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@conradhuebler
conradhuebler committed May 9, 2023
1 parent f4dd00a commit 440d29b
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Showing 9 changed files with 311 additions and 102 deletions.
143 changes: 67 additions & 76 deletions src/capabilities/confscan.cpp
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24 changes: 12 additions & 12 deletions src/capabilities/confscan.h
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Original file line number Diff line number Diff line change
Expand Up @@ -56,12 +56,12 @@ static const json ConfScanJson = {
{ "preventreorder", false },
{ "scaleLoose", 1.5 },
{ "scaleTight", 0.1 },
{ "scaleLooseEnergy", 1.2 },
{ "scaleTightEnergy", 0.1 },
{ "scaleLooseRotational", 1.2 },
{ "scaleTightRotational", 0.1 },
{ "scaleLooseRipser", 1.2 },
{ "scaleTightRipser", 0.1 },
{ "sLE", 1.2 },
{ "sTE", 0.1 },
{ "sLI", 1.2 },
{ "sTI", 0.1 },
{ "sLH", 1.2 },
{ "sTH", 0.1 },
{ "skip", 0 },
{ "allxyz", false },
{ "update", false },
Expand Down Expand Up @@ -315,13 +315,13 @@ class ConfScan : public CurcumaMethod {
std::map<double, int> m_ordered_list;
std::vector<std::pair<std::string, Molecule*>> m_molecules;
double m_rmsd_threshold = 1.0, m_nearly_missed = 0.8, m_energy_cutoff = -1, m_reference_last_energy = 0, m_target_last_energy = 0, m_lowest_energy = 1, m_current_energy = 0;
double m_scaleTightEnergy = 0.1, m_scaleLooseEnergy = 1.5;
double m_scaleTightRotational = 0.1, m_scaleLooseRotational = 1.5;
double m_scaleTightRipser = 0.1, m_scaleLooseRipser = 1.5;
double m_sTE = 0.1, m_sLE = 1.5;
double m_sTI = 0.1, m_sLI = 1.5;
double m_sTH = 0.1, m_sLH = 1.5;

double m_reference_restored_energy = -1e10, m_target_restored_energy = -1e10;
double m_diff_rot_threshold_loose = 0.0, m_diff_ripser_threshold_loose = 0.0, m_diff_energy_threshold_loose = 0.0;
double m_diff_rot_threshold_tight = 0.0, m_diff_ripser_threshold_tight = 0.0, m_diff_energy_threshold_tight = 0.0;
double m_dLI = 0.0, m_dLH = 0.0, m_dLE = 0.0;
double m_dTI = 0.0, m_dTH = 0.0, m_dTE = 0.0;

std::vector<Molecule*> m_result, m_rejected_structures, m_stored_structures, m_previously_accepted;
std::vector<const Molecule*> m_threshold;
Expand All @@ -336,7 +336,7 @@ class ConfScan : public CurcumaMethod {
std::string m_molalign = "molalign";

double m_domolalign = -1;
double m_last_diff = 0.0, m_last_ripser = 0.0, m_last_dE = -1, m_dE = -1, m_damping = 0.8;
double m_lastDI = 0.0, m_lastDH = 0.0, m_lastdE = -1, m_dE = -1, m_damping = 0.8;
int m_maxmol = 0;
int m_maxrank = 10000;
int m_maxParam = -1;
Expand Down
91 changes: 88 additions & 3 deletions src/capabilities/persistentdiagram.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@

using json = nlohmann::json;

PersistentDiagram::PersistentDiagram(const json config)
PersistentDiagram::PersistentDiagram(const json& config)
{
json j = MergeJson(RipserJson, config);
// std::cout << j << std::endl;
Expand All @@ -43,13 +43,15 @@ PersistentDiagram::PersistentDiagram(const json config)
m_std_x = j["ripser_stdx"];
m_std_y = j["ripser_stdy"];
m_dimension = j["ripser_dimension"];
m_epsilon = j["ripser_epsilon"];

m_threshold = std::numeric_limits<float>::max();
}

dpairs PersistentDiagram::generatePairs()
{
coefficient_t modulus = 2;

std::vector<float> distance = m_compressed_lower_distance_matrix;
compressed_lower_distance_matrix dist(std::move(m_compressed_lower_distance_matrix));

value_t enclosing_radius = std::numeric_limits<value_t>::infinity();
Expand All @@ -75,6 +77,68 @@ dpairs PersistentDiagram::generatePairs()
return final;
}

triples PersistentDiagram::generateTriples()
{
coefficient_t modulus = 2;
std::vector<float> distance = m_compressed_lower_distance_matrix;
compressed_lower_distance_matrix dist(std::move(m_compressed_lower_distance_matrix));

value_t enclosing_radius = std::numeric_limits<value_t>::infinity();
if (m_threshold == std::numeric_limits<value_t>::max()) {
for (size_t i = 0; i < dist.size(); ++i) {
value_t r_i = -std::numeric_limits<value_t>::infinity();
for (size_t j = 0; j < dist.size(); ++j)
r_i = std::max(r_i, dist(i, j));
enclosing_radius = std::min(enclosing_radius, r_i);
}
}

auto result = ripser<compressed_lower_distance_matrix>(std::move(dist), m_dimension, enclosing_radius,
m_ratio, modulus)
.compute_barcodes();

triples final;
for (const auto& a : result)
if (a.first != 0) {
for (const auto& b : a.second) {
triple t;
t.start = b.first;
t.end = b.second;
final.push_back(t);
}
} else {
int counter = 0;
std::vector<int> indices;
for (const auto& b : a.second)

{
bool found = false;
for (int i = 0; i < distance.size(); ++i) {
if (std::abs(distance[i] - b.second) < 1e-6 && std::find(indices.begin(), indices.end(), i) == indices.end()) {
// std::cout << i << " " << distance[i] << " " << m_en_scaling[i] << " " << counter++ << std::endl;
indices.push_back(i);
triple t;
t.start = b.first;
t.end = b.second;
t.scaling = m_en_scaling[i] + m_epsilon;
final.push_back(t);

found = true;
break;
}
}
if (found == false) {
triple t;
t.start = b.first;
t.end = b.second;
final.push_back(t);
}
}
}

return final;
}

Eigen::MatrixXd PersistentDiagram::generateImage(const dpairs& pairs)
{
Eigen::MatrixXd matrix = Eigen::MatrixXd::Zero(m_bins, m_bins);
Expand All @@ -86,7 +150,6 @@ Eigen::MatrixXd PersistentDiagram::generateImage(const dpairs& pairs)
for (int j = 0; j < matrix.rows(); ++j) // iteration over x values
{
double cur_x = (m_xmax - m_xmin) * i_bins * (j);

for (const auto& pair : pairs) {
double x = pair.first;
double y = pair.second;
Expand All @@ -96,3 +159,25 @@ Eigen::MatrixXd PersistentDiagram::generateImage(const dpairs& pairs)
}
return matrix;
}

Eigen::MatrixXd PersistentDiagram::generateImage(const triples& pairs)
{
Eigen::MatrixXd matrix = Eigen::MatrixXd::Zero(m_bins, m_bins);

double i_bins = 1 / double(m_bins);
for (int i = 0; i < matrix.cols(); ++i) // iteration over y values
{
double cur_y = m_ymax - (m_ymax - m_ymin) * i_bins * (i);
for (int j = 0; j < matrix.rows(); ++j) // iteration over x values
{
double cur_x = (m_xmax - m_xmin) * i_bins * (j);
for (const auto& triple : pairs) {
double x = triple.start;
double y = triple.end;
double std = triple.scaling;
matrix(i, j) += m_scaling * exp(-((cur_x - x) * (cur_x - x) * m_std_x / std)) * exp((-(cur_y - y) * (cur_y - y) * m_std_y / std));
}
}
}
return matrix;
}
22 changes: 20 additions & 2 deletions src/capabilities/persistentdiagram.h
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Original file line number Diff line number Diff line change
Expand Up @@ -26,9 +26,17 @@

#include <Eigen/Dense>

struct triple {
double start = 0;
double end = 0;
double scaling = 1;
};

typedef std::pair<double, double> dpair;

typedef std::vector<dpair> dpairs;
typedef std::vector<triple> triples;

using json = nlohmann::json;

static const json RipserJson = {
Expand All @@ -41,18 +49,24 @@ static const json RipserJson = {
{ "ripser_stdx", 10 },
{ "ripser_stdy", 10 },
{ "ripser_ratio", 1 },
{ "ripser_dimension", 2 }
{ "ripser_dimension", 2 },
{ "ripser_epsilon", 0.4 }
};

class PersistentDiagram {
public:
PersistentDiagram(const json config = RipserJson);
PersistentDiagram(const json& config = RipserJson);

inline void setDistanceMatrix(const std::vector<float>& vector)
{
m_compressed_lower_distance_matrix = vector;
}

inline void setENScaling(const std::vector<double>& en_scaling)
{
m_en_scaling = en_scaling;
}

inline void setDimension(int dim)
{
m_dimension = dim;
Expand All @@ -69,6 +83,7 @@ class PersistentDiagram {
}

dpairs generatePairs();
triples generateTriples();

inline void setXRange(double xmin, double xmax)
{
Expand All @@ -83,6 +98,7 @@ class PersistentDiagram {
}

Eigen::MatrixXd generateImage(const dpairs& pairs);
Eigen::MatrixXd generateImage(const triples& pairs);

void setScaling(double scaling) { m_scaling = scaling; }
void setBins(int bins) { m_bins = bins; }
Expand All @@ -98,5 +114,7 @@ class PersistentDiagram {
double m_scaling = 0.1;
double m_std_x = 10;
double m_std_y = 10;
double m_epsilon = 0.4;
std::vector<float> m_compressed_lower_distance_matrix;
std::vector<double> m_en_scaling;
};
89 changes: 89 additions & 0 deletions src/core/elements.h
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Original file line number Diff line number Diff line change
Expand Up @@ -486,6 +486,95 @@ static const std::vector<double> CovalentRadius = {
1.46 // At - taken from Bi
};

static const std::vector<double> PaulingEN = {
-1, // leading index
2.2, // H
0, // He
0.98, // Li
1.57, // Be
2.04, // B
2.55, // C
3.04, // N
3.44, // O
3.98, // F
0, // Ne
0.93, // Na
1.31, // Mg
1.61, // Al
1.9, // S
2.19, // P
2.58, // S
3.16, // Cl
0, // Ar
0.82, // K
1.0, // Ca
1.36, // Sc
1.54, // Ti
1.63, // V
1.66, // Cr
1.55, // Mn
1.83, // Fe
1.88, // Co
1.91, // Ni
1.9, // Cu
1.65, // Zn
1.81, // Ga
2.01, // Ge
2.18, // As
2.55, // Se
2.96, // Br
0, // Kr
0.82, // Rb
0.95, // Sr
1.22, // Y
1.33, // Zr
1.6, // Nb
2.16, // Mo
1.9, // Tc
2.2, // Ru
2.28, // Rh
2.20, // Pd
1.93, // Ag
1.69, // Cd
1.78, // In
1.96, // Sn
2.05, // Sb
2.1, // Te
2.66, // I
0, // Xe
0.79, // Cs
0.89, // Ba
1.1, // La
1.12, // Ce - taken from La
1.13, // Pr - taken from La
1.14, // Nd - taken from La
1.13, // Pm - taken from La
1.17, // Sm - taken from La
1.2, // Eu - taken from La
1.2, // Gd - taken from La
1.2, // Tb - taken from La
1.22, // Dy - taken from La
1.23, // Ho - taken from La
1.24, // Er - taken from La
1.25, // Tm - taken from La
1.1, // Yb - taken from La
1.27, // Lu
1.3, // Hf
1.5, // Ta
2.36, // W
1.9, // Re
2.2, // Os
2.2, // Ir
2.28, // Pt
2.54, // Au
2, // Hg
2.04, // Tl
2.33, // Pb
2.02, // Bi
2.0, // Po - taken from Bi
2.2 // At - taken from Bi
};

// The old ones
/* for now, taken from here
* https://de.wikipedia.org/wiki/Van-der-Waals-Radius */
Expand Down
11 changes: 11 additions & 0 deletions src/core/molecule.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -769,6 +769,17 @@ std::vector<float> Molecule::LowerDistanceVector() const
return vector;
}

std::vector<double> Molecule::DeltaEN() const
{
std::vector<double> vector;
for (int i = 0; i < AtomCount(); ++i) {
for (int j = 0; j < i; ++j) {
vector.push_back(std::abs(Elements::PaulingEN[m_atoms[i]] - Elements::PaulingEN[m_atoms[j]]));
}
}
return vector;
}

Position Molecule::Centroid(bool protons, int fragment) const
{
return GeometryTools::Centroid(getGeometryByFragment(fragment, protons));
Expand Down
1 change: 1 addition & 0 deletions src/core/molecule.h
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,7 @@ class Molecule

std::string LowerDistanceMatrix() const;
std::vector<float> LowerDistanceVector() const;
std::vector<double> DeltaEN() const;

bool setGeometry(const Geometry &geometry);
bool setGeometryByFragment(const Geometry& geometry, int fragment, bool protons = true);
Expand Down
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