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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"MMCif behavior when auth_seq_id is missing","articleBody":"A discussion came up in PR #774 regarding the correct behavior when parsing an mmCif file without `auth_seq_id`.\r\n\r\nBioJava 4.2.11 requires the `auth_seq_id` column. This is a problem because it is optional according to the spec and omitted by PyMOL.\r\n\r\nIn b207d34 I added code to use the `label_seq_id` column for creating the ResidueNumber for each group if `auth_seq_id` is missing. There was some concern that this could lead to inconsistent residue numbers if some residues used '?' (defaulting to `label_`) while the rest used the `auth_` values specified. This worry is actually not justified due to *another* bug, which causes a NumberFormatException if '?' is used in that column.\r\n\r\n@josemduarte suggested only doing the `label_` fallback if ALL groups have null ResidueNumbers. This is probably the right solution, but it seems like such an edge case it might not be worth the hour it will take to fix it.","author":{"url":"https://github.com/sbliven","@type":"Person","name":"sbliven"},"datePublished":"2018-06-15T10:23:10.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":11},"url":"https://github.com/775/biojava/issues/775"}