From 5e2626ed43ae66fbb63b4daafb50b70a9117acaa Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Tue, 2 Jan 2024 10:19:27 +0100
Subject: [PATCH] fix: SCHWED-6108 read other as CHAINTYPE_POLY
This allows the mmCIF writer to save the entity_poly.type as "other"
rater than error on an unknown type.
We can do this because there is no "other" in _entity_poly.type.
Added a comment about the risks of chain_type for reading/writing mmCIF
files.
---
modules/mol/base/src/chain_type.cc | 4 +++-
modules/mol/base/src/chain_type.hh | 5 +++++
2 files changed, 8 insertions(+), 1 deletion(-)
diff --git a/modules/mol/base/src/chain_type.cc b/modules/mol/base/src/chain_type.cc
index 6694aa017..0820407c7 100644
--- a/modules/mol/base/src/chain_type.cc
+++ b/modules/mol/base/src/chain_type.cc
@@ -59,7 +59,9 @@ ChainType ChainTypeFromString(StringRef identifier)
} else if (StringRef("oligosaccharide", 15) == identifier) {
return CHAINTYPE_OLIGOSACCHARIDE;
} else if (StringRef("other", 5) == identifier) {
- return CHAINTYPE_UNKNOWN;
+ // According to the mmCIF dictionary, "other" only exists in
+ // _entity_poly.type. Therefore, "other" can only be a generic polymer.
+ return CHAINTYPE_POLY;
}
throw Error("Unrecognised chain type descriptor found: '" +
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
index 08ce4dcc6..27e1910e6 100644
--- a/modules/mol/base/src/chain_type.hh
+++ b/modules/mol/base/src/chain_type.hh
@@ -28,6 +28,11 @@
namespace ost { namespace mol {
/// \enum different kinds of chains
+///
+/// Warning: this class mixes vocabulary from _entity.type and
+// _entity_poly.type, which is more detailed. As a result it cannot be used to
+/// to read/write mmCIF entity types accurately.
+
typedef enum {
CHAINTYPE_POLY, ///< polymer
CHAINTYPE_NON_POLY, ///< non-polymer
--
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