From 2c14a4a91a076063bce0ffcb974f5fb0356f52e7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 24 Mar 2021 12:35:48 +0100
Subject: [PATCH] reduce code duplication and use PagedArray from ost
---
loop/src/CMakeLists.txt | 1 -
loop/src/frag_db.cc | 2 +-
loop/src/frag_db.hh | 1 -
loop/src/fragger.cc | 14 +++++++-------
loop/src/fragger.hh | 2 +-
loop/src/structure_db.hh | 34 +++++++++++++++++-----------------
6 files changed, 26 insertions(+), 28 deletions(-)
diff --git a/loop/src/CMakeLists.txt b/loop/src/CMakeLists.txt
index 6c874f58..39da6810 100644
--- a/loop/src/CMakeLists.txt
+++ b/loop/src/CMakeLists.txt
@@ -17,7 +17,6 @@ set(LOOP_HEADERS
idx_handler.hh
loop_object_loader.hh
mm_system_creator.hh
- paged_array.hh
psipred_prediction.hh
stem_geom.hh
structure_db.hh
diff --git a/loop/src/frag_db.cc b/loop/src/frag_db.cc
index 4e0bfdd7..8467f5cc 100644
--- a/loop/src/frag_db.cc
+++ b/loop/src/frag_db.cc
@@ -258,7 +258,7 @@ void FragDB::AddFragments(uint fragment_length,
//extract all stem information of this chain to create the
//stem geoms later on
- const PagedArray<PeptideCoords, 65536>& db_coords = structure_db->GetCoords();
+ const ost::PagedArray<PeptideCoords, 65536>& db_coords = structure_db->GetCoords();
stem_coords.clear();
for(uint j = 0; j < size; ++j){
const PeptideCoords& coords = db_coords[offset + j];
diff --git a/loop/src/frag_db.hh b/loop/src/frag_db.hh
index 8deb7b19..75195312 100644
--- a/loop/src/frag_db.hh
+++ b/loop/src/frag_db.hh
@@ -28,7 +28,6 @@
#include <ost/mol/entity_view.hh>
#include <ost/mol/mol.hh>
-#include <promod3/loop/paged_array.hh>
#include <promod3/loop/data_bag.hh>
#include <promod3/loop/ushort_vec.hh>
#include <promod3/loop/structure_db.hh>
diff --git a/loop/src/fragger.cc b/loop/src/fragger.cc
index 7f5ed5d1..fa1054ed 100644
--- a/loop/src/fragger.cc
+++ b/loop/src/fragger.cc
@@ -500,14 +500,14 @@ void Fragger::FillProfiles(StructureDBPtr db,
break;
}
case SequenceProfile:{
- const PagedArray<AAFreq, 65536>& frequencies =
+ const ost::PagedArray<AAFreq, 65536>& frequencies =
db->GetAAFrequencies();
this->GenerateProfileProfile(db, profiles[i], chain_idx, frequencies,
profiles_[i]);
break;
}
case StructureProfile:{
- const PagedArray<AAFreq, 65536>& frequencies =
+ const ost::PagedArray<AAFreq, 65536>& frequencies =
db->GetAAStructFrequencies();
this->GenerateProfileProfile(db, profiles[i], chain_idx, frequencies,
profiles_[i]);
@@ -553,7 +553,7 @@ void Fragger::GenerateSeqSimProfile(StructureDBPtr db,
const ost::seq::alg::SubstWeightMatrix& subst) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<char, 65536>& full_db_seq = db->GetSeq();
+ const ost::PagedArray<char, 65536>& full_db_seq = db->GetSeq();
profile.clear();
@@ -591,7 +591,7 @@ void Fragger::GenerateSeqIDProfile(StructureDBPtr db,
uint index) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<char, 65536>& full_db_seq = db->GetSeq();
+ const ost::PagedArray<char, 65536>& full_db_seq = db->GetSeq();
profile.clear();
@@ -622,7 +622,7 @@ void Fragger::GenerateSSAgreementProfile(StructureDBPtr db,
const std::vector<int>& confidence) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<char, 65536>& full_db_dssp = db->GetDSSP();
+ const ost::PagedArray<char, 65536>& full_db_dssp = db->GetDSSP();
profile.clear();
@@ -658,7 +658,7 @@ void Fragger::GenerateTorsionProbabilityProfile(StructureDBPtr db,
const std::vector<int>& t_sampler_indices) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<DihedralInfo, 65536>& full_db_dihedrals = db->GetDihedrals();
+ const ost::PagedArray<DihedralInfo, 65536>& full_db_dihedrals = db->GetDihedrals();
profile.clear();
@@ -693,7 +693,7 @@ void Fragger::GenerateTorsionProbabilityProfile(StructureDBPtr db,
void Fragger::GenerateProfileProfile(StructureDBPtr db,
std::vector<Real>& profile,
uint index,
- const PagedArray<AAFreq,65536>& frequencies,
+ const ost::PagedArray<AAFreq,65536>& frequencies,
short** prof) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
diff --git a/loop/src/fragger.hh b/loop/src/fragger.hh
index dfe545f4..205f10dc 100644
--- a/loop/src/fragger.hh
+++ b/loop/src/fragger.hh
@@ -134,7 +134,7 @@ private:
void GenerateProfileProfile(StructureDBPtr db, std::vector<Real>& profile,
uint index,
- const PagedArray<AAFreq, 65536>& frequencies,
+ const ost::PagedArray<AAFreq, 65536>& frequencies,
short** prof) const;
diff --git a/loop/src/structure_db.hh b/loop/src/structure_db.hh
index 89395b36..075d0a3f 100644
--- a/loop/src/structure_db.hh
+++ b/loop/src/structure_db.hh
@@ -24,6 +24,7 @@
#include <list>
#include <ost/base.hh>
+#include <ost/paged_array.hh>
#include <ost/fixed_string.hh>
#include <ost/mol/entity_view.hh>
#include <ost/mol/mol.hh>
@@ -34,7 +35,6 @@
#include <ost/seq/profile_handle.hh>
#include <ost/mol/surface_handle.hh>
-#include <promod3/loop/paged_array.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/core/message.hh>
#include <promod3/core/superpose.hh>
@@ -249,15 +249,15 @@ public:
const std::vector<CoordInfo>& GetCoordToc() const { return coord_toc_; }
- const PagedArray<char, 65536>& GetSeq() const {
+ const ost::PagedArray<char, 65536>& GetSeq() const {
return seq_;
}
- const PagedArray<PeptideCoords, 65536>& GetCoords() const {
+ const ost::PagedArray<PeptideCoords, 65536>& GetCoords() const {
return coords_;
}
- const PagedArray<DihedralInfo, 65536>& GetDihedrals() const {
+ const ost::PagedArray<DihedralInfo, 65536>& GetDihedrals() const {
if(!this->HasData(Dihedrals)) {
throw promod3::Error("StructureDB does not contain dihedrals!");
@@ -266,7 +266,7 @@ public:
return dihedrals_;
}
- const PagedArray<unsigned short, 65536>& GetSolvAcc() const {
+ const ost::PagedArray<unsigned short, 65536>& GetSolvAcc() const {
if(!this->HasData(SolventAccessibilities)) {
throw promod3::Error("StructureDB does not contain "
@@ -276,7 +276,7 @@ public:
return solv_acc_;
}
- const PagedArray<unsigned short, 65536>& GetResDepth() const {
+ const ost::PagedArray<unsigned short, 65536>& GetResDepth() const {
if(!this->HasData(ResidueDepths)) {
throw promod3::Error("StructureDB does not contain residue depths!");
@@ -285,7 +285,7 @@ public:
return res_depths_;
}
- const PagedArray<char, 65536>& GetDSSP() const {
+ const ost::PagedArray<char, 65536>& GetDSSP() const {
if(!this->HasData(DSSP)) {
throw promod3::Error("StructureDB does not contain dssp assignments!");
@@ -294,7 +294,7 @@ public:
return dssp_;
}
- const PagedArray<AAFreq, 65536>& GetAAFrequencies() const {
+ const ost::PagedArray<AAFreq, 65536>& GetAAFrequencies() const {
if(!this->HasData(AAFrequencies)) {
throw promod3::Error("StructureDB does not contain amino acid "
@@ -304,7 +304,7 @@ public:
return aa_frequencies_;
}
- const PagedArray<AAFreq, 65536>& GetAAStructFrequencies() const {
+ const ost::PagedArray<AAFreq, 65536>& GetAAStructFrequencies() const {
if(!this->HasData(AAFrequenciesStruct)) {
throw promod3::Error("StructureDB does not contain amino acid "
@@ -336,30 +336,30 @@ private:
std::vector<CoordInfo> coord_toc_;
// one letter codes
- PagedArray<char, 65536> seq_;
+ ost::PagedArray<char, 65536> seq_;
// backbone coordinates
- PagedArray<PeptideCoords, 65536> coords_;
+ ost::PagedArray<PeptideCoords, 65536> coords_;
// phi and psi dihedrals
- PagedArray<DihedralInfo, 65536> dihedrals_;
+ ost::PagedArray<DihedralInfo, 65536> dihedrals_;
// solvent accessibility in A^2 as calculated by Lee & Richards implementation
// in ost
- PagedArray<uint16_t, 65536> solv_acc_;
+ ost::PagedArray<uint16_t, 65536> solv_acc_;
// distance towards closest surface residue in A multiplied by 10 to allow
// accuracy of 0.1
- PagedArray<uint16_t, 65536> res_depths_;
+ ost::PagedArray<uint16_t, 65536> res_depths_;
// dssp state, which is a member of {H,B,E,G,I,T,S}
- PagedArray<char, 65536> dssp_;
+ ost::PagedArray<char, 65536> dssp_;
// Amino acid frequencies as given as input profile
- PagedArray<AAFreq, 65536> aa_frequencies_;
+ ost::PagedArray<AAFreq, 65536> aa_frequencies_;
// Amino acid frequencies as derived from structural information
- PagedArray<AAFreq, 65536> aa_frequencies_struct_;
+ ost::PagedArray<AAFreq, 65536> aa_frequencies_struct_;
};
}}
--
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