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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.
*/
/*
Created by: Maarten L. Hekkelman
Date: dinsdag 22 mei, 2018
*/
#pragma once
#include <set>
#include <cif++/point.hpp>
#include <pdb-redo/MapMaker.hpp>
namespace pdb_redo
{
using DPoint = cif::point_type<double>;
// --------------------------------------------------------------------
class AtomLocationProvider;
class DFCollector;
// --------------------------------------------------------------------
typedef std::size_t AtomRef;
typedef typename Map<float>::Xmap Xmap;
// --------------------------------------------------------------------
struct Restraint
{
virtual ~Restraint() {}
virtual double f(const AtomLocationProvider &atoms) const = 0;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const = 0;
virtual void print(const AtomLocationProvider &atoms) const = 0;
};
struct BondRestraint : public Restraint
{
BondRestraint(AtomRef a, AtomRef b, double distance, double esd)
: mA(a)
, mB(b)
, mDist(distance)
, mDistESD(esd)
{
}
virtual double f(const AtomLocationProvider &atoms) const;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const;
virtual void print(const AtomLocationProvider &atoms) const;
AtomRef mA, mB;
double mDist, mDistESD;
};
struct AngleRestraint : public Restraint
{
AngleRestraint(AtomRef a, AtomRef b, AtomRef c, double angle, double esd)
: mA(a)
, mB(b)
, mC(c)
, mAngle(angle)
, mESD(esd)
{
}
virtual double f(const AtomLocationProvider &atoms) const;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const;
virtual void print(const AtomLocationProvider &atoms) const;
AtomRef mA, mB, mC;
double mAngle, mESD;
};
struct TorsionRestraint : public Restraint
{
TorsionRestraint(AtomRef a, AtomRef b, AtomRef c, AtomRef d, double target, double esd, int periodicity)
: mA(a)
, mB(b)
, mC(c)
, mD(d)
, mPeriodicity(periodicity)
, mTarget(target)
, mESD(esd)
{
}
virtual double f(const AtomLocationProvider &atoms) const;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const;
virtual void print(const AtomLocationProvider &atoms) const;
AtomRef mA, mB, mC, mD;
int mPeriodicity;
double mTarget, mESD;
private:
std::tuple<DPoint, DPoint, DPoint, DPoint> CalculateTorsionGradients(float theta, DPoint p[4]) const;
};
struct TransPeptideRestraint : public TorsionRestraint
{
TransPeptideRestraint(AtomRef a, AtomRef b, AtomRef c, AtomRef d, double esd = 2.0)
: TorsionRestraint(a, b, c, d, 180.0, esd, 2)
{
}
};
const double kChiralVolumeESD = 0.2; // according to coot that's a reasonable value...
struct ChiralVolumeRestraint : public Restraint
{
ChiralVolumeRestraint(AtomRef c, AtomRef a1, AtomRef a2, AtomRef a3, double volume)
: mCentre(c)
, mA1(a1)
, mA2(a2)
, mA3(a3)
, mVolume(volume)
{
}
virtual double f(const AtomLocationProvider &atoms) const;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const;
virtual void print(const AtomLocationProvider &atoms) const;
AtomRef mCentre, mA1, mA2, mA3;
double mVolume, mESD = kChiralVolumeESD;
};
struct PlanarityRestraint : public Restraint
{
PlanarityRestraint(std::vector<AtomRef> &&atoms, double esd)
: mAtoms(std::move(atoms))
, mESD(esd)
{
if (mAtoms.size() < 3)
throw std::runtime_error("Insufficient number of atoms in planar restraint");
}
virtual double f(const AtomLocationProvider &atoms) const;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const;
virtual void print(const AtomLocationProvider &atoms) const;
void calculatePlaneFunction(const AtomLocationProvider &atoms, double abcd[4]) const;
std::vector<AtomRef> mAtoms;
double mESD;
};
struct NonBondedContactRestraint : public Restraint
{
NonBondedContactRestraint(AtomRef a, AtomRef b, double minDist, double esd)
: mA(a)
, mB(b)
, mMinDist(minDist)
, mMinDistSq(minDist * minDist)
, mDistESD(esd)
{
}
virtual double f(const AtomLocationProvider &atoms) const;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const;
virtual void print(const AtomLocationProvider &atoms) const;
AtomRef mA, mB;
double mMinDist, mMinDistSq, mDistESD;
};
struct DensityRestraint : public Restraint
{
DensityRestraint(std::vector<std::pair<AtomRef, double>> &&atoms,
const Xmap &xMap, double mapWeight = 60);
virtual double f(const AtomLocationProvider &atoms) const;
virtual void df(const AtomLocationProvider &atoms, DFCollector &d) const;
virtual void print(const AtomLocationProvider &atoms) const;
std::vector<std::pair<AtomRef, double>> mAtoms;
const Xmap &mXMap;
double mMapWeight;
bool mElectronScattering = false;
};
} // namespace pdb_redo
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