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shape_functions1.cpp
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shape_functions1.cpp
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/* $Id: shape_functions1.cpp 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
*
* ===========================================================================
*/
// C++ Includes
#include <cmath>
#include <vector>
#include <map>
#include <set>
#include <cstring>
#include <iostream>
#include <algorithm>
#include "shape_functions.hpp"
namespace Align3D {
void VRotTransMatrixNew( Uint8& packed,
const float* m )
{
packed = 0;
double trace = 1.0 + m[ 0 ] + m[ 4 ] + m[ 8 ];
double s, qw, qx, qy, qz;
if ( 0.1 < trace ) { // Default
s = 2.0 * sqrt( trace );
qw = 0.25 * s;
double s_invert = 1.0 / s;
qx = ( m[ 7 ] - m[ 5 ] ) * s_invert;
qy = ( m[ 2 ] - m[ 6 ] ) * s_invert;
qz = ( m[ 3 ] - m[ 1 ] ) * s_invert;
////// PUBCHEM_INFO( "0 trace: " << trace
// << " (Q: " << qw << " " << qx << " " << qy << " " << qz << ")"
// << " (M: " << m[0] << " " << m[4] << " " << m[8] << ")" );
} else if ( 0.005 < ( m[ 0 ] - m[ 4 ] ) &&
0.005 < ( m[ 0 ] - m[ 8 ] ) ) { // X is largest
s = 2.0 * sqrt( 1.0 + m[ 0 ] - m[ 4 ] - m[ 8 ] );
double s_invert = 1.0 / s;
qw = ( m[ 7 ] - m[ 5 ] ) * s_invert;
qx = 0.25 * s;
qy = ( m[ 3 ] + m[ 1 ] ) * s_invert;
qz = ( m[ 2 ] + m[ 6 ] ) * s_invert;
////// PUBCHEM_INFO( "1 trace: " << trace
// << " (Q: " << qw << " " << qx << " " << qy << " " << qz << ")"
// << " (M: " << m[0] << " " << m[4] << " " << m[8] << ")" );
} else if ( 0.005 < ( m[ 4 ] - m[ 8 ] ) ) { // Y is largest
s = 2.0 * sqrt( 1.0 + m[ 4 ] - m[ 0 ] - m[ 8 ] );
double s_invert = 1.0 / s;
qw = ( m[ 2 ] - m[ 6 ] ) * s_invert;
qx = ( m[ 3 ] + m[ 1 ] ) * s_invert;
qy = 0.25 * s;
qz = ( m[ 7 ] + m[ 5 ] ) * s_invert;
////// PUBCHEM_INFO( "2 trace: " << trace
// << " (Q: " << qw << " " << qx << " " << qy << " " << qz << ")"
// << " (M: " << m[0] << " " << m[4] << " " << m[8] << ")" );
} else { // Z is largest
s = 2.0 * sqrt( 1.0 + m[ 8 ] - m[ 0 ] - m[ 4 ] );
double s_invert = 1.0 / s;
qw = ( m[ 3 ] - m[ 1 ] ) * s_invert;
qx = ( m[ 2 ] + m[ 6 ] ) * s_invert;
qy = ( m[ 7 ] + m[ 5 ] ) * s_invert;
qz = 0.25 * s;
////// PUBCHEM_INFO( "3 trace: " << trace
// << " (Q: " << qw << " " << qx << " " << qy << " " << qz << ")"
// << " (M: " << m[0] << " " << m[4] << " " << m[8] << ")" );
}
// Encode Quaternion
static const unsigned rbase = 0xFF; // Rotation base
static const double cr = static_cast< double >( rbase ) / 2.0;
// Normalize
s = cr / sqrt( qw * qw + qx * qx + qy * qy + qz * qz );
Uint8 p1 = static_cast< Uint8 >( rint( cr + ( qw * s ) ) );
Uint8 p2 = static_cast< Uint8 >( rint( cr + ( qx * s ) ) );
Uint8 p3 = static_cast< Uint8 >( rint( cr + ( qy * s ) ) );
Uint8 p4 = static_cast< Uint8 >( rint( cr + ( qz * s ) ) );
if ( rbase < p1 ) {
//// //// PUBCHEM_WARN( "Qw encoding is corrupt (0-255 range)! " << p1 << " " << qw * s );
}
if ( rbase < p2 ) {
//// //// PUBCHEM_WARN( "Qx encoding is corrupt (0-255 range)! " << p2 << " " << qx * s );
}
if ( rbase < p3 ) {
//// //// PUBCHEM_WARN( "Qy encoding is corrupt (0-255 range)! " << p3 << " " << qy * s );
}
if ( rbase < p4 ) {
//// //// PUBCHEM_WARN( "Qz encoding is corrupt (0-255 range)! " << p4 << " " << qz * s );
}
// Encode Translation
static const unsigned tbase = static_cast< unsigned >( pow( static_cast< double >( 0x1FFFFFFF ), ( 1.0 / 3.0 ) ) );
static const unsigned tbase2 = tbase * tbase;
static const double itresolution = static_cast< double >( tbase ) / log( 101. );
double x = m[ 9 ]; // X
if ( x < 0.0 ) {
packed |= 0x01;
x = -x;
}
x = log( 1.0 + x );
Uint8 p5 = static_cast< Uint8 >( rint( x * itresolution ) );
if ( p5 >= tbase ) { // Range check
p5 = tbase - 1;
//// //// PUBCHEM_WARN( "X axis translation abs(" << m[ 9 ] << ") is beyond maximum range of " << PubChem::Data::expPackedNew2[ p5 ] );
}
double y = m[ 10 ]; // Y
if ( y < 0.0 ) {
packed |= 0x02;
y = -y;
}
y = log( 1.0 + y );
Uint8 p6 = static_cast< Uint8 >( rint( y * itresolution ) );
if ( p6 >= tbase ) { // Range check
p6 = tbase - 1;
//// //// PUBCHEM_WARN( "Y axis translation abs(" << m[ 10 ] << ") is beyond maximum range of " << PubChem::Data::expPackedNew2[ p6 ] );
}
double z = m[ 11 ]; // Z
if ( z < 0.0 ) {
packed |= 0x04;
z = -z;
}
z = log( 1.0 + z );
Uint8 p7 = static_cast< Uint8 >( rint( z * itresolution ) );
if ( p7 >= tbase ) { // Range check
p7 = tbase - 1;
//// //// PUBCHEM_WARN( "Z axis translation abs(" << m[ 11 ] << ") is beyond maximum range of " << PubChem::Data::expPackedNew2[ p7 ] );
}
Uint8 pt = p5 * tbase2 + p6 * tbase + p7;
// Pack matrix
packed |= ( ( p1 & rbase ) << 56 ); // Qw
packed |= ( ( p2 & rbase ) << 48 ); // Qy
packed |= ( ( p3 & rbase ) << 40 ); // Qx
packed |= ( ( p4 & rbase ) << 32 ); // Qz
packed |= ( ( pt & 0x1FFFFFFF ) << 3 ); // X,Y,Z
}
void VQuaternionTransArray2RotTransMatrix( double* m,
const double* q,
const bool normalize )
{
double q00 = q[ 0 ];
double q01 = q[ 1 ];
double q02 = q[ 2 ];
double q03 = q[ 3 ];
// Normalize quaternion
if ( true == normalize ) {
double s = 1.0 / sqrt( q00 * q00 + q01 * q01 + q02 * q02 + q03 * q03 );
q00 *= s;
q01 *= s;
q02 *= s;
q03 *= s;
}
double sqw = q00 * q00;
double sqx = q01 * q01;
double sqy = q02 * q02;
double sqz = q03 * q03;
double qxqy = q01 * q02;
double qwqz = q00 * q03;
double qxqz = q01 * q03;
double qwqy = q00 * q02;
double qyqz = q02 * q03;
double qwqx = q00 * q01;
// Left-handed rotation matrix
m[ 0 ] = sqw + sqx - sqy - sqz; // X X
m[ 1 ] = 2.0 * ( qxqy - qwqz ); // X Y
m[ 2 ] = 2.0 * ( qxqz + qwqy ); // X Z
m[ 3 ] = 2.0 * ( qxqy + qwqz ); // Y X
m[ 4 ] = sqw - sqx + sqy - sqz; // Y Y
m[ 5 ] = 2.0 * ( qyqz - qwqx ); // Y Z
m[ 6 ] = 2.0 * ( qxqz - qwqy ); // Z X
m[ 7 ] = 2.0 * ( qyqz + qwqx ); // Z Y
m[ 8 ] = sqw - sqx - sqy + sqz; // Z Z
m[ 9 ] = q[ 4 ];
m[ 10 ] = q[ 5 ];
m[ 11 ] = q[ 6 ];
}
void VQuaternionTransArray2RotTransMatrix( float* m,
const double* q,
const bool normalize )
{
double q00 = q[ 0 ];
double q01 = q[ 1 ];
double q02 = q[ 2 ];
double q03 = q[ 3 ];
// Normalize quaternion
if ( true == normalize ) {
double s = 1.0 / sqrt( q00 * q00 + q01 * q01 + q02 * q02 + q03 * q03 );
q00 *= s;
q01 *= s;
q02 *= s;
q03 *= s;
}
double sqw = q00 * q00;
double sqx = q01 * q01;
double sqy = q02 * q02;
double sqz = q03 * q03;
double qxqy = q01 * q02;
double qwqz = q00 * q03;
double qxqz = q01 * q03;
double qwqy = q00 * q02;
double qyqz = q02 * q03;
double qwqx = q00 * q01;
// Left-handed rotation matrix
m[ 0 ] = sqw + sqx - sqy - sqz; // X X
m[ 1 ] = 2.0 * ( qxqy - qwqz ); // X Y
m[ 2 ] = 2.0 * ( qxqz + qwqy ); // X Z
m[ 3 ] = 2.0 * ( qxqy + qwqz ); // Y X
m[ 4 ] = sqw - sqx + sqy - sqz; // Y Y
m[ 5 ] = 2.0 * ( qyqz - qwqx ); // Y Z
m[ 6 ] = 2.0 * ( qxqz - qwqy ); // Z X
m[ 7 ] = 2.0 * ( qyqz + qwqx ); // Z Y
m[ 8 ] = sqw - sqx - sqy + sqz; // Z Z
m[ 9 ] = q[ 4 ];
m[ 10 ] = q[ 5 ];
m[ 11 ] = q[ 6 ];
}
void VCombineRotTransMatrixMatrix( double* t,
const double* t1,
const double* t2 )
{
// Rotation Matrix
t[ 0 ] = t1[ 0] * t2[ 0] + t1[ 1] * t2[ 3] + t1[ 2] * t2[ 6];
t[ 1 ] = t1[ 0] * t2[ 1] + t1[ 1] * t2[ 4] + t1[ 2] * t2[ 7];
t[ 2 ] = t1[ 0] * t2[ 2] + t1[ 1] * t2[ 5] + t1[ 2] * t2[ 8];
t[ 3 ] = t1[ 3] * t2[ 0] + t1[ 4] * t2[ 3] + t1[ 5] * t2[ 6];
t[ 4 ] = t1[ 3] * t2[ 1] + t1[ 4] * t2[ 4] + t1[ 5] * t2[ 7];
t[ 5 ] = t1[ 3] * t2[ 2] + t1[ 4] * t2[ 5] + t1[ 5] * t2[ 8];
t[ 6 ] = t1[ 6] * t2[ 0] + t1[ 7] * t2[ 3] + t1[ 8] * t2[ 6];
t[ 7 ] = t1[ 6] * t2[ 1] + t1[ 7] * t2[ 4] + t1[ 8] * t2[ 7];
t[ 8 ] = t1[ 6] * t2[ 2] + t1[ 7] * t2[ 5] + t1[ 8] * t2[ 8];
// Translation Matrix
t[ 9 ] = t1[ 0] * t2[ 9] + t1[ 1] * t2[10] + t1[ 2] * t2[11] + t1[ 9];
t[ 10 ] = t1[ 3] * t2[ 9] + t1[ 4] * t2[10] + t1[ 5] * t2[11] + t1[10];
t[ 11 ] = t1[ 6] * t2[ 9] + t1[ 7] * t2[10] + t1[ 8] * t2[11] + t1[11];
}
void VRotTransMatrix2QuaternionTransArray( double* q,
const double* m )
{
double trace = 1.0 + m[ 0 ] + m[ 4 ] + m[ 8 ];
double s, qw, qx, qy, qz;
if ( trace > 0.00001 ) {
s = 2.0 * sqrt( trace );
qw = 0.25 * s;
double s_invert = 1.0 / s;
qx = ( m[ 7 ] - m[ 5 ] ) * s_invert;
qy = ( m[ 2 ] - m[ 6 ] ) * s_invert;
qz = ( m[ 3 ] - m[ 1 ] ) * s_invert;
////// PUBCHEM_INFO( "0 trace: " << trace << " " << qw << " " << qx << " " << qy << " " << qz );
} else if ( m[ 0 ] > m[ 4 ] &&
m[ 0 ] > m[ 8 ] ) {
s = 2.0 * sqrt( 1.0 + m[ 0 ] - m[ 4 ] - m[ 8 ] );
double s_invert = 1.0 / s;
qw = ( m[ 7 ] - m[ 5 ] ) * s_invert;
qx = 0.25 * s;
qy = ( m[ 3 ] + m[ 1 ] ) * s_invert;
qz = ( m[ 2 ] + m[ 6 ] ) * s_invert;
////// PUBCHEM_INFO( "1 trace: " << trace << " " << qw << " " << qx << " " << qy << " " << qz );
} else if ( m[ 4 ] > m[ 8 ] ) {
s = 2.0 * sqrt( 1.0 + m[ 4 ] - m[ 0 ] - m[ 8 ] );
double s_invert = 1.0 / s;
qw = ( m[ 2 ] - m[ 6 ] ) * s_invert;
qx = ( m[ 3 ] + m[ 1 ] ) * s_invert;
qy = 0.25 * s;
qz = ( m[ 7 ] + m[ 5 ] ) * s_invert;
////// PUBCHEM_INFO( "2 trace: " << trace << " " << qw << " " << qx << " " << qy << " " << qz );
} else {
s = 2.0 * sqrt( 1.0 + m[ 8 ] - m[ 0 ] - m[ 4 ] );
double s_invert = 1.0 / s;
qw = ( m[ 3 ] - m[ 1 ] ) * s_invert;
qx = ( m[ 2 ] + m[ 6 ] ) * s_invert;
qy = ( m[ 7 ] + m[ 5 ] ) * s_invert;
qz = 0.25 * s;
////// PUBCHEM_INFO( "3 trace: " << trace << " " << qw << " " << qx << " " << qy << " " << qz );
}
// Normalize
s = 1.0 / sqrt( qw * qw + qx * qx + qy * qy + qz * qz );
q[ 0 ] = qw * s;
q[ 1 ] = qx * s;
q[ 2 ] = qy * s;
q[ 3 ] = qz * s;
q[ 4 ] = m[ 9 ];
q[ 5 ] = m[ 10 ];
q[ 6 ] = m[ 11 ];
}
void VStericFrameRotation( float* m, // float[ 9 ]
const float* coord, // float[ n * 3 ]
const unsigned n,
float* ev ) // float[ 3 ]
{
/*
std::cerr << "*** COORDINATES: " << std::endl;
for ( unsigned i = 0; i < n; ++i ) {
std::cerr << "\t" << coord[3*i]
<< "\t" << coord[3*i+1]
<< "\t" << coord[3*i+2]
<< std::endl;
}
*/
// Compute initial inertial tensor
double it[ 3 ][ 3 ];
double sx = coord[ 0 ], sy = coord[ 1 ], sz = coord[ 2 ];
double xx = sx * sx, yy = sy * sy, zz = sz * sz;
it[ 0 ][ 0 ] = yy + zz;
it[ 1 ][ 1 ] = xx + zz;
it[ 2 ][ 2 ] = xx + yy;
it[ 0 ][ 1 ] = sx * sy;
it[ 0 ][ 2 ] = sx * sz;
it[ 1 ][ 2 ] = sy * sz;
for ( unsigned i = 1; i < n; ++i ) {
sx = coord[ i * 3 ];
sy = coord[ 1 + i * 3 ];
sz = coord[ 2 + i * 3 ];
xx = sx * sx;
yy = sy * sy;
zz = sz * sz;
it[ 0 ][ 0 ] += yy + zz;
it[ 1 ][ 1 ] += xx + zz;
it[ 2 ][ 2 ] += xx + yy;
it[ 0 ][ 1 ] += sx * sy;
it[ 0 ][ 2 ] += sx * sz;
it[ 1 ][ 2 ] += sy * sz;
}
/*
std::cerr << "*** Begin MATRIX: " << std::endl;
for ( unsigned i = 0; i < 3; ++i ) {
for ( unsigned j = 0; j < 3; ++j ) {
std::cerr << "\t" << it[i][j];
}
std::cerr << std::endl;
}
*/
// Diagonalize 3x3 steric inertial tensor matrix using Jacobi Diagonalization method
// Initialize eigenvectors
m[ 0 ] = 1.0;
m[ 1 ] = 0.0;
m[ 2 ] = 0.0;
m[ 3 ] = 0.0;
m[ 4 ] = 1.0;
m[ 5 ] = 0.0;
m[ 6 ] = 0.0;
m[ 7 ] = 0.0;
m[ 8 ] = 1.0;
m[ 9 ] = 0.0;
m[ 10 ] = 0.0;
m[ 11 ] = 0.0;
// Initialize eigenvalues
double e[ 3 ];
e[ 0 ] = it[ 0 ][ 0 ];
e[ 1 ] = it[ 1 ][ 1 ];
e[ 2 ] = it[ 2 ][ 2 ];
// Main iteration loop for numerical modification
const unsigned max_iter = 50;
const double convergence_threshold = 0.000001;
double sum; // Sum of off-diagonal elements
double s, c, t; // sin, cos, tan of rotation angle
double g, h, tz, tau, theta; // More temporary storage
double thresh, thresh_val = 1.0 / ( 5.0 * 3.0 * 3.0 );
if ( n > 1 ) {
for ( unsigned iter = 0; iter++ < max_iter; ) {
// Test for convergence
sum = fabs( it[ 0 ][ 1 ] ) + fabs( it[ 0 ][ 2 ] ) + fabs( it[ 1 ][ 2 ] );
if ( sum < convergence_threshold ) {
break; // Convergence reached
}
if ( 4 > iter ) {
thresh = sum * thresh_val;
} else {
thresh = 0.0;
}
// Modify off diagonal elements in the attempt to make them (near) zero
for ( unsigned p = 0; p < 2; p++ ) {
for ( unsigned q = p + 1; q < 3; q++ ) {
g = 100.0 * fabs( it[ p ][ q ] );
if ( 4 < iter &&
g < convergence_threshold ) {
it[ p ][ q ] = 0.0; // Almost or at zero... so make it zero
} else if ( thresh < fabs( it[ p ][ q ] ) ) {
// Calculate Jacobi transformation
if ( g < convergence_threshold ) {
t = it[ p ][ q ] / ( e[ q ] - e[ p ] );
} else {
theta = ( e[ q ] - e[ p ] ) / ( 2.0 * it[ p ][ q ] );
if ( 0.0 > theta ) {
t = -1.0 / ( sqrt( 1.0 + ( theta * theta ) ) - theta );
} else {
t = 1.0 / ( sqrt( 1.0 + ( theta * theta ) ) + theta );
}
}
c = 1.0 / sqrt( 1.0 + ( t * t ) );
s = t * c;
tau = s / ( 1.0 + c );
tz = t * it[ p ][ q ];
it[ p ][ q ] = 0.0;
// Apply Jacobi transformation
for ( unsigned r = 0; r < p; r++ ) {
g = it[ r ][ p ];
h = it[ r ][ q ];
it[ r ][ p ] = g - s * ( h + g * tau );
it[ r ][ q ] = h + s * ( g - h * tau );
}
for ( unsigned r = p + 1; r < q; r++ ) {
g = it[ p ][ r ];
h = it[ r ][ q ];
it[ p ][ r ] = g - s * ( h + g * tau );
it[ r ][ q ] = h + s * ( g - h * tau );
}
for ( unsigned r = q + 1; r < 3; r++ ) {
g = it[ p ][ r ];
h = it[ q ][ r ];
it[ p ][ r ] = g - s * ( h + g * tau );
it[ q ][ r ] = h + s * ( g - h * tau );
}
// Update eigenvalues/eigenvectors
e[ p ] -= tz;
e[ q ] += tz;
for ( unsigned r = 0; r < 3; r++ ) {
g = m[ r * 3 + p ];
h = m[ r * 3 + q ];
m[ r * 3 + p ] = g - s * ( h + g * tau );
m[ r * 3 + q ] = h + s * ( g - h * tau );
}
}
}
}
}
if ( sum > convergence_threshold ) {
///// PUBCHEM_WARN( "Convergence (" << sum << ") failed for inertial tensor diagonalization" );
}
// Sort Eigenvalue/eigenvectors
double diff = e[ 0 ] - e[ 1 ]; // Be wary of degenerate axes
if ( diff > 0.0001 ) {
std::swap( e[ 0 ], e[ 1 ] );
double tmp;
tmp = - m[ 0 ];
m[ 0 ] = m[ 3 ];
m[ 3 ] = tmp;
tmp = - m[ 1 ];
m[ 1 ] = m[ 4 ];
m[ 4 ] = tmp;
tmp = - m[ 2 ];
m[ 2 ] = m[ 5 ];
m[ 5 ] = tmp;
//PUBCHEM_INFO( "Swap x->y" );
}
diff = e[ 1 ] - e[ 2 ];
if ( diff > 0.0001 ) {
std::swap( e[ 1 ], e[ 2 ] );
double tmp;
tmp = - m[ 3 ];
m[ 3 ] = m[ 6 ];
m[ 6 ] = tmp;
tmp = - m[ 4 ];
m[ 4 ] = m[ 7 ];
m[ 7 ] = tmp;
tmp = - m[ 5 ];
m[ 5 ] = m[ 8 ];
m[ 8 ] = tmp;
//PUBCHEM_INFO( "Swap y->z" );
diff = e[ 0 ] - e[ 1 ];
if ( diff > 0.0001 ) {
std::swap( e[ 0 ], e[ 1 ] );
tmp = - m[ 0 ];
m[ 0 ] = m[ 3 ];
m[ 3 ] = tmp;
tmp = - m[ 1 ];
m[ 1 ] = m[ 4 ];
m[ 4 ] = tmp;
tmp = - m[ 2 ];
m[ 2 ] = m[ 5 ];
m[ 5 ] = tmp;
//PUBCHEM_INFO( "Swap x->y" );
}
}
}
/*
std::cerr << "*** End MATRIX: " << std::endl;
for ( unsigned i = 0; i < 3; ++i ) {
for ( unsigned j = 0; j < 3; ++j ) {
std::cerr << "\t" << it[i][j];
}
std::cerr << std::endl;
}
*/
if ( NULL != ev ) {
ev[ 0 ] = e[ 0 ];
ev[ 1 ] = e[ 1 ];
ev[ 2 ] = e[ 2 ];
}
}
void VTransform2StericFrame( float* m, // float[ 12 ]
float* coord, // float[ n * 3 ]
const unsigned n,
float* ev ) // float[ 3 ]
{
// Determine rotation necessary to put into inertial frame of reference
VStericFrameRotation( m, coord, n, ev );
// Rotate molecule into inertial frame of reference
VApplyRotTransMatrix( coord, n, m );
// Determine molecule steric center
Get3dStericCenterOfGravity( &( m[ 9 ] ), coord, n );
m[ 9 ] = - m[ 9 ];
m[ 10 ] = - m[ 10 ];
m[ 11 ] = - m[ 11 ];
// PUBCHEM_INFO( "PMI :: " << e[ 0 ] << " " << e[ 1 ] << " " << e[ 2 ] );
// PUBCHEM_INFO( "Rot :: " << m[ 0 ] << " " << m[ 1 ] << " " << m[ 2 ]
// << " " << m[ 3 ] << " " << m[ 4 ] << " " << m[ 5 ]
// << " " << m[ 6 ] << " " << m[ 7 ] << " " << m[ 8 ] );
// PUBCHEM_INFO( "Trans: " << m[ 9 ] << " " << m[ 10 ] << " " << m[ 11 ] );
// Translate molecule to the steric center
Translate3dCoords( coord, &( m[ 9 ] ), n );
}
void VApplyRotTransMatrix( float* c,
const unsigned n,
const float* m )
{
return VApplyRotTransMatrix( c, c, n, m );
}
// Avoids need to copy array
void VApplyRotTransMatrix( float* c,
const float* d,
const unsigned n,
const float* m )
{
double m00 = m[ 0 ];
double m01 = m[ 1 ];
double m02 = m[ 2 ];
double m03 = m[ 3 ];
double m04 = m[ 4 ];
double m05 = m[ 5 ];
double m06 = m[ 6 ];
double m07 = m[ 7 ];
double m08 = m[ 8 ];
double m09 = m[ 9 ];
double m10 = m[ 10 ];
double m11 = m[ 11 ];
double x, y, z;
unsigned n3 = n * 3;
for ( unsigned i = 0; i < n3; i += 3 ) {
x = d[ i ];
y = d[ 1 + i ];
z = d[ 2 + i ];
c[ i ] = static_cast< float >( m09 + m00 * x + m01 * y + m02 * z );
c[ 1 + i ] = static_cast< float >( m10 + m03 * x + m04 * y + m05 * z );
c[ 2 + i ] = static_cast< float >( m11 + m06 * x + m07 * y + m08 * z );
}
}
void TransformCoordToStericFrameAndCalculateEigenvalues(
const unsigned natom,
float* coord, // float[ natom * 3 ]
float* ev // float[ 3 ]
){
float m[12];
VTransform2StericFrame( m, coord, natom, ev );
}
void TransformCoordToStericFrameAndCalculateQrat(
const unsigned natom,
const float threshold,
float* coord, // float[ natom * 3 ]
unsigned& qrat
){
float ev[3];
TransformCoordToStericFrameAndCalculateEigenvalues( natom, coord, ev );
qrat = CalculateQrat( ev, threshold );
}
unsigned CalculateQrat( const float* ev_ncbi, const float threshold ){
float double_ev_oe[3];
double_ev_oe[0] = ev_ncbi[1] + ev_ncbi[2] - ev_ncbi[0];
double_ev_oe[1] = ev_ncbi[0] + ev_ncbi[2] - ev_ncbi[1];
double_ev_oe[2] = ev_ncbi[0] + ev_ncbi[1] - ev_ncbi[2];
///// std::cerr << "** 1 ** double_EV_oe: " << double_ev_oe[0] << " " << double_ev_oe[1] << " " << double_ev_oe[2] << std::endl;
std::sort( double_ev_oe, double_ev_oe+3, std::greater<float>());
//// std::cerr << "** 2 ** double_EV_oe: " << double_ev_oe[0] << " " << double_ev_oe[1] << " " << double_ev_oe[2] << std::endl;
Uint8 u_rqyx, u_rqzy;
unsigned qrat = 1000;
if( double_ev_oe[1] > 0 ){
if ( threshold < ( double_ev_oe[1] / double_ev_oe[0] ) ) {
u_rqyx = 1;
} else {
u_rqyx = 0;
}
if ( threshold < ( double_ev_oe[2] / double_ev_oe[1] ) ) {
u_rqzy = 1;
} else {
u_rqzy = 0;
}
qrat = u_rqyx + u_rqzy;
}
return qrat;
}
} // namespace Align3D