From 445c2c42d81d8f67fc952e0913e4e7a5ac9aa98b Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 6 Jun 2024 15:17:57 +0200
Subject: [PATCH] doc: items were checked to be mandatory/optional per mmCIF
dictionary
---
modules/io/src/mol/mmcif_reader.cc | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index f4e2057b0..f04e15f37 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -301,27 +301,31 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
cat_available = true;
} else if (header.GetCategory() == "struct_ref") {
category_ = STRUCT_REF;
+ // mandatory items
this->TryStoreIdx(SR_ENTITY_ID, "entity_id", header);
this->TryStoreIdx(SR_ID, "id", header);
this->TryStoreIdx(SR_DB_NAME, "db_name", header);
this->TryStoreIdx(SR_DB_CODE, "db_code", header);
+ // optional items
indices_[SR_DB_ACCESS]=header.GetIndex("pdbx_db_accession");
cat_available = true;
} else if (header.GetCategory() == "struct_ref_seq") {
- category_ = STRUCT_REF_SEQ;
+ category_ = STRUCT_REF_SEQ;
+ // mandatory items
this->TryStoreIdx(SRS_ALIGN_ID, "align_id", header);
this->TryStoreIdx(SRS_STRUCT_REF_ID, "ref_id", header);
this->TryStoreIdx(SRS_ENT_ALIGN_BEG, "seq_align_beg", header);
this->TryStoreIdx(SRS_ENT_ALIGN_END, "seq_align_end", header);
this->TryStoreIdx(SRS_DB_ALIGN_BEG, "db_align_beg", header);
this->TryStoreIdx(SRS_DB_ALIGN_END, "db_align_end", header);
+ // optional items
indices_[SRS_PDBX_STRAND_ID]=header.GetIndex("pdbx_strand_id");
cat_available = true;
} else if (header.GetCategory()=="struct_ref_seq_dif") {
category_ = STRUCT_REF_SEQ_DIF;
- // mandatory
+ // mandatory items
this->TryStoreIdx(SRSD_ALIGN_ID, "align_id", header);
- // optional
+ // optional items
indices_[SRSD_SEQ_RNUM]=header.GetIndex("seq_num");
indices_[SRSD_DB_RNUM]=header.GetIndex("pdbx_seq_db_seq_num");
indices_[SRSD_DETAILS]=header.GetIndex("details");
--
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