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// Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
// Biozentrum - University of Basel
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
#include <promod3/loop/all_atom_env.hh>
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/conop/heuristic.hh>
#include <ost/mol/builder.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/seq/sequence_op.hh>
BOOST_AUTO_TEST_SUITE( loop );
using namespace promod3::loop;
namespace {
ost::mol::EntityHandle LoadTestStructure(const String& pdb_name) {
ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
reader.Import(test_ent);
ost::conop::HeuristicProcessor heu_proc;
heu_proc.Process(test_ent);
return test_ent;
}
AllAtomEnv GenerateAllAtomEnv(
const String& seqresstr = "MGSLVREWVGFQQFPAATQEKLIEFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGEQVVRVSPFQAEGLRPVMVSRTMGGFTINIIDTPGLVEAGYVNHQALELIKGFLVNRTIDVLLYVDRLDVYAVDELDKQVVIAITQTFGKEIWCKTLLVLTHAQFSPPDELSYETFSSKRSDSLLKTIRAGSKMRKQEFEDSAIAVVYAENSGRCSKNDKDEKALPNGEAWIPNLVKAITDVATNQRKAIHVDAAALEHHHHHH") {
ost::seq::SequenceHandle seqres = ost::seq::CreateSequence("A", seqresstr);
ost::seq::SequenceList seqres_list = ost::seq::CreateSequenceList();
seqres_list.AddSequence(seqres);
AllAtomEnv env(seqres_list);
return env;
}
// test listener: checks for predefined expected outcome
class TestListener: public AllAtomEnvListener {
public:
// all public data for convenience
TestListener(String myid = "TestListener"): init_done(false),
reset_done(false),
myid_(myid) { }
bool init_done;
bool reset_done;
std::vector<uint> last_update;
// AllAtomEnvListener interface
virtual void Init(const AllAtomEnv& base_env) {
init_done = true;
}
virtual void ResetEnvironment(const AllAtomEnv& base_env) {
reset_done = true;
}
virtual void UpdateEnvironment(const AllAtomEnv& base_env,
const std::vector<uint>& res_indices) {
last_update = res_indices;
}
virtual String WhoAmI() const { return myid_; }
private:
String myid_;
};
typedef boost::shared_ptr<TestListener> TestListenerPtr;
} // anon ns
BOOST_AUTO_TEST_CASE(test_all_atom_env_setup) {
// check normal setup
ost::mol::EntityHandle test_ent = LoadTestStructure("data/3DEFA.pdb");
AllAtomEnv env = GenerateAllAtomEnv();
BOOST_CHECK_NO_THROW(env.SetInitialEnvironment(test_ent));
// check invalid olc
BOOST_CHECK_THROW(GenerateAllAtomEnv("MUX"), promod3::Error);
// check inconsistent env.
String wrong_seqres = "MGSLVAAAVGFQQFPAATQEKLIEFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGEQVVRVSPFQAEGLRPVMVSRTMGGFTINIIDTPGLVEAGYVNHQALELIKGFLVNRTIDVLLYVDRLDVYAVDELDKQVVIAITQTFGKEIWCKTLLVLTHAQFSPPDELSYETFSSKRSDSLLKTIRAGSKMRKQEFEDSAIAVVYAENSGRCSKNDKDEKALPNGEAWIPNLVKAITDVATNQRKAIHVDAAALEHHHHHH";
AllAtomEnv wrong_env = GenerateAllAtomEnv(wrong_seqres);
BOOST_CHECK_THROW(wrong_env.SetInitialEnvironment(test_ent), promod3::Error);
// check wrong numbering
test_ent.EditXCS().RenumberAllResidues(42, true);
BOOST_CHECK_THROW(env.SetInitialEnvironment(test_ent), promod3::Error);
// same thing, this time with AllAtomPositions
AllAtomPositions new_pos("LVREWVGF");
BOOST_CHECK_NO_THROW(env.SetEnvironment(new_pos, 4, 0));
BOOST_CHECK_THROW(env.SetEnvironment(new_pos, 5, 0), promod3::Error);
BOOST_CHECK_THROW(env.SetEnvironment(new_pos, -1, 0), promod3::Error);
BOOST_CHECK_THROW(env.SetEnvironment(new_pos, 260, 0), promod3::Error);
BOOST_CHECK_THROW(wrong_env.SetEnvironment(new_pos, 4, 0), promod3::Error);
// same thing with BackboneList
ConstAllAtomPositionsPtr env_all_pos = env.GetAllPosData();
AllAtomPositionsPtr ref_all_pos = env_all_pos->Copy();
BackboneList my_loop("KLIEFFGKLK");
env.SetEnvironment(my_loop, 21);
BOOST_CHECK(*env_all_pos != *ref_all_pos);
BOOST_CHECK(*env_all_pos->Extract(0, 20) == *ref_all_pos->Extract(0, 20));
BOOST_CHECK(*env_all_pos->Extract(20, 30) != *ref_all_pos->Extract(20, 30));
BOOST_CHECK(*env_all_pos->Extract(20, 30) == AllAtomPositions(my_loop));
BOOST_CHECK(env_all_pos->ExtractBackbone(20, 30) == my_loop);
const uint N = env_all_pos->GetNumResidues();
BOOST_CHECK(*env_all_pos->Extract(30, N) == *ref_all_pos->Extract(30, N));
// check exceptions
BOOST_CHECK_THROW(env.SetEnvironment(my_loop, 5, 0), promod3::Error);
BOOST_CHECK_THROW(env.SetEnvironment(my_loop, -1, 0), promod3::Error);
BOOST_CHECK_THROW(env.SetEnvironment(my_loop, 260, 0), promod3::Error);
BOOST_CHECK_THROW(wrong_env.SetEnvironment(my_loop, 4, 0), promod3::Error);
// check AllAtomEnvPositions
AllAtomEnvPositions new_env_pos;
BOOST_CHECK_THROW(env.SetEnvironment(new_env_pos), promod3::Error);
new_env_pos.all_pos = ref_all_pos;
new_env_pos.res_indices = env.GetIdxHandlerData()->ToIdxVector(1, N, 0);
env.SetEnvironment(new_env_pos);
BOOST_CHECK(*env_all_pos == *ref_all_pos);
}
BOOST_AUTO_TEST_CASE(test_all_atom_env_listener) {
// setup (note: start res. num. = 6, gap at num. 70)
ost::mol::EntityHandle test_ent = LoadTestStructure("data/3DEFA.pdb");
AllAtomEnv env = GenerateAllAtomEnv();
// check missing listener
BOOST_CHECK(env.GetListener("TestListener") == NULL);
// add unique listener
TestListenerPtr listener = env.UniqueListener<TestListener>("TestListener");
BOOST_CHECK(listener != NULL);
BOOST_CHECK(env.GetListener("TestListener") == listener);
BOOST_CHECK(env.UniqueListener<TestListener>("TestListener") == listener);
BOOST_CHECK(listener->init_done);
BOOST_CHECK(listener->reset_done);
// set initial env. -> should call ResetEnvironment
listener->reset_done = false;
env.SetInitialEnvironment(test_ent);
BOOST_CHECK(listener->reset_done);
BOOST_CHECK(listener->last_update.empty());
// keep subset for later
AllAtomPositionsPtr new_pos = env.GetAllPosData()->Extract(7,12);
new_pos->ClearResidue(0);
new_pos->ClearPos(1, BB_O_INDEX); // should have no effect
// clear res. nums 10,11 (indices = num - 1)
std::vector<uint> exp_res_indices;
exp_res_indices.push_back(9);
exp_res_indices.push_back(10);
env.ClearEnvironment(10, 2);
BOOST_CHECK(listener->last_update == exp_res_indices);
// reset nums 8-12 (indices = num - 1)
exp_res_indices.clear();
exp_res_indices.push_back(7);
exp_res_indices.push_back(8);
exp_res_indices.push_back(9);
exp_res_indices.push_back(10);
exp_res_indices.push_back(11);
// stretch
env.SetEnvironment(*new_pos, 8);
BOOST_CHECK(listener->last_update == exp_res_indices);
// res. indices
listener->last_update.clear();
env.SetEnvironment(*new_pos, exp_res_indices);
BOOST_CHECK(listener->last_update == exp_res_indices);
// AllAtomEnvPositions
AllAtomEnvPositions new_env_pos;
new_env_pos.all_pos = new_pos;
new_env_pos.res_indices = exp_res_indices;
listener->last_update.clear();
env.SetEnvironment(new_env_pos);
BOOST_CHECK(listener->last_update == exp_res_indices);
// BackboneList
listener->last_update.clear();
env.SetEnvironment(BackboneList(new_pos->GetSequence()), 8);
BOOST_CHECK(listener->last_update == exp_res_indices);
// attach new listener (should set all)
TestListenerPtr listener2(new TestListener("TL2"));
env.AttachListener(listener2);
BOOST_CHECK(listener2->init_done);
BOOST_CHECK(listener2->reset_done);
BOOST_CHECK(listener2->last_update.empty());
}
BOOST_AUTO_TEST_SUITE_END();
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