record_composition
Read-only
What the subject record is MADE OF: molecular weight under its own topology and strand count, GC and AT over the resolved bases, and the per-symbol census with the ambiguity codes broken out. The nucleic-acid counterpart of protein_properties, and the same derivation the editor's Properties panel, its inspector and the alignment inspector all draw (Biopython's mass model; ProtParam for a protein subject).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| doubleStranded | No | weigh BOTH strands (a plasmid or any dsDNA record) rather than the one strand written in the file (an oligo, an RNA, an alignment row). The two answers differ by about a factor of two, which is why it is a parameter and not a guess. Defaults to true, or false when the record is RNA (U and no T), which is also weighed with RNA residue masses. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| length | Yes | symbols in the record, non-standard ones included | |
| strands | Yes | how many strands the mass was taken over: 2, 1, or 0 for a protein where the question does not arise | |
| atPercent | Yes | percent A+T over the same denominator. Null for a protein | |
| gcPercent | Yes | percent G+C over the RESOLVED A/C/G/T bases (`standardCount`), which is Biopython's gc_fraction default (ambiguous="remove") — not over the full length, so it complements `atPercent` exactly. Null for a protein | |
| extinction | Yes | protein subjects only: e280 under both cystine conventions; null otherwise | |
| composition | Yes | one row per standard symbol: code, label, count, and its percent of `standardCount` | |
| nonStandard | Yes | the symbols the alphabet does not define — Ns, IUPAC ambiguity codes, gaps — with counts and NO share, because they are excluded from the denominator | |
| standardCount | Yes | how many of `length` are standard — the denominator every share here is over | |
| molecularWeight | Yes | molecular weight — g/mol for a nucleic acid under `doubleStranded` and the record's own topology, Da for a protein | |
| isoelectricPoint | Yes | protein subjects only (ProtParam, Bjellqvist); null otherwise |