
     indigo.setOption("ignore-stereochemistry-errors", "true")
     rxn = indigo.loadReactionFromFile(