@datagrok/helm 2.13.8 → 3.0.0

package/files/samples/helm-showcase.csv

@@ -0,0 +1,56 @@
+Name,Category,HELM
+Dipeptide,Peptide / linear,PEPTIDE1{A.C}$$$$
+Linear 10-mer,Peptide / linear,PEPTIDE1{A.C.D.E.F.G.H.I.K.L}$$$$
+Protein 50-mer (all 20 AAs),Peptide / linear,PEPTIDE1{A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y.A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y.A.C.D.E.F.G.H.I.K.L}$$$$
+Protein 100-mer (all 20 AAs),Peptide / linear,PEPTIDE1{A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y.A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y.A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y.A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y.A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y}$$$$
+Homopolymer poly-A (20),Peptide / linear,PEPTIDE1{A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A}$$$$
+Modified residues (meL/meY),Peptide / modified,PEPTIDE1{[meL].A.G.[meY].T}$$$$
+Head-to-tail cyclic (5),Peptide / cyclic,"PEPTIDE1{A.C.D.E.F}$PEPTIDE1,PEPTIDE1,5:R2-1:R1$$$V2.0"
+Disulfide cyclic,Peptide / cyclic,"PEPTIDE1{A.C.D.E.F.C}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0"
+Cyclic head-to-tail (32-mer),Peptide / cyclic,"PEPTIDE1{A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y.A.C.D.E.F.G.H.I.K.L.M.N}$PEPTIDE1,PEPTIDE1,32:R2-1:R1$$$V2.0"
+Inner side-chain cycle (R3-R3),Peptide / cyclic,"PEPTIDE1{A.C.D.E.F.G.H.I.K.L}$PEPTIDE1,PEPTIDE1,3:R3-7:R3$$$V2.0"
+Two side-chain bridges (bicyclic),Peptide / multicyclic,"PEPTIDE1{A.C.D.E.F.G.H.I.K.L.M.N}$PEPTIDE1,PEPTIDE1,2:R3-6:R3|PEPTIDE1,PEPTIDE1,7:R3-11:R3$$$V2.0"
+"Stapled helix (i, i+4)",Peptide / cyclic,"PEPTIDE1{A.C.D.E.C.G.H.I}$PEPTIDE1,PEPTIDE1,2:R3-5:R3$$$V2.0"
+Branched tri-ring (R3-R3 bridges),Peptide / multicyclic,"PEPTIDE1{C.A.C.A.C.A}|PEPTIDE2{C.A.C.A.C.A}|PEPTIDE3{C.A.C.A.C.A}$PEPTIDE1,PEPTIDE2,1:R3-1:R3|PEPTIDE2,PEPTIDE3,3:R3-3:R3|PEPTIDE3,PEPTIDE1,5:R3-5:R3$$$V2.0"
+Disulfide-rich (insulin-like),Peptide / multicyclic,"PEPTIDE1{G.I.V.E.Q.C.C.T.S.I.C.S.L.Y.Q.L.E.N.Y.C.N}|PEPTIDE2{F.V.N.Q.H.L.C.G.S.H.L.V.E.A.L.Y.L.V.C.G.E.R.G.F.F.Y.T.P.K.T}$PEPTIDE1,PEPTIDE2,7:R3-7:R3|PEPTIDE1,PEPTIDE2,20:R3-19:R3|PEPTIDE1,PEPTIDE1,6:R3-11:R3$$$V2.0"
+Two disconnected chains,Peptide / linear,PEPTIDE1{A.C}|PEPTIDE2{G.H}$$$$V2.0
+"Ambiguous position (A,G,C)",Peptide / ambiguity,"PEPTIDE1{(A,G,C)}$$$$"
+RNA tetramer (ribose),Nucleic acid / single,RNA1{r(A)p.r(C)p.r(G)p.r(U)p}$$$$V2.0
+DNA tetramer (deoxy),Nucleic acid / single,RNA1{d(A)p.d(C)p.d(G)p.d(T)p}$$$$V2.0
+RNA 30-mer,Nucleic acid / single,RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p}$$$$V2.0
+2'-Fluoro modified ribose,Nucleic acid / modified,RNA1{[fl2r](A)p.[fl2r](C)p.r(G)p.r(U)p}$$$$V2.0
+Phosphorothioate (PS) backbone,Nucleic acid / modified,RNA1{m(G)[sP].m(A)[sP].m(C)[sP].m(U)[sP]}$$$$V2.0
+2'-OMe gapmer (PS wings),Nucleic acid / modified,RNA1{m(A)[sP].m(C)[sP].d(G)p.d(A)p.d(T)p.d(C)p.m(G)[sP].m(U)[sP]}$$$$V2.0
+Bracket repeat (rA)x3,Nucleic acid / modified,RNA1{(r(A)p)'3'}$$$$V2.0
+Mini duplex (2bp),Nucleic acid / duplex,"RNA1{r(A)p.r(C)p}|RNA2{r(G)p.r(U)p}$RNA1,RNA2,2:pair-5:pair$$$V2.0"
+Blunt duplex (8bp),Nucleic acid / duplex,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}|RNA2{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-23:pair|RNA1,RNA2,5:pair-20:pair|RNA1,RNA2,8:pair-17:pair|RNA1,RNA2,11:pair-14:pair|RNA1,RNA2,14:pair-11:pair|RNA1,RNA2,17:pair-8:pair|RNA1,RNA2,20:pair-5:pair|RNA1,RNA2,23:pair-2:pair$$$V2.0"
+Blunt duplex (12bp),Nucleic acid / duplex,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}|RNA2{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-35:pair|RNA1,RNA2,5:pair-32:pair|RNA1,RNA2,8:pair-29:pair|RNA1,RNA2,11:pair-26:pair|RNA1,RNA2,14:pair-23:pair|RNA1,RNA2,17:pair-20:pair|RNA1,RNA2,20:pair-17:pair|RNA1,RNA2,23:pair-14:pair|RNA1,RNA2,26:pair-11:pair|RNA1,RNA2,29:pair-8:pair|RNA1,RNA2,32:pair-5:pair|RNA1,RNA2,35:pair-2:pair$$$V2.0"
+siRNA 19-mer blunt duplex,Nucleic acid / siRNA,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p}|RNA2{r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-56:pair|RNA1,RNA2,5:pair-53:pair|RNA1,RNA2,8:pair-50:pair|RNA1,RNA2,11:pair-47:pair|RNA1,RNA2,14:pair-44:pair|RNA1,RNA2,17:pair-41:pair|RNA1,RNA2,20:pair-38:pair|RNA1,RNA2,23:pair-35:pair|RNA1,RNA2,26:pair-32:pair|RNA1,RNA2,29:pair-29:pair|RNA1,RNA2,32:pair-26:pair|RNA1,RNA2,35:pair-23:pair|RNA1,RNA2,38:pair-20:pair|RNA1,RNA2,41:pair-17:pair|RNA1,RNA2,44:pair-14:pair|RNA1,RNA2,47:pair-11:pair|RNA1,RNA2,50:pair-8:pair|RNA1,RNA2,53:pair-5:pair|RNA1,RNA2,56:pair-2:pair$$$V2.0"
+"siRNA 21-mer, 2-nt 3′ overhangs",Nucleic acid / siRNA,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(U)p}|RNA2{r(A)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-59:pair|RNA1,RNA2,5:pair-56:pair|RNA1,RNA2,8:pair-53:pair|RNA1,RNA2,11:pair-50:pair|RNA1,RNA2,14:pair-47:pair|RNA1,RNA2,17:pair-44:pair|RNA1,RNA2,20:pair-41:pair|RNA1,RNA2,23:pair-38:pair|RNA1,RNA2,26:pair-35:pair|RNA1,RNA2,29:pair-32:pair|RNA1,RNA2,32:pair-29:pair|RNA1,RNA2,35:pair-26:pair|RNA1,RNA2,38:pair-23:pair|RNA1,RNA2,41:pair-20:pair|RNA1,RNA2,44:pair-17:pair|RNA1,RNA2,47:pair-14:pair|RNA1,RNA2,50:pair-11:pair|RNA1,RNA2,53:pair-8:pair|RNA1,RNA2,56:pair-5:pair$$$V2.0"
+"siRNA 23-mer, 2-nt 3′ overhangs",Nucleic acid / siRNA,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p}|RNA2{r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-65:pair|RNA1,RNA2,5:pair-62:pair|RNA1,RNA2,8:pair-59:pair|RNA1,RNA2,11:pair-56:pair|RNA1,RNA2,14:pair-53:pair|RNA1,RNA2,17:pair-50:pair|RNA1,RNA2,20:pair-47:pair|RNA1,RNA2,23:pair-44:pair|RNA1,RNA2,26:pair-41:pair|RNA1,RNA2,29:pair-38:pair|RNA1,RNA2,32:pair-35:pair|RNA1,RNA2,35:pair-32:pair|RNA1,RNA2,38:pair-29:pair|RNA1,RNA2,41:pair-26:pair|RNA1,RNA2,44:pair-23:pair|RNA1,RNA2,47:pair-20:pair|RNA1,RNA2,50:pair-17:pair|RNA1,RNA2,53:pair-14:pair|RNA1,RNA2,56:pair-11:pair|RNA1,RNA2,59:pair-8:pair|RNA1,RNA2,62:pair-5:pair$$$V2.0"
+siRNA with ss/as strand annotations,Nucleic acid / siRNA,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p}|RNA2{r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-56:pair|RNA1,RNA2,5:pair-53:pair|RNA1,RNA2,8:pair-50:pair|RNA1,RNA2,11:pair-47:pair|RNA1,RNA2,14:pair-44:pair|RNA1,RNA2,17:pair-41:pair|RNA1,RNA2,20:pair-38:pair|RNA1,RNA2,23:pair-35:pair|RNA1,RNA2,26:pair-32:pair|RNA1,RNA2,29:pair-29:pair|RNA1,RNA2,32:pair-26:pair|RNA1,RNA2,35:pair-23:pair|RNA1,RNA2,38:pair-20:pair|RNA1,RNA2,41:pair-17:pair|RNA1,RNA2,44:pair-14:pair|RNA1,RNA2,47:pair-11:pair|RNA1,RNA2,50:pair-8:pair|RNA1,RNA2,53:pair-5:pair|RNA1,RNA2,56:pair-2:pair$${""RNA1"":{""strandtype"":""ss""},""RNA2"":{""strandtype"":""as""}}$V2.0"
+Long anti-parallel pair (25-mer),Nucleic acid / duplex,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p}|RNA2{r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-74:pair|RNA1,RNA2,5:pair-71:pair|RNA1,RNA2,8:pair-68:pair|RNA1,RNA2,11:pair-65:pair|RNA1,RNA2,14:pair-62:pair|RNA1,RNA2,17:pair-59:pair|RNA1,RNA2,20:pair-56:pair|RNA1,RNA2,23:pair-53:pair|RNA1,RNA2,26:pair-50:pair|RNA1,RNA2,29:pair-47:pair|RNA1,RNA2,32:pair-44:pair|RNA1,RNA2,35:pair-41:pair|RNA1,RNA2,38:pair-38:pair|RNA1,RNA2,41:pair-35:pair|RNA1,RNA2,44:pair-32:pair|RNA1,RNA2,47:pair-29:pair|RNA1,RNA2,50:pair-26:pair|RNA1,RNA2,53:pair-23:pair|RNA1,RNA2,56:pair-20:pair|RNA1,RNA2,59:pair-17:pair|RNA1,RNA2,62:pair-14:pair|RNA1,RNA2,65:pair-11:pair|RNA1,RNA2,68:pair-8:pair|RNA1,RNA2,71:pair-5:pair|RNA1,RNA2,74:pair-2:pair$$$V2.0"
+Hairpin (3-bp stem + loop),Nucleic acid / structure,"RNA1{r(G)p.r(A)p.r(C)p.r(U)p.r(A)p.r(C)p.r(G)p.r(G)p.r(U)p.r(C)p}$RNA1,RNA1,2:pair-29:pair|RNA1,RNA1,5:pair-26:pair|RNA1,RNA1,8:pair-23:pair$$$V2.0"
+Internal-loop stem,Nucleic acid / structure,"RNA1{r(G)p.r(C)p.r(A)p.r(U)p.r(A)p.r(A)p.r(G)p.r(C)p.r(A)p.r(U)p.r(U)p.r(C)p.r(G)p.r(U)p.r(G)p.r(C)p.r(A)p.r(U)p.r(G)p.r(C)p}$RNA1,RNA1,2:pair-59:pair|RNA1,RNA1,5:pair-56:pair|RNA1,RNA1,8:pair-53:pair|RNA1,RNA1,11:pair-50:pair|RNA1,RNA1,20:pair-47:pair|RNA1,RNA1,23:pair-44:pair|RNA1,RNA1,26:pair-41:pair$$$V2.0"
+Cloverleaf — three-arm junction,Nucleic acid / structure,"RNA1{r(G)p.r(C)p.r(A)p.r(U)p.r(G)p.r(C)p.r(A)p.r(U)p.r(C)p.r(C)p.r(A)p.r(A)p.r(U)p.r(G)p.r(C)p.r(G)p.r(C)p.r(A)p.r(U)p.r(C)p.r(U)p.r(A)p.r(C)p.r(U)p.r(A)p.r(U)p.r(A)p.r(U)p.r(G)p.r(C)p.r(A)p.r(U)p.r(G)p.r(C)p}$RNA1,RNA1,2:pair-101:pair|RNA1,RNA1,5:pair-98:pair|RNA1,RNA1,8:pair-95:pair|RNA1,RNA1,11:pair-92:pair|RNA1,RNA1,14:pair-44:pair|RNA1,RNA1,17:pair-41:pair|RNA1,RNA1,20:pair-38:pair|RNA1,RNA1,23:pair-35:pair|RNA1,RNA1,47:pair-89:pair|RNA1,RNA1,50:pair-86:pair|RNA1,RNA1,53:pair-83:pair|RNA1,RNA1,56:pair-80:pair$$$V2.0"
+Cloverleaf — four-arm tRNA,Nucleic acid / structure,"RNA1{r(G)p.r(C)p.r(A)p.r(U)p.r(G)p.r(C)p.r(A)p.r(C)p.r(U)p.r(A)p.r(G)p.r(U)p.r(G)p.r(C)p.r(G)p.r(C)p.r(A)p.r(U)p.r(C)p.r(A)p.r(U)p.r(A)p.r(G)p.r(A)p.r(U)p.r(G)p.r(C)p.r(G)p.r(C)p.r(A)p.r(U)p.r(U)p.r(A)p.r(C)p.r(G)p.r(A)p.r(U)p.r(G)p.r(C)p.r(A)p.r(U)p.r(G)p.r(C)p}$RNA1,RNA1,2:pair-128:pair|RNA1,RNA1,5:pair-125:pair|RNA1,RNA1,8:pair-122:pair|RNA1,RNA1,11:pair-119:pair|RNA1,RNA1,14:pair-41:pair|RNA1,RNA1,17:pair-38:pair|RNA1,RNA1,20:pair-35:pair|RNA1,RNA1,44:pair-80:pair|RNA1,RNA1,47:pair-77:pair|RNA1,RNA1,50:pair-74:pair|RNA1,RNA1,53:pair-71:pair|RNA1,RNA1,83:pair-116:pair|RNA1,RNA1,86:pair-113:pair|RNA1,RNA1,89:pair-110:pair|RNA1,RNA1,92:pair-107:pair$$$V2.0"
+CHEM only (PEG2),Conjugate / CHEM,CHEM1{[PEG2]}$$$$V2.0
+Peptide – PEG2 conjugate,Conjugate / CHEM,"PEPTIDE1{A.C.D}|CHEM1{[PEG2]}$PEPTIDE1,CHEM1,3:R2-1:R1$$$V2.0"
+Peptide – RNA direct conjugate,Conjugate / peptide-RNA,"PEPTIDE1{A.W.Y}|RNA1{r(A)p.r(C)p}$PEPTIDE1,RNA1,3:R2-1:R1$$$V2.0"
+Peptide – SMCC – RNA conjugate,Conjugate / peptide-RNA,"PEPTIDE1{A.C.D.E.F.G.H.I.K.L.M.N.P.Q.R.S.T.V.W.Y}|RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p}|CHEM1{[SMCC]}$PEPTIDE1,CHEM1,20:R2-1:R1|CHEM1,RNA1,1:R2-1:R1$$$V2.0"
+Cholesterol-conjugated oligo (Chol/L3),Conjugate / siRNA,RNA1{[Chol].r(A)p.r(C)p.r(G)p.r(U)p.[L3]}$$$$V2.0
+BLOB (gold nanoparticle),Conjugate / blob,BLOB1{Gold}$$$$V2.0
+BLOB bead – PEG2 conjugate,Conjugate / blob,"BLOB1{Bead}|CHEM1{[PEG2]}$BLOB1,CHEM1,1:R1-1:R2$$$V2.0"
+Huge mixed conjugate (peptide+2 RNA+CHEM+blob),Conjugate / mixed,"PEPTIDE1{A.C.D.E.F.G.H.I.K.L}|RNA1{r(A)p.r(C)p.r(G)p.r(U)p}|RNA2{r(A)p.r(C)p.r(G)p.r(U)p}|CHEM1{[SMCC]}|CHEM2{[PEG2]}|BLOB1{Bead}$PEPTIDE1,CHEM1,10:R2-1:R1|CHEM1,RNA1,1:R2-1:R1|CHEM2,RNA2,1:R2-1:R1|RNA1,RNA2,2:pair-2:pair|RNA1,RNA2,5:pair-5:pair|BLOB1,CHEM2,1:R1-1:R2$$$V2.0"
+PEGylated peptide (N-term),Conjugate / CHEM,"PEPTIDE1{A.C.D.E.F}|CHEM1{[PEG2]}$PEPTIDE1,CHEM1,1:R1-1:R2$$$V2.0"
+Peptide with gap (*),Peptide / linear,PEPTIDE1{A.*.C}$$$$
+Asymmetric duplex (21 sense / 19 anti),Nucleic acid / siRNA,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(U)p}|RNA2{r(A)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p}$RNA1,RNA2,2:pair-56:pair|RNA1,RNA2,5:pair-53:pair|RNA1,RNA2,8:pair-50:pair|RNA1,RNA2,11:pair-47:pair|RNA1,RNA2,14:pair-44:pair|RNA1,RNA2,17:pair-41:pair|RNA1,RNA2,20:pair-38:pair|RNA1,RNA2,23:pair-35:pair|RNA1,RNA2,26:pair-32:pair|RNA1,RNA2,29:pair-29:pair|RNA1,RNA2,32:pair-26:pair|RNA1,RNA2,35:pair-23:pair|RNA1,RNA2,38:pair-20:pair|RNA1,RNA2,41:pair-17:pair|RNA1,RNA2,44:pair-14:pair|RNA1,RNA2,47:pair-11:pair|RNA1,RNA2,50:pair-8:pair|RNA1,RNA2,53:pair-5:pair|RNA1,RNA2,56:pair-2:pair$$$V2.0"
+Palindromic self-pairing duplex,Nucleic acid / duplex,"RNA1{r(G)p.r(C)p.r(G)p.r(C)p.r(G)p.r(C)p.r(G)p.r(C)p}|RNA2{r(G)p.r(C)p.r(G)p.r(C)p.r(G)p.r(C)p.r(G)p.r(C)p}$RNA1,RNA2,2:pair-23:pair|RNA1,RNA2,5:pair-20:pair|RNA1,RNA2,8:pair-17:pair|RNA1,RNA2,11:pair-14:pair|RNA1,RNA2,14:pair-11:pair|RNA1,RNA2,17:pair-8:pair|RNA1,RNA2,20:pair-5:pair|RNA1,RNA2,23:pair-2:pair$$$V2.0"
+DNA blunt duplex (10bp),Nucleic acid / duplex,"RNA1{d(A)p.d(C)p.d(G)p.d(T)p.d(A)p.d(C)p.d(G)p.d(T)p.d(A)p.d(C)p}|RNA2{d(G)p.d(T)p.d(A)p.d(C)p.d(G)p.d(T)p.d(A)p.d(C)p.d(G)p.d(T)p}$RNA1,RNA2,2:pair-29:pair|RNA1,RNA2,5:pair-26:pair|RNA1,RNA2,8:pair-23:pair|RNA1,RNA2,11:pair-20:pair|RNA1,RNA2,14:pair-17:pair|RNA1,RNA2,17:pair-14:pair|RNA1,RNA2,20:pair-11:pair|RNA1,RNA2,23:pair-8:pair|RNA1,RNA2,26:pair-5:pair|RNA1,RNA2,29:pair-2:pair$$$V2.0"
+Tricyclic peptide (3 disulfide bridges),Peptide / multicyclic,"PEPTIDE1{C.A.C.A.C.A.C.A.C.A.C.A}$PEPTIDE1,PEPTIDE1,1:R3-5:R3|PEPTIDE1,PEPTIDE1,3:R3-9:R3|PEPTIDE1,PEPTIDE1,7:R3-11:R3$$$V2.0"
+Lasso peptide (macrolactam + tail),Peptide / cyclic,"PEPTIDE1{A.C.D.E.F.G.H.I}$PEPTIDE1,PEPTIDE1,4:R2-1:R1$$$V2.0"
+RNA 40-mer single strand,Nucleic acid / single,RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$$$$V2.0
+Two peptides bridged by one disulfide,Peptide / multicyclic,"PEPTIDE1{A.C.D.E}|PEPTIDE2{F.G.C.H}$PEPTIDE1,PEPTIDE2,2:R3-3:R3$$$V2.0"
+"siRNA 25-mer, 2-nt 3′ overhangs",Nucleic acid / siRNA,"RNA1{r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p}|RNA2{r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p}$RNA1,RNA2,2:pair-71:pair|RNA1,RNA2,5:pair-68:pair|RNA1,RNA2,8:pair-65:pair|RNA1,RNA2,11:pair-62:pair|RNA1,RNA2,14:pair-59:pair|RNA1,RNA2,17:pair-56:pair|RNA1,RNA2,20:pair-53:pair|RNA1,RNA2,23:pair-50:pair|RNA1,RNA2,26:pair-47:pair|RNA1,RNA2,29:pair-44:pair|RNA1,RNA2,32:pair-41:pair|RNA1,RNA2,35:pair-38:pair|RNA1,RNA2,38:pair-35:pair|RNA1,RNA2,41:pair-32:pair|RNA1,RNA2,44:pair-29:pair|RNA1,RNA2,47:pair-26:pair|RNA1,RNA2,50:pair-23:pair|RNA1,RNA2,53:pair-20:pair|RNA1,RNA2,56:pair-17:pair|RNA1,RNA2,59:pair-14:pair|RNA1,RNA2,62:pair-11:pair|RNA1,RNA2,65:pair-8:pair|RNA1,RNA2,68:pair-5:pair$$$V2.0"
+"Hairpin, long apical loop",Nucleic acid / structure,"RNA1{r(G)p.r(C)p.r(G)p.r(A)p.r(A)p.r(A)p.r(A)p.r(A)p.r(A)p.r(C)p.r(G)p.r(C)p}$RNA1,RNA1,2:pair-35:pair|RNA1,RNA1,5:pair-32:pair|RNA1,RNA1,8:pair-29:pair$$$V2.0"
+Peptide–PEG2–RNA triple conjugate,Conjugate / mixed,"PEPTIDE1{A.C.D.E.F}|RNA1{r(A)p.r(C)p.r(G)p}|CHEM1{[PEG2]}$PEPTIDE1,CHEM1,5:R2-1:R1|CHEM1,RNA1,1:R2-1:R1$$$V2.0"

package/package.json

@@ -1,24 +1,19 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.13.8",
+  "version": "3.0.0",
   "author": {
     "name": "Maria Dolotova",
     "email": "mdolotova@datagrok.ai"
   },
   "description": "Provides support for HELM notation (importing, detecting, rendering, conversion).",
-  "sources-backup": [
-    "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js.uncompressed.js",
-    "helm/JSDraw/Scilligence.JSDraw2.Lite-uncompressed.js",
-    "helm/JSDraw/Pistoia.HELM-uncompressed.js"
-  ],
   "sources": [
     "css/helm.css"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.65.2",
+    "@datagrok-libraries/bio": "^6.0.0",
     "@datagrok-libraries/chem-meta": "^1.2.9",
-    "@datagrok-libraries/helm-web-editor": "^1.1.16",
+    "@datagrok-libraries/hwe": "^1.0.0",
     "@datagrok-libraries/utils": "^4.6.9",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.26.0",
@@ -29,7 +24,6 @@
     "@datagrok-libraries/test": "^1.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/bio": "^2.25.1",
     "@datagrok/chem": "^1.17.0",
     "@types/node": "17.0.45",
@@ -37,13 +31,15 @@
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^7.16.0",
     "@typescript-eslint/parser": "^7.16.0",
-    "datagrok-tools": "^5.0.0",
+    "css-loader": "^6.7.3",
+    "datagrok-tools": "^6.3.0",
     "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-deprecation": "^3.0.0",
     "eslint-plugin-rxjs": "^5.0.3",
     "path": "^0.12.7",
     "source-map-loader": "^5.0.0",
+    "style-loader": "^3.3.1",
     "ts-loader": "^9.5.1",
     "typescript": "^5.6.3",
     "webpack": "^5.76.3",