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shape_functions.hpp
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shape_functions.hpp
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/* $Id: shape_functions.hpp 685605 2024-07-26 12:29:33Z thiessen $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Authors: Evan Bolton, Leonid Zaslavsky, Paul Thiessen
*
* ===========================================================================
*/
#ifndef ALIGN3D_SHAPE_FUNCTIONS__HPP
#define ALIGN3D_SHAPE_FUNCTIONS__HPP
#include "types.hpp"
namespace Align3D {
void Neighbor_Conformers(
const float* ref_coord,
const std::vector<double>& alpha_ref_vector,
const std::vector< unsigned >& ref_volumeAtomIndexVector,
const std::map< unsigned, std::vector< unsigned > >& ref_colorAtomType2IndexVectorMap,
const double ref_sov,
const double ref_sof,
const float* fit_coord,
const std::vector<double>& alpha_fit_vector,
const std::vector< unsigned >& fit_volumeAtomIndexVector,
const std::map< unsigned, std::vector< unsigned > >& fit_colorAtomType2IndexVectorMap,
const double fit_sov,
const double fit_sof,
const bool considerColorAtoms,
const unsigned max_preiters,
const unsigned max_postiters,
const double opt_param,
float* matrix,
double& nbr_st,
double& nbr_ct
);
// *** Gradients
void ComputeOverlapAndAnalyticGradient(
double& o, // overlap
double* g, // gradient[ 7 ]
const double* m, // rotation/translation matrix [ 12 ]
const float* ref_coord, // per ref atom, XYZ coordinates [3*nref]
const std::vector<double>& alpha_ref_vector,
const std::vector< unsigned >& ref_volume_atom_index_vector,
const float* fit_coord, // original per fit atom, XYZ coordinates [3*nfit]
const std::vector<double>& alpha_fit_vector,
const std::vector< unsigned >& fit_volume_atom_index_vector,
bool needGrad = true
);
// *** Interconvert quaternion/rotational matrix with translational matrix along for the ride
void VQuaternionTransArray2RotTransMatrix( double* m, // double[ 12 ]
const double* q, // double[ 7 ]
const bool normalize = false );
void VRotTransMatrix2QuaternionTransArray( double* q, // double[ 7 ]
const double* m ); // double[ 12 ]
void VQuaternionTransArray2RotTransMatrix( float* m, // float[ 12 ]
const double* q, // float[ 7 ]
const bool normalize = false );
// *** Rotational/Translational matrix handling (3x3 matrix + 1x3 matrix == 12 floats)
// Combine (matrix multiply) two rotational/translational matrices
void VCombineRotTransMatrixMatrix( double* t, // double[ 12 ]
const double* t1, // double[ 12 ]
const double* t2 ); // double[ 12 ]
void VRotTransMatrixNew( Uint8& packed,
const float* m ); // float[ 12 ]
double ComputeFeatureOverlap( const float* ref_coord, // per ref atom, XYZ coordinates
const std::vector<double>& alpha_ref_vector,
const std::map< unsigned, std::vector< unsigned > >& ref_atom_type_to_index_vector_map,
const float* fit_coord, // per fit atom, XYZ coordinates
const std::vector<double>& alpha_fit_vector,
const std::map< unsigned, std::vector< unsigned > >& fit_atom_type_to_index_vector_map,
const double* m
);
double ComputeFeatureOverlap(
const float* ref_coord,
const std::vector<double>& alpha_ref_vector,
const std::map< unsigned, std::vector< unsigned > >& ref_atom_type_to_index_vector_map,
const float* fit_coord,
const std::vector<double>& alpha_fit_vector,
const std::map< unsigned, std::vector< unsigned > >& fit_atom_type_to_index_vector_map
);
double ComputeShapeOverlap( const float* ref_coord, // per ref atom, XYZ coordinates
const std::vector<double>& alpha_ref_vector,
const std::vector< unsigned >& ref_volume_atom_index_vector,
const float* fit_coord,
const std::vector<double>& alpha_fit_vector,
const std::vector< unsigned >& fit_volume_atom_index_vector
);
// Get Steric Center of Gravity
template< class T > void Get3dStericCenterOfGravity( T* center,
const T* coord,
const unsigned ncoord )
{
if ( 0 == ncoord ) {
center[ 0 ] = static_cast< T >( 0.0 );
center[ 1 ] = static_cast< T >( 0.0 );
center[ 2 ] = static_cast< T >( 0.0 );
return; // Nothing more to do...
}
// Loop over coordinates
T x = coord[ 0 ];
T y = coord[ 1 ];
T z = coord[ 2 ];
for ( unsigned icoord = 1; icoord != ncoord; ++icoord ) {
x += coord[ icoord * 3 ];
y += coord[ 1 + ( icoord * 3 ) ];
z += coord[ 2 + ( icoord * 3 ) ];
}
center[ 0 ] = x / static_cast< T >( ncoord );
center[ 1 ] = y / static_cast< T >( ncoord );
center[ 2 ] = z / static_cast< T >( ncoord );
}
template< class T, class W > void Get3dCenterOfMass( T* center,
const T* coord,
const W* weight,
const unsigned ncoord )
{
if ( 0 == ncoord ) {
center[ 0 ] = static_cast< T >( 0.0 );
center[ 1 ] = static_cast< T >( 0.0 );
center[ 2 ] = static_cast< T >( 0.0 );
return; // Nothing more to do...
}
// Loop over coordinates
T x = static_cast< T >( coord[ 0 ] * weight[ 0 ] );
T y = static_cast< T >( coord[ 1 ] * weight[ 0 ] );
T z = static_cast< T >( coord[ 2 ] * weight[ 0 ] );
for ( unsigned icoord = 1; icoord != ncoord; ++icoord ) {
x += static_cast< T >( coord[ ( icoord * 3 ) ] * weight[ icoord ] );
y += static_cast< T >( coord[ 1 + ( icoord * 3 ) ] * weight[ icoord ] );
z += static_cast< T >( coord[ 2 + ( icoord * 3 ) ] * weight[ icoord ] );
}
center[ 0 ] = x / static_cast< T >( ncoord );
center[ 1 ] = y / static_cast< T >( ncoord );
center[ 2 ] = z / static_cast< T >( ncoord );
}
// Translate 3D Coordinates
template< class T > void Translate3dCoords( T* coord,
const T* translate,
const unsigned ncoord )
{
T x = translate[ 0 ];
T y = translate[ 1 ];
T z = translate[ 2 ];
for( unsigned icoord = 0; icoord != ncoord; ++icoord ) {
coord[ ( icoord * 3 ) ] += x;
coord[ 1 + ( icoord * 3 ) ] += y;
coord[ 2 + ( icoord * 3 ) ] += z;
}
}
// Translate 3D Coordinates to molecule center
template< class T > void Translate3D2Center( T* coord,
const unsigned natoms )
{
// Get steric center
T cne[ 3 ];
Get3dStericCenterOfGravity( cne, coord, natoms );
// Translate to steric center
cne[ 0 ] = -cne[ 0 ];
cne[ 1 ] = -cne[ 1 ];
cne[ 2 ] = -cne[ 2 ];
Translate3dCoords( coord, cne, natoms );
}
void VStericFrameRotation( float* m, // float[ 9 ]
const float* coord, // float[ n * 3 ]
const unsigned n,
float* ev ); // float[ 3 ]
void VTransform2StericFrame( float* m, // float[ 12 ]
float* coord, // float[ n * 3 ]
const unsigned n,
float* ev ); // float[ 3 ]
void VApplyRotTransMatrix( float* c,
const unsigned n,
const float* m );
// Avoids need to copy array
void VApplyRotTransMatrix( float* c,
const float* d,
const unsigned n,
const float* m );
void TransformCoordToStericFrameAndCalculateEigenvalues(
const unsigned natom,
float* coord, // float[ natom * 3 ]
float* ev // float[ 3 ]
);
unsigned CalculateQrat( const float* ev, const float threshold );
void TransformCoordToStericFrameAndCalculateQrat(
const unsigned natom,
const float threshold,
float* coord, // float[ natom * 3 ]
unsigned& qrat
);
void getJointColorTypeSet( const unsigned* ref_atom_types,
const unsigned ref_natom,
const unsigned* fit_atom_types,
const unsigned fit_natom,
std::set<unsigned>& joint_color_atom_type_set );
void getVolumeAtomIndexVector( const unsigned* atom_types,
const unsigned natom,
std::vector< unsigned >& atomIndexVector );
void getColorAtomType2IndexVectorMap( const unsigned* atom_types,
const unsigned natom,
std::map< unsigned, std::vector< unsigned > >& atomType2IndexVectorMap );
void restrictColorAtomType2IndexVectorMap(
std::map< unsigned, std::vector< unsigned > >& atom_type_to_index_vector_map,
const std::set<unsigned>& joint_color_atom_type_set );
void setUseCutOff( bool useCutOff );
double getD2CutOff();
double getAlpha( double r );
double getA_ak( double alpha1, double alpha2 );
double getOverlap0( double alpha1, double alpha2 );
void setAlpha( const double* rad, const unsigned natom, std::vector< double >& alpha_vec );
}
#endif // ALIGN3D_SHAPE_FUNCTIONS__HPP