#1184 Support monomer templates export into KET-format (#1251)

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

@@ -3,5 +3,10 @@
 1046-imp_hydrogen.ket:SUCCEED
 SgroupDifferent.ket:SUCCEED
 atropisomer.ket:SUCCEED
+chem.ket:SUCCEED
+cysteine.ket:SUCCEED
+dcysteine.ket:SUCCEED
+dthymine.ket:SUCCEED
 non_atrop.ket:SUCCEED
 suplabel.ket:SUCCEED
+thymine.ket:SUCCEED

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

@@ -30,6 +30,11 @@ def find_diff(a, b):
     "suplabel",
     "atropisomer",
     "non_atrop",
+    "cysteine",
+    "dcysteine",
+    "thymine",
+    "dthymine",
+    "chem",
 ]
 
 files.sort()

api/tests/integration/tests/formats/molecules/chem.mol

@@ -0,0 +1,47 @@
+
+  -INDIGO-09062309442D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 3 CHEM/cch/cch
+M  V30 BEGIN CTAB
+M  V30 COUNTS 9 8 4 0 1
+M  V30 BEGIN ATOM
+M  V30 1 H 9.2012 -7.1587 0 0
+M  V30 2 H 8.3747 -7.9854 0 0
+M  V30 3 O 10.0281 -7.9854 0 0
+M  V30 4 S 9.7182 -6.7372 0 0
+M  V30 5 C 9.1949 -7.6427 0 0 CFG=2
+M  V30 6 O 9.6984 -8.5803 0 0
+M  V30 7 C 9.6984 -7.9763 0 0
+M  V30 8 C 9.1949 -7.0388 0 0
+M  V30 9 N 8.7041 -7.9947 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 4 1
+M  V30 2 1 7 3
+M  V30 3 1 9 2
+M  V30 4 2 7 6
+M  V30 5 1 5 8 CFG=1
+M  V30 6 1 8 4
+M  V30 7 1 5 7
+M  V30 8 1 9 5
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(1 2) XBONDS=(1 3) LABEL=H CSTATE=(4 3 0.8265 0 0) -
+M  V30 CLASS=LGRP
+M  V30 2 SUP 2 ATOMS=(1 3) XBONDS=(1 2) LABEL=OH CSTATE=(4 2 -0.825 0 0) -
+M  V30 CLASS=LGRP
+M  V30 3 SUP 3 ATOMS=(1 1) XBONDS=(1 1) LABEL=H CSTATE=(4 1 0 -0.8267 0) -
+M  V30 CLASS=LGRP
+M  V30 4 SUP 4 ATOMS=(6 4 5 6 7 8 9) XBONDS=(3 1 2 3) LABEL=Cys CSTATE=(4 3 -
+M  V30 -0.8265 0 0) CSTATE=(4 2 0.825 0 0) CSTATE=(4 1 0 0.8267 0) CLASS=AA -
+M  V30 SAP=(3 9 2 Br) SAP=(3 7 3 Cx) SAP=(3 4 1 Ex)
+M  V30 END SGROUP
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END
+

api/tests/integration/tests/formats/molecules/cysteine.mol

@@ -0,0 +1,47 @@
+
+  -INDIGO-09062309442D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 3 AA/cys/C
+M  V30 BEGIN CTAB
+M  V30 COUNTS 9 8 4 0 1
+M  V30 BEGIN ATOM
+M  V30 1 H 9.2012 -7.1587 0 0
+M  V30 2 H 8.3747 -7.9854 0 0
+M  V30 3 O 10.0281 -7.9854 0 0
+M  V30 4 S 9.7182 -6.7372 0 0
+M  V30 5 C 9.1949 -7.6427 0 0 CFG=2
+M  V30 6 O 9.6984 -8.5803 0 0
+M  V30 7 C 9.6984 -7.9763 0 0
+M  V30 8 C 9.1949 -7.0388 0 0
+M  V30 9 N 8.7041 -7.9947 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 4 1
+M  V30 2 1 7 3
+M  V30 3 1 9 2
+M  V30 4 2 7 6
+M  V30 5 1 5 8 CFG=1
+M  V30 6 1 8 4
+M  V30 7 1 5 7
+M  V30 8 1 9 5
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(1 2) XBONDS=(1 3) LABEL=H CSTATE=(4 3 0.8265 0 0) -
+M  V30 CLASS=LGRP
+M  V30 2 SUP 2 ATOMS=(1 3) XBONDS=(1 2) LABEL=OH CSTATE=(4 2 -0.825 0 0) -
+M  V30 CLASS=LGRP
+M  V30 3 SUP 3 ATOMS=(1 1) XBONDS=(1 1) LABEL=H CSTATE=(4 1 0 -0.8267 0) -
+M  V30 CLASS=LGRP
+M  V30 4 SUP 4 ATOMS=(6 4 5 6 7 8 9) XBONDS=(3 1 2 3) LABEL=Cys CSTATE=(4 3 -
+M  V30 -0.8265 0 0) CSTATE=(4 2 0.825 0 0) CSTATE=(4 1 0 0.8267 0) CLASS=AA -
+M  V30 SAP=(3 9 2 Al) SAP=(3 7 3 Br) SAP=(3 4 1 Cx)
+M  V30 END SGROUP
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END
+

api/tests/integration/tests/formats/molecules/dala.mol

@@ -0,0 +1,43 @@
+
+  ACCLDraw09281611442D
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 23 dAA/ala/a/ NATREPLACE=AA/A
+M  V30 BEGIN CTAB
+M  V30 COUNTS 7 6 3 0 1
+M  V30 BEGIN ATOM
+M  V30 1 O 6.6266 -2.0662 0 0 
+M  V30 2 H 5.0016 -2.0876 0 0 
+M  V30 3 N 5.1358 -2.0784 0 0 CFG=3 
+M  V30 4 C 5.7844 -1.5983 0 0 CFG=1 
+M  V30 5 C 6.4753 -2.0653 0 0 
+M  V30 6 O 6.4753 -2.8977 0 0 
+M  V30 7 C 5.7844 -0.7662 0 0 
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 3 4 
+M  V30 2 1 4 5 
+M  V30 3 2 5 6 
+M  V30 4 1 4 7 CFG=3 
+M  V30 5 1 3 2 
+M  V30 6 1 5 1 
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(1 1) XBONDS=(1 6) BRKXYZ=(9 7.02 -2.26 0 7.02 -1.85 0 -
+M  V30 0 0 0) CSTATE=(4 6 -0.82 -0.01 0) LABEL=OH CLASS=LGRP 
+M  V30 2 SUP 2 ATOMS=(1 2) XBONDS=(1 5) BRKXYZ=(9 4.58 -1.87 0 4.6 -2.28 0 -
+M  V30 0 0 0) CSTATE=(4 5 0.8 0.02 0) LABEL=H CLASS=LGRP 
+M  V30 3 SUP 3 ATOMS=(5 3 4 5 6 7) XBONDS=(2 5 6) BRKXYZ=(9 3.95 -3.33 0 3.95 -
+M  V30 -0.38 0 0 0 0) CSTATE=(4 5 -0.8 -0.02 0) CSTATE=(4 6 0.82 0.01 -
+M  V30 0) LABEL=a CLASS=AA SAP=(3 3 2 Al) SAP=(3 5 1 Br) NATREPLACE=AA/A
+M  V30 END SGROUP
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(1 4)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END

api/tests/integration/tests/formats/molecules/dcysteine.mol

@@ -0,0 +1,50 @@
+
+  -INDIGO-09062309442D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 27 dAA/cys/c/ NATREPLACE=AA/C
+M  V30 BEGIN CTAB
+M  V30 COUNTS 9 8 4 0 0
+M  V30 BEGIN ATOM
+M  V30 1 H 9.2012 -7.1587 0 0 
+M  V30 2 H 8.3747 -7.9854 0 0 
+M  V30 3 O 10.0281 -7.9854 0 0 
+M  V30 4 S 9.7182 -6.7372 0 0 
+M  V30 5 C 9.1949 -7.6427 0 0 CFG=1 
+M  V30 6 O 9.6984 -8.5803 0 0 
+M  V30 7 C 9.6984 -7.9763 0 0 
+M  V30 8 C 9.1949 -7.0388 0 0 
+M  V30 9 N 8.7041 -7.9947 0 0 CFG=3 
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 4 1 
+M  V30 2 1 7 3 
+M  V30 3 1 9 2 
+M  V30 4 2 7 6 
+M  V30 5 1 5 8 CFG=3 
+M  V30 6 1 8 4 
+M  V30 7 1 5 7 
+M  V30 8 1 9 5 
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(1 2) XBONDS=(1 3) CSTATE=(4 3 0.83 -0 0) LABEL=H -
+M  V30 CLASS=LGRP 
+M  V30 2 SUP 2 ATOMS=(1 3) XBONDS=(1 2) CSTATE=(4 2 -0.83 -0 0) LABEL=OH -
+M  V30 CLASS=LGRP 
+M  V30 3 SUP 3 ATOMS=(1 1) XBONDS=(1 1) CSTATE=(4 1 0 -0.83 0) LABEL=H -
+M  V30 CLASS=LGRP 
+M  V30 4 SUP 4 ATOMS=(6 9 5 6 7 8 4) XBONDS=(3 3 2 1) CSTATE=(4 3 -0.83 0 0) -
+M  V30 CSTATE=(4 2 0.83 0 0) CSTATE=(4 1 -0 0.83 0) LABEL=c SAP=(3 -
+M  V30 9 2 Al) SAP=(3 7 3 Br) SAP=(3 4 1 Cx) NATREPLACE=AA/C
+M  V30 END SGROUP
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(1 5)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END
+

api/tests/integration/tests/formats/molecules/dthymine.mol

@@ -0,0 +1,76 @@
+
+  -INDIGO-09062309442D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 45 DNA/T
+M  V30 BEGIN CTAB
+M  V30 COUNTS 22 23 3 0 0
+M  V30 BEGIN ATOM
+M  V30 1 O 13.2102 -15.3772 0 0 
+M  V30 2 N 14.5655 -12.6378 0 0 CFG=3 
+M  V30 3 O 13.616 -13.0138 0 0 
+M  V30 4 C 14.2945 -13.5123 0 0 CFG=2 
+M  V30 5 C 14.0424 -14.2836 0 0 
+M  V30 6 C 13.2102 -14.2836 0 0 CFG=1 
+M  V30 7 C 12.9472 -13.5013 0 0 CFG=1 
+M  V30 8 C 12.1657 -13.2555 0 0 
+M  V30 9 O 11.9165 -12.4635 0 0 
+M  V30 10 P 10.9413 -12.1135 0 0 CFG=3 
+M  V30 11 O 10.9413 -11.2885 0 0 
+M  V30 12 O 10.9413 -12.9385 0 0 
+M  V30 13 C 15.4027 -12.3728 0 0 
+M  V30 14 C 13.8243 -11.9705 0 0 
+M  V30 15 N 15.6751 -11.494 0 0 CFG=3 
+M  V30 16 O 16.0606 -13.0135 0 0 
+M  V30 17 C 14.0967 -11.0918 0 0 
+M  V30 18 C 14.9733 -10.8443 0 0 
+M  V30 19 O 15.2442 -9.9702 0 0 
+M  V30 20 C 13.4376 -10.4484 0 0 
+M  V30 21 O 10.8008 -13.7454 0 0 
+M  V30 22 H 13.3787 -13.7454 0 0 
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 22 
+M  V30 2 1 7 6 
+M  V30 3 1 10 11 
+M  V30 4 1 3 4 
+M  V30 5 2 10 12 
+M  V30 6 1 6 5 
+M  V30 7 1 4 5 
+M  V30 8 1 7 8 CFG=1 
+M  V30 9 1 4 2 CFG=1 
+M  V30 10 1 6 1 CFG=3 
+M  V30 11 1 8 9 
+M  V30 12 1 2 13 
+M  V30 13 1 2 14 
+M  V30 14 1 13 15 
+M  V30 15 2 13 16 
+M  V30 16 2 14 17 
+M  V30 17 1 15 18 
+M  V30 18 2 18 19 
+M  V30 19 1 17 18 
+M  V30 20 1 7 3 
+M  V30 21 1 17 20 
+M  V30 22 1 10 21 
+M  V30 23 1 9 10 
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(20 2 1 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20) -
+M  V30 XBONDS=(2 22 1) CSTATE=(4 22 -1.27 -0 0) CSTATE=(4 1 1.3 -0 -
+M  V30 0) LABEL=T CLASS=DNA SAP=(3 10 21 Al) SAP=(3 1 22 Br) 
+M  V30 2 SUP 2 ATOMS=(1 21) XBONDS=(1 22) CSTATE=(4 22 1.27 0 0) LABEL="5'" -
+M  V30 CLASS=LGRP 
+M  V30 3 SUP 3 ATOMS=(1 22) XBONDS=(1 1) CSTATE=(4 1 -1.3 0 0) LABEL="3'" -
+M  V30 CLASS=LGRP 
+M  V30 END SGROUP
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(3 4 6 7)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END
+

api/tests/integration/tests/formats/molecules/thymine.mol

@@ -0,0 +1,78 @@
+
+  -INDIGO-09062309442D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 131 RNA/T
+M  V30 BEGIN CTAB
+M  V30 COUNTS 23 24 3 0 0
+M  V30 BEGIN ATOM
+M  V30 1 O 12.7602 -15.7147 0 0 
+M  V30 2 O 14.0825 -15.2617 0 0 
+M  V30 3 N 14.1088 -12.9483 0 0 CFG=3 
+M  V30 4 O 13.166 -13.3263 0 0 
+M  V30 5 C 13.8445 -13.8248 0 0 CFG=2 
+M  V30 6 C 13.5924 -14.5961 0 0 CFG=1 
+M  V30 7 C 12.7602 -14.5961 0 0 CFG=1 
+M  V30 8 C 12.4972 -13.8138 0 0 CFG=1 
+M  V30 9 C 11.7157 -13.568 0 0 
+M  V30 10 O 11.4665 -12.776 0 0 
+M  V30 11 P 10.4913 -12.376 0 0 CFG=3 
+M  V30 12 O 10.1163 -11.551 0 0 
+M  V30 13 O 10.4913 -13.201 0 0 
+M  V30 14 C 14.9439 -12.6769 0 0 
+M  V30 15 C 13.3625 -12.2866 0 0 
+M  V30 16 N 15.2096 -11.7959 0 0 CFG=3 
+M  V30 17 O 15.6067 -13.3125 0 0 
+M  V30 18 C 13.6281 -11.4059 0 0 
+M  V30 19 C 14.5028 -11.1516 0 0 
+M  V30 20 O 14.767 -10.2755 0 0 
+M  V30 21 C 12.9642 -10.7675 0 0 
+M  V30 22 O 10.5257 -14.0454 0 0 
+M  V30 23 H 12.5598 -14.0454 0 0 
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 23 
+M  V30 2 1 8 7 
+M  V30 3 1 11 12 
+M  V30 4 1 4 5 
+M  V30 5 2 11 13 
+M  V30 6 1 7 6 
+M  V30 7 1 5 6 
+M  V30 8 1 8 9 CFG=1 
+M  V30 9 1 5 3 CFG=1 
+M  V30 10 1 6 2 CFG=3 
+M  V30 11 1 7 1 CFG=3 
+M  V30 12 1 9 10 
+M  V30 13 1 3 14 
+M  V30 14 1 3 15 
+M  V30 15 1 14 16 
+M  V30 16 2 14 17 
+M  V30 17 2 15 18 
+M  V30 18 1 16 19 
+M  V30 19 2 19 20 
+M  V30 20 1 18 19 
+M  V30 21 1 8 4 
+M  V30 22 1 18 21 
+M  V30 23 1 11 22 
+M  V30 24 1 10 11 
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(21 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21-
+M  V30 ) XBONDS=(2 23 1) CSTATE=(4 23 -1.1 -0 0) CSTATE=(4 1 0.93 -0 0) -
+M  V30 LABEL=T CLASS=RNA SAP=(3 11 22 Al) SAP=(3 1 23 Br) 
+M  V30 2 SUP 2 ATOMS=(1 22) XBONDS=(1 23) CSTATE=(4 23 1.1 0 0) LABEL="5'" -
+M  V30 CLASS=LGRP 
+M  V30 3 SUP 3 ATOMS=(1 23) XBONDS=(1 1) CSTATE=(4 1 -0.93 0 0) LABEL="3'" -
+M  V30 CLASS=LGRP 
+M  V30 END SGROUP
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(4 5 6 7 8)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END
+