From 9825e096159cb08555a8eeba61439d8e8ff412f2 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 21 Dec 2023 11:31:35 +0100
Subject: [PATCH] mmcif writer: Use controlled vocabulary for _chem_comp.type
---
modules/io/src/mol/mmcif_writer.cc | 31 +++++++++++++++---------------
1 file changed, 16 insertions(+), 15 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index faaaa5c05..ccdc1e483 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -288,47 +288,48 @@ namespace {
String type = "";
switch(chem_class) {
case 'P': {
- type = "peptide linking";
+ type = "PEPTIDE LINKING";
break;
}
case 'D': {
- type = "D-peptide linking";
+ type = "D-PEPTIDE LINKING";
break;
}
case 'L': {
- type = "L-peptide linking";
+ type = "L-PEPTIDE LINKING";
break;
}
case 'R': {
- type = "RNA linking";
+ type = "RNA LINKING";
break;
}
case 'S': {
- type = "DNA linking";
+ type = "DNA LINKING";
break;
}
case 'N': {
- type = "non-polymer";
+ type = "NON-POLYMER";
break;
}
case 'X': {
- type = "L-saccharide";
+ type = "L-SACCHARIDE";
break;
}
case 'Y': {
- type = "D-saccharide";
+ type = "D-SACCHARIDE";
break;
}
case 'Z': {
- type = "saccharide";
+ type = "SACCHARIDE";
break;
}
case 'W': {
- type = "non-polymer";
+ type = "NON-POLYMER"; // yes, water is a non-polymer
+ // https://www.rcsb.org/ligand/HOH
break;
}
case 'U': {
- type = "non-polymer";
+ type = "OTHER";
break;
}
default: {
@@ -1164,7 +1165,7 @@ namespace {
const std::map<String, CompInfo>& comp_infos) {
std::vector<ost::io::StarWriterLoopDataItem> comp_data;
comp_data.push_back(ost::io::StarWriterLoopDataItem("ALA"));
- comp_data.push_back(ost::io::StarWriterLoopDataItem("L-peptide linking"));
+ comp_data.push_back(ost::io::StarWriterLoopDataItem("L-PEPTIDE LINKING"));
for(auto it = comp_infos.begin(); it != comp_infos.end(); ++it) {
comp_data[0] = it->first;
comp_data[1] = it->second.type;
@@ -1351,7 +1352,7 @@ namespace {
entity_infos[entity_idx].seq_can_olcs[mon_id_idx] = "X";
if(comp_infos.find("UNK") == comp_infos.end()) {
CompInfo info;
- info.type = "L-peptide linking";
+ info.type = "L-PEPTIDE LINKING";
comp_infos["UNK"] = info;
}
}
@@ -1362,7 +1363,7 @@ namespace {
entity_infos[entity_idx].seq_can_olcs[mon_id_idx] = "N";
if(comp_infos.find("DN") == comp_infos.end()) {
CompInfo info;
- info.type = "DNA linking";
+ info.type = "DNA LINKING";
comp_infos["DN"] = info;
}
}
@@ -1373,7 +1374,7 @@ namespace {
entity_infos[entity_idx].seq_can_olcs[mon_id_idx] = "N";
if(comp_infos.find("N") == comp_infos.end()) {
CompInfo info;
- info.type = "RNA linking";
+ info.type = "RNA LINKING";
comp_infos["N"] = info;
}
}
--
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