From e350a7e9e03f6cebb973d2420d506d644d293d05 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 Jan 2024 13:48:52 +0100
Subject: [PATCH] mmcif writer: cleanup
---
modules/io/src/mol/mmcif_writer.cc | 41 +++++++++++++++---------------
1 file changed, 21 insertions(+), 20 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 3cfd364d3..35dd15c6b 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -470,6 +470,25 @@ namespace {
}
}
+ bool MatchEntity(const ost::mol::ResidueHandleList& res_list,
+ const ost::io::MMCifWriterEntity& info) {
+ // checks if the residue names in res_list are an exact match
+ // with mon_ids in info
+ std::vector<String> mon_ids;
+ for(auto res : res_list) {
+ mon_ids.push_back(res.GetName());
+ }
+ return mon_ids == info.mon_ids;
+ }
+
+ void AddAsym(const String& asym_chain_name,
+ ost::io::MMCifWriterEntity& info) {
+ // adds asym_chain_name to info under the assumption that mon_ids
+ // exactly match => just add a copy of mon_ids to asym_alns
+ info.asym_ids.push_back(asym_chain_name);
+ info.asym_alns.push_back(info.mon_ids);
+ }
+
bool MatchEntityResnum(const ost::mol::ResidueHandleList& res_list,
const ost::io::MMCifWriterEntity& info,
Real beyond_frac = 0.05) {
@@ -521,25 +540,6 @@ namespace {
}
}
- bool MatchEntity(const ost::mol::ResidueHandleList& res_list,
- const ost::io::MMCifWriterEntity& info) {
- // checks if the residue names in res_list are an exact match
- // with mon_ids in info
- std::vector<String> mon_ids;
- for(auto res : res_list) {
- mon_ids.push_back(res.GetName());
- }
- return mon_ids == info.mon_ids;
- }
-
- void AddAsym(const String& asym_chain_name,
- ost::io::MMCifWriterEntity& info) {
- // adds asym_chain_name to info under the assumption that mon_ids
- // exactly match => just add a copy of mon_ids to asym_alns
- info.asym_ids.push_back(asym_chain_name);
- info.asym_alns.push_back(info.mon_ids);
- }
-
void AddAsymResnum(const String& asym_chain_name,
const ost::mol::ResidueHandleList& res_list,
ost::io::MMCifWriterEntity& info) {
@@ -729,7 +729,8 @@ namespace {
const ost::mol::ResidueHandleList& res_list,
bool resnum_alignment,
std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
-
+ // use chem types in res_list to determine _entity.type and
+ // _entity_poly.type
String type = GuessEntityType(res_list);
bool is_poly = type == "polymer";
String poly_type = "";
--
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