diff --git a/src/nplinker/genomics/bgc.py b/src/nplinker/genomics/bgc.py index f1eb0635..08978587 100644 --- a/src/nplinker/genomics/bgc.py +++ b/src/nplinker/genomics/bgc.py @@ -35,7 +35,7 @@ class BGC: gives product information. For MIBiG metadata, its biosynthetic class provides such info. mibig_bgc_class: A tuple of MIBiG biosynthetic classes to which the BGC belongs. - Defaults to None. + Defaults to None, which means the class is unknown. MIBiG defines 6 major biosynthetic classes for natural products, including `NRP`, `Polyketide`, `RiPP`, `Terpene`, `Saccharide` @@ -142,7 +142,21 @@ def bigscape_classes(self) -> set[str | None]: """Get BiG-SCAPE's BGC classes. BiG-SCAPE's BGC classes are similar to those defined in MiBIG but have - more categories (7 classes). More details see: + more categories (7 classes), including: + + - NRPS + - PKS-NRP_Hybrids + - PKSI + - PKSother + - RiPPs + - Saccharides + - Terpene + + For BGC falls outside of these categories, the value is "Others". + + Default is None, which means the class is unknown. + + More details see: https://doi.org/10.1038%2Fs41589-019-0400-9. """ return {p.bigscape_class for p in self.parents} diff --git a/src/nplinker/genomics/gcf.py b/src/nplinker/genomics/gcf.py index 3a1759c4..33e38a4d 100644 --- a/src/nplinker/genomics/gcf.py +++ b/src/nplinker/genomics/gcf.py @@ -22,7 +22,21 @@ class GCF: bgc_ids: a set of BGC ids that belongs to the GCF. bigscape_class: BiG-SCAPE's BGC class. BiG-SCAPE's BGC classes are similar to those defined in MiBIG - but have more categories (7 classes). More details see: + but have more categories (7 classes), including: + + - NRPS + - PKS-NRP_Hybrids + - PKSI + - PKSother + - RiPPs + - Saccharides + - Terpene + + For BGC falls outside of these categories, the value is "Others". + + Default is None, which means the class is unknown. + + More details see: https://doi.org/10.1038%2Fs41589-019-0400-9. """