From 766884be4fb3728291fee75860b5e4a749913085 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 Jan 2024 11:30:22 +0100
Subject: [PATCH] mmcif writer: CHAINTYPE_OLIGOSACCHARIDE is strictly
entity.type 'branched'
---
modules/io/src/mol/mmcif_writer.cc | 6 +++---
modules/mol/base/src/chain_type.cc | 2 ++
modules/mol/base/src/chain_type.hh | 3 ++-
3 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 59d30f2e0..be209e559 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -241,15 +241,15 @@ namespace {
case ost::mol::CHAINTYPE_POLY_PEPTIDE_L: return "polymer";
case ost::mol::CHAINTYPE_POLY_DN: return "polymer";
case ost::mol::CHAINTYPE_POLY_RN: return "polymer";
- case ost::mol::CHAINTYPE_POLY_SAC_D: return "polymer"; // branched?
- case ost::mol::CHAINTYPE_POLY_SAC_L: return "polymer"; // branched?
+ case ost::mol::CHAINTYPE_POLY_SAC_D: return "polymer";
+ case ost::mol::CHAINTYPE_POLY_SAC_L: return "polymer";
case ost::mol::CHAINTYPE_POLY_DN_RN: return "polymer";
case ost::mol::CHAINTYPE_UNKNOWN: return "unknown";
case ost::mol::CHAINTYPE_MACROLIDE: return "macrolide";
case ost::mol::CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE: return "polymer";
case ost::mol::CHAINTYPE_POLY_PEPTIDE_DN_RN: return "polymer";
case ost::mol::CHAINTYPE_BRANCHED: return "branched";
- case ost::mol::CHAINTYPE_OLIGOSACCHARIDE: return "polymer"; // branched?
+ case ost::mol::CHAINTYPE_OLIGOSACCHARIDE: return "branched";
default: return "unknown";
}
}
diff --git a/modules/mol/base/src/chain_type.cc b/modules/mol/base/src/chain_type.cc
index 8b1c444bc..7604bbc50 100644
--- a/modules/mol/base/src/chain_type.cc
+++ b/modules/mol/base/src/chain_type.cc
@@ -108,8 +108,10 @@ String StringFromChainType(ChainType type)
return "cyclic-pseudo-peptide";
} else if (CHAINTYPE_POLY_PEPTIDE_DN_RN == type) {
return "peptide nucleic acid";
+ // chain types as found in the pdbx_entity_branch category of a mmcif file
} else if (CHAINTYPE_OLIGOSACCHARIDE == type) {
return "oligosaccharide";
+ // other...
} else if (CHAINTYPE_UNKNOWN == type) {
return "other";
}
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
index f062606ec..839844827 100644
--- a/modules/mol/base/src/chain_type.hh
+++ b/modules/mol/base/src/chain_type.hh
@@ -50,7 +50,8 @@ typedef enum {
CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE, ///< cyclic-pseudo-peptide
CHAINTYPE_POLY_PEPTIDE_DN_RN, ///< peptide nucleic acid
CHAINTYPE_BRANCHED, ///< carbohydrate
- CHAINTYPE_OLIGOSACCHARIDE, ///< oligosaccharide (branched carbohydrate)
+ CHAINTYPE_OLIGOSACCHARIDE, ///< oligosaccharide (branched carbohydrate,
+ ///< i.e. _entity.type is strictly 'branched')
CHAINTYPE_N_CHAINTYPES ///< no. of chain types
} ChainType;
--
GitLab