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/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#pragma once
#include <pdb-redo/BondMap.hpp>
#include "pdb-redo/MapMaker.hpp"
namespace pdb_redo
{
// --------------------------------------------------------------------
struct AtomData;
class BoundingBox;
struct ResidueStatistics
{
std::string asymID;
int seqID;
std::string compID;
std::string authSeqID;
double RSR, SRSR, RSCCS, EDIAm, OPIA;
int ngrid;
};
std::ostream &operator<<(std::ostream &os, const ResidueStatistics &st);
// --------------------------------------------------------------------
template <typename F, typename FTYPE = float>
void iterateGrid(const clipper::Coord_orth &p, float r, const clipper::Xmap<FTYPE> &m, F &&func)
{
using namespace clipper;
Coord_frac fp = p.coord_frac(m.cell());
Coord_frac o = Coord_orth(r, r, r).coord_frac(m.cell());
o[0] = std::abs(o[0]);
o[1] = std::abs(o[1]);
o[2] = std::abs(o[2]);
Coord_frac fMin = fp - o, fMax = fp + o;
Coord_map mMin = fMin.coord_map(m.grid_sampling()), mMax = fMax.coord_map(m.grid_sampling());
Coord_grid gMin = mMin.floor(), gMax = mMax.ceil();
auto i0 = Xmap_base::Map_reference_coord(m, gMin);
for (auto iu = i0; iu.coord().u() <= gMax[0]; iu.next_u())
for (auto iv = iu; iv.coord().v() <= gMax[1]; iv.next_v())
for (auto iw = iv; iw.coord().w() <= gMax[2]; iw.next_w())
func(iw);
}
// --------------------------------------------------------------------
class StatsCollector
{
public:
StatsCollector(const StatsCollector &) = delete;
StatsCollector &operator=(const StatsCollector &) = delete;
StatsCollector(const MapMaker<float> &mm,
cif::mm::structure &structure, bool electronScattering);
virtual std::vector<ResidueStatistics> collect() const;
virtual std::vector<ResidueStatistics> collect(const std::string &asymID) const;
virtual std::vector<ResidueStatistics> collect(const std::string &asymID,
int resFirst, int resLast, bool authNameSpace = false) const;
virtual ResidueStatistics collect(std::initializer_list<const cif::mm::residue *> residues) const;
virtual ResidueStatistics collect(std::initializer_list<cif::mm::atom> atoms) const;
virtual ResidueStatistics collect(const std::vector<cif::mm::atom> &atoms) const;
protected:
using residue_list = std::vector<std::tuple<std::string, int, std::string>>;
// asym-seqid-compid
std::vector<ResidueStatistics> collect(const residue_list &residues, BoundingBox &bbox, bool addWaters) const;
void initialize();
virtual void calculate(std::vector<AtomData> &atomData) const;
struct cmpGPt
{
bool operator()(const clipper::Coord_grid &a, const clipper::Coord_grid &b) const
{
int d = a.u() - b.u();
if (d == 0)
d = a.v() - b.v();
if (d == 0)
d = a.w() - b.w();
return d < 0;
}
};
typedef std::map<clipper::Coord_grid, double, cmpGPt> GridPtDataMap;
cif::mm::structure &mStructure;
const MapMaker<float> &mMapMaker;
clipper::Spacegroup mSpacegroup;
clipper::Cell mCell;
clipper::Grid_sampling mGrid;
float mResHigh, mResLow;
bool mElectronScattering;
std::map<std::string, std::pair<double, double>> mRmsScaled;
void collectSums(std::vector<AtomData> &atomData, GridPtDataMap &gridPointDensity) const;
void sumDensity(std::vector<AtomData> &atomData,
GridPtDataMap &gridPointDensity, std::map<std::string, std::vector<double>> &zScoresPerAsym) const;
// Other variables we cache
double mMeanDensityFb, mRMSDensityFb, mRMSDensityFd;
double mSZ; // average electron density in cell
double mVF; // degrees of freedom
double mVC; // cell volume?
};
// --------------------------------------------------------------------
class EDIAStatsCollector : public StatsCollector
{
public:
EDIAStatsCollector(const MapMaker<float> &mm,
cif::mm::structure &structure, bool electronScattering);
protected:
virtual void calculate(std::vector<AtomData> &atomData) const;
BondMap createBondMap(std::vector<AtomData> &atomData) const;
std::map<cif::atom_type, float> mRadii;
};
} // namespace pdb_redo
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