diff --git a/modules/io/pymod/export_omf_io.cc b/modules/io/pymod/export_omf_io.cc
index 974211d4542b97c6ecd92942fd37fa911873eafa..bb3e8169c1e61cff430c82fb1c42562702119568 100644
--- a/modules/io/pymod/export_omf_io.cc
+++ b/modules/io/pymod/export_omf_io.cc
@@ -66,14 +66,14 @@ void export_omf_io() {
class_<OMF, OMFPtr>("OMF",no_init)
.def("FromEntity", &OMF::FromEntity, (arg("ent"), arg("options")=0)).staticmethod("FromEntity")
- .def("FromMMCIF", &OMF::FromMMCIF, (arg("ent"), arg("mmcif_info"), arg("options")=0)).staticmethod("FromMMCIF")
.def("FromFile", &OMF::FromFile).staticmethod("FromFile")
.def("FromBytes", &wrap_from_bytes).staticmethod("FromBytes")
.def("ToFile", &OMF::ToFile)
.def("ToBytes", &wrap_to_bytes)
.def("GetAU", &OMF::GetAU)
+ .def("GetEntity", &OMF::GetEntity)
.def("GetAUChain", &OMF::GetAUChain)
- .def("GetBU", &OMF::GetBU)
+ .def("GetEntityChain", &OMF::GetEntityChain)
.def("GetName", &OMF::GetName)
.def("GetChainNames", &wrap_get_chain_names)
.def("GetPositions", &OMF::GetPositions, return_value_policy<reference_existing_object>(),(arg("cname")))
diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc
index 35ee9ce2d57671de321c96569b6264f6bb79fc5c..310857d4d82ad2904e530f7fbd1a12e20a4fd92b 100644
--- a/modules/io/src/mol/omf.cc
+++ b/modules/io/src/mol/omf.cc
@@ -877,52 +877,6 @@ namespace{
}
}
- // generates as many chain names as you want (potentially multiple characters)
- struct ChainNameGenerator{
- ChainNameGenerator() {
- chain_names = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz";
- n_chain_names = chain_names.size();
- indices.push_back(-1);
- }
-
- String Get() {
- int idx = indices.size() - 1;
- indices[idx] += 1;
- bool more_digits = false;
- while(idx >= 0) {
- if(indices[idx] >= n_chain_names) {
- indices[idx] = 0;
- if(idx>0) {
- indices[idx-1] += 1;
- --idx;
- } else {
- more_digits = true;
- break;
- }
- } else {
- break;
- }
- }
- if(more_digits) {
- indices.insert(indices.begin(), 0);
- }
- String ch_name(indices.size(), 'X');
- for(uint i = 0; i < indices.size(); ++i) {
- ch_name[i] = chain_names[indices[i]];
- }
- return ch_name;
- }
-
- void Reset() {
- indices.clear();
- indices.push_back(-1);
- }
-
- String chain_names;
- int n_chain_names;
- std::vector<int> indices;
- };
-
// delta/runlength encodings/decodings
void DeltaEncoding(const std::vector<int>& in, std::vector<int>& out) {
out.clear();
@@ -1299,17 +1253,6 @@ namespace{
}
}
- // dump and load vectors with BioUnitDefinition
- void Load(std::istream& stream,
- std::vector<ost::io::BioUnitDefinition>& vec) {
- uint32_t size;
- stream.read(reinterpret_cast<char*>(&size), sizeof(uint32_t));
- vec.resize(size);
- for(uint i = 0; i < size; ++i) {
- vec[i].FromStream(stream);
- }
- }
-
void Dump(std::ostream& stream,
const std::vector<bool>& vec) {
uint32_t size = vec.size();
@@ -1337,34 +1280,6 @@ namespace{
}
}
- void Dump(std::ostream& stream,
- const std::vector<ost::io::BioUnitDefinition>& vec) {
- uint32_t size = vec.size();
- stream.write(reinterpret_cast<char*>(&size), sizeof(uint32_t));
- for(uint i = 0; i < size; ++i) {
- vec[i].ToStream(stream);
- }
- }
-
- // dump and load vectors with Mat4
- void Load(std::istream& stream, std::vector<geom::Mat4>& vec) {
- uint32_t size;
- stream.read(reinterpret_cast<char*>(&size), sizeof(uint32_t));
- vec.resize(size);
- for(uint i = 0; i < size; ++i) {
- stream.read(reinterpret_cast<char*>(vec[i].Data()),16*sizeof(Real));
- }
- }
-
- void Dump(std::ostream& stream, const std::vector<geom::Mat4>& vec) {
- uint32_t size = vec.size();
- stream.write(reinterpret_cast<char*>(&size), sizeof(uint32_t));
- for(uint i = 0; i < size; ++i) {
- stream.write(reinterpret_cast<const char*>(vec[i].Data()),
- 16*sizeof(Real));
- }
- }
-
// knowledge based dump and load functions, i.e. awesome compressions
void LoadIsHetatm(std::istream& stream, std::vector<bool>& vec) {
std::vector<int> run_length_encoded;
@@ -1845,61 +1760,6 @@ void ResidueDefinition::_AddAtomRule(int a_idx, int anch_one_idx,
sidechain_atom_rules.push_back(rule);
}
-BioUnitDefinition::BioUnitDefinition(const ost::io::MMCifInfoBioUnit& bu) {
-
- au_chains = bu.GetChainList();
-
- const std::vector<std::pair<int, int> >& bu_ch_intvl =
- bu.GetChainIntervalList();
- for(auto it = bu_ch_intvl.begin(); it != bu_ch_intvl.end(); ++it) {
- chain_intvl.push_back(it->first);
- chain_intvl.push_back(it->second);
- }
-
- const std::vector<std::vector<MMCifInfoTransOpPtr> >& bu_op_list =
- bu.GetOperations();
- for(auto i = bu_op_list.begin(); i != bu_op_list.end(); ++i) {
- std::vector<geom::Mat4> mat_list;
- for(auto j = i->begin(); j != i->end(); ++j) {
- geom::Mat4 m;
- m.PasteRotation((*j)->GetMatrix());
- m.PasteTranslation((*j)->GetVector());
- mat_list.push_back(m);
- }
- operations.push_back(mat_list);
- }
-
- const std::vector<std::pair<int, int> >& bu_op_intvl =
- bu.GetOperationsIntervalList();
- for(auto it = bu_op_intvl.begin(); it != bu_op_intvl.end(); ++it) {
- op_intvl.push_back(it->first);
- op_intvl.push_back(it->second);
- }
-}
-
-void BioUnitDefinition::ToStream(std::ostream& stream) const {
- Dump(stream, au_chains);
- Dump(stream, chain_intvl);
- uint32_t size = operations.size();
- stream.write(reinterpret_cast<char*>(&size), sizeof(uint32_t));
- for(auto it = operations.begin(); it != operations.end(); ++it) {
- Dump(stream, *it);
- }
- Dump(stream, op_intvl);
-}
-
-void BioUnitDefinition::FromStream(std::istream& stream) {
- Load(stream, au_chains);
- Load(stream, chain_intvl);
- uint32_t size = 0;
- stream.read(reinterpret_cast<char*>(&size), sizeof(uint32_t));
- operations.resize(size);
- for(uint i = 0; i < size; ++i) {
- Load(stream, operations[i]);
- }
- Load(stream, op_intvl);
-}
-
ChainData::ChainData(const ost::mol::ChainHandle& chain,
const std::vector<ResidueDefinition>& residue_definitions,
const std::unordered_map<unsigned long, int>& res_idx_map,
@@ -4934,18 +4794,6 @@ OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent,
return omf;
}
-OMFPtr OMF::FromMMCIF(const ost::mol::EntityHandle& ent,
- const MMCifInfo& info,
- uint8_t options) {
-
- OMFPtr p = OMF::FromEntity(ent, options);
- const std::vector<MMCifInfoBioUnit>& biounits = info.GetBioUnits();
- for(auto it = biounits.begin(); it != biounits.end(); ++it) {
- p->biounit_definitions_.push_back(BioUnitDefinition(*it));
- }
- return p;
-}
-
OMFPtr OMF::FromFile(const String& fn) {
std::ifstream in_stream(fn.c_str(), std::ios::binary);
if (!in_stream) {
@@ -5014,67 +4862,6 @@ ost::mol::EntityHandle OMF::GetAUChain(const String& name) const{
return ent;
}
-ost::mol::EntityHandle OMF::GetBU(int bu_idx) const{
- if(bu_idx < 0 || bu_idx >= static_cast<int>(biounit_definitions_.size())) {
- throw ost::Error("Invalid biounit idx");
- }
-
- const BioUnitDefinition& bu = biounit_definitions_[bu_idx];
- ost::mol::EntityHandle ent = mol::CreateEntity();
- std::stringstream ss;
- ss << name_ << " " << bu_idx;
- ent.SetName(ss.str());
- ost::mol::XCSEditor ed = ent.EditXCS(mol::BUFFERED_EDIT);
-
- std::vector<String> au_chain_names;
- std::vector<geom::Mat4> transforms;
-
- // The code below is pure magic and heavily inspired by
- // the biounit buildup in modules/io/pymod/__init__.py
- int n_intervals = bu.chain_intvl.size() / 2;
- for(int intvl_idx = 0; intvl_idx < n_intervals; ++intvl_idx) {
- std::vector<geom::Mat4> rts;
- int op_start = bu.op_intvl[2*intvl_idx];
- int op_end = bu.op_intvl[2*intvl_idx+1];
- int n_intv_ops = op_end - op_start;
- if(n_intv_ops) {
- for(auto it = bu.operations[op_start].begin();
- it != bu.operations[op_start].end(); ++it) {
- rts.push_back(*it);
- }
- ++op_start;
- while(op_start < op_end) {
- std::vector<geom::Mat4> tmp_rts;
- for(auto i = bu.operations[op_start].begin();
- i != bu.operations[op_start].end(); ++i) {
- for(auto j = rts.begin(); j != rts.end(); ++j) {
- tmp_rts.push_back((*j)*(*i));
- }
- }
- rts = tmp_rts;
- ++op_start;
- }
- }
- for(int ch_idx = bu.chain_intvl[2*intvl_idx];
- ch_idx < bu.chain_intvl[2*intvl_idx+1]; ++ch_idx) {
- for(auto it = rts.begin(); it != rts.end(); ++it) {
- au_chain_names.push_back(bu.au_chains[ch_idx]);
- transforms.push_back(*it);
- }
- }
- }
-
- ChainNameGenerator gen;
- for(uint bu_ch_idx = 0; bu_ch_idx < au_chain_names.size(); ++bu_ch_idx) {
- String bu_ch_name = gen.Get();
- ost::mol::ChainHandle added_chain = ed.InsertChain(bu_ch_name);
- this->FillChain(added_chain, ed, chain_data_.at(au_chain_names[bu_ch_idx]),
- transforms[bu_ch_idx]);
- }
-
- return ent;
-}
-
void OMF::ToStream(std::ostream& stream) const {
uint32_t magic_number = 42;
@@ -5099,7 +4886,6 @@ void OMF::ToStream(std::ostream& stream) const {
Dump(stream, residue_definitions_);
}
- Dump(stream, biounit_definitions_);
Dump(stream, chain_data_, residue_definitions_, OptionSet(LOSSY),
OptionSet(AVG_BFACTORS), OptionSet(ROUND_BFACTORS), OptionSet(SKIP_SS),
OptionSet(INFER_POS));
@@ -5143,7 +4929,6 @@ void OMF::FromStream(std::istream& stream) {
Load(stream, residue_definitions_);
}
- Load(stream, biounit_definitions_);
Load(stream, chain_data_, residue_definitions_, version_, OptionSet(LOSSY),
OptionSet(AVG_BFACTORS), OptionSet(ROUND_BFACTORS), OptionSet(SKIP_SS),
OptionSet(INFER_POS));
diff --git a/modules/io/src/mol/omf.hh b/modules/io/src/mol/omf.hh
index c912bcec35525078d6310240f7bf12770027d539..aa5eb6c2d0d2233d58611be7b323f17dba185caf 100644
--- a/modules/io/src/mol/omf.hh
+++ b/modules/io/src/mol/omf.hh
@@ -33,11 +33,9 @@ namespace ost { namespace io {
const int OMF_VERSION = 2;
class ChainData;
-class BioUnitData;
class OMF;
typedef boost::shared_ptr<OMF> OMFPtr;
typedef boost::shared_ptr<ChainData> ChainDataPtr;
-typedef boost::shared_ptr<BioUnitData> BioUnitDataPtr;
struct SidechainAtomRule {
int sidechain_atom_idx;
@@ -120,23 +118,6 @@ struct ResidueDefinition {
std::vector<SidechainAtomRule> sidechain_atom_rules;
};
-
-struct BioUnitDefinition {
- BioUnitDefinition() { }
-
- BioUnitDefinition(const ost::io::MMCifInfoBioUnit& bu);
-
- void ToStream(std::ostream& stream) const;
-
- void FromStream(std::istream& stream);
-
- std::vector<String> au_chains;
- std::vector<int> chain_intvl;
- std::vector<std::vector<geom::Mat4> > operations;
- std::vector<int> op_intvl;
-};
-
-
struct ChainData {
ChainData(): ch_name(""), chain_type(ost::mol::CHAINTYPE_UNKNOWN) { }
@@ -210,10 +191,6 @@ public:
static OMFPtr FromEntity(const ost::mol::EntityHandle& ent,
uint8_t options = 0);
- static OMFPtr FromMMCIF(const ost::mol::EntityHandle& ent,
- const MMCifInfo& info,
- uint8_t options = 0);
-
static OMFPtr FromFile(const String& fn);
static OMFPtr FromString(const String& s);
@@ -224,8 +201,16 @@ public:
ost::mol::EntityHandle GetAU() const;
+ ost::mol::EntityHandle GetEntity() const {
+ return this->GetAU();
+ }
+
ost::mol::EntityHandle GetAUChain(const String& name) const;
+ ost::mol::EntityHandle GetEntityChain(const String& name) const {
+ return this->GetAUChain(name);
+ }
+
ost::mol::EntityHandle GetBU(int bu_idx) const;
int GetVersion() const { return version_; }
@@ -261,7 +246,6 @@ private:
String name_;
std::vector<ResidueDefinition> residue_definitions_;
- std::vector<BioUnitDefinition> biounit_definitions_;
std::map<String, ChainDataPtr> chain_data_;
// bond features - only for bonds that are inter-chain
diff --git a/modules/io/tests/test_io_omf.py b/modules/io/tests/test_io_omf.py
index 8d519c5084969316d2aeab844aeac45cdd89d8bd..81c19f2e889bbd5dd9601bd69e0ae23bbbedc665 100644
--- a/modules/io/tests/test_io_omf.py
+++ b/modules/io/tests/test_io_omf.py
@@ -118,17 +118,16 @@ class TestOMF(unittest.TestCase):
self.ent.SetName("This is a name 123")
def test_AU(self):
- omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
loaded_omf = io.OMF.FromBytes(omf_bytes)
loaded_ent = loaded_omf.GetAU()
self.assertTrue(compare_ent(self.ent, loaded_ent))
def test_default_peplib(self):
- omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
- omf_def_pep = io.OMF.FromMMCIF(self.ent, self.info,
- io.OMFOption.DEFAULT_PEPLIB)
+ omf_def_pep = io.OMF.FromEntity(self.ent, io.OMFOption.DEFAULT_PEPLIB)
omf_def_pep_bytes = omf_def_pep.ToBytes()
loaded_omf_def_pep = io.OMF.FromBytes(omf_def_pep_bytes)
loaded_ent = loaded_omf_def_pep.GetAU()
@@ -137,10 +136,9 @@ class TestOMF(unittest.TestCase):
self.assertTrue(compare_ent(self.ent, loaded_ent))
def test_lossy(self):
- omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
- omf_lossy = io.OMF.FromMMCIF(self.ent, self.info,
- io.OMFOption.LOSSY)
+ omf_lossy = io.OMF.FromEntity(self.ent, io.OMFOption.LOSSY)
omf_lossy_bytes = omf_lossy.ToBytes()
loaded_omf_lossy = io.OMF.FromBytes(omf_lossy_bytes)
loaded_ent = loaded_omf_lossy.GetAU()
@@ -152,10 +150,9 @@ class TestOMF(unittest.TestCase):
at_dist_thresh=max_dist))
def test_avg_bfactors(self):
- omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
- omf_avg_bfac = io.OMF.FromMMCIF(self.ent, self.info,
- io.OMFOption.AVG_BFACTORS)
+ omf_avg_bfac = io.OMF.FromEntity(self.ent, io.OMFOption.AVG_BFACTORS)
omf_avg_bfac_bytes = omf_avg_bfac.ToBytes()
loaded_omf_avg_bfac = io.OMF.FromBytes(omf_avg_bfac_bytes)
loaded_ent = loaded_omf_avg_bfac.GetAU()
@@ -174,10 +171,9 @@ class TestOMF(unittest.TestCase):
self.assertTrue(abs(a.b_factor - exp_bfac) < 0.008)
def test_round_bfactors(self):
- omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
- omf_round_bfac = io.OMF.FromMMCIF(self.ent, self.info,
- io.OMFOption.ROUND_BFACTORS)
+ omf_round_bfac = io.OMF.FromEntity(self.ent, io.OMFOption.ROUND_BFACTORS)
omf_round_bfac_bytes = omf_round_bfac.ToBytes()
loaded_omf_round_bfac = io.OMF.FromBytes(omf_round_bfac_bytes)
loaded_ent = loaded_omf_round_bfac.GetAU()
@@ -188,10 +184,9 @@ class TestOMF(unittest.TestCase):
at_bfactor_thresh=0.5))
def test_skip_ss(self):
- omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
- omf_skip_ss = io.OMF.FromMMCIF(self.ent, self.info,
- io.OMFOption.SKIP_SS)
+ omf_skip_ss = io.OMF.FromEntity(self.ent, io.OMFOption.SKIP_SS)
omf_skip_ss_bytes = omf_skip_ss.ToBytes()
loaded_omf_skip_ss = io.OMF.FromBytes(omf_skip_ss_bytes)
loaded_ent = loaded_omf_skip_ss.GetAU()
@@ -201,10 +196,10 @@ class TestOMF(unittest.TestCase):
self.assertTrue(compare_ent(self.ent, loaded_ent, skip_ss=True))
def test_infer_pep_bonds(self):
- omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf = io.OMF.FromEntity(self.ent)
omf_bytes = omf.ToBytes()
- omf_infer_pep_bonds = io.OMF.FromMMCIF(self.ent, self.info,
- io.OMFOption.INFER_PEP_BONDS)
+ omf_infer_pep_bonds = io.OMF.FromEntity(self.ent,
+ io.OMFOption.INFER_PEP_BONDS)
omf_infer_pep_bonds_bytes = omf_infer_pep_bonds.ToBytes()
loaded_omf_infer_pep_bonds = io.OMF.FromBytes(omf_infer_pep_bonds_bytes)
loaded_ent = loaded_omf_infer_pep_bonds.GetAU()
@@ -212,40 +207,6 @@ class TestOMF(unittest.TestCase):
self.assertTrue(len(omf_infer_pep_bonds_bytes) < len(omf_bytes))
self.assertTrue(compare_ent(self.ent, loaded_ent))
- def test_multiple_BU(self):
- ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3imj.cif.gz",
- seqres=True,
- info=True)
-
- omf = io.OMF.FromMMCIF(ent, info)
- omf_bytes = omf.ToBytes()
- omf_loaded = io.OMF.FromBytes(omf_bytes)
-
- # there are quite some discrepancies between PDBize and OMF
- # - chain names: PDBize has specific chain names for ligands and
- # water etc. OMF just iterates A, B, C, D, ...
- # - skip_bonds: Thats qualified atom name based. PDBize used rnums
- # and insertion codes for waters...
- # - skip_rnums: Again, insertion codes for waters...
- self.assertTrue(compare_ent(info.GetBioUnits()[0].PDBize(ent),
- omf_loaded.GetBU(0),
- skip_cnames=True, skip_bonds=True,
- skip_rnums=True, bu_idx = 0))
-
- self.assertTrue(compare_ent(info.GetBioUnits()[1].PDBize(ent),
- omf_loaded.GetBU(1),
- skip_cnames=True, skip_bonds=True,
- skip_rnums=True, bu_idx = 1))
-
- # no check for the full guy... problem: PDBize throws all water
- # molecules in the same chain, whereas OMF keeps them separate
- # as in the chains from the assymetric unit... maybe needs some
- # thinking on how to resolve discrepancies between PDBize and OMF
- #self.assertTrue(compare_ent(omf_loaded.GetBU(2),
- # info.GetBioUnits()[2].PDBize(ent),
- # skip_cnames=True, skip_bonds=True,
- # skip_rnums=True))
-
if __name__== '__main__':
from ost import testutils
if testutils.DefaultCompoundLibIsSet():