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update ff, and essential step for rmsd atom indices permutation
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Signed-off-by: Conrad Hübler <[email protected]>
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@conradhuebler
conradhuebler committed Feb 23, 2024
1 parent c3f6aa5 commit 14e5df1
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Showing 9 changed files with 952 additions and 240 deletions.
10 changes: 5 additions & 5 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -164,9 +164,9 @@ set(curcuma_core_SRC
src/core/eigen_uff.cpp
src/core/qmdff.cpp
src/core/eht.cpp
#src/core/forcefield.h
#src/core/forcefield.cpp
#src/core/forcefieldfunctions.h
src/core/forcefieldthread.cpp
src/core/forcefield.cpp
src/core/forcefieldfunctions.h
#src/core/forcefield_terms/qmdff_terms.h
src/tools/formats.h
src/tools/geometry.h
Expand Down Expand Up @@ -277,12 +277,12 @@ if(USE_D3)
if(NOT TARGET s-dftd3)
add_subdirectory(external/simple-dftd3)
endif()
#if(HELPERS)
if(HELPERS)
add_executable(dftd3_helper
src/helpers/dftd3_helper.cpp
)
target_link_libraries(dftd3_helper PUBLIC s-dftd3 gfortran pthread)
#endif()
endif()
set(curcuma_D3_SRC
src/core/dftd3interface.cpp
)
Expand Down
124 changes: 69 additions & 55 deletions src/capabilities/rmsd.cpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/*
* <RMSD calculator for chemical structures.>
* Copyright (C) 2019 - 2023 Conrad Hübler <[email protected]>
* Copyright (C) 2019 - 2024 Conrad Hübler <[email protected]>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand Down Expand Up @@ -37,6 +37,7 @@
#include <map>
#include <mutex>
#include <queue>
#include <random>
#include <string>
#include <vector>

Expand Down Expand Up @@ -803,32 +804,35 @@ void RMSDDriver::HeavyTemplate()

void RMSDDriver::TemplateFree()
{

Molecule ref_mol = m_reference;
Molecule tar_mol = m_target;
for (int i = 0; i < 2; ++i) {

Geometry cached_reference = m_reference.getGeometry();
Geometry cached_target = m_target.getGeometry();

Geometry tref = GeometryTools::TranslateMolecule(m_reference, m_reference.Centroid(true), Position{ 0, 0, 0 });
Geometry tget = GeometryTools::TranslateMolecule(m_target, m_target.Centroid(true), Position{ 0, 0, 0 });
ref_mol.setGeometry(tref);
tar_mol.setGeometry(tget);

if (m_moi) {
ref_mol.CalculateRotationalConstants();
tar_mol.CalculateRotationalConstants();

Eigen::MatrixXd tar = tget.transpose();
Eigen::MatrixXd ref = tref.transpose();

Geometry rotated_reference = ref.transpose() * ref_mol.AlignmentAxes();
Geometry rotated_target = tar.transpose() * tar_mol.AlignmentAxes();
Geometry cached_reference = m_reference.getGeometry();
Geometry cached_target = m_target.getGeometry();

ref_mol.setGeometry(rotated_reference);
tar_mol.setGeometry(rotated_target);
ref_mol.writeXYZFile("reference.moi.xyz");
tar_mol.writeXYZFile("target.moi.xyz");
} else {
Geometry tref = GeometryTools::TranslateMolecule(m_reference, m_reference.Centroid(true), Position{ 0, 0, 0 });
Geometry tget = GeometryTools::TranslateMolecule(m_target, m_target.Centroid(true), Position{ 0, 0, 0 });
ref_mol.setGeometry(tref);
tar_mol.setGeometry(tget);
/*
if (m_moi) {
ref_mol.CalculateRotationalConstants();
tar_mol.CalculateRotationalConstants();
Eigen::MatrixXd tar = tget.transpose();
Eigen::MatrixXd ref = tref.transpose();
Geometry rotated_reference = ref.transpose() * ref_mol.AlignmentAxes();
Geometry rotated_target = tar.transpose() * tar_mol.AlignmentAxes();
ref_mol.setGeometry(rotated_reference);
tar_mol.setGeometry(rotated_target);
ref_mol.writeXYZFile("reference.moi.xyz");
tar_mol.writeXYZFile("target.moi.xyz");
} else {
*/
auto operators = GetOperateVectors(ref_mol, tar_mol);
Eigen::Matrix3d R = operators.first;
Eigen::MatrixXd tar = tget.transpose();
Expand All @@ -839,14 +843,17 @@ void RMSDDriver::TemplateFree()
ref_mol.setGeometry(tref);
Molecule tar_mol = m_target;
tar_mol.setGeometry(rotated);
ref_mol.writeXYZFile("reference.nomoi.xyz");
tar_mol.writeXYZFile("target.nomoi.xyz");
// ref_mol.writeXYZFile("reference.nomoi.xyz");
// tar_mol.writeXYZFile("target.nomoi.xyz");
// }

std::vector<int> new_order = DistanceReorder(ref_mol, tar_mol);
auto rules = ApplyOrder(new_order, m_target);
double rmsd = Rules2RMSD(new_order);
m_target = rules;
m_target_aligned = m_target;
m_reorder_rules = new_order;
}
std::vector<int> new_order = DistanceReorder(ref_mol, tar_mol);
m_target_reordered = ApplyOrder(new_order, m_target);
m_target = m_target_reordered;
m_target_aligned = m_target;
m_reorder_rules = new_order;
}

void RMSDDriver::FinaliseTemplate(std::pair<std::vector<int>, std::vector<int>> pairs)
Expand All @@ -863,13 +870,15 @@ void RMSDDriver::FinaliseTemplate(std::pair<std::vector<int>, std::vector<int>>
auto result = AlignByVectorPair(pairs);
m_reorder_rules = result;
m_target_reordered = ApplyOrder(m_reorder_rules, target);
local_results.insert(std::pair<double, std::vector<int>>(Rules2RMSD(m_reorder_rules), m_reorder_rules));
double rmsd = Rules2RMSD(m_reorder_rules);
// std::cout << rmsd << " ";
local_results.insert(std::pair<double, std::vector<int>>(rmsd, m_reorder_rules));
/*std::set<int> s(result.second.begin(), result.second.end());
if (s.size() != result.second.size()) // make sure, that only results with non-duplicate vectors are accepted
continue;*/
result = AlignByVectorPair(tmp, m_reorder_rules);
if (m_reorder_rules == result)
break;
// if (m_reorder_rules == result)
// break;
m_reorder_rules = result;
m_target_reordered = ApplyOrder(m_reorder_rules, target);
StructComp structcomp = Rule2RMSD(m_reorder_rules);
Expand Down Expand Up @@ -1158,7 +1167,7 @@ bool RMSDDriver::TemplateReorder()
std::vector<int> RMSDDriver::DistanceReorder(const Molecule& reference, const Molecule& target)
{
std::map<double, std::vector<int>> rules;

/*
std::vector<int> orderV1 = DistanceReorderV1(reference, target);
std::vector<int> orderV2 = DistanceReorderV2(reference, target);
Expand All @@ -1167,24 +1176,25 @@ std::vector<int> RMSDDriver::DistanceReorder(const Molecule& reference, const Mo
rules.insert(std::pair<double, std::vector<int>>(rmsdV1, orderV1));
rules.insert(std::pair<double, std::vector<int>>(rmsdV2, orderV2));

*/
if (m_nomunkres == false) {
std::vector<int> munkress = Munkress(reference, target);
double rmsdM = Rules2RMSD(munkress);
// std::cout << rmsdM << ": " << std::endl;
rules.insert(std::pair<double, std::vector<int>>(rmsdM, munkress));
}

if (m_update_rotation) {
auto orderV3 = DistanceReorderV3(reference, target);
double rmsdV3 = Rules2RMSD(orderV3.first);

rules.insert(std::pair<double, std::vector<int>>(rmsdV3, orderV3.first));
if (m_split) {
double rmsdV4 = Rules2RMSD(orderV3.second);
rules.insert(std::pair<double, std::vector<int>>(rmsdV4, orderV3.first));
/*
if (m_update_rotation) {
auto orderV3 = DistanceReorderV3(reference, target);
double rmsdV3 = Rules2RMSD(orderV3.first);
rules.insert(std::pair<double, std::vector<int>>(rmsdV3, orderV3.first));
if (m_split) {
double rmsdV4 = Rules2RMSD(orderV3.second);
rules.insert(std::pair<double, std::vector<int>>(rmsdV4, orderV3.first));
}
}
}

*/
for (auto iter : rules)
m_stored_rules.push_back(iter.second);

Expand Down Expand Up @@ -1391,19 +1401,25 @@ std::vector<int> RMSDDriver::Munkress(const Molecule& reference, const Molecule&
Eigen::MatrixXd distance = Eigen::MatrixXd::Zero(reference.AtomCount(), reference.AtomCount());
std::vector<int> element_reference = reference.Atoms();
std::vector<int> element_target = target.Atoms();

double min = penalty;
static std::random_device rd{};
static std::mt19937 gen{ rd() };
static std::normal_distribution<> d{ 0, 3 };
for (int i = 0; i < reference.AtomCount(); ++i) {
for (int j = 0; j < target.AtomCount(); ++j) {
distance(i, j) = GeometryTools::Distance(target.Atom(j).second, reference.Atom(i).second) + penalty * (target.Atom(j).first != reference.Atom(i).first);

distance(i, j) = GeometryTools::Distance(target.Atom(j).second, reference.Atom(i).second) * GeometryTools::Distance(target.Atom(j).second, reference.Atom(i).second)
// + (target.Atom(j).second.norm() - reference.Atom(i).second.norm())*(target.Atom(j).second.norm() - reference.Atom(i).second.norm())
// + d(gen)
+ penalty * (target.Atom(j).first != reference.Atom(i).first);
}
}
if (m_dmix <= 1 && 0 < m_dmix) {
Matrix d = target.DistanceMatrix().first;
distance = (1 - m_dmix) * distance + m_dmix * d;
}
// std::cout << distance << std::endl;

auto result = MunkressAssign(distance);
// std::cout << result << std::endl;

for (int i = 0; i < result.cols(); ++i) {
for (int j = 0; j < result.rows(); ++j) {
Expand All @@ -1413,9 +1429,6 @@ std::vector<int> RMSDDriver::Munkress(const Molecule& reference, const Molecule&
}
}
}
// for(auto i : new_order)
// std::cout << i << " ";
// std::cout << std::endl;
return new_order;
}

Expand All @@ -1425,7 +1438,7 @@ bool RMSDDriver::MolAlignLib()
m_target.writeXYZFile("molalign_tar.xyz");

FILE* FileOpen;
std::string command = m_molalign + " molaign_ref.xyz " + " molalign_tar.xyz -reorder -fast -tol " + std::to_string(m_molaligntol) + " 2>&1";
std::string command = m_molalign + " molaign_ref.xyz " + " molalign_tar.xyz -sort -fast -tol " + std::to_string(m_molaligntol) + " 2>&1";
if (!m_silent)
std::cout << command << std::endl;
FileOpen = popen(command.c_str(), "r");
Expand All @@ -1447,10 +1460,11 @@ bool RMSDDriver::MolAlignLib()
fmt::print(fg(fmt::color::green) | fmt::emphasis::bold, "\nPlease cite the follow research report!\nJ. Chem. Inf. Model. 2023, 63, 4, 1157–1165 - DOI: 10.1021/acs.jcim.2c01187\n\n");
}
FileIterator file("aligned.xyz", true);
file.Next();
m_target_reordered = file.Next();
m_target_aligned = m_target_reordered;
m_target = m_target_reordered;
std::filesystem::remove("aligned.xyz");
// std::filesystem::remove("aligned.xyz");
} else {
if (!rndm && !error) {
fmt::print(fg(fmt::color::salmon) | fmt::emphasis::bold, "Molalign was not found. Consider getting it from\nhttps://github.com/qcuaeh/molalignlib\nEither adding the location of the binary to the path for executables or append\n-molalignbin /yourpath/molalign\nto your argument list!\n");
Expand Down
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