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88 lines
2.8 KiB
C++
88 lines
2.8 KiB
C++
//
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// Copyright (C) 2004-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef __RD_NONBONDED_H__
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#define __RD_NONBONDED_H__
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#include <ForceField/Contrib.h>
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namespace ForceFields {
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namespace UFF {
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class AtomicParams;
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//! the van der Waals term for the Universal Force Field
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/*!
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<b>The Distance Threshold</b>
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For the sake of efficiency, each vdwContrib maintains a threshold
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distance. When the distance between the two atoms exceeds this
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threshold, the vdwContrib makes no contribution to either the
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energy or the gradient.
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The threshold is set to a multiple of the vdW distance's preferred
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length. This multiplier can be supplied to the constructor.
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*/
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class RDKIT_FORCEFIELD_EXPORT vdWContrib : public ForceFieldContrib {
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public:
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vdWContrib() {}
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//! Constructor
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/*!
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\param owner pointer to the owning ForceField
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\param idx1 index of end1 in the ForceField's positions
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\param idx2 index of end2 in the ForceField's positions
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\param at1Params pointer to the parameters for end1
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\param at2Params pointer to the parameters for end2
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\param threshMultiplier (optional) multiplier for the threshold
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calculation. See class documentation for details.
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*/
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vdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
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const AtomicParams *at1Params, const AtomicParams *at2Params,
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double threshMultiplier = 10.0);
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double getEnergy(double *pos) const override;
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void getGrad(double *pos, double *grad) const override;
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vdWContrib *copy() const override { return new vdWContrib(*this); }
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private:
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int d_at1Idx{-1};
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int d_at2Idx{-1};
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double d_xij; //!< the preferred length of the contact
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double d_wellDepth; //!< the vdW well depth (strength of the interaction)
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double d_thresh; //!< the distance threshold
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};
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namespace Utils {
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//! calculates and returns the UFF minimum position for a vdW contact
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/*!
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\param at1Params pointer to the parameters for end1
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\param at2Params pointer to the parameters for end2
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\return the position of the minimum
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*/
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RDKIT_FORCEFIELD_EXPORT double calcNonbondedMinimum(
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const AtomicParams *at1Params, const AtomicParams *at2Params);
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//! calculates and returns the UFF well depth for a vdW contact
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/*!
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\param at1Params pointer to the parameters for end1
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\param at2Params pointer to the parameters for end2
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\return the depth of the well
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*/
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RDKIT_FORCEFIELD_EXPORT double calcNonbondedDepth(
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const AtomicParams *at1Params, const AtomicParams *at2Params);
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} // namespace Utils
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} // namespace UFF
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} // namespace ForceFields
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#endif
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