mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
* Allow fragments to be groups in CDXML * Add support for grouped reactants * run clang-format * Change github issue to 7528 * Add documents to the code * response to review, check grouped reactants in cdxml against rxn file * Remove unused code * Add missing file --------- Co-authored-by: Brian Kelley <bkelley@relaytx.com>
608 lines
12 KiB
XML
608 lines
12 KiB
XML
<?xml version="1.0" encoding="UTF-8" ?>
|
|
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
|
|
<CDXML
|
|
CreationProgram="ChemDraw 21.0.0.28"
|
|
Name="github7467-grouped-fragments.cdxml"
|
|
BoundingBox="0.88 69.39 453.90 168.20"
|
|
WindowPosition="0 0"
|
|
WindowSize="0 0"
|
|
FractionalWidths="yes"
|
|
InterpretChemically="yes"
|
|
ShowAtomQuery="yes"
|
|
ShowAtomStereo="no"
|
|
ShowAtomEnhancedStereo="yes"
|
|
ShowAtomNumber="no"
|
|
ShowResidueID="no"
|
|
ShowBondQuery="yes"
|
|
ShowBondRxn="yes"
|
|
ShowBondStereo="no"
|
|
ShowTerminalCarbonLabels="no"
|
|
ShowNonTerminalCarbonLabels="no"
|
|
HideImplicitHydrogens="no"
|
|
Magnification="666"
|
|
LabelFont="58"
|
|
LabelSize="10"
|
|
LabelFace="96"
|
|
CaptionFont="58"
|
|
CaptionSize="10"
|
|
HashSpacing="2.50"
|
|
MarginWidth="1.60"
|
|
LineWidth="0.60"
|
|
BoldWidth="2"
|
|
BondLength="14.40"
|
|
BondSpacing="18"
|
|
ChainAngle="120"
|
|
LabelJustification="Auto"
|
|
CaptionJustification="Left"
|
|
AminoAcidTermini="HOH"
|
|
ShowSequenceTermini="yes"
|
|
ShowSequenceBonds="yes"
|
|
ShowSequenceUnlinkedBranches="no"
|
|
ResidueWrapCount="40"
|
|
ResidueBlockCount="10"
|
|
ResidueZigZag="yes"
|
|
NumberResidueBlocks="no"
|
|
PrintMargins="36 36 36 36"
|
|
MacPrintInfo="0003000000480048000000000300024CFFF4FFF4030C02580367052803FC0002000000480048000000000300024C000100000064000000010001010100000001270F000100010000000000000000000000000002001901900000000000400000000000000000000100000000000000000000000000000000"
|
|
ChemPropName=""
|
|
ChemPropFormula="Chemical Formula: "
|
|
ChemPropExactMass="Exact Mass: "
|
|
ChemPropMolWt="Molecular Weight: "
|
|
ChemPropMOverZ="m/z: "
|
|
ChemPropAnalysis="Elemental Analysis: "
|
|
ChemPropBoilingPt="Boiling Point: "
|
|
ChemPropMeltingPt="Melting Point: "
|
|
ChemPropCritTemp="Critical Temp: "
|
|
ChemPropCritPres="Critical Pres: "
|
|
ChemPropCritVol="Critical Vol: "
|
|
ChemPropGibbs="Gibbs Energy: "
|
|
ChemPropLogP="Log P: "
|
|
ChemPropMR="MR: "
|
|
ChemPropHenry="Henry's Law: "
|
|
ChemPropEForm="Heat of Form: "
|
|
ChemProptPSA="tPSA: "
|
|
ChemPropID=""
|
|
ChemPropFragmentLabel=""
|
|
color="0"
|
|
bgcolor="1"
|
|
RxnAutonumberStart="1"
|
|
RxnAutonumberConditions="no"
|
|
RxnAutonumberStyle="Roman"
|
|
RxnAutonumberFormat="(#)"
|
|
><colortable>
|
|
<color r="1" g="1" b="1"/>
|
|
<color r="0" g="0" b="0"/>
|
|
<color r="1" g="0" b="0"/>
|
|
<color r="1" g="1" b="0"/>
|
|
<color r="0" g="1" b="0"/>
|
|
<color r="0" g="1" b="1"/>
|
|
<color r="0" g="0" b="1"/>
|
|
<color r="1" g="0" b="1"/>
|
|
</colortable><fonttable>
|
|
<font id="21" charset="x-mac-roman" name="Helvetica"/>
|
|
<font id="58" charset="x-mac-roman" name="Arial"/>
|
|
</fonttable><page
|
|
id="82"
|
|
BoundingBox="0 0 776 240"
|
|
Width="776"
|
|
Height="240"
|
|
HeaderPosition="36"
|
|
FooterPosition="36"
|
|
PageOverlap="0"
|
|
PrintTrimMarks="yes"
|
|
HeightPages="1"
|
|
WidthPages="2"
|
|
DrawingSpace="poster"
|
|
><fragment
|
|
id="5"
|
|
BoundingBox="280.82 71.59 350.61 133.18"
|
|
Z="65"
|
|
><n
|
|
id="2"
|
|
p="333.97 109.58"
|
|
Z="63"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="330.64 113.26"
|
|
BoundingBox="331.10 105.90 350.61 115.56"
|
|
LabelJustification="Left"
|
|
LabelAlignment="Left"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="6"
|
|
p="323.79 119.77"
|
|
Z="64"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="319.90 123.45"
|
|
BoundingBox="320.29 116.09 327.28 123.66"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="7"
|
|
p="309.39 119.77"
|
|
Z="66"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="310.50 123.45"
|
|
BoundingBox="291 116.09 309.82 125.75"
|
|
LabelJustification="Right"
|
|
Justification="Right"
|
|
LabelAlignment="Right"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="8"
|
|
p="299.21 109.58"
|
|
Z="67"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="295.32 113.26"
|
|
BoundingBox="295.71 105.90 302.70 113.47"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="10"
|
|
p="299.21 95.18"
|
|
Z="68"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="300.32 98.86"
|
|
BoundingBox="280.82 91.50 299.64 101.16"
|
|
LabelJustification="Right"
|
|
Justification="Right"
|
|
LabelAlignment="Right"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="12"
|
|
p="309.39 85"
|
|
Z="69"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="305.50 88.68"
|
|
BoundingBox="305.89 81.32 312.88 88.89"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="14"
|
|
p="323.79 85"
|
|
Z="70"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="320.46 88.68"
|
|
BoundingBox="320.92 81.32 340.43 90.98"
|
|
LabelJustification="Left"
|
|
LabelAlignment="Left"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="16"
|
|
p="333.97 95.18"
|
|
Z="71"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="330.08 98.86"
|
|
BoundingBox="330.47 91.50 337.46 99.07"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="18"
|
|
p="347.28 89.67"
|
|
Z="72"
|
|
AS="N"
|
|
/><n
|
|
id="20"
|
|
p="303.88 71.70"
|
|
Z="73"
|
|
AS="N"
|
|
/><n
|
|
id="22"
|
|
p="285.91 115.09"
|
|
Z="74"
|
|
AS="N"
|
|
/><n
|
|
id="24"
|
|
p="329.30 133.07"
|
|
Z="75"
|
|
AS="N"
|
|
/><b
|
|
id="26"
|
|
Z="76"
|
|
B="2"
|
|
E="6"
|
|
BS="N"
|
|
/><b
|
|
id="27"
|
|
Z="77"
|
|
B="6"
|
|
E="7"
|
|
BS="N"
|
|
/><b
|
|
id="28"
|
|
Z="78"
|
|
B="7"
|
|
E="8"
|
|
BS="N"
|
|
/><b
|
|
id="29"
|
|
Z="79"
|
|
B="8"
|
|
E="10"
|
|
BS="N"
|
|
/><b
|
|
id="30"
|
|
Z="80"
|
|
B="10"
|
|
E="12"
|
|
BS="N"
|
|
/><b
|
|
id="31"
|
|
Z="81"
|
|
B="12"
|
|
E="14"
|
|
BS="N"
|
|
/><b
|
|
id="32"
|
|
Z="82"
|
|
B="14"
|
|
E="16"
|
|
BS="N"
|
|
/><b
|
|
id="33"
|
|
Z="83"
|
|
B="2"
|
|
E="16"
|
|
BS="N"
|
|
/><b
|
|
id="34"
|
|
Z="84"
|
|
B="16"
|
|
E="18"
|
|
BS="N"
|
|
/><b
|
|
id="35"
|
|
Z="85"
|
|
B="12"
|
|
E="20"
|
|
BS="N"
|
|
/><b
|
|
id="36"
|
|
Z="86"
|
|
B="8"
|
|
E="22"
|
|
BS="N"
|
|
/><b
|
|
id="37"
|
|
Z="87"
|
|
B="6"
|
|
E="24"
|
|
BS="N"
|
|
/></fragment><fragment
|
|
id="46"
|
|
BoundingBox="58.53 69.39 128.32 130.98"
|
|
Z="94"
|
|
><n
|
|
id="47"
|
|
p="111.68 107.38"
|
|
Z="92"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="108.35 111.06"
|
|
BoundingBox="108.81 103.70 128.32 113.36"
|
|
LabelJustification="Left"
|
|
LabelAlignment="Left"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="48"
|
|
p="101.50 117.57"
|
|
Z="93"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="97.61 121.25"
|
|
BoundingBox="98 113.89 104.99 121.46"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="49"
|
|
p="87.10 117.57"
|
|
Z="95"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="88.21 121.25"
|
|
BoundingBox="68.71 113.89 87.53 123.55"
|
|
LabelJustification="Right"
|
|
Justification="Right"
|
|
LabelAlignment="Right"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="50"
|
|
p="76.92 107.38"
|
|
Z="96"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="73.03 111.06"
|
|
BoundingBox="73.42 103.70 80.41 111.27"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="51"
|
|
p="76.92 92.98"
|
|
Z="97"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="78.03 96.66"
|
|
BoundingBox="58.53 89.30 77.35 98.96"
|
|
LabelJustification="Right"
|
|
Justification="Right"
|
|
LabelAlignment="Right"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="52"
|
|
p="87.10 82.80"
|
|
Z="98"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="83.21 86.48"
|
|
BoundingBox="83.60 79.12 90.59 86.69"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="53"
|
|
p="101.50 82.80"
|
|
Z="99"
|
|
Element="14"
|
|
NumHydrogens="2"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="98.17 86.48"
|
|
BoundingBox="98.63 79.12 118.14 88.78"
|
|
LabelJustification="Left"
|
|
LabelAlignment="Left"
|
|
><s font="21" size="10" color="0" face="96">SiH2</s></t></n><n
|
|
id="54"
|
|
p="111.68 92.98"
|
|
Z="100"
|
|
Warning="An atom in this label has an invalid valence."
|
|
Element="8"
|
|
NumHydrogens="0"
|
|
NeedsClean="yes"
|
|
AS="N"
|
|
><t
|
|
p="107.79 96.66"
|
|
BoundingBox="108.18 89.30 115.17 96.87"
|
|
LabelJustification="Left"
|
|
><s font="21" size="10" color="0" face="96">O</s></t></n><n
|
|
id="55"
|
|
p="124.99 87.47"
|
|
Z="101"
|
|
AS="N"
|
|
/><n
|
|
id="56"
|
|
p="81.59 69.50"
|
|
Z="102"
|
|
AS="N"
|
|
/><n
|
|
id="57"
|
|
p="63.62 112.89"
|
|
Z="103"
|
|
AS="N"
|
|
/><n
|
|
id="58"
|
|
p="107.01 130.87"
|
|
Z="104"
|
|
AS="N"
|
|
/><b
|
|
id="59"
|
|
Z="105"
|
|
B="47"
|
|
E="48"
|
|
BS="N"
|
|
/><b
|
|
id="60"
|
|
Z="106"
|
|
B="48"
|
|
E="49"
|
|
BS="N"
|
|
/><b
|
|
id="61"
|
|
Z="107"
|
|
B="49"
|
|
E="50"
|
|
BS="N"
|
|
/><b
|
|
id="62"
|
|
Z="108"
|
|
B="50"
|
|
E="51"
|
|
BS="N"
|
|
/><b
|
|
id="63"
|
|
Z="109"
|
|
B="51"
|
|
E="52"
|
|
BS="N"
|
|
/><b
|
|
id="64"
|
|
Z="110"
|
|
B="52"
|
|
E="53"
|
|
BS="N"
|
|
/><b
|
|
id="65"
|
|
Z="111"
|
|
B="53"
|
|
E="54"
|
|
BS="N"
|
|
/><b
|
|
id="66"
|
|
Z="112"
|
|
B="47"
|
|
E="54"
|
|
BS="N"
|
|
/><b
|
|
id="67"
|
|
Z="113"
|
|
B="54"
|
|
E="55"
|
|
BS="N"
|
|
/><b
|
|
id="68"
|
|
Z="114"
|
|
B="52"
|
|
E="56"
|
|
BS="N"
|
|
/><b
|
|
id="69"
|
|
Z="115"
|
|
B="50"
|
|
E="57"
|
|
BS="N"
|
|
/><b
|
|
id="70"
|
|
Z="116"
|
|
B="48"
|
|
E="58"
|
|
BS="N"
|
|
/></fragment><t
|
|
id="38"
|
|
p="315.48 166.12"
|
|
BoundingBox="223.17 158.75 407.58 168.20"
|
|
Z="88"
|
|
Warning="Chemical Interpretation is not possible for this label"
|
|
CaptionJustification="Center"
|
|
Justification="Center"
|
|
LineHeight="auto"
|
|
><s font="21" size="10" color="0">Caution: Valence appears to be exceeded</s></t><t
|
|
id="39"
|
|
p="317.48 146.19"
|
|
BoundingBox="236.34 139 398.49 148.29"
|
|
Z="89"
|
|
InterpretChemically="no"
|
|
CaptionJustification="Center"
|
|
Justification="Center"
|
|
LineHeight="auto"
|
|
><s font="58" size="10" color="0">2,4,6,8-tetramethylcyclotetrasiloxane</s></t><t
|
|
id="45"
|
|
p="201.42 121.13"
|
|
BoundingBox="201.98 115.24 206.70 119.97"
|
|
Z="91"
|
|
Warning="Chemical Interpretation is not possible for this label"
|
|
LineHeight="auto"
|
|
><s font="58" size="10" color="0">+</s></t><t
|
|
id="71"
|
|
p="93.19 163.92"
|
|
BoundingBox="0.88 156.55 185.29 166"
|
|
Z="117"
|
|
Warning="Chemical Interpretation is not possible for this label"
|
|
CaptionJustification="Center"
|
|
Justification="Center"
|
|
LineHeight="auto"
|
|
><s font="21" size="10" color="0">Caution: Valence appears to be exceeded</s></t><t
|
|
id="72"
|
|
p="95.19 143.99"
|
|
BoundingBox="14.05 136.80 176.20 146.09"
|
|
Z="118"
|
|
InterpretChemically="no"
|
|
CaptionJustification="Center"
|
|
Justification="Center"
|
|
LineHeight="auto"
|
|
><s font="58" size="10" color="0">2,4,6,8-tetramethylcyclotetrasiloxane</s></t><t
|
|
id="74"
|
|
p="93.40 61.84"
|
|
BoundingBox="93.40 61.84 93.45 61.89"
|
|
Z="120"
|
|
Visible="no"
|
|
IgnoreWarnings="yes"
|
|
InterpretChemically="no"
|
|
CaptionJustification="Center"
|
|
Justification="Center"
|
|
LineHeight="auto"
|
|
><s font="58" size="10" color="0"></s></t><t
|
|
id="76"
|
|
p="315.70 62.10"
|
|
BoundingBox="310.82 54.94 320.61 64.09"
|
|
Z="121"
|
|
Visible="no"
|
|
InterpretChemically="no"
|
|
CaptionJustification="Center"
|
|
Justification="Center"
|
|
LineHeight="auto"
|
|
><s font="58" size="10" color="0">[II]</s></t><graphic
|
|
id="80"
|
|
SupersededBy="83"
|
|
BoundingBox="453.90 119.54 423.70 119.54"
|
|
Z="62"
|
|
GraphicType="Line"
|
|
ArrowType="FullHead"
|
|
HeadSize="1500"
|
|
/><scheme
|
|
id="84"
|
|
><step
|
|
id="85"
|
|
ReactionStepReactants="46 5"
|
|
ReactionStepArrows="80"
|
|
/></scheme><chemicalproperty
|
|
id="75"
|
|
ChemicalPropertyDisplayID="74"
|
|
ChemicalPropertyIsActive="yes"
|
|
ChemicalPropertyType="24"
|
|
BasisObjects="47 48 46 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70"
|
|
/><chemicalproperty
|
|
id="77"
|
|
ChemicalPropertyDisplayID="76"
|
|
ChemicalPropertyIsActive="yes"
|
|
ChemicalPropertyType="24"
|
|
BasisObjects="2 6 5 7 8 10 12 14 16 18 20 22 24 26 27 28 29 30 31 32 33 34 35 36 37"
|
|
/><arrow
|
|
id="83"
|
|
BoundingBox="423.70 116.62 453.90 121.79"
|
|
Z="62"
|
|
FillType="None"
|
|
ArrowheadHead="Full"
|
|
ArrowheadType="Solid"
|
|
HeadSize="1500"
|
|
ArrowheadCenterSize="1313"
|
|
ArrowheadWidth="375"
|
|
Head3D="453.90 119.54 0"
|
|
Tail3D="423.70 119.54 0"
|
|
Center3D="641.05 179.38 0"
|
|
MajorAxisEnd3D="671.25 179.38 0"
|
|
MinorAxisEnd3D="641.05 209.58 0"
|
|
/><annotation
|
|
Keyword="Fragment Label"
|
|
Content="[I]"
|
|
/></page></CDXML> |