From a002412aecdab94015351ccbb50e27f691279663 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Tue, 9 Apr 2019 11:44:36 +0200
Subject: [PATCH] Ignore missing
(struct_conf|struct_sheet_range).(beg|end)_label_seq_id data item in
fault_tolerant mode of mmCIF reader.
---
modules/io/src/mol/mmcif_reader.cc | 31 ++++++++++++++++++++++--------
1 file changed, 23 insertions(+), 8 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 5ed09e1ed..a232e3711 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -1312,10 +1312,18 @@ void MMCifReader::ParseStructConf(const std::vector<StringRef>& columns)
if (restrict_chains_.size() == 0 ||
restrict_chains_.find(chain_name.str()) != String::npos) {
// fetch start and end
- s_res_num = this->TryGetInt(columns[indices_[SC_BEG_LABEL_SEQ_ID]],
- "struct_conf.beg_label_seq_id");
- e_res_num = this->TryGetInt(columns[indices_[SC_END_LABEL_SEQ_ID]],
- "struct_conf.end_label_seq_id");
+ std::pair<bool,int> s_beg = this->TryGetInt(columns[indices_[SC_BEG_LABEL_SEQ_ID]], // s_res_num
+ "struct_conf.beg_label_seq_id",
+ profile_.fault_tolerant);
+ std::pair<bool,int> s_end = this->TryGetInt(columns[indices_[SC_END_LABEL_SEQ_ID]], // e_res_num
+ "struct_conf.end_label_seq_id",
+ profile_.fault_tolerant);
+ if (!(s_beg.first && s_end.first)) {
+ return;
+ }
+ s_res_num = s_beg.second;
+ e_res_num = s_end.second;
+
MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
to_res_num(e_res_num, ' '),
chain_name.str()};
@@ -1353,10 +1361,17 @@ void MMCifReader::ParseStructSheetRange(const std::vector<StringRef>& columns)
if (restrict_chains_.size() == 0 ||
restrict_chains_.find(chain_name.str()) != String::npos) {
- s_res_num = this->TryGetInt(columns[indices_[SSR_BEG_LABEL_SEQ_ID]],
- "struct_sheet_range.beg_label_seq_id");
- e_res_num = this->TryGetInt(columns[indices_[SSR_END_LABEL_SEQ_ID]],
- "struct_sheet_range.end_label_seq_id");
+ std::pair<bool,int> s_beg = this->TryGetInt(columns[indices_[SSR_BEG_LABEL_SEQ_ID]], // s_res_num
+ "struct_sheet_range.beg_label_seq_id",
+ profile_.fault_tolerant);
+ std::pair<bool,int> s_end = this->TryGetInt(columns[indices_[SSR_END_LABEL_SEQ_ID]], // e_res_num
+ "struct_sheet_range.end_label_seq_id",
+ profile_.fault_tolerant);
+ if (!(s_beg.first && s_end.first)) {
+ return;
+ }
+ s_res_num = s_beg.second;
+ e_res_num = s_end.second;
MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
to_res_num(e_res_num, ' '),
--
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