@datagrok/helm 0.0.4

package/README.md

@@ -0,0 +1,36 @@
+# HELM
+
+Provides support for [HELM notation](https://pistoiaalliance.atlassian.net/wiki/spaces/HELM/overview) 
+(Hierarchical Editing Language for Macromolecules) -
+a single notation that can encode the structure of complex biomolecules including diverse polymers, 
+non-natural monomers and complex attachment points.
+
+[Andrew Skalkin](https://github.com/skalkin) | 
+[issue tracker](https://github.com/datagrok-ai/public/issues/700) | beta
+
+![](images/helm-rendering.png)
+
+### Features
+* Automatic detection of HELM values in datasets
+* Rendering in the spreadsheet
+* Editing
+* Conversion to SMARTS and MOLBLOCK
+* Substructure search
+* Similarity search
+* Calculators (mol weight, mol formula, extinction coefficient, )
+* Data augmentation (show relevant information in the property panel)
+
+### Advanced features
+* Integration with the [HELM2WebService](https://github.com/PistoiaHELM/HELM2WebService) (calculations, images, etc)
+* Support for company-specific monomer libraries
+* Management tool for monomer libraries (integrated with the security and privileges)
+* Similarity and diversity analyses
+* HELM space (UMAP or t-SNE based on the distance)
+* Activity cliffs analysis (based on the HELM space)
+
+Kudos to Pistoia alliance for open-sourcing the [HELM Web Editor](https://github.com/PistoiaHELM/HELMWebEditor) 
+that is used in this integration. 
+
+See also:
+* https://pistoiaalliance.atlassian.net/wiki/spaces/HELM/overview
+* https://github.com/PistoiaHELM/HELMWebEditor

package/css/helm.css

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+.d4-g-cell[semType="HELM"] * {
+    pointer-events: none !important;
+}

package/detectors.js

@@ -0,0 +1,22 @@
+/**
+ * The class contains semantic type detectors.
+ * Detectors are functions tagged with `DG.FUNC_TYPES.SEM_TYPE_DETECTOR`.
+ * See also: https://datagrok.ai/help/develop/how-to/define-semantic-type-detectors
+ * The class should follow the `<PackageName>Detectors` notation, otherwise it won't be loaded.
+ */
+class HelmPackageDetectors extends DG.Package {
+
+  /** @param s {String} - string to check
+   * @returns {boolean} */
+  static isHelm(s) {
+    return s.startsWith('PEPTIDE1{') || s.startsWith('RNA1{') || s.startsWith('CHEM1{') || s.startsWith('BLOB1{');
+  }
+
+  //tags: semTypeDetector
+  //input: column col
+  //output: string semType
+  detectHelm(col) {
+    if (DG.Detector.sampleCategories(col, (s) => HelmPackageDetectors.isHelm(s)))
+      return 'HELM';
+  }
+}

package/files/samples/helm2.csv

@@ -0,0 +1,86 @@
+ID,Category,Test type,HELM string,Valid?,Mol Weight,Mol Formula,Cannonical SMILES
+,Ambiguous monomers,Use of * PEPTIDE,PEPTIDE1{A.*.G.C}$$$$V2.0,yes,NA,NA,NA
+,Ambiguous monomers,Use of * CHEM,CHEM1{*}$$$$V2.0,yes,NA,NA,NA
+,Ambiguous monomers,Use of * multiple CHEMs,"CHEM1{*}|CHEM2{[SMCC]}$CHEM2,CHEM1,1:R1-1:R1$$$V2.0",yes,NA,NA,NA
+,Ambiguous monomers,Use of * RNA ,RNA1{*.R(A)P.R(C)P}$$$$V2.0,yes,NA,NA,NA
+,Ambiguous monomers,Use of X,PEPTIDE1{A.X.G.C}$$$$V2.0,yes,NA,NA,NA
+,Ambiguous monomers,Use of N,RNA1{R(A)P.R(N)P.R(C)P.R(C)P.R(C)}$$$$V2.0,yes,NA,NA,NA
+,Ambiguous monomers,Use of _ as an alternative in PEPTIDE,"PEPTIDE1{A.(A,_).G.C}$$$$V2.0",,,,
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating single monomer - absolute value,PEPTIDE1{A'2'}$$$$V2.0,yes,160.17,C6H12N2O3,C[C@@H](C(=O)N[C@@H](C)C(=O)O)N[H] 
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating single monomer - absolute value,PEPTIDE1{A'11'}$$$$V2.0,yes,799.87,C33H57N11O12,C[C@@H](C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)O)N[H] 
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating monomer in larger polymer - absolute value,PEPTIDE1{A.G.A.C'5'.A}$$$$V2.0,yes,804.02,C26H45N9O10S5,C[C@@H](C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@@H](CS[H])C(=O)N[C@@H](CS[H])C(=O)N[C@@H](CS[H])C(=O)N[C@@H](CS[H])C(=O)N[C@@H](CS[H])C(=O)N[C@@H](C)C(=O)O)N[H] 
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating monomerin larger polymer - range,PEPTIDE1{A.G.A.C.A'5-30'}$$$$V2.0,yes,NA,NA,NA
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating CHEM monomer - not valid,CHEM1{[Az]'3'}$$$$V2.0,no,NA,NA,NA
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating partial RNA monomer - not valid,RNA1{R'3'}$$$$V2.0,no,NA,NA,NA
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating combo RNA - absolute value,RNA1{R(C)P.(R(U)P)'3'.R(A)P}$$$$V2.0,yes,1570.9,C46H59N14O38P5 ,C1=CN([C@H]2[C@@H]([C@@H]([C@@H](CO[H])O2)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@H](N4C=CC(=O)NC4=O)O3)O)OP(=O)(O)OC[C@@H]5[C@H]([C@H]([C@H](N6C=CC(=O)NC6=O)O5)O)OP(=O)(O)OC[C@@H]7[C@H]([C@H]([C@H](N8C=CC(=O)NC8=O)O7)O)OP(=O)(O)OC[C@@H]9[C@H]([C@H]([C@H](N%10C=NC%11=C%10N=CN=C%11N)O9)O)OP(=O)(O)O)O)C(=O)N=C1N
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),"Repeating combo RNA - range, plus absolute",RNA1{R(A)P.(R(N)P)'4'.(R(G)P)'3-7'}$$$$V2.0,yes,NA,NA,NA
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),repeating single monomer peptide with multicharacter symbol,PEPTIDE1{[Bal]'11'}$$$$V2.0,yes,799.87,C33H57N11O12,C(CN[H])C(=O)NCCC(=O)NCCC(=O)NCCC(=O)NCCC(=O)NCCC(=O)NCCC(=O)NCCC(=O)NCCC(=O)NCCC(=O)NCCC(=O)O
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),repeating single monomer peptide with annotation,"PEPTIDE1{A.G'70-100'""repeatingMonomer""}$$$$V2.0",yes,NA,NA,NA
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating section of peptide polymer,PEPTIDE1{A.(G.A.C)'3'.A}$$$$V2.0,yes,839.96,C29H49N11O12S3,C[C@@H](C(NCC(N[C@H](C(N[C@@H](CS[H])C(NCC(N[C@H](C(N[C@@H](CS[H])C(NCC(N[C@H](C(N[C@@H](CS[H])C(NCC(O)=O)=O)=O)C)=O)=O)=O)C)=O)=O)=O)C)=O)=O)N[H]
+,Brackets and repeating groups (NB repeating CHEMs are not allowed),Repeating section of RNA polymer,RNA1{R(A)P.R(C)P.(R(T)P)'2'.R(G)}$$$$V2.0,yes,1612.06,C49H69N17O37P4,O[C@H]1[C@H](N(C=N2)C3=C2C(N)=NC=N3)O[C@H](CO[H])[C@H]1OP(O)(OC[C@H]4O[C@@H](N5C=CC(N)=NC5=O)[C@H](O)[C@@H]4OP(O)(OC[C@H]6O[C@@H](N(C7=O)C=C(C)C(N7)=O)[C@H](O)[C@@H]6OP(O)(OC[C@H]8O[C@@H](N(C9=O)C=C(C)C(N9)=O)[C@H](O)[C@@H]8OP(OC[C@H]%10O[C@@H](N(C=N%11)C(N=C(N)N%12)=C%11C%12=O)[C@H](O)[C@@H]%10O[H])(O)=O)=O)=O)=O
+,Monomer mixtures and alternatives,Mixture,PEPTIDE1{A.(A+G+C).G.C}$$$$V2.0,yes,NA,NA,NA
+,Monomer mixtures and alternatives,Mixture with ratios,PEPTIDE1{A.(A:1+G:2+C:3).G.C}$$$$V2.0,yes,NA,NA,NA
+,Monomer mixtures and alternatives,Multiple mixtures in a molecules,PEPTIDE1{A.A.A.A.(A+G).A.A.A.A.(A+G+L).A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D}$$$$V2.0,yes,NA,NA,NA
+,Monomer mixtures and alternatives,List of alternatives,"PEPTIDE1{A.(A,G,L).G.C}$$$$V2.0",yes,NA,NA,NA
+,Monomer mixtures and alternatives,Peptide with alternative monomers and multicharacter monomers,"PEPTIDE1{[fmoc].D.(V,[dV]).Y.A}$$$$V2.0",yes,NA,NA,NA
+,Monomer mixtures and alternatives,List of alternatives with ambiguous monomers,"PEPTIDE1{A.A.(X,*).A.A.C.D.D.E.E}$$$$V2.0",yes,NA,NA,NA
+,Monomer mixtures and alternatives,Alternatives with ratios,"PEPTIDE1{A.(A:1,G:9).G.C}$$$$V2.0",yes,NA,NA,NA
+,Monomer mixtures and alternatives,Alternatives with more complex ratios and multicharacter monomers,"PEPTIDE1{A.A.A.A.(A:1.1,G:69.5,W:25.5,[Nal]:3.9).A.A.C.D.D.E.E}$$$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Peptide alternatives,"PEPTIDE1{A.C.D}|PEPTIDE2{D.A.C}$$G3(PEPTIDE1,PEPTIDE2)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Peptide alternatives with ratios,PEPTIDE1{A.C.D}|PEPTIDE2{D.A.C}$$G3(PEPTIDE1:2+PEPTIDE2:1)$$V2.0,yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Peptide alternatives with annotation,"PEPTIDE1{A.C.D}""Polymer 1""|PEPTIDE2{D.A.C}""Polymer 2""$$G3(PEPTIDE1,PEPTIDE2)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Peptide alternatives with ratios and annotation,"PEPTIDE1{A.C.D}""Polymer 1""|PEPTIDE2{D.A.C}""Polymer 2""$$G3(PEPTIDE1:2,PEPTIDE2:5)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Peptide mixture,PEPTIDE1{A.C.D}|PEPTIDE2{D.A.C}$$G3(PEPTIDE1+PEPTIDE2)$$V2.0,yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,RNA alternatives,"RNA1{R(A)P.R(C)P.R(G)}|RNA2{R(A)P.R(C)P.R(G)}$$G3(RNA1,RNA2)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,RNA mixture,RNA1{R(A)P.R(C)P.R(G)}|RNA2{R(A)P.R(C)P.R(G)}$$G3(RNA1+RNA2)$$V2.0,yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,RNA and CHEM mixture with ratios and annotation,"CHEM1{*}|RNA1{R(C)P.R(C)P}|RNA2{R(A)P.R(G)P.R(C)P}$G3,CHEM1,?:?-1:?$G3(RNA2+RNA1)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Alternative peptides attached to unknown chem,"PEPTIDE1{A.C.D.E}|PEPTIDE2{G.C.S.P.P.K}|CHEM1{*}$G1,CHEM1,C:R3-1:?$G1(PEPTIDE1,PEPTIDE2)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Mixture of peptides attached to unknown chem,"PEPTIDE1{A.C.D.E.E}|PEPTIDE2{G.C.S.S.P.P.K}|CHEM1{[SMCC]}$G1,CHEM1,?:?-?:?$G1(PEPTIDE1+PEPTIDE2)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Peptide and chem connected ratio 1:2.5,"PEPTIDE1{A.A.A.A.A.C.D.D.D.D.D.D.D.E.E.E}|CHEM1{[PEG2]}$PEPTIDE1,CHEM1,C:R3-1:R1$G1(PEPTIDE1+CHEM1:2.5)$$V2.0",yes,NA,NA,NA
+,Group (polymer) mixtures and alternatives,Connected chem and peptide ratio 1:2.5 two unconnected instances,"PEPTIDE1{A.A.A.A.A.C.D.D.D.D.D.E.E.E.E}|PEPTIDE2{G.G.G.C.S.S.S.S.S.P.P.K.K.K.K}|CHEM1{[PEG2]}|CHEM2{[SMCC]}$PEPTIDE1,CHEM1,C:R3-1:R1|PEPTIDE2,CHEM2,C:R3-1:R1$G1(PEPTIDE1+CHEM1:2.5)|G2(PEPTIDE2+CHEM2:1.5)$$V2.0",yes,NA,NA,NA
+,Unknown monomers,Blobs with direct bond,"BLOB1{Bead}|PEPTIDE1{A.G.T}$PEPTIDE1,BLOB1,1:R1-?:?$$$V2.0",yes,NA,NA,NA
+,Unknown monomers,Blob and PEPTIDE no connection with annotation,"BLOB1{Bead}""Aminated Polystyrene""|PEPTIDE1{A.G.T}$$$$V2.0",yes,NA,NA,NA
+,Single monomer annotations,Monomer annotation peptide,"PEPTIDE1{A.A.C""mutation"".D.E.E}$$$$V2.0",yes,636.63,C23H36N6O13S,C[C@@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CS[H])C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](CCC(=O)O)C(=O)O)N[H]
+,Single monomer annotations,Unknown monomer with annotation,"PEPTIDE1{*""IL6""}$$$$V2.0",yes,NA,NA,NA
+,Single monomer annotations,Monomer annotation on RNA base,"RNA1{R(A""mutation"")P.R(U)P.R(G)P}$$$$V2.0",yes,998.59,C29H37N12O22P3,O[C@H]1[C@H](N(C=N2)C3=C2C(N)=NC=N3)O[C@H](CO[H])[C@H]1OP(O)(OC[C@H]4O[C@@H](N(C5=O)C=CC(N5)=O)[C@H](O)[C@@H]4OP(O)(OC[C@H]6O[C@@H](N(C=N7)C(N=C(N)N8)=C7C8=O)[C@H](O)[C@@H]6OP(O)(O)=O)=O)=O
+,Single monomer annotations,Monomer annnotation on RNA  sugar,"RNA1{R(A)P.R""mutation""(U)P.R(G)P}$$$$V2.0",yes,998.59,C29H37N12O22P3,O[C@H]1[C@H](N(C=N2)C3=C2C(N)=NC=N3)O[C@H](CO[H])[C@H]1OP(O)(OC[C@H]4O[C@@H](N(C5=O)C=CC(N5)=O)[C@H](O)[C@@H]4OP(O)(OC[C@H]6O[C@@H](N(C=N7)C(N=C(N)N8)=C7C8=O)[C@H](O)[C@@H]6OP(O)(O)=O)=O)=O
+,Single monomer annotations,Monomer annnotation on RNA  phosphate,"RNA1{R(A)P.R(G)P""mutation"".R(U)P}$$$$V2.0",yes,998.59,C29H37N12O22P3,O[C@H]1[C@H](N(C=N2)C3=C2C(N)=NC=N3)O[C@H](CO[H])[C@H]1OP(O)(OC[C@H]4O[C@@H](N(C=N5)C(N=C(N)N6)=C5C6=O)[C@H](O)[C@@H]4OP(O)(OC[C@H]7O[C@@H](N(C8=O)C=CC(N8)=O)[C@H](O)[C@@H]7OP(O)(O)=O)=O)=O
+,Single monomer annotations,Monomer annotation on CHEM,"CHEM1{[hxy]""Annotation""}|PEPTIDE1{A.C.V.L.L}$CHEM1,PEPTIDE1,1:R1-1:R1$$$V2.0",yes,613.81,C29H51N5O7S,O(CCCCC#C)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC(C)C)C(=O)O)C(C)C)CS[H]
+,Single monomer annotations,Monomer annotation blob,"BLOB1{BEAD}""Animated Polystyrene""$$$$V2.0",yes,NA,NA,NA
+,Annotations on polymers,Simple polymer annotation,"PEPTIDE1{A.C.D.D.E}""HC""|PEPTIDE2{G.C.S.S.S.P.K.K.V.K}""LC""$$$$V2.0",yes,1571.73,C61H106N18O26S2,CC(C)[C@@H](C(=O)N[C@@H](CCCCN[H])C(=O)O)NC(=O)[C@H](CCCCN[H])NC(=O)[C@H](CCCCN[H])NC(=O)[C@@H]1CCCN1C(=O)[C@H](CO)NC(=O)[C@H](CO)NC(=O)[C@H](CO)NC(=O)[C@H](CS[H])NC(=O)CN[H].C[C@@H](C(=O)N[C@@H](CS[H])C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CCC(=O)O)C(=O)O)N[H]
+,Annotations on polymers,Simple polymer annotation - RNA,"RNA1{R(A)P.R(C)P.R(G)P}""Test annotation""$$$$V2.0",yes,997.61,C29H38N13O21P3,O=P(O)(O)O[C@@H]1[C@@H](COP(O)(O[C@@H]2[C@@H](COP(O)(O[C@@H]3[C@@H](CO[H])O[C@@H](N(C=N4)C5=C4C(N)=NC=N5)[C@@H]3O)=O)O[C@@H](N6C=CC(N)=NC6=O)[C@@H]2O)=O)O[C@@H](N(C=N7)C(N=C(N)N8)=C7C8=O)[C@@H]1O
+,Annotations on polymers,Simple polymer annotation - CHEM,"CHEM1{[A6OH]}""Test annotation""$$$$V2.0",yes,117.19,C6H15NO,[H]NCCCCCCO[H]
+,Annotations on polymers,Group annotation - middle section of peptide,"PEPTIDE1{A.A.A.C.C}|PEPTIDE2{D.L.L.L.V.V.V}|PEPTIDE3{C.D.D}""Test annotation""$PEPTIDE1,PEPTIDE3,5:R2-1:R1|PEPTIDE3,PEPTIDE2,3:R2-1:R1$$$V2.0",yes,1522.81,C63H107N15O22S3,CC(C)C[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](C(C)C)C(=O)O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CC(=O)O)NC(=O)[C@H](CC(=O)O)NC(=O)[C@H](CC(=O)O)NC(=O)[C@H](CS[H])NC(=O)[C@H](CS[H])NC(=O)[C@H](CS[H])NC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@H](C)N[H] 
+,Annotations on polymers,Group annotation - middle section of peptide with CHEM ambiguous bond,"CHEM1{[Az]}|PEPTIDE1{A.A.A.A.A.A.A.A.A}|PEPTIDE2{A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D}|PEPTIDE3{A.A.A.A.A.A.A.A.A.A.A}""Test Annotation""$PEPTIDE1,PEPTIDE3,9:R2-1:R1|PEPTIDE3,PEPTIDE2,11:R2-1:R1|PEPTIDE3,CHEM1,?:?-1:R1$$$V2.0",yes,NA,NA,NA
+,Annotations on bonds,Annotation on ambiguous bond between peptide group and CHEM,"CHEM1{[SMCC]}|PEPTIDE1{A.A.A.C.D.D.E.E}$PEPTIDE1,CHEM1,C:R3-1:R1""Specific Conjugation""$$$V2.0",yes,NA,NA,NA
+,Annotations on bonds,Annotation on bond between Chem and RNA,"CHEM1{[SMCC]}|RNA1{R(A)P.R(C)P.R(G)}$CHEM1,RNA1,1:R1-?:?""my annotation""$$$V2.0",yes,NA,NA,NA
+,Third section annotations,PEPTIDE JSON annotation,"PEPTIDE1{L.V.A}$$${""PEPTIDE1"":{""ChainType"":""hc""}}$V2.0",yes,301.38,C14H27N3O4,CC(C)C[C@@H](C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](C)C(=O)O)N[H] 
+,Third section annotations,BLOB JSON annotation,"BLOB1{Bead}$$${""Name"":""Gold particle conjugated with peptides"",""Load"":26}$V2.0",yes,NA,NA,NA
+,Third section annotations,RNA annotation,"RNA1{R(A)P.R(C)P.R(G)}$$${""my annotation""}$V2.0",yes,917.63,C29H37N13O18P2,C1=CN([C@H]2[C@@H]([C@@H]([C@@H](COP(=O)(O)O[C@@H]3[C@@H](CO[H])O[C@H]([C@@H]3O)N4C=NC5=C4N=CN=C5N)O2)OP(=O)(O)OC[C@@H]6[C@H]([C@H]([C@H](N7C=NC8=C7N=C(N)NC8=O)O6)O)O[H])O)C(=O)N=C1N
+,Third section annotations,BLOB annotation and third section annotation. Ambiguous peptide and blob bond,"PEPTIDE1{C.C}|BLOB1{Gold Particle}""Au10, Diameter:10nm""$PEPTIDE1,BLOB1,C:R3-?:?$G1(PEPTIDE1:20-34+BLOB1)${""Name"":""Gold particle conjugated with peptides"",""Load"":26}$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB unspecified, PEPTIDE unspecified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,?:?-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB location specified, PEPTIDE unspecified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,1:?-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB R group specified, PEPTIDE unspecified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,?:R1-?:?$$$V2.0",no,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB unspecified, PEPTIDE location specified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,?:?-1:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB unspecified, PEPTIDE R group specified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,?:?-?:R1$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB specified, PEPTIDE unspecified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,1:R1-?:?$$$V2.0",no,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB unspecified, PEPTIDE specified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,?:?-1:R1$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Blob-peptide - BLOB specified, PEPTIDE specified","BLOB1{Bead}|PEPTIDE1{A.G.T}$BLOB1,PEPTIDE1,1:R1-1:R1$$$V2.0",no,NA,NA,NA
+,Connection ambiguity,Chem-peptide connection to unknown cys,"CHEM1{[SMCC]}|PEPTIDE1{A.A.A.C.A.C.D.D.D.E.E.E.E.E}$PEPTIDE1,CHEM1,C:?-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,PEPTIDE-PEPTIDE one side fully specified,"PEPTIDE1{A}|PEPTIDE2{A.C}$PEPTIDE1,PEPTIDE2,1:R1-?:?$$$V2.0 ",yes,NA,NA,NA
+,Connection ambiguity,"PEPTIDE - RNA, peptide fully specified","PEPTIDE1{A.C}|RNA1{P}$RNA1,PEPTIDE1,1:R2-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"PEPTIDE - different RNA, peptide fully specified","PEPTIDE1{A.C}|RNA1{R}$RNA1,PEPTIDE1,1:R2-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Unknown PEPTIDE-PEPTIDE, PEPTIDE side fully specified","PEPTIDE1{*}|PEPTIDE2{A.C}$PEPTIDE1,PEPTIDE2,1:?-?:R1$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Unknown PEPTIDE-PEPTIDE, unknown PEPTIDE side incorrectly specified","PEPTIDE1{*}|PEPTIDE2{A.C}$PEPTIDE1,PEPTIDE2,1:R1-?:?$$$V2.0",no,NA,NA,NA
+,Connection ambiguity,"PEPTIDE - unknown RNA, peptide fully specified","PEPTIDE1{A.C}|RNA1{*}$RNA1,PEPTIDE1,?:?-1:R2$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,Chem-peptide entirely unspecified,"PEPTIDE1{A.A.A.A.A.C.D.D.D.E.E.E.E.E}|PEPTIDE2{G.G.G.C.S.S.S.P.P.P.P.K.K.K.K.K}|CHEM1{[SMCC]}$PEPTIDE1,CHEM1,?:?-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Unspecified PEPTIDE connection, specified CHEM","CHEM1{*}|PEPTIDE1{A.C}$CHEM1,PEPTIDE1,1:R1-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Specified PEPTIDE connection, unspecified CHEM","CHEM1{*}|PEPTIDE1{A.C}$CHEM1,PEPTIDE1,?:?-1:R1$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Unspecified PEPTIDE connection, unspecified CHEM","CHEM1{*}|PEPTIDE1{A.C}$CHEM1,PEPTIDE1,?:?-?:?$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,"Specified PEPTIDE connection, specified CHEM","CHEM1{*}|PEPTIDE1{A.C}$CHEM1,PEPTIDE1,1:R1-1:R1$$$V2.0",no,NA,NA,NA
+,Connection ambiguity,RNA * to RNA strand both ends (incorrectly) fully specified,"RNA1{*}|RNA2{R(A)P.R(C)P}$RNA1,RNA2,1:R1-1:R1$$$V2.0",no,NA,NA,NA
+,Connection ambiguity,RNA * to RNA strand RNA end fully specified,"RNA1{*}|RNA2{R(A)P.R(C)P}$RNA1,RNA2,?:?-1:R1$$$V2.0",yes,NA,NA,NA
+,Connection ambiguity,RNA * to RNA strand RNA * end fully specified,"RNA1{*}|RNA2{R(A)P.R(C)P}$RNA1,RNA2,1:R1-?:?$$$V2.0",no,NA,NA,NA
+,Other cases,Large simple peptide,PEPTIDE1{D.I.Q.M.T.Q.S.P.S.S.L.S.A.S.V.G.D.R.V.T.I.T.C.R.A.S.Q.D.V.N.T.A.V.A.W.Y.Q.Q.K.P.G.K.A.P.K.L.L.I.Y.S.A.S.F.L.Y.S.G.V.P.S.R.F.S.G.S.R.S.G.T.D.F.T.L.T.I.S.S.L.Q.P.E.D.F.A.T.Y.Y.C.Q.Q.H.Y.T.T.P.P.T.F.G.Q.G.T.K.V.E.I.K.R.T.V.A.A.P.S.V.F.I.F.P.P.S.D.E.Q.L.K.S.G.T.A.S.V.V.C.L.L.N.N.F.Y.P.R.E.A.K.V.Q.W.K.V.D.N.A.L.Q.S.G.N.S.Q.E.S.V.T.E.Q.D.S.K.D.S.T.Y.S.L.S.S.T.L.T.L.S.K.A.D.Y.E.K.H.K.V.Y.A.C.E.V.T.H.Q.G.L.S.S.P.V.T.K.S.F.N.R.G.E.C.E.V.Q.L.V.E.S.G.G.G.L.V.Q.P.G.G.S.L.R.L.S.C.A.A.S.G.F.N.I.K.D.T.Y.I.H.W.V.R.Q.A.P.G.K.G.L.E.W.V.A.R.I.Y.P.T.N.G.Y.T.R.Y.A.D.S.V.K.G.R.F.T.I.S.A.D.T.S.K.N.T.A.Y.L.Q.M.N.S.L.R.A.E.D.T.A.V.Y.Y.C.S.R.W.G.G.D.G.F.Y.A.M.D.Y.W.G.Q.G.T.L.V.T.V.S.S.A.S.T.K.G.P.S.V.F.P.L.A.P.S.S.K.S.T.S.G.G.T.A.A.L.G.C.L.V.K.D.Y.F.P.E.P.V.T.V.S.W.N.S.G.A.L.T.S.G.V.H.T.F.P.A.V.L.Q.S.S.G.L.Y.S.L.S.S.V.V.T.V.P.S.S.S.L.G.T.Q.T.Y.I.C.N.V.N.H.K.P.S.N.T.K.V.D.K.K.V.E.P.P.K.S.C.D.K.T.H.T.C.P.P.C.P.A.P.E.L.L.G.G.P.S.V.F.L.F.P.P.K.P.K.D.T.L.M.I.S.R.T.P.E.V.T.C.V.V.V.D.V.S.H.E.D.P.E.V.K.F.N.W.Y.V.D.G.V.E.V.H.N.A.K.T.K.P.R.E.E.Q.Y.N.S.T.Y.R.V.V.S.V.L.T.V.L.H.Q.D.W.L.N.G.K.E.Y.K.C.K.V.S.N.K.A.L.P.A.P.I.E.K.T.I.S.K.A.K.G.Q.P.R.E.P.Q.V.Y.T.L.P.P.S.R.D.E.L.T.K.N.Q.V.S.L.T.C.L.V.K.G.F.Y.P.S.D.I.A.V.E.W.E.S.N.G.Q.P.E.N.N.Y.K.T.T.P.P.V.L.D.S.D.G.S.F.F.L.Y.S.K.L.T.V.D.K.S.R.W.Q.Q.G.N.V.F.S.C.S.V.M.H.E.A.L.H.N.H.Y.T.Q.K.S.L.S.L.S.P.G.K.E.V.Q.L.V.E.S.G.G.G.L.V.Q.P.G.G.S.L.R.L.S.C.A.A.S.G.F.N.I.K.D.T.Y.I.H.W.V.R.Q.A.P.G.K.G.L.E.W.V.A.R.I.Y.P.T.N.G.Y.T.R.Y.A.D.S.V.K.G.R.F.T.I.S.A.D.T.S.K.N.T.A.Y.L.Q.M.N.S.L.R.A.E.D.T.A.V.Y.Y.C.S.R.W.G.G.D.G.F.Y.A.M.D.Y.W.G.Q.G.T.L.V.T.V.S.S.A.S.T.K.G.P.S.V.F.P.L.A.P.S.S.K.S.T.S.G.G.T.A.A.L.G.C.L.V.K.D.Y.F.P.E.P.V.T.V.S.W.N.S.G.A.L.T.S.G.V.H.T.F.P.A.V.L.Q.S.S.G.L.Y.S.L.S.S.V.V.T.V.P.S.S.S.L.G.T.Q.T.Y.I.C.N.V.N.H.K.P.S.N.T.K.V.D.K.K.V.E.P.P.K.S.C.D.K.T.H.T.C.P.P.C.P.A.P.E.L.L.G.G.P.S.V.F.L.F.P.P.K.P.K.D.T.L.M.I.S.R.T.P.E.V.T.C.V.V.V.D.V.S.H.E.D.P.E.V.K.F.N.W.Y.V.D.G.V.E.V.H.N.A.K.T.K.P.R.E.E.Q.Y.N.S.T.Y.R.V.V.S.V.L.T.V.L.H.Q.D.W.L.N.G.K.E.Y.K.C.K.V.S.N.K.A.L.P.A.P.I.E.K.T.I.S.K.A.K.G.Q.P.R.E.P.Q.V.Y.T.L.P.P.S.R.D.E.L.T.K.N.Q.V.S.L.T.C.L.V.K.G.F.Y.P.S.D.I.A.V.E.W.E.S.N.G.Q.P.E.N.N.Y.K.T.T.P.P.V.L.D.S.D.G.S.F.F.L.Y.S.K.L.T.V.D.K.S.R.W.Q.Q.G.N.V.F.S.C.S.V.M.H.E.A.L.H.N.H.Y.T.Q.K.S.L.S.L.S.P.G.K.D.I.Q.M.T.Q.S.P.S.S.L.S.A.S.V.G.D.R.V.T.I.T.C.R.A.S.Q.D.V.N.T.A.V.A.W.Y.Q.Q.K.P.G.K.A.P.K.L.L.I.Y.S.A.S.F.L.Y.S.G.V.P.S.R.F.S.G.S.R.S.G.T.D.F.T.L.T.I.S.S.L.Q.P.E.D.F.A.T.Y.Y.C.Q.Q.H.Y.T.T.P.P.T.F.G.Q.G.T.K.V.E.I.K.R.T.V.A.A.P.S.V.F.I.F.P.P.S.D.E.Q.L.K.S.G.T.A.S.V.V.C.L.L.N.N.F.Y.P.R.E.A.K.V.Q.W.K.V.D.N.A.L.Q.S.G.N.S.Q.E.S.V.T.E.Q.D.S.K.D.S.T.Y.S.L.S.S.T.L.T.L.S.K.A.D.Y.E.K.H.K.V.Y.A.C.E.V.T.H.Q.G.L.S.S.P.V.T.K.S.F.N.R.G.E.C}$$$$V2.0,yes,145529.41,C6470H10012N1726O2013S42,Not calculated
+,Other cases,Large mol with ambiguity (antibody structure),"PEPTIDE1{D.I.Q.M.T.Q.S.P.S.S.L.S.A.S.V.G.D.R.V.T.I.T.C.R.A.S.Q.D.V.N.T.A.V.A.W.Y.Q.Q.K.P.G.K.A.P.K.L.L.I.Y.S.A.S.F.L.Y.S.G.V.P.S.R.F.S.G.S.R.S.G.T.D.F.T.L.T.I.S.S.L.Q.P.E.D.F.A.T.Y.Y.C.Q.Q.H.Y.T.T.P.P.T.F.G.Q.G.T.K.V.E.I.K.R.T.V.A.A.P.S.V.F.I.F.P.P.S.D.E.Q.L.K.S.G.T.A.S.V.V.C.L.L.N.N.F.Y.P.R.E.A.K.V.Q.W.K.V.D.N.A.L.Q.S.G.N.S.Q.E.S.V.T.E.Q.D.S.K.D.S.T.Y.S.L.S.S.T.L.T.L.S.K.A.D.Y.E.K.H.K.V.Y.A.C.E.V.T.H.Q.G.L.S.S.P.V.T.K.S.F.N.R.G.E.C}|PEPTIDE2{E.V.Q.L.V.E.S.G.G.G.L.V.Q.P.G.G.S.L.R.L.S.C.A.A.S.G.F.N.I.K.D.T.Y.I.H.W.V.R.Q.A.P.G.K.G.L.E.W.V.A.R.I.Y.P.T.N.G.Y.T.R.Y.A.D.S.V.K.G.R.F.T.I.S.A.D.T.S.K.N.T.A.Y.L.Q.M.N.S.L.R.A.E.D.T.A.V.Y.Y.C.S.R.W.G.G.D.G.F.Y.A.M.D.Y.W.G.Q.G.T.L.V.T.V.S.S.A.S.T.K.G.P.S.V.F.P.L.A.P.S.S.K.S.T.S.G.G.T.A.A.L.G.C.L.V.K.D.Y.F.P.E.P.V.T.V.S.W.N.S.G.A.L.T.S.G.V.H.T.F.P.A.V.L.Q.S.S.G.L.Y.S.L.S.S.V.V.T.V.P.S.S.S.L.G.T.Q.T.Y.I.C.N.V.N.H.K.P.S.N.T.K.V.D.K.K.V.E.P.P.K.S.C.D.K.T.H.T.C.P.P.C.P.A.P.E.L.L.G.G.P.S.V.F.L.F.P.P.K.P.K.D.T.L.M.I.S.R.T.P.E.V.T.C.V.V.V.D.V.S.H.E.D.P.E.V.K.F.N.W.Y.V.D.G.V.E.V.H.N.A.K.T.K.P.R.E.E.Q.Y.N.S.T.Y.R.V.V.S.V.L.T.V.L.H.Q.D.W.L.N.G.K.E.Y.K.C.K.V.S.N.K.A.L.P.A.P.I.E.K.T.I.S.K.A.K.G.Q.P.R.E.P.Q.V.Y.T.L.P.P.S.R.D.E.L.T.K.N.Q.V.S.L.T.C.L.V.K.G.F.Y.P.S.D.I.A.V.E.W.E.S.N.G.Q.P.E.N.N.Y.K.T.T.P.P.V.L.D.S.D.G.S.F.F.L.Y.S.K.L.T.V.D.K.S.R.W.Q.Q.G.N.V.F.S.C.S.V.M.H.E.A.L.H.N.H.Y.T.Q.K.S.L.S.L.S.P.G.K}|PEPTIDE3{E.V.Q.L.V.E.S.G.G.G.L.V.Q.P.G.G.S.L.R.L.S.C.A.A.S.G.F.N.I.K.D.T.Y.I.H.W.V.R.Q.A.P.G.K.G.L.E.W.V.A.R.I.Y.P.T.N.G.Y.T.R.Y.A.D.S.V.K.G.R.F.T.I.S.A.D.T.S.K.N.T.A.Y.L.Q.M.N.S.L.R.A.E.D.T.A.V.Y.Y.C.S.R.W.G.G.D.G.F.Y.A.M.D.Y.W.G.Q.G.T.L.V.T.V.S.S.A.S.T.K.G.P.S.V.F.P.L.A.P.S.S.K.S.T.S.G.G.T.A.A.L.G.C.L.V.K.D.Y.F.P.E.P.V.T.V.S.W.N.S.G.A.L.T.S.G.V.H.T.F.P.A.V.L.Q.S.S.G.L.Y.S.L.S.S.V.V.T.V.P.S.S.S.L.G.T.Q.T.Y.I.C.N.V.N.H.K.P.S.N.T.K.V.D.K.K.V.E.P.P.K.S.C.D.K.T.H.T.C.P.P.C.P.A.P.E.L.L.G.G.P.S.V.F.L.F.P.P.K.P.K.D.T.L.M.I.S.R.T.P.E.V.T.C.V.V.V.D.V.S.H.E.D.P.E.V.K.F.N.W.Y.V.D.G.V.E.V.H.N.A.K.T.K.P.R.E.E.Q.Y.N.S.T.Y.R.V.V.S.V.L.T.V.L.H.Q.D.W.L.N.G.K.E.Y.K.C.K.V.S.N.K.A.L.P.A.P.I.E.K.T.I.S.K.A.K.G.Q.P.R.E.P.Q.V.Y.T.L.P.P.S.R.D.E.L.T.K.N.Q.V.S.L.T.C.L.V.K.G.F.Y.P.S.D.I.A.V.E.W.E.S.N.G.Q.P.E.N.N.Y.K.T.T.P.P.V.L.D.S.D.G.S.F.F.L.Y.S.K.L.T.V.D.K.S.R.W.Q.Q.G.N.V.F.S.C.S.V.M.H.E.A.L.H.N.H.Y.T.Q.K.S.L.S.L.S.P.G.K}|PEPTIDE4{D.I.Q.M.T.Q.S.P.S.S.L.S.A.S.V.G.D.R.V.T.I.T.C.R.A.S.Q.D.V.N.T.A.V.A.W.Y.Q.Q.K.P.G.K.A.P.K.L.L.I.Y.S.A.S.F.L.Y.S.G.V.P.S.R.F.S.G.S.R.S.G.T.D.F.T.L.T.I.S.S.L.Q.P.E.D.F.A.T.Y.Y.C.Q.Q.H.Y.T.T.P.P.T.F.G.Q.G.T.K.V.E.I.K.R.T.V.A.A.P.S.V.F.I.F.P.P.S.D.E.Q.L.K.S.G.T.A.S.V.V.C.L.L.N.N.F.Y.P.R.E.A.K.V.Q.W.K.V.D.N.A.L.Q.S.G.N.S.Q.E.S.V.T.E.Q.D.S.K.D.S.T.Y.S.L.S.S.T.L.T.L.S.K.A.D.Y.E.K.H.K.V.Y.A.C.E.V.T.H.Q.G.L.S.S.P.V.T.K.S.F.N.R.G.E.C}|CHEM1{[SMCC]}|CHEM2{[PEG2]}$CHEM1,CHEM2,1:R2-1:R1|PEPTIDE1,PEPTIDE1,23:R3-88:R3|PEPTIDE2,PEPTIDE2,371:R3-429:R3|PEPTIDE4,PEPTIDE4,134:R3-194:R3|PEPTIDE1,PEPTIDE1,134:R3-194:R3|PEPTIDE3,PEPTIDE3,265:R3-325:R3|PEPTIDE3,PEPTIDE4,224:R3-214:R3|PEPTIDE2,PEPTIDE3,233:R3-233:R3|PEPTIDE2,PEPTIDE2,265:R3-325:R3|PEPTIDE2,PEPTIDE2,147:R3-203:R3|PEPTIDE2,PEPTIDE3,230:R3-230:R3|PEPTIDE2,PEPTIDE1,224:R3-214:R3|PEPTIDE3,PEPTIDE3,147:R3-203:R3|PEPTIDE2,PEPTIDE2,22:R3-96:R3|PEPTIDE3,PEPTIDE3,22:R3-96:R3|PEPTIDE3,PEPTIDE3,371:R3-429:R3|PEPTIDE4,PEPTIDE4,23:R3-88:R3|G1,CHEM1,K:R3-1:R1$G1(PEPTIDE1+PEPTIDE2+PEPTIDE3+PEPTIDE4)|G2(CHEM1:3.5+G1:1)$$V2.0",yes,NA,NA,NA
+,Other cases,Large mol without ambiguity (antibody structure),"PEPTIDE1{D.I.Q.M.T.Q.S.P.S.S.L.S.A.S.V.G.D.R.V.T.I.T.C.R.A.S.Q.D.V.N.T.A.V.A.W.Y.Q.Q.K.P.G.K.A.P.K.L.L.I.Y.S.A.S.F.L.Y.S.G.V.P.S.R.F.S.G.S.R.S.G.T.D.F.T.L.T.I.S.S.L.Q.P.E.D.F.A.T.Y.Y.C.Q.Q.H.Y.T.T.P.P.T.F.G.Q.G.T.K.V.E.I.K.R.T.V.A.A.P.S.V.F.I.F.P.P.S.D.E.Q.L.K.S.G.T.A.S.V.V.C.L.L.N.N.F.Y.P.R.E.A.K.V.Q.W.K.V.D.N.A.L.Q.S.G.N.S.Q.E.S.V.T.E.Q.D.S.K.D.S.T.Y.S.L.S.S.T.L.T.L.S.K.A.D.Y.E.K.H.K.V.Y.A.C.E.V.T.H.Q.G.L.S.S.P.V.T.K.S.F.N.R.G.E.C}|PEPTIDE2{E.V.Q.L.V.E.S.G.G.G.L.V.Q.P.G.G.S.L.R.L.S.C.A.A.S.G.F.N.I.K.D.T.Y.I.H.W.V.R.Q.A.P.G.K.G.L.E.W.V.A.R.I.Y.P.T.N.G.Y.T.R.Y.A.D.S.V.K.G.R.F.T.I.S.A.D.T.S.K.N.T.A.Y.L.Q.M.N.S.L.R.A.E.D.T.A.V.Y.Y.C.S.R.W.G.G.D.G.F.Y.A.M.D.Y.W.G.Q.G.T.L.V.T.V.S.S.A.S.T.K.G.P.S.V.F.P.L.A.P.S.S.K.S.T.S.G.G.T.A.A.L.G.C.L.V.K.D.Y.F.P.E.P.V.T.V.S.W.N.S.G.A.L.T.S.G.V.H.T.F.P.A.V.L.Q.S.S.G.L.Y.S.L.S.S.V.V.T.V.P.S.S.S.L.G.T.Q.T.Y.I.C.N.V.N.H.K.P.S.N.T.K.V.D.K.K.V.E.P.P.K.S.C.D.K.T.H.T.C.P.P.C.P.A.P.E.L.L.G.G.P.S.V.F.L.F.P.P.K.P.K.D.T.L.M.I.S.R.T.P.E.V.T.C.V.V.V.D.V.S.H.E.D.P.E.V.K.F.N.W.Y.V.D.G.V.E.V.H.N.A.K.T.K.P.R.E.E.Q.Y.N.S.T.Y.R.V.V.S.V.L.T.V.L.H.Q.D.W.L.N.G.K.E.Y.K.C.K.V.S.N.K.A.L.P.A.P.I.E.K.T.I.S.K.A.K.G.Q.P.R.E.P.Q.V.Y.T.L.P.P.S.R.D.E.L.T.K.N.Q.V.S.L.T.C.L.V.K.G.F.Y.P.S.D.I.A.V.E.W.E.S.N.G.Q.P.E.N.N.Y.K.T.T.P.P.V.L.D.S.D.G.S.F.F.L.Y.S.K.L.T.V.D.K.S.R.W.Q.Q.G.N.V.F.S.C.S.V.M.H.E.A.L.H.N.H.Y.T.Q.K.S.L.S.L.S.P.G.K}|PEPTIDE3{E.V.Q.L.V.E.S.G.G.G.L.V.Q.P.G.G.S.L.R.L.S.C.A.A.S.G.F.N.I.K.D.T.Y.I.H.W.V.R.Q.A.P.G.K.G.L.E.W.V.A.R.I.Y.P.T.N.G.Y.T.R.Y.A.D.S.V.K.G.R.F.T.I.S.A.D.T.S.K.N.T.A.Y.L.Q.M.N.S.L.R.A.E.D.T.A.V.Y.Y.C.S.R.W.G.G.D.G.F.Y.A.M.D.Y.W.G.Q.G.T.L.V.T.V.S.S.A.S.T.K.G.P.S.V.F.P.L.A.P.S.S.K.S.T.S.G.G.T.A.A.L.G.C.L.V.K.D.Y.F.P.E.P.V.T.V.S.W.N.S.G.A.L.T.S.G.V.H.T.F.P.A.V.L.Q.S.S.G.L.Y.S.L.S.S.V.V.T.V.P.S.S.S.L.G.T.Q.T.Y.I.C.N.V.N.H.K.P.S.N.T.K.V.D.K.K.V.E.P.P.K.S.C.D.K.T.H.T.C.P.P.C.P.A.P.E.L.L.G.G.P.S.V.F.L.F.P.P.K.P.K.D.T.L.M.I.S.R.T.P.E.V.T.C.V.V.V.D.V.S.H.E.D.P.E.V.K.F.N.W.Y.V.D.G.V.E.V.H.N.A.K.T.K.P.R.E.E.Q.Y.N.S.T.Y.R.V.V.S.V.L.T.V.L.H.Q.D.W.L.N.G.K.E.Y.K.C.K.V.S.N.K.A.L.P.A.P.I.E.K.T.I.S.K.A.K.G.Q.P.R.E.P.Q.V.Y.T.L.P.P.S.R.D.E.L.T.K.N.Q.V.S.L.T.C.L.V.K.G.F.Y.P.S.D.I.A.V.E.W.E.S.N.G.Q.P.E.N.N.Y.K.T.T.P.P.V.L.D.S.D.G.S.F.F.L.Y.S.K.L.T.V.D.K.S.R.W.Q.Q.G.N.V.F.S.C.S.V.M.H.E.A.L.H.N.H.Y.T.Q.K.S.L.S.L.S.P.G.K}|PEPTIDE4{D.I.Q.M.T.Q.S.P.S.S.L.S.A.S.V.G.D.R.V.T.I.T.C.R.A.S.Q.D.V.N.T.A.V.A.W.Y.Q.Q.K.P.G.K.A.P.K.L.L.I.Y.S.A.S.F.L.Y.S.G.V.P.S.R.F.S.G.S.R.S.G.T.D.F.T.L.T.I.S.S.L.Q.P.E.D.F.A.T.Y.Y.C.Q.Q.H.Y.T.T.P.P.T.F.G.Q.G.T.K.V.E.I.K.R.T.V.A.A.P.S.V.F.I.F.P.P.S.D.E.Q.L.K.S.G.T.A.S.V.V.C.L.L.N.N.F.Y.P.R.E.A.K.V.Q.W.K.V.D.N.A.L.Q.S.G.N.S.Q.E.S.V.T.E.Q.D.S.K.D.S.T.Y.S.L.S.S.T.L.T.L.S.K.A.D.Y.E.K.H.K.V.Y.A.C.E.V.T.H.Q.G.L.S.S.P.V.T.K.S.F.N.R.G.E.C}|CHEM1{[SMCC]}|CHEM2{[PEG2]}$CHEM1,CHEM2,1:R2-1:R1|PEPTIDE1,PEPTIDE1,23:R3-88:R3|PEPTIDE2,PEPTIDE2,371:R3-429:R3|PEPTIDE4,PEPTIDE4,134:R3-194:R3|PEPTIDE1,PEPTIDE1,134:R3-194:R3|PEPTIDE3,PEPTIDE3,265:R3-325:R3|PEPTIDE3,PEPTIDE4,224:R3-214:R3|PEPTIDE2,PEPTIDE3,233:R3-233:R3|PEPTIDE2,PEPTIDE2,265:R3-325:R3|PEPTIDE2,PEPTIDE2,147:R3-203:R3|PEPTIDE2,PEPTIDE3,230:R3-230:R3|PEPTIDE2,PEPTIDE1,224:R3-214:R3|PEPTIDE3,PEPTIDE3,147:R3-203:R3|PEPTIDE2,PEPTIDE2,22:R3-96:R3|PEPTIDE3,PEPTIDE3,22:R3-96:R3|PEPTIDE3,PEPTIDE3,371:R3-429:R3|PEPTIDE4,PEPTIDE4,23:R3-88:R3|G1,CHEM1,K:R3-1:R1$G1(PEPTIDE1+PEPTIDE2+PEPTIDE3+PEPTIDE4)$$V2.0",yes,145877.57,C6486H10010N1727O2022S42,Not calculated

package/files/samples/peptide-inline.csv

@@ -0,0 +1,28 @@
+Category,Test type,Example HELM,,Expected validation,Expected image,Expected  mol wt calculation,,
+Single monomer in-line HELM one connection point,"Unnumbered connection point, no brackets",PEPTIDE1{[C(=O)[C@H](C)N(*)C]}$$$$,,fail,No display,None,,
+Single monomer in-line HELM one connection point,"Unnumbered connection point, brackets",PEPTIDE1{[C(=O)[C@H](C)N([*])C]}$$$$,,fail,No display,None,,
+Single monomer in-line HELM one connection point,"Numbered connection point, square brackets",PEPTIDE1{[C(=O)[C@H](C)N([*:1])C]}$$$$,,pass,Structure with connection point,None,,
+Single monomer in-line HELM one connection point,"Numbered connection point, ChemAxon SMILES",PEPTIDE1{[C(=O)[C@H](C)N(*)C |$_;;;;;;;_R1;;;$]}$$$$,,pass,Structure with connection point,None,,
+Single monomer in-line HELM one connection point,"Numbered connection point, square brackets ChemAxon SMILES",PEPTIDE1{[C(=O)[C@H](C)N([*])C |$_;;;;;;;_R1;;;$]}$$$$,,pass,Structure with connection point,None,,
+Single monomer in-line HELM two connection points,"Unnumbered connection point, no brackets",PEPTIDE1{[*C(=O)[C@H](C)N(*)C]}$$$$,,fail,No display,None,,
+Single monomer in-line HELM two connection points,"Unnumbered connection point, brackets",PEPTIDE1{[[*]C(=O)[C@H](C)N([*])C]}$$$$,,fail,No display,None,,
+Single monomer in-line HELM two connection points,"Numbered connection point, square brackets",PEPTIDE1{[[*:2]C(=O)[C@H](C)N([*:1])C]}$$$$,,pass,Structure with 2 connection points,None,,
+Single monomer in-line HELM two connection points,"Numbered connection point, ChemAxon SMILES",PEPTIDE1{[*C(=O)[C@H](C)N(*)C |$_R2;;;;;;_R1;;;$]}$$$$,,pass,Structure with 2 connection points,None,,
+Single monomer in-line HELM two connection points,"Numbered connection point, square brackets ChemAxon SMILES",PEPTIDE1{[[*]C(=O)[C@H](C)N([*])C |$_R2;;;;;;_R1;;;$]}$$$$,,pass,Structure with 2 connection points,None,,
+Two monomers one in-line HELM one connection point,"Unnumbered connection point, no brackets",PEPTIDE1{A.[C(=O)[C@H](C)N(*)C]}$$$$,,fail,No display,None,,
+Two monomers one in-line HELM one connection point,"Unnumbered connection point, brackets",PEPTIDE1{A.[C(=O)[C@H](C)N([*])C]}$$$$,,fail,No display,None,,
+Two monomers one in-line HELM one connection point,"Numbered connection point, square brackets",PEPTIDE1{A.[C(=O)[C@H](C)N([*:1])C]}$$$$,,pass,Complete structure,158.2,,
+Two monomers one in-line HELM one connection point,"Numbered connection point, ChemAxon SMILES",PEPTIDE1{A.[C[C@@H](C=O)N(C)(*) |$;;;;;;_R1$|]}$$$$,,pass,Complete structure,158.2,,
+Two monomers one in-line HELM one connection point,"Numbered connection point, square brackets ChemAxon SMILES",PEPTIDE1{A.[C(=O)[C@H](C)N([*])C |$;;;;;;;_R1;;;$]}$$$$,,pass,Complete structure,158.2,,
+Two monomers one in-line HELM two connection points,"Unnumbered connection point, no brackets",PEPTIDE1{A.[*C(=O)[C@H](C)N(*)C]}$$$$,,fail,No display,None,,
+Two monomers one in-line HELM two connection points,"Unnumbered connection point, brackets",PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C]}$$$$,,fail,No display,None,,
+Two monomers one in-line HELM two connection points,"Numbered connection point, square brackets",PEPTIDE1{A.[[*:2]C(=O)[C@H](C)N([*:1])C]}$$$$,,pass,Structure with connection point,None,,
+Two monomers one in-line HELM two connection points,"Numbered connection point, ChemAxon SMILES",PEPTIDE1{A.[*C(=O)[C@H](C)N(*)C |$_R2;;;;;;_R1;;;$]}$$$$,,pass,Structure with connection point,None,,
+Two monomers one in-line HELM two connection points,"Numbered connection point, square brackets ChemAxon SMILES",PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C |$_R2;;;;;;_R1;;;$]}$$$$,,pass,Structure with connection point,None,,
+Three monomers one in-line HELM,"Unnumbered connection point, no brackets",PEPTIDE1{A.[*C(=O)[C@H](C)N(*)C].A}$$$$,,fail,No display,None,,
+Three monomers one in-line HELM,"Unnumbered connection point, brackets",PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C].A}$$$$,,fail,No display,None,,
+Three monomers one in-line HELM,"Numbered connection point, square brackets",PEPTIDE1{A.[[*:2]C(=O)[C@H](C)N([*:1])C].A}$$$$,,pass,Complete structure,245.27,,
+Three monomers one in-line HELM,"Numbered connection point, ChemAxon SMILES",PEPTIDE1{A.[*C(=O)[C@H](C)N(*)C |$_R2;;;;;;_R1;;;$].A}$$$$,,pass,Complete structure,245.27,,
+Three monomers one in-line HELM,"Numbered connection point, square brackets ChemAxon SMILES",PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C |$_R2;;;;;;_R1;;;$].A}$$$$,,pass,Complete structure,245.27,,
+in-line HELM connected to in-line HELM,in-line HELM connected to in-line HELM,PEPTIDE1{[C[C@@H](N*)C(*)=O |$;;;_R1;;_R2;;$|].[O=C(*)[C@@H](C(C)C)N* |$;;_R2;;;;;;_R1;$|].[O=C(*)[C@@H](CC(C)C)N* |$;;_R2;;;;;;;_R1;$|]}$$$$V2.0,,pass,structure with two connection points,None,,
+in-line HELM with incorrectly numbered R groups,in-line HELM with incorrectly numbered R groups,PEPTIDE1{A.[[*:4]C(=O)[C@H](C)N([*:1])C].A}$$$$V2.0 ,,fail,error,None,,

package/files/samples/rna-and-chem-inline.csv

@@ -0,0 +1,20 @@
+Category,Test type,Example HELM,,Expected validation,Expected image,Expected  mol wt calculation,Expected SMILES,
+RNA with in-line HELM for base,no dots between monomers,RNA1{R([NC1=NC(N([*:1])C=C1)=O])P}$$$$,,pass ,Complete structure,323.2,O1[C@@H]([C@H]([C@H]([C@@H]1N2C(N=C(N)C=C2)=O)O)OP(=O)(O)O)CO[H] ,
+RNA with in-line HELM for base,Dot before the branch,RNA1{R.([NC1=NC(N([*:1])C=C1)=O])P}$$$$,,fail,No display,None,,
+RNA with in-line HELM for base,Dot after the branch,RNA1{R([NC1=NC(N([*:1])C=C1)=O])P}$$$$,,pass ,Complete structure,323.2,O1[C@@H]([C@H]([C@H]([C@@H]1N2C(N=C(N)C=C2)=O)O)OP(=O)(O)O)CO[H] ,
+RNA with in-line HELM for base,Dot before and after the branch,RNA1{R.([NC1=NC(N([*:1])C=C1)=O]).P}$$$$,,pass ,Complete structure,323.2,O1[C@@H]([C@H]([C@H]([C@@H]1N2C(N=C(N)C=C2)=O)O)OP(=O)(O)O)CO[H] ,
+RNA with in-line HELM for ribose,un-numbered connection points,RNA1{[O[C@H]1[C@H]([*])O[C@H](CO[*])[C@H]1O[*]](C)P}$$$$V2.0,,fail,none,None,,
+RNA with in-line HELM for ribose,numbered connection points,RNA1{[O[C@H]1[C@H]([*:3])O[C@H](CO[*:1])[C@H]1O[*:2]](C)P}$$$$V2.0,,pass,structure with one connection point,322.2,,
+RNA with in-line HELM for ribose,ChemAxon SMILES with no square brackets,RNA1{[O[C@H]1[C@H](*)O[C@H](CO*)[C@H]1O* |$;;;;;;R3;;;;;R1;;;R2$](C)P}$$$$V2.0,,pass,structure with one connection point,322.2,,
+RNA with in-line HELM for ribose,ChemAxon SMILES with  square brackets,RNA1{[O[C@H]1[C@H]([*])O[C@H](CO[*])[C@H]1O[*] |$;;;;;;R3;;;;;R1;;;R2$](C)P}$$$$V2.0,,pass,structure with one connection point,322.2,,
+RNA with in-line HELM for ribose and more monomers,no dots,RNA1{P[O[C@H]1[C@H]([*:1])O[C@H](CO[*:2])[C@H]1O[*:3]](U)P.R(T)}$$$$V2.0,,pass,structure ,644.37,,
+RNA with in-line HELM for ribose and more monomers,Dot before the in-line backbone,RNA1{P.[O[C@H]1[C@H]([*:1])O[C@H](CO[*:2])[C@H]1O[*:3]](U)P.R(T)}$$$$V2.0,,pass,structure ,644.37,,
+RNA with in-line HELM for ribose and more monomers,Dot after the in-line backbone and before the branch,RNA1{P[O[C@H]1[C@H]([*:1])O[C@H](CO[*:2])[C@H]1O[*:3]].(U)P.R(T)}$$$$V2.0,,fail,No display,None,,
+RNA with in-line HELM for ribose and more monomers,"Dot before and after the inline backbone, before branch",RNA1{P.[O[C@H]1[C@H]([*:1])O[C@H](CO[*:2])[C@H]1O[*:3]].(U)P.R(T)}$$$$V2.0,,fail,No display,None,,
+RNA with in-line HELM for phosphate,un-numbered connection points,RNA1{R(C)[OP([*])([*])=O]}$$$$V2.0,,fail,No display,None,,
+RNA with in-line HELM for phosphate,numbered connection points,RNA1{R(C)[OP([*:1])([*:2])=O]}$$$$V2.0,,pass,structure with one connection point,306.19,,
+CHEM single in-line HELM,1 connection point,CHEM1{[[*:1]OCCCCC=C]}$$$$,,pass,structure with one connection point,99.15,,
+CHEM single in-line HELM,2 connection points,CHEM1{[[*:2]C(=O)[C@H](C)N([*:1])CC]}$$$$,,pass,structure with one connection point,99.15,,
+CHEM single in-line HELM,connection between CHEMs,"CHEM1{[[R1]OCCCCC=C]}|CHEM2{[[R2]C(=O)[C@H](C)N([R1])CC]}$CHEM1,CHEM2,1:R1-1:R1$$$V2.0",,pass,structure with one connection point,198.28,,
+CHEM single in-line HELM,connection between CHEMs,"CHEM1{[[*:1]OCCCCC=C]}|CHEM2{[[*:2]C(=O)[C@H](C)N([*:1])CC]}$CHEM1,CHEM2,1:R1-1:R1$$$V2.0",,pass,structure with one connection point,198.28,,
+in-line HELM connected to in-line HELM,two monomers each with 2 connection points,PEPTIDE1{[C[C@@H](N*)C(*)=O |$;;;_R1;;_R2;;$|].[O=C(*)[C@@H](C(C)C)N* |$;;_R2;;;;;;_R1;$|].[O=C(*)[C@@H](CC(C)C)N* |$;;_R2;;;;;;;_R1;$|]}$$$$V2.0,,pass,structure with two connection points,287.36,,

package/files/samples/test-set-1.csv

@@ -0,0 +1,25 @@
+ID,Test type,HELM string,Valid?,Mol Weight,Mol Formula,SMILES
+RNA,Simple RNA ,RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$,yes,1543.98,C48H61N17O34P4,[H]OCC1OC(N2C=CC(=O)NC2=O)C(O)C1OP(=O)(O)OCC3OC(N4C=C(C(=O)NC4=O)C)C(O)C3OP(=O)(O)OCC5OC(N6C=NC=7C(=O)NC(=NC76)N)C(O)C5OP(=O)(O)OCC8OC(N9C=CC(=NC9=O)N)C(O)C8OP(=O)(O)OCC%10OC(N%11C=NC=%12C(=NC=NC%12%11)N)C(O)C%10O[H] 
+RNA,Simple RNA with multicharacter monomer,RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R([daA])}$$$$,yes,1572.04,C50H65N17O34P4,[H]OCC1OC(N2C=CC(=O)NC2=O)C(O)C1OP(=O)(O)OCC3OC(N4C=C(C(=O)NC4=O)C)C(O)C3OP(=O)(O)OCC5OC(N6C=NC=7C(=O)NC(=NC76)N)C(O)C5OP(=O)(O)OCC8OC(N9C=CC(=NC9=O)N)C(O)C8OP(=O)(O)OCC%10OC(N%11C=NC=%12C%11=NC=NC%12N(C)C)C(O)C%10O[H] 
+Different arrangements of dots,Only dots beween the backbone monomers,RNA1{P.R(U)P.R(T)}$$$$,yes,644.37,C19H26N4O17P2,OP(O)(OC[C@H]1O[C@@H](N(C2=O)C=CC(N2)=O)[C@H](O)[C@@H]1OP(O)(OC[C@H]3O[C@@H](N(C4=O)C=C(C)C(N4)=O)[C@H](O)[C@@H]3O[H])=O)=O
+Different arrangements of dots,Dot before the branch (invalid notation),RNA1{P.R.(U)P.R(T)}$$$$,no ,,,
+Different arrangements of dots,Dot after the branch,RNA1{P.R(U).P.R(T)}$$$$,yes,644.37,C19H26N4O17P2,OP(O)(OC[C@H]1O[C@@H](N(C2=O)C=CC(N2)=O)[C@H](O)[C@@H]1OP(O)(OC[C@H]3O[C@@H](N(C4=O)C=C(C)C(N4)=O)[C@H](O)[C@@H]3O[H])=O)=O
+Different arrangements of dots,Dot before and after the branch (invalid notation),RNA1{P.R.(U).P.R(T)}$$$$,no,,,
+Different arrangements of dots,Triple phosphate at the terminus (note: structure is not chemically sensible),RNA1{P.R(U)P.R(T)P.P.P}$$$$,yes,852.31,C19H29N4O24P5,OP(O)(OC[C@H]1O[C@@H](N(C2=O)C=CC(N2)=O)[C@H](O)[C@@H]1OP(O)(OC[C@H]3O[C@@H](N(C4=O)C=C(C)C(N4)=O)[C@H](O)[C@@H]3OP(O)(P(O)(P(O)(O)=O)=O)=O)=O)=O
+Hydrogen bonding,RNA with hydrogen bonding,"RNA1{R(A)P.R(C)P.R(G)P}|RNA2{P.R(C)P.R(G)P.R(T)}$RNA1,RNA2,2:pair-9:pair|RNA1,RNA2,5:pair-6:pair|RNA1,RNA2,8:pair-3:pair$$$",yes,1986.2,C58H77N23O44P6,NA
+Hydrogen bonding,Shorter RNA with H bonding,"RNA1{R(U)P.R(T)P}|RNA2{P.R(A)P.R(A)}$RNA1,RNA2,2:pair-6:pair|RNA1,RNA2,5:pair-3:pair$$$",yes,1320.8,C39H52N14O30P4,NA
+Hydrogen bonding,annotated H bonding annotated sense strand,"RNA1{R(A)P.R(C)P.R(G)P}|RNA2{P.R(C)P.R(G)P.R(T)}$RNA1,RNA2,2:pair-9:pair|RNA1,RNA2,5:pair-6:pair|RNA1,RNA2,8:pair-3:pair$${""RNA1"":{""strandtype"":""ss""}}$",yes,1986.2,C58H77N23O44P6,NA
+PEPTIDE  ,Simple Peptide,PEPTIDE1{A.L.C}$$$$,yes,305.395,C12H23N3O4S,[H]SCC(NC(=O)C(NC(=O)C(N[H])C)CC(C)C)C(=O)O 
+PEPTIDE  ,Simple Peptide with multicharacter monomer,PEPTIDE1{A.[meA].C}$$$$,yes,277.342,C10H19N3O4S,[H]SCC(NC(=O)C(N(C(=O)C(N[H])C)C)C)C(=O)O 
+PEPTIDE  ,Branched peptide,"PEPTIDE1{D.E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0",yes,698.7,C28H38N6O13S,O=C(O)C[C@H](N[H])C(N[C@@H](CCC(N[C@@H](CS[H])C(N[C@@H](CCC(O)=O)C(O)=O)=O)=O)C(N[C@H](C(NCC(O)=O)=O)CC1=CC=CC=C1)=O)=O
+PEPTIDE  ,Cyclic peptide,"PEPTIDE1{L.M.P.Q.R.S.T}$PEPTIDE1,PEPTIDE1,7:R2-1:R1$$$",yes,813.96,C34H59N11O10S,O=C(N)CCC1NC(=O)C2N(C(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC1=O)CCCNC(=N)N)CO)C(O)C)CC(C)C)CCSC)CCC2 
+PEPTIDE  ,Cyclic peptide with non-natural amino acid,"PEPTIDE1{N.P.F.V.L.P.[dV]}$PEPTIDE1,PEPTIDE1,7:R2-1:R1$$$",yes,766.92,C39H58N8O8,CC(C)C[C@H]1C(=O)N2CCC[C@H]2C(=O)N[C@H]([C@@H](C)C)C(=O)N[C@@H](CC(=O)N)C(=O)N3CCC[C@H]3C(=O)N[C@@H](CC4=CC=CC=C4)C(=O)N[C@@H](C(C)C)C(=O)N1 
+PEPTIDE  ,Cyclic peptide with branch to CHEM,"CHEM1{[PEG2]}|PEPTIDE1{W.N.D.[Pen].G.[Orn].D.A.D.G.S.G.[Cap]}$PEPTIDE1,PEPTIDE1,13:R2-4:R3|PEPTIDE1,CHEM1,1:R1-1:R1$$$",yes,1521.6,C64H96N16O25S,C[C@H]1C(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@@H](CO)C(=O)NCC(=O)N[C@@H](CCC2CCCCC2)[C@H](C(=O)SC(C)(C)[C@@H](C(=O)NCC(=O)N[C@@H](CCCN[H])C(=O)N[C@@H](CC(=O)O)C(=O)N1)NC(=O)[C@H](CC(=O)O)NC(=O)[C@H](CC(=O)N)NC(=O)[C@H](CC3=CNC4=C3C=CC=C4)NOCCOCCO[H])O
+PEPTIDE  ,Peptide with Cys-Cys bond,"PEPTIDE1{A.R.C.A.A.K.T.C.D.A}$PEPTIDE1,PEPTIDE1,8:R3-3:R3$$$",yes,1007.14,C38H66N14O14S2,C[C@H](N[H])C(=O)N[C@H](C(=O)N[C@@H]1C(=O)N([C@@H](C)C(=O)N[C@H](C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C=O)CC(O)=O)CSSC1)[C@@H](C)O)CCCCN[H])[C@@H](C)C(=O)O)CCCNC(N)=N
+CHEM,Single CHEM,CHEM1{[sDBl]}$$$$,yes,290.356,C13H26N2O5,[H]OCCCCC(=O)NCC(O[H])CNC(=O)CCCCO[H] 
+CHEM,CHEMs connected to each other,"CHEM1{[SMCC]}|CHEM2{[EG]}$CHEM1,CHEM2,1:R1-1:R1$$$",yes,283.32,C14H21NO5,O=C1N(C(CC1[H])=O)CC2CCC(C(OCCO)=O)CC2
+CHEM,CHEMs connected to each other - incorrectly joined,CHEM1{[Az].[MCC]}$$$$,no,NA,NA,NA
+CHEM,"Combo PEPTIDE, RNA, CHEM","CHEM1{[SMCC]}|PEPTIDE1{L.M}|RNA1{R(C)P.R(A)P}$RNA1,PEPTIDE1,6:R2-1:R1|PEPTIDE1,CHEM1,2:R2-1:R1$$$",yes,1102.01,C42H61N11O18P2S,CC(C)C[C@@H](C(=O)N[C@@H](CCSC)C(=O)C(=O)C1CCC(CC1)CN2C(=O)CC([H])C2=O)NP(=O)(O)O[C@@H]3[C@@H](COP(=O)(O)O[C@@H]4[C@@H](CO[H])O[C@H]([C@@H]4O)N5C=CC(=NC5=O)N)O[C@H]([C@@H]3O)N6C=NC7=C6N=CN=C7N
+CHEM,Disconnected fragments - all CHEM,"CHEM1{[SMPEG2]}|CHEM2{[SMCC]}|CHEM3{[PEG2]}|CHEM4{[MCC]}$CHEM4,CHEM3,1:R1-1:R1|CHEM2,CHEM1,1:R1-1:R1$$$",yes,860.94,C42H60N4O15,C1CC(CCC1CN2C(=O)CC([H])C2=O)C(=O)C(=O)CCOCCOCCNC(=O)CCN3C(=O)CC([H])C3=O.C1CC(CCC1CN2C(=O)C=CC2=O)C(=O)OCCOCCO[H]
+CHEM,Disconnected fragments - mixture,CHEM1{[SMPEG2]}|PEPTIDE1{A}|RNA1{R(A)P}$$$$,yes,766.65,C27H43N8O16P,C[C@@H](C(=O)O)N[H].C1C([H])C(=O)N(CCC(=O)NCCOCCOCCC(=O)O)C1=O.C([C@@H]1[C@H]([C@H]([C@H](N2C=NC3=C2N=CN=C3N)O1)O)OP(=O)(O)O)O[H] 
+CHEM,Disconnected fragments - PEPTIDE,PEPTIDE1{L.V.A}|PEPTIDE2{L.V.A}$$$$,yes,602.76,C28H54N6O8,CC(C)C[C@@H](C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](C)C(=O)O)N[H].CC(C)C[C@@H](C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](C)C(=O)O)N[H]

package/files/samples/test.csv

@@ -0,0 +1,6 @@
+ID,Test type,HELM string,Valid?,Mol Weight,Mol Formula,SMILES
+RNA,Simple RNA ,RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$,yes,1543.98,C48H61N17O34P4,[H]OCC1OC(N2C=CC(=O)NC2=O)C(O)C1OP(=O)(O)OCC3OC(N4C=C(C(=O)NC4=O)C)C(O)C3OP(=O)(O)OCC5OC(N6C=NC=7C(=O)NC(=NC76)N)C(O)C5OP(=O)(O)OCC8OC(N9C=CC(=NC9=O)N)C(O)C8OP(=O)(O)OCC%10OC(N%11C=NC=%12C(=NC=NC%12%11)N)C(O)C%10O[H] 
+Different arrangements of dots,Only dots beween the backbone monomers,RNA1{P.R(U)P.R(T)}$$$$,yes,644.37,C19H26N4O17P2,OP(O)(OC[C@H]1O[C@@H](N(C2=O)C=CC(N2)=O)[C@H](O)[C@@H]1OP(O)(OC[C@H]3O[C@@H](N(C4=O)C=C(C)C(N4)=O)[C@H](O)[C@@H]3O[H])=O)=O
+Different arrangements of dots,Dot after the branch,RNA1{P.R(U).P.R(T)}$$$$,yes,644.37,C19H26N4O17P2,OP(O)(OC[C@H]1O[C@@H](N(C2=O)C=CC(N2)=O)[C@H](O)[C@@H]1OP(O)(OC[C@H]3O[C@@H](N(C4=O)C=C(C)C(N4)=O)[C@H](O)[C@@H]3O[H])=O)=O
+Hydrogen bonding,RNA with hydrogen bonding,"RNA1{R(A)P.R(C)P.R(G)P}|RNA2{P.R(C)P.R(G)P.R(T)}$RNA1,RNA2,2:pair-9:pair|RNA1,RNA2,5:pair-6:pair|RNA1,RNA2,8:pair-3:pair$$$",yes,1986.2,C58H77N23O44P6,NA
+Hydrogen bonding,Shorter RNA with H bonding,"RNA1{R(U)P.R(T)P}|RNA2{P.R(A)P.R(A)}$RNA1,RNA2,2:pair-6:pair|RNA1,RNA2,5:pair-3:pair$$$",yes,1320.8,C39H52N14O30P4,NA