xHELM string not accepted

[ClairePA]

I created the following xHELM string and validated it using the toolkit. The editor returns an error 'null' when I try to load it. As the monomer definitions are contained within the file there should be no monomer set incompatibilities.

RNA1{R(A)p.r(C)p.r(G)p.r(U)p}$$$$V2.0 r H4sIAAAAAAAAA52UTWoDMQyF9z6FTyD0a1vL0mSZFmbRG5RSKOn9d/WMHZKJs2g8iEF6wp+fxoPD6ffneP76Pn9iZqZEooUPIUTiNSLexPVx9/jBiBjWSgHZrWXkymuGULsYX+Me8Tg6RTPrmjFkyThHMXA37hQsNEdJoC7SJ9Iss144F20ZJis3lPf/UxjMkZuX5DzpRcBMt29KYMw854VAxbnxkqvPUfqK/r/I7Ukvz0yUUPOe9zwlQUkp99nMaW6iDG6obaJ6WjLjpW7N23unVklGtUo6qlWyUW3SvVrrdNdou+VL76rWooyEKvmo5kj4yC/RyNXthtl7eNmul7DQlhGGhVvGYZFwivH4dgh/nwOM+LUEAAA= r Backbone RNA R1-H R1 H R2-H R2 H R3-OH R3 OH r H4sIAAAAAAAAA52UTWoDMQyF9z6FTyD0a1vL0mSZFmbRG5RSKOn9d/WMHZKJs2g8iEF6wp+fxoPD6ffneP76Pn9iZqZEooUPIUTiNSLexPVx9/jBiBjWSgHZrWXkymuGULsYX+Me8Tg6RTPrmjFkyThHMXA37hQsNEdJoC7SJ9Iss144F20ZJis3lPf/UxjMkZuX5DzpRcBMt29KYMw854VAxbnxkqvPUfqK/r/I7Ukvz0yUUPOe9zwlQUkp99nMaW6iDG6obaJ6WjLjpW7N23unVklGtUo6qlWyUW3SvVrrdNdou+VL76rWooyEKvmo5kj4yC/RyNXthtl7eNmul7DQlhGGhVvGYZFwivH4dgh/nwOM+LUEAAA= r Backbone RNA R1-H R1 H R2-H R2 H R3-OH R3 OH A H4sIAAAAAAAAA6WUQY7CMAxF9zmFTxDZjpPYSwQsYcGCG4xGSIi5/26SFJjSdMGEKqrcX/fpf6etO/xc97fvy+0LMzMlCqK8cw6IgBgAZ+vvMDM4MyK6ehV8SmS1Es8YpFboy12ELbwi1lejsA/CNvFEGD+gaK3IG9kgpSXKE4Vinic6vk8Rb4r54UV1zEujPOdCOuYFvVqkyYuIxlFKe6LNOd2z/T9R8xKmREY8mKjuEbdE0WdOg3uEXljia7Z7dXqXUr4UrOelCqnMqVe577VVtUihJ+SmLnuLJL1apNgTYnO27C1cXVPLj6BT9WF5pm7qu0XuRO4AsD/u3C89s9wSWwQAAA== A Branch RNA R1-H R1 H p H4sIAAAAAAAAA5WQPQ7CMAyFd5/inSCynR/IiNSOBZSBGyCEhMr9N9q0iKTKQCPLcl6cT8+m4f3qx8dzvPNBVYJYd9SOCPCAA7iI34kx4qbMTPONzVTldzFeAhdaQo1oB61/1X4pqrGgXHdRVgfWsPMl5bLPS4z1bPsps4PATd7fexFAc67USbI5b1XX7PVb9ZRNUZKl8pSUBqA/d/QB3UJaRRECAAA= p Backbone RNA R1-OH R1 OH R2-OH R2 OH C H4sIAAAAAAAAA6WRzQ7CIAyA730KnoAUGIwejdtxM9nBNzDGxMz3v1nY4uTnMCdpSPkCHy3A8Hr28/0x37DVWjllGq87ACEoBn7FNohIXDUiQlhp6TgNmZGtXTKUGNgoUkU9MouWOrWc91uUNGhxySwerWU98Wctm6V4l0MdNXlHhyzuU9Xv77JZMLdM+y1GeqL6H132WhR/TZwTysiUlFFTUkY2nkgoI1fuVZHmexm11dt8tTLKDafQuIdJwSBEP3bwBtcnPO2NAwAA C Branch RNA R1-H R1 H G H4sIAAAAAAAAA62UO27DMAyGd52CJxD4kGRqLJqMSYEMuUEQFCjS+2+lH4HqSIOjxBAE+jf1+ScJ2x1+f/a36/ftggMzJZKgvHMOiIEEAP+tcuWc4cyI6Ma74DMOcYzEi6qMEXp7inCENaK9HijkdU353E4Rn4hwppDEoc8Le3mDl0Kp+vJkRRznDpH0UpYTk6v0AkWVl4o09k66VBQfvXxtpyTPmNJ90r1eSkXkA0ftpQSavZQ+L9FpK4VsNNO+Uk2SaV+pJoU616RY55qU6lxqqva5aJOgda4dz3Wu/TWw5Yyo9baGahJVffgY58PuRO4AsD/u3B9fTFBDtwQAAA== G Branch RNA R1-H R1 H U H4sIAAAAAAAAA6WRTQqDMBBG9zlFThAmExMzy1JdasFFb1BKodj77zpR0eZnIakMMj4yz29UDJ93Pz9f8wNaRO20aTx2QkhJS8FPHRcRyTsCgAhPqBy3oTOqtWsHCgIbZawoV2JBhbHlet6ilQELa2ehNss28WeWw5J9l6qNmnSjKovbU22WW40FUst03mKUJ9LFf3Q6C4/jco8oI5NTRk1OGdllIqKMXH5WFymjNjfw23wxGaVnL2FxLyYtBin7sRNfXJLfG40DAAA= U Branch RNA R1-H R1 H

[scilligence]

I save the xhelm as a file, and then try to load it to the demo site. The app complains R is an unknown monomer.

The HELM string is the file is RNA1{R(A)p.r(C)p.r(G)p.r(U)p}$$$$V2.0, where R is not defined in Monomers list.

[ClairePA]

xHELM should be independent of the monomers since they are defined in the monomer list, tried again with a file generated by the web-editor version which is using the old monomer list and it still complains. I think the issue is the mismatch between base64 encoded molfiles expected by the toolkit and non-base64 encoded xHELM file generated by the web-editor. The HELM notation currently specifies base64 encoding. Discussing with Tianhong.

[scilligence]

The web editor does accept both base64-encoded and plaintext mol string

[ClairePA]

It does accept both formats, but needs to create the encoded version. I am using the version via these links http://elncloud.com/helm/helm/index.htm and it is giving me a non-encoded file.

[ClairePA]

Confirmed fixed. xHELM can be generated and read into both editors and new monomers are recognised. Perfect.