From acca041d290120f868c8e71994e44b5f1f1b8880 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 15 Feb 2023 17:43:53 +0100
Subject: [PATCH] OMF - raw data access for per residue bfactor averages
---
modules/io/pymod/export_omf_io.cc | 1 +
modules/io/src/mol/omf.cc | 25 +++++++++++++++++++++++++
modules/io/src/mol/omf.hh | 2 ++
3 files changed, 28 insertions(+)
diff --git a/modules/io/pymod/export_omf_io.cc b/modules/io/pymod/export_omf_io.cc
index fb98237b0..43355a4a9 100644
--- a/modules/io/pymod/export_omf_io.cc
+++ b/modules/io/pymod/export_omf_io.cc
@@ -77,6 +77,7 @@ void export_omf_io() {
.def("GetChainNames", &wrap_get_chain_names)
.def("GetPositions", &OMF::GetPositions, return_value_policy<reference_existing_object>(),(arg("cname")))
.def("GetBFactors", &OMF::GetBFactors, return_value_policy<reference_existing_object>(),(arg("cname")))
+ .def("GetAvgBFactors", &OMF::GetAvgBFactors,(arg("cname")))
.def("GetSequence", &OMF::GetSequence, (arg("cname")))
;
}
diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc
index 973595161..91fdca413 100644
--- a/modules/io/src/mol/omf.cc
+++ b/modules/io/src/mol/omf.cc
@@ -3833,6 +3833,31 @@ const std::vector<Real>& OMF::GetBFactors(const String& cname) const {
return it->second->bfactors;
}
+std::vector<Real> OMF::GetAvgBFactors(const String& cname) const {
+ auto it = chain_data_.find(cname);
+ if(it == chain_data_.end()) {
+ throw ost::Error("Provided chain name not in OMF structure");
+ }
+ const std::vector<Real>& bfactors = it->second->bfactors;
+ const std::vector<int>& res_def_indices = it->second->res_def_indices;
+ std::vector<Real> avg_bfactors;
+ avg_bfactors.reserve(it->second->res_def_indices.size());
+ int current_atom_idx = 0;
+ for(auto i = res_def_indices.begin(); i != res_def_indices.end(); ++i) {
+ int size = residue_definitions_[*i].anames.size();
+ Real summed_bfac = 0.0;
+ for(int j = 0; j < size; ++j) {
+ summed_bfac += bfactors[current_atom_idx];
+ ++current_atom_idx;
+ }
+ if(size > 0) {
+ summed_bfac /= size;
+ }
+ avg_bfactors.push_back(summed_bfac);
+ }
+ return avg_bfactors;
+}
+
String OMF::GetSequence(const String& cname) const {
auto it = chain_data_.find(cname);
if(it == chain_data_.end()) {
diff --git a/modules/io/src/mol/omf.hh b/modules/io/src/mol/omf.hh
index f5bb8b996..9503b1f54 100644
--- a/modules/io/src/mol/omf.hh
+++ b/modules/io/src/mol/omf.hh
@@ -199,6 +199,8 @@ public:
const std::vector<Real>& GetBFactors(const String& cname) const;
+ std::vector<Real> GetAvgBFactors(const String& cname) const;
+
String GetSequence(const String& cname) const;
private:
--
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