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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/idx_handler.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
BOOST_AUTO_TEST_SUITE( loop );
using namespace promod3::loop;
namespace {
bool HasLoop(const std::vector<uint>& loop_start_indices,
const std::vector<uint>& loop_lengths,
uint exp_start_idx, uint exp_length) {
// check if exp_... appear in vector
const uint num_loops = loop_start_indices.size();
for (uint i_loop = 0; i_loop < num_loops; ++i_loop) {
if (loop_start_indices[i_loop] == exp_start_idx
&& loop_lengths[i_loop] == exp_length) return true;
}
return false;
}
} // anon ns
BOOST_AUTO_TEST_CASE(test_idx_handler) {
// setup
std::vector<size_t> chain_sizes;
chain_sizes.push_back(3);
chain_sizes.push_back(0);
chain_sizes.push_back(2);
IdxHandler idx_handler(chain_sizes);
// global checks
BOOST_CHECK_EQUAL(idx_handler.GetNumChains(), size_t(3));
BOOST_CHECK_EQUAL(idx_handler.GetNumResidues(), size_t(5));
// per chain tests
BOOST_CHECK_EQUAL(idx_handler.GetChainSize(0), size_t(3));
BOOST_CHECK_EQUAL(idx_handler.GetChainSize(1), size_t(0));
BOOST_CHECK_EQUAL(idx_handler.GetChainSize(2), size_t(2));
BOOST_CHECK_EQUAL(idx_handler.GetChainStartIdx(0), uint(0));
BOOST_CHECK_EQUAL(idx_handler.GetChainStartIdx(1), uint(3));
BOOST_CHECK_EQUAL(idx_handler.GetChainStartIdx(2), uint(3));
BOOST_CHECK_EQUAL(idx_handler.GetChainLastIdx(0), uint(2));
BOOST_CHECK_EQUAL(idx_handler.GetChainLastIdx(2), uint(4));
// per residue tests
BOOST_CHECK_EQUAL(idx_handler.ToIdx(1,0), uint(0));
BOOST_CHECK_EQUAL(idx_handler.ToIdx(2,0), uint(1));
BOOST_CHECK_EQUAL(idx_handler.ToIdx(3,0), uint(2));
BOOST_CHECK_EQUAL(idx_handler.ToIdx(1,2), uint(3));
BOOST_CHECK_EQUAL(idx_handler.ToIdx(2,2), uint(4));
BOOST_CHECK_EQUAL(idx_handler.GetChainIdx(0), uint(0));
BOOST_CHECK_EQUAL(idx_handler.GetChainIdx(1), uint(0));
BOOST_CHECK_EQUAL(idx_handler.GetChainIdx(2), uint(0));
BOOST_CHECK_EQUAL(idx_handler.GetChainIdx(3), uint(2));
BOOST_CHECK_EQUAL(idx_handler.GetChainIdx(4), uint(2));
// vector
std::vector<uint> res_indices = idx_handler.ToIdxVector(1, 3, 0);
BOOST_CHECK_EQUAL(res_indices.size(), size_t(3));
BOOST_CHECK_EQUAL(res_indices[0], uint(0));
BOOST_CHECK_EQUAL(res_indices[1], uint(1));
BOOST_CHECK_EQUAL(res_indices[2], uint(2));
// exceptions
BOOST_CHECK_THROW(idx_handler.ToIdx(4, 0), promod3::Error);
BOOST_CHECK_THROW(idx_handler.ToIdx(1, 1), promod3::Error);
BOOST_CHECK_THROW(idx_handler.ToIdx(0, 2), promod3::Error);
BOOST_CHECK_THROW(idx_handler.ToIdx(1, 3), promod3::Error);
BOOST_CHECK_THROW(idx_handler.ToIdxVector(1, 4, 0), promod3::Error);
BOOST_CHECK_THROW(idx_handler.ToIdxVector(1, 1, 1), promod3::Error);
BOOST_CHECK_THROW(idx_handler.ToIdxVector(0, 1, 2), promod3::Error);
BOOST_CHECK_THROW(idx_handler.ToIdxVector(1, 1, 3), promod3::Error);
}
BOOST_AUTO_TEST_CASE(test_idx_handler_bb_list) {
// setup
std::vector<size_t> chain_sizes;
chain_sizes.push_back(10);
IdxHandler idx_handler(chain_sizes);
String seq = "HELLYEAH";
BackboneList bb_list(seq);
// check
uint bb_list_size, start_idx, end_idx;
idx_handler.SetupScoreCalculation(bb_list, 1, 0, bb_list_size, start_idx,
end_idx);
BOOST_CHECK_EQUAL(bb_list_size, uint(8));
BOOST_CHECK_EQUAL(start_idx, uint(0));
BOOST_CHECK_EQUAL(end_idx, uint(7));
idx_handler.SetupScoreCalculation(bb_list, 3, 0, bb_list_size, start_idx,
end_idx);
BOOST_CHECK_EQUAL(bb_list_size, uint(8));
BOOST_CHECK_EQUAL(start_idx, uint(2));
BOOST_CHECK_EQUAL(end_idx, uint(9));
// exceptions
BOOST_CHECK_THROW(idx_handler.SetupScoreCalculation(bb_list, 0, 0,
bb_list_size, start_idx,
end_idx), promod3::Error);
BOOST_CHECK_THROW(idx_handler.SetupScoreCalculation(bb_list, 4, 0,
bb_list_size, start_idx,
end_idx), promod3::Error);
BOOST_CHECK_THROW(idx_handler.SetupScoreCalculation(bb_list, 1, 1,
bb_list_size, start_idx,
end_idx), promod3::Error);
}
BOOST_AUTO_TEST_CASE(test_idx_handler_overlaps) {
// setup
std::vector<uint> loop_start_indices;
std::vector<uint> loop_lengths;
loop_start_indices.push_back(10);
loop_start_indices.push_back(5);
loop_start_indices.push_back(15);
loop_lengths.push_back(2);
loop_lengths.push_back(2);
loop_lengths.push_back(3);
// check
std::vector<uint> loop_start_indices_res = loop_start_indices;
std::vector<uint> loop_lengths_res = loop_lengths;
IdxHandler::ResolveOverlaps(loop_start_indices_res, loop_lengths_res);
BOOST_CHECK(loop_start_indices == loop_start_indices_res);
BOOST_CHECK(loop_lengths == loop_lengths_res);
// check empty loop
loop_lengths[1] = 0;
loop_start_indices_res = loop_start_indices;
loop_lengths_res = loop_lengths;
IdxHandler::ResolveOverlaps(loop_start_indices_res, loop_lengths_res);
BOOST_CHECK_EQUAL(loop_start_indices_res.size(), 2u);
BOOST_CHECK_EQUAL(loop_lengths_res.size(), 2u);
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 10, 2));
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 15, 3));
// check touch (no overlap)
loop_lengths[1] = 5;
loop_start_indices_res = loop_start_indices;
loop_lengths_res = loop_lengths;
IdxHandler::ResolveOverlaps(loop_start_indices_res, loop_lengths_res);
BOOST_CHECK(loop_start_indices == loop_start_indices_res);
BOOST_CHECK(loop_lengths == loop_lengths_res);
// check partial overlap
loop_lengths[1] = 6;
loop_start_indices_res = loop_start_indices;
loop_lengths_res = loop_lengths;
IdxHandler::ResolveOverlaps(loop_start_indices_res, loop_lengths_res);
BOOST_CHECK_EQUAL(loop_start_indices_res.size(), 2u);
BOOST_CHECK_EQUAL(loop_lengths_res.size(), 2u);
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 5, 7));
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 15, 3));
// check full overlap
loop_lengths[1] = 8;
loop_start_indices_res = loop_start_indices;
loop_lengths_res = loop_lengths;
IdxHandler::ResolveOverlaps(loop_start_indices_res, loop_lengths_res);
BOOST_CHECK_EQUAL(loop_start_indices_res.size(), 2u);
BOOST_CHECK_EQUAL(loop_lengths_res.size(), 2u);
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 5, 8));
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 15, 3));
// check double overlap
loop_lengths[1] = 20;
loop_start_indices_res = loop_start_indices;
loop_lengths_res = loop_lengths;
IdxHandler::ResolveOverlaps(loop_start_indices_res, loop_lengths_res);
BOOST_CHECK_EQUAL(loop_start_indices_res.size(), 1u);
BOOST_CHECK_EQUAL(loop_lengths_res.size(), 1u);
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 5, 20));
// check double overlap with loop in loop
loop_lengths[1] = 12;
loop_start_indices_res = loop_start_indices;
loop_lengths_res = loop_lengths;
IdxHandler::ResolveOverlaps(loop_start_indices_res, loop_lengths_res);
BOOST_CHECK_EQUAL(loop_start_indices_res.size(), 1u);
BOOST_CHECK_EQUAL(loop_lengths_res.size(), 1u);
BOOST_CHECK(HasLoop(loop_start_indices_res, loop_lengths_res, 5, 13));
}
BOOST_AUTO_TEST_CASE(test_idx_handler_multi_loops) {
// setup
std::vector<size_t> chain_sizes;
chain_sizes.push_back(10);
chain_sizes.push_back(0);
chain_sizes.push_back(8);
IdxHandler idx_handler(chain_sizes);
// input data
std::vector<uint> start_resnums;
std::vector<uint> num_residues;
std::vector<uint> chain_indices;
start_resnums.push_back(1);
num_residues.push_back(2);
chain_indices.push_back(2);
start_resnums.push_back(6);
num_residues.push_back(2);
chain_indices.push_back(0);
start_resnums.push_back(6);
num_residues.push_back(3);
chain_indices.push_back(2);
// output data
std::vector<uint> loop_start_indices;
std::vector<uint> loop_lengths;
// check
idx_handler.ToLoopIndices(start_resnums, num_residues, chain_indices,
loop_start_indices, loop_lengths);
BOOST_CHECK_EQUAL(loop_start_indices.size(), 3u);
BOOST_CHECK_EQUAL(loop_lengths.size(), 3u);
BOOST_CHECK(HasLoop(loop_start_indices, loop_lengths, 10, 2));
BOOST_CHECK(HasLoop(loop_start_indices, loop_lengths, 5, 2));
BOOST_CHECK(HasLoop(loop_start_indices, loop_lengths, 15, 3));
// check overlap fixing (just one of the cases)
num_residues[0] = 6;
idx_handler.ToLoopIndices(start_resnums, num_residues, chain_indices,
loop_start_indices, loop_lengths);
BOOST_CHECK_EQUAL(loop_start_indices.size(), 2u);
BOOST_CHECK_EQUAL(loop_lengths.size(), 2u);
BOOST_CHECK(HasLoop(loop_start_indices, loop_lengths, 10, 8));
BOOST_CHECK(HasLoop(loop_start_indices, loop_lengths, 5, 2));
// check ToIdxVector
std::vector<uint> res_indices
= idx_handler.ToIdxVector(start_resnums, num_residues, chain_indices,
loop_start_indices, loop_lengths);
BOOST_CHECK_EQUAL(res_indices.size(), 10u);
BOOST_CHECK_EQUAL(loop_start_indices.size(), 2u);
BOOST_CHECK_EQUAL(loop_lengths.size(), 2u);
BOOST_CHECK_EQUAL(loop_start_indices[0], 0u);
BOOST_CHECK_EQUAL(loop_start_indices[1], loop_lengths[0]);
// we cannot assume any order so we need to resolve both options
if (loop_lengths[0] == 8) {
BOOST_CHECK_EQUAL(loop_lengths[1], 2u);
for (uint i = 0; i < 10; ++i) {
if (i < 8) BOOST_CHECK_EQUAL(res_indices[i], 10 + i);
else BOOST_CHECK_EQUAL(res_indices[i], 5 + i - 8);
}
} else {
BOOST_CHECK_EQUAL(loop_lengths[0], 2u);
BOOST_CHECK_EQUAL(loop_lengths[1], 8u);
for (uint i = 0; i < 10; ++i) {
if (i < 2) BOOST_CHECK_EQUAL(res_indices[i], 5 + i);
else BOOST_CHECK_EQUAL(res_indices[i], 10 + i - 2);
}
}
// exceptions
num_residues[0] = 2;
start_resnums[0] = 9;
BOOST_CHECK_THROW(idx_handler.ToLoopIndices(start_resnums, num_residues,
chain_indices, loop_start_indices,
loop_lengths), promod3::Error);
start_resnums[0] = 8;
BOOST_CHECK_THROW(idx_handler.ToLoopIndices(start_resnums, num_residues,
chain_indices, loop_start_indices,
loop_lengths), promod3::Error);
start_resnums[0] = 0;
BOOST_CHECK_THROW(idx_handler.ToLoopIndices(start_resnums, num_residues,
chain_indices, loop_start_indices,
loop_lengths), promod3::Error);
start_resnums[0] = 1;
// bad chain
chain_indices[0] = 1;
BOOST_CHECK_THROW(idx_handler.ToLoopIndices(start_resnums, num_residues,
chain_indices, loop_start_indices,
loop_lengths), promod3::Error);
chain_indices[0] = 3;
BOOST_CHECK_THROW(idx_handler.ToLoopIndices(start_resnums, num_residues,
chain_indices, loop_start_indices,
loop_lengths), promod3::Error);
chain_indices[0] = 2;
// bad vector sizes
start_resnums.push_back(1);
BOOST_CHECK_THROW(idx_handler.ToLoopIndices(start_resnums, num_residues,
chain_indices, loop_start_indices,
loop_lengths), promod3::Error);
}
BOOST_AUTO_TEST_SUITE_END();
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