From c0c46ec3f4dc4d344f13d4e63d80eb9a2555d29f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 3 Feb 2016 14:45:25 +0100
Subject: [PATCH] make saving/loading or rotamer libraries faster
---
sidechain/src/bb_dep_rotamer_lib.cc | 11 +++--------
sidechain/src/rotamer_lib.cc | 8 ++------
sidechain/src/rotamer_lib_entry.hh | 12 ------------
3 files changed, 5 insertions(+), 26 deletions(-)
diff --git a/sidechain/src/bb_dep_rotamer_lib.cc b/sidechain/src/bb_dep_rotamer_lib.cc
index 8637c35a..357a5ce2 100644
--- a/sidechain/src/bb_dep_rotamer_lib.cc
+++ b/sidechain/src/bb_dep_rotamer_lib.cc
@@ -133,10 +133,7 @@ void BBDepRotamerLib::Save(const String& filename){
}
out_stream.write(reinterpret_cast<char*>(&total_num_rotamers_),sizeof(uint64_t));
- for(uint i = 0; i < total_num_rotamers_; ++i){
- out_stream << static_data_[i];
- }
-
+ out_stream.write(reinterpret_cast<char*>(&static_data_[0]),total_num_rotamers_ * sizeof(RotamerLibEntry));
out_stream.close();
}
@@ -198,10 +195,8 @@ BBDepRotamerLibPtr BBDepRotamerLib::Load(const String& filename){
in_stream.read(reinterpret_cast<char*>(&p->total_num_rotamers_),sizeof(uint64_t));
p->static_data_ = new RotamerLibEntry[p->total_num_rotamers_];
- for(uint i = 0; i < p->total_num_rotamers_; ++i){
- in_stream >> p->static_data_[i];
- }
- in_stream.close();
+ in_stream.read(reinterpret_cast<char*>(&p->static_data_[0]),p->total_num_rotamers_ * sizeof(RotamerLibEntry));
+
return p;
}
diff --git a/sidechain/src/rotamer_lib.cc b/sidechain/src/rotamer_lib.cc
index c6bd203c..4e2a567a 100644
--- a/sidechain/src/rotamer_lib.cc
+++ b/sidechain/src/rotamer_lib.cc
@@ -57,9 +57,7 @@ void RotamerLib::Save(const String& filename){
}
out_stream.write(reinterpret_cast<char*>(&total_num_rotamers_),sizeof(uint64_t));
- for(uint i = 0; i < total_num_rotamers_; ++i){
- out_stream << static_data_[i];
- }
+ out_stream.write(reinterpret_cast<char*>(&static_data_[0]),total_num_rotamers_ * sizeof(RotamerLibEntry));
out_stream.close();
}
@@ -112,9 +110,7 @@ RotamerLibPtr RotamerLib::Load(const String& filename){
in_stream.read(reinterpret_cast<char*>(&p->total_num_rotamers_),sizeof(uint64_t));
p->static_data_ = new RotamerLibEntry[p->total_num_rotamers_];
- for(uint i = 0; i < p->total_num_rotamers_; ++i){
- in_stream >> p->static_data_[i];
- }
+ in_stream.read(reinterpret_cast<char*>(&p->static_data_[0]),p->total_num_rotamers_ * sizeof(RotamerLibEntry));
in_stream.close();
return p;
}
diff --git a/sidechain/src/rotamer_lib_entry.hh b/sidechain/src/rotamer_lib_entry.hh
index 31e271ca..7e8afd80 100644
--- a/sidechain/src/rotamer_lib_entry.hh
+++ b/sidechain/src/rotamer_lib_entry.hh
@@ -69,18 +69,6 @@ struct RotamerLibEntry{
bool SimilarDihedral(RotamerLibEntryPtr other, uint dihedral_idx,
Real thresh, const String& res_name);
- friend std::ofstream& operator<<(std::ofstream& os, RotamerLibEntry& entry){
- //assumes all variables being in memory in a consecutive order...
- os.write(reinterpret_cast<char*>(&entry.probability),9*sizeof(Real));
- return os;
- }
-
- friend std::ifstream& operator>>(std::ifstream& is, RotamerLibEntry& entry){
- //assumes all variables being in memory in a consecutive order...
- is.read(reinterpret_cast<char*>(&entry.probability),9*sizeof(Real));
- return is;
- }
-
// portable serialization
// (cleanly element by element with fixed-width base-types)
template <typename DS>
--
GitLab