From 6d8cecbb7f462660acf8b93ab6c0cc2bbb5fdceb Mon Sep 17 00:00:00 2001 From: Timofei Ermak Date: Wed, 21 Jul 2021 22:18:14 +0300 Subject: [PATCH] ASN hydrogen almost right names added to support correct bond restoring (#58) * Added ASN hydrogen names sometimes set by Scho --- ChangeLog.md | 4 ++++ package.yaml | 2 +- src/Bio/PDB/BondRestoring.hs | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 815fa65..9aa6c13 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -2,6 +2,10 @@ ## [Unreleased] +## [0.1.3.23] - 2021-07-06 +### Added +Added ASN hydrogen names sometimes set by Scho + ## [0.1.3.22] - 2021-07-06 ### Changed - `*` -> `Type` for GHC-9. diff --git a/package.yaml b/package.yaml index 8a094ca..9e39b72 100644 --- a/package.yaml +++ b/package.yaml @@ -1,5 +1,5 @@ name: cobot-io -version: 0.1.3.22 +version: 0.1.3.23 github: "biocad/cobot-io" license: BSD3 category: Bio diff --git a/src/Bio/PDB/BondRestoring.hs b/src/Bio/PDB/BondRestoring.hs index f246b4a..fec3908 100644 --- a/src/Bio/PDB/BondRestoring.hs +++ b/src/Bio/PDB/BondRestoring.hs @@ -168,7 +168,7 @@ caCbBonds aminoacid = case aminoacid of sideChainBonds :: Text -> [(Text, Text)] sideChainBonds "ALA" = bwhMany [("CB", ["HB1", "HB2", "HB3"])] sideChainBonds "ARG" = [("CB", "CG"), ("CG", "CD"), ("CD", "NE"), ("NE", "CZ"), ("CZ", "NH2"), ("CZ", "NH1")] ++ bwhMany[("CB", ["HB3", "HB2"]), ("CG", ["HG3", "HG2"]), ("CD", ["HD3", "HD2"]), ("NE", ["HE"]), ("NH1", ["HH12", "HH11"]), ("NH2", ["HH22", "HH21"])] -sideChainBonds "ASN" = [("CB", "CG"), ("CG", "OD1"), ("CG", "ND2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("ND2", ["HD22", "HD21"])] +sideChainBonds "ASN" = [("CB", "CG"), ("CG", "OD1"), ("CG", "ND2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("ND2", ["HD22", "HD21"]), ("ND2", ["HD2", "HD1"])] sideChainBonds "ASP" = [("CB", "CG"), ("CG", "OD1"), ("CG", "OD2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("OD2", ["HD2"])] -- in fact, these are bonds for ASH, but sometimes ASH called just ASP... sideChainBonds "ASH" = [("CB", "CG"), ("CG", "OD1"), ("CG", "OD2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("OD2", ["HD2"])] sideChainBonds "CYS" = [("CB", "SG")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("SG", ["HG"])]