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.gitattributes CHANGED
@@ -41,3 +41,5 @@ data/reaction_rule.csv filter=lfs diff=lfs merge=lfs -text
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  data/relaxed_rule_noduplic.csv filter=lfs diff=lfs merge=lfs -text
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  data/Test_KEGG_all_grp.mat filter=lfs diff=lfs merge=lfs -text
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  CC/data_cc/equilibrator_compounds.json filter=lfs diff=lfs merge=lfs -text
 
 
 
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  data/relaxed_rule_noduplic.csv filter=lfs diff=lfs merge=lfs -text
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  data/Test_KEGG_all_grp.mat filter=lfs diff=lfs merge=lfs -text
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  CC/data_cc/equilibrator_compounds.json filter=lfs diff=lfs merge=lfs -text
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figures/analyze_groups.mrv ADDED
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figures/linear_cc_groups.png ADDED
figures/linear_regression_cc.png ADDED
figures/not_covered.mrv ADDED
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order="1"></bond><bond id="b31" atomRefs2="a31 a32" order="2"></bond><bond id="b32" atomRefs2="a32 a33" order="1"></bond><bond id="b33" atomRefs2="a32 a34" order="1"></bond><bond id="b34" atomRefs2="a34 a35" order="2"></bond><bond id="b35" atomRefs2="a35 a36" order="1"></bond><bond id="b36" atomRefs2="a36 a37" order="2"></bond><bond id="b37" atomRefs2="a28 a37" order="1"></bond><bond id="b38" atomRefs2="a31 a37" order="1"></bond><bond id="b39" atomRefs2="a4 a38" order="1"></bond><bond id="b40" atomRefs2="a38 a39" order="1"><bondStereo>H</bondStereo></bond><bond id="b41" atomRefs2="a38 a40" order="1"></bond><bond id="b42" atomRefs2="a40 a41" order="2"></bond><bond id="b43" atomRefs2="a40 a42" order="1"></bond><bond id="b44" atomRefs2="a42 a43" order="1"></bond><bond id="b45" atomRefs2="a43 a44" order="1"></bond><bond id="b46" atomRefs2="a44 a45" order="1"></bond><bond id="b47" atomRefs2="a45 a46" order="2"></bond><bond id="b48" atomRefs2="a45 a47" order="1"></bond><bond id="b49" atomRefs2="a47 a48" order="1"></bond><bond id="b50" atomRefs2="a48 a49" order="1"></bond><bond id="b51" atomRefs2="a49 a3" order="1"></bond></bondArray><AttachmentPointArray><attachmentPoint atom="a3" order="1" bond="b1"></attachmentPoint></AttachmentPointArray></molecule></molecule><molecule molID="m6"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8" elementType="N N C O C C O C" x2="22.49415294069711 21.160473818869075 23.827832062525147 25.16151118435318 23.827832062525147 19.826794697041038 18.493115575213004 19.82679469704104" y2="2.6046485996246336 1.8346485996246336 1.8346485996246336 2.6046485996246336 0.29464859962463374 2.604648599624634 1.834648599624634 4.1446485996246345"></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"></bond><bond id="b2" atomRefs2="a1 a3" order="1"></bond><bond id="b3" atomRefs2="a2 a6" order="1"></bond><bond id="b4" atomRefs2="a3 a4" order="2"></bond><bond id="b5" atomRefs2="a3 a5" order="1"></bond><bond id="b6" atomRefs2="a6 a7" order="2"></bond><bond id="b7" atomRefs2="a6 a8" order="1"></bond></bondArray></molecule></productList></reaction></MChemicalStruct><MReactionSign id="o2" fontScale="18.0" halign="CENTER" valign="CENTER" autoSize="true"><Field name="text"><![CDATA[{D font=SansSerif,size=18,bold}+]]></Field><MPoint x="-1.9684960879004656" y="2.6002963366302314"></MPoint><MPoint x="-1.1984960879004696" y="2.6002963366302314"></MPoint><MPoint x="-1.1984960879004696" y="1.3902963366302323"></MPoint><MPoint x="-1.9684960879004656" y="1.3902963366302323"></MPoint></MReactionSign><MReactionSign id="o3" fontScale="18.0" halign="CENTER" valign="CENTER" autoSize="true"><Field name="text"><![CDATA[{D font=SansSerif,size=18,bold}+]]></Field><MPoint x="15.92491662339727" y="2.633411415841511"></MPoint><MPoint x="16.694916623397265" y="2.633411415841511"></MPoint><MPoint x="16.694916623397265" y="1.423411415841512"></MPoint><MPoint x="15.92491662339727" y="1.423411415841512"></MPoint></MReactionSign></MDocument>
4
+ </cml>
figures/pathway_example.mrv ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ <?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_16_02_15.xsd" version="ChemAxon file format v16.02.15, generated by v17.3.13.0">
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+ <MHead><MarvinGUI><mprop name="saveproperties" dataType="xsd:boolean" value="true"></mprop><mprop name="aminoAcidBondColoringEnabled" dataType="xsd:boolean" value="true"></mprop><mprop name="automaticReactionEnabled" dataType="xsd:boolean" value="true"></mprop><mprop name="setColoringEnabled" dataType="xsd:boolean" value="true"></mprop><mprop name="atomNumberingType" dataType="xsd:integer" value="0"></mprop><mprop name="fogFactor" dataType="xsd:integer" value="66"></mprop><mprop name="automaticFogEnabled" dataType="xsd:boolean" value="false"></mprop><mprop name="atomPropertiesVisible" dataType="xsd:boolean" value="true"></mprop><mprop name="atomMappingVisible" dataType="xsd:boolean" value="true"></mprop><mprop name="EZVisible" dataType="xsd:boolean" value="false"></mprop><mprop name="mpVisible" dataType="xsd:boolean" value="false"></mprop><mprop name="bondLength" dataType="xsd:double" value="28.0"></mprop><mprop name="bondLengthVisible" dataType="xsd:boolean" value="false"></mprop><mprop name="valenceErrorVisible" dataType="xsd:boolean" value="true"></mprop><mprop name="valenceErrorVisibleInView" dataType="xsd:boolean" value="false"></mprop><mprop name="atomSymbolVisible3D" dataType="xsd:boolean" value="true"></mprop><mprop name="rgroupsVisible" dataType="xsd:boolean" value="true"></mprop><mprop name="lonePairsAutoCalc" dataType="xsd:boolean" value="true"></mprop><mprop name="lonePairsAsLine" dataType="xsd:boolean" value="false"></mprop><mprop name="chargeWithCircle" dataType="xsd:boolean" value="false"></mprop><mprop name="molbg" value="#ffffff"></mprop><mprop name="chiralitySupport" dataType="xsd:integer" value="0"></mprop><mprop name="atomsize" dataType="xsd:double" value="0.35714285714"></mprop><mprop name="boldBondWidth" dataType="xsd:double" value="5.0"></mprop><mprop name="bondSpacing" dataType="xsd:double" value="0.180375"></mprop><mprop name="bondHashSpacing" dataType="xsd:double" value="0.15"></mprop><mprop name="wireThickness" dataType="xsd:double" value="0.066666"></mprop><mprop name="stickThickness" dataType="xsd:double" value="0.1"></mprop><mprop name="ballRadius" dataType="xsd:double" value="0.5"></mprop><mprop name="rendering" value="wireframe"></mprop><mprop name="downWedge" value="mdl"></mprop><mprop name="coordinateBondStyle" value="arrow"></mprop><mprop name="coordinateBondStyleAtMulticenter" value="hashed"></mprop><mprop name="anybond" value="auto"></mprop><mprop name="sketchAnyBond" value="auto"></mprop><mprop name="viewAnyBond" value="auto"></mprop><mprop name="atomFont" dataType="xsd:mfont" value="SansSerif-PLAIN-10"></mprop><mprop name="sketchImplicitH" value="hetero"></mprop><mprop name="lonePairsVisible" dataType="xsd:boolean" value="false"></mprop><mprop name="autoscale" dataType="xsd:boolean" value="false"></mprop><mprop name="absLabelVisible" dataType="xsd:boolean" value="false"></mprop><mprop name="colorScheme" value="cpk"></mprop><mprop name="viewCarbonVisibility" value="inChain"></mprop><mprop name="sketchCarbonVisibility" value="off"></mprop><mprop name="viewLigandOrderVisibility" value="showOnlyWithDefinition"></mprop><mprop name="sketchLigandOrderVisibility" value="showOnlyWithDefinition"></mprop><mprop name="rLogicVisible" value="off"></mprop><mprop name="peptideDisplayType" value="3-letter"></mprop><mprop name="zeroBasedAtomIndexing" dataType="xsd:boolean" value="false"></mprop><mprop name="valencePropertyVisible" dataType="xsd:boolean" value="true"></mprop><mprop name="ligandErrorVisible" dataType="xsd:boolean" value="true"></mprop><mprop name="sketchArrowHeadLength" dataType="xsd:double" value="0.8"></mprop><mprop name="sketchArrowHeadWidth" dataType="xsd:double" value="0.5"></mprop><mprop name="sketchArrowTailLength" dataType="xsd:double" value="0.8"></mprop><mprop name="sketchArrowTailWidth" dataType="xsd:double" value="0.5"></mprop></MarvinGUI></MHead>
3
+ <MDocument><MChemicalStruct><molecule molID="m1"><propertyList><property dictRef="type" title="type"><scalar>systematic</scalar></property></propertyList><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55 a56 a57 a58 a59 a60 a61 a62 a63 a64 a65 a66 a67 a68 a69 a70 a71 a72 a73 a74 a75 a76 a77 a78 a79 a80 a81 a82 a83 a84 a85 a86 a87 a88" elementType="C C C C O O C C O C O O C C C C C C C C N O C O C C C C C C C C C N C C C C C C C C C C N N N N O O O O O C C C C C C C C C C N N N N O O O O O O C C C C C C C C C C C N O O O" x2="2.555705152146543 1.2220260303185093 1.2220260303185104 -0.11165309150952375 2.5557051521465435 3.962565156916147 9.574701859840074 8.804701859840078 9.574701859840076 7.264701859840083 6.494701859840085 6.494701859840075 4.049512571309678 4.954701859840084 4.049512571309674 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4
+ </cml>
figures/ridge_groups.png ADDED
figures/ridge_regression.png ADDED
figures/test.png ADDED
figures/test_cc.png ADDED