From 101ee42483b00173c0166ddc90a3bd1f1b938402 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 6 May 2021 22:06:03 +0200
Subject: [PATCH] hacks to reduce omf file size
---
modules/io/src/mol/omf.cc | 71 ++++++++++++++++++++++++++++++---------
1 file changed, 55 insertions(+), 16 deletions(-)
diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc
index c28e4087b..a5c21ba34 100644
--- a/modules/io/src/mol/omf.cc
+++ b/modules/io/src/mol/omf.cc
@@ -266,6 +266,7 @@ namespace{
outliers.push_back(*it);
outliers.push_back(vec[*it]);
}
+
DumpIntVec(stream, int8_vec);
DumpIntVec(stream, outliers);
} else if(n_bytes_16 < n_bytes_32) {
@@ -278,7 +279,7 @@ namespace{
outliers.push_back(vec[*it]);
}
DumpIntVec(stream, int16_vec);
- DumpIntVec(stream, outliers);
+ DumpIntVec(stream, outliers);
} else {
int8_t encoding = 32;
stream.write(reinterpret_cast<char*>(&encoding), sizeof(int8_t));
@@ -386,6 +387,18 @@ namespace{
Dump(stream, run_length_encoded);
}
+ void LoadBonds(std::istream& stream, std::vector<int>& vec) {
+ std::vector<int> delta_encoded;
+ Load(stream, delta_encoded);
+ DeltaDecoding(delta_encoded, vec);
+ }
+
+ void DumpBonds(std::ostream& stream, const std::vector<int>& vec) {
+ std::vector<int> delta_encoded;
+ DeltaEncoding(vec, delta_encoded);
+ Dump(stream, delta_encoded);
+ }
+
void LoadBondOrders(std::istream& stream, std::vector<int>& vec) {
std::vector<int> run_length_encoded;
Load(stream, run_length_encoded);
@@ -442,19 +455,47 @@ namespace{
}
void LoadBFactors(std::istream& stream, std::vector<Real>& bfactors) {
- std::vector<int> delta_encoded;
- Load(stream, delta_encoded);
- std::vector<int> int_vec;
- DeltaDecoding(delta_encoded, int_vec);
- IntToRealVec(int_vec, bfactors, 0.01);
+
+ int8_t bfactor_encoding = 0;
+ stream.read(reinterpret_cast<char*>(&bfactor_encoding), sizeof(int8_t));
+ if(bfactor_encoding == 0) {
+ std::vector<int> delta_encoded;
+ Load(stream, delta_encoded);
+ std::vector<int> int_vec;
+ DeltaDecoding(delta_encoded, int_vec);
+ IntToRealVec(int_vec, bfactors, 0.01);
+ } else if(bfactor_encoding == 42) {
+ std::vector<int> runlength_encoded;
+ Load(stream, runlength_encoded);
+ std::vector<int> int_vec;
+ RunLengthDecoding(runlength_encoded, int_vec);
+ IntToRealVec(int_vec, bfactors, 0.01);
+ } else {
+ throw ost::Error("Observed invalid bfactor encoding");
+ }
}
void DumpBFactors(std::ostream& stream, const std::vector<Real>& bfactors) {
std::vector<int> int_vec;
RealToIntVec(bfactors, int_vec, 100);
- std::vector<int> delta_encoded;
- DeltaEncoding(int_vec, delta_encoded);
- Dump(stream, delta_encoded);
+
+ // Hack: some structures (e.g. EM) have all bfactors set to 0.0
+ // this efficiently compresses with runlength encoding.
+ // Let's sacrifice a byte to mark that
+ std::vector<int> run_length_encoded;
+ RunLengthEncoding(int_vec, run_length_encoded);
+ if(static_cast<float>(run_length_encoded.size())/int_vec.size() < 0.42) {
+ int8_t bfactor_encoding = 42;
+ stream.write(reinterpret_cast<char*>(&bfactor_encoding), sizeof(int8_t));
+ Dump(stream, run_length_encoded);
+ } else {
+ // continue with delta encoding
+ int8_t bfactor_encoding = 0;
+ stream.write(reinterpret_cast<char*>(&bfactor_encoding), sizeof(int8_t));
+ std::vector<int> delta_encoded;
+ DeltaEncoding(int_vec, delta_encoded);
+ Dump(stream, delta_encoded);
+ }
}
void LoadOccupancies(std::istream& stream, std::vector<Real>& occupancies) {
@@ -584,7 +625,7 @@ void ResidueDefinition::FromStream(std::istream& stream) {
Load(stream, anames);
Load(stream, elements);
LoadIsHetatm(stream, is_hetatm);
- Load(stream, bonds);
+ LoadBonds(stream, bonds);
LoadBondOrders(stream, bond_orders);
}
@@ -596,7 +637,7 @@ void ResidueDefinition::ToStream(std::ostream& stream) const{
Dump(stream, anames);
Dump(stream, elements);
DumpIsHetatm(stream, is_hetatm);
- Dump(stream, bonds);
+ DumpBonds(stream, bonds);
DumpBondOrders(stream, bond_orders);
}
@@ -661,8 +702,7 @@ ChainData::ChainData(const ost::mol::ChainHandle& chain,
ch_name = chain.GetName();
- // some mappers to deal with the bonds later on
- std::unordered_map<unsigned long, int> residue_idx_mapper;
+ // mapper to deal with the bonds later on
std::unordered_map<unsigned long, int> atom_idx_mapper;
// process residues
@@ -677,7 +717,6 @@ ChainData::ChainData(const ost::mol::ChainHandle& chain,
// process atoms of that residue
for(auto a_it = def.anames.begin(); a_it != def.anames.end(); ++a_it) {
ost::mol::AtomHandle at = res_it->FindAtom(*a_it);
- residue_idx_mapper[at.GetHashCode()] = rnums.size() - 1;
atom_idx_mapper[at.GetHashCode()] = positions.size();
occupancies.push_back(at.GetOccupancy());
bfactors.push_back(at.GetBFactor());
@@ -716,7 +755,7 @@ void ChainData::ToStream(std::ostream& stream) const {
DumpOccupancies(stream, occupancies);
DumpBFactors(stream, bfactors);
DumpPositions(stream, positions);
- Dump(stream, bonds);
+ DumpBonds(stream, bonds);
DumpBondOrders(stream, bond_orders);
DumpIntVec(stream, sec_structures);
}
@@ -729,7 +768,7 @@ void ChainData::FromStream(std::istream& stream) {
LoadOccupancies(stream, occupancies);
LoadBFactors(stream, bfactors);
LoadPositions(stream, positions);
- Load(stream, bonds);
+ LoadBonds(stream, bonds);
LoadBondOrders(stream, bond_orders);
LoadIntVec(stream, sec_structures);
}
--
GitLab