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/* Copyright (C) 2001-2003 Damir Zucic */
/*=============================================================================
build_chain.c
Purpose:
Build the extended polypeptide chain. Moving of a single residue
consists of three steps:
(1) Translate the chain to bring N atom to the correct position.
(2) Rotate the new residue to bring CA atom to correct position.
(3) Rotate the residue about N-CA bond, to fix C atom position.
Input:
(1) Pointer to MolComplexS structure, with macromolecular data.
Output:
(1) The extended chain formed.
(2) Return value.
Return value:
(1) Positive on success.
(2) Negative on failure.
========includes:============================================================*/
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <X11/Xlib.h>
#include <X11/Xutil.h>
#include <X11/Xos.h>
#include <X11/Xatom.h>
#include "defines.h"
#include "typedefs.h"
/*======function prototypes:=================================================*/
int ExtractNCAC_ (VectorS *, VectorS *, VectorS *,
AtomS *, size_t, size_t);
double AbsoluteValue_ (VectorS *);
void VectorProduct_ (VectorS *, VectorS *, VectorS *);
void TranslateRange_ (AtomS *, size_t, size_t,
double, double, double);
double ScalarProduct_ (VectorS *, VectorS *);
void RotateRange_ (AtomS *, size_t, size_t,
VectorS *, VectorS *, double);
int ParallelPart_ (VectorS *, VectorS *, VectorS *);
/*======move residues to build extended chain:===============================*/
int BuildChain_ (MolComplexS *mol_complexSP)
{
size_t vector_struct_size;
double angle;
double cn1, cn2, nca1, nca2, cac1, cac2;
int residuesN;
int residueI;
ResidueS *curr_residueSP;
size_t atom_startI, atom_endI;
int n;
static VectorS N_old_vectorS, CA_old_vectorS, C_old_vectorS;
static VectorS N_vectorS, CA_vectorS, C_vectorS;
VectorS vector1S, vector2S;
double abs_value, reciprocal_abs_value;
VectorS unit_vector1S, unit_vector2S, unit_vector3S;
double x, y, z;
double delta_x, delta_y, delta_z;
double denominator, ratio;
VectorS axis_vectorS;
VectorS parallel_vectorS, perpendicular_vectorS;
/* The size of VectorS structure: */
vector_struct_size = sizeof (VectorS);
/* Prepare the auxilliary parameters: */
angle = DEG_TO_RAD * (180.0 - CACN_ANGLE);
cn1 = CN_BOND_LENGTH * cos (angle);
cn2 = CN_BOND_LENGTH * sin (angle);
angle = DEG_TO_RAD * (180.0 - CNCA_ANGLE);
nca1 = NCA_BOND_LENGTH * cos (angle);
nca2 = NCA_BOND_LENGTH * sin (angle);
angle = DEG_TO_RAD * (180.0 - NCAC_ANGLE);
cac1 = CAC_BOND_LENGTH * cos (angle);
cac2 = CAC_BOND_LENGTH * sin (angle);
/* Prepare the number of residues: */
residuesN = mol_complexSP->residuesN;
/* If there is only one residue (or less), return: */
if (residuesN <= 1) return 1;
/* Prepare N, CA and C coordinates for the first residue: */
atom_startI = mol_complexSP->residueSP->residue_startI;
atom_endI = mol_complexSP->residueSP->residue_endI;
n = ExtractNCAC_ (&N_old_vectorS, &CA_old_vectorS, &C_old_vectorS,
mol_complexSP->atomSP, atom_startI, atom_endI);
/* All three atomic positions are required to properly initiate the chain: */
if (n < 3) return -1;
/* Scan residues, skipping the first one: */
for (residueI = 1; residueI < residuesN; residueI++)
{
/* Pointer to the current residue: */
curr_residueSP = mol_complexSP->residueSP + residueI;
/* Prepare the atomic index range: */
atom_startI = curr_residueSP->residue_startI;
atom_endI = curr_residueSP->residue_endI;
/*------translation:-------------------------------------------------*/
/* Extract N, CA and C coordinates: */
n = ExtractNCAC_ (&N_vectorS, &CA_vectorS, &C_vectorS,
mol_complexSP->atomSP, atom_startI, atom_endI);
/* Three atoms are required to properly place the current residue: */
if (n < 3) continue;
/* Prepare the vector parallel to CA-C bond of the previous residue: */
vector1S.x = C_old_vectorS.x - CA_old_vectorS.x;
vector1S.y = C_old_vectorS.y - CA_old_vectorS.y;
vector1S.z = C_old_vectorS.z - CA_old_vectorS.z;
/* Prepare the first unit vector, required to place the N atom: */
abs_value = AbsoluteValue_ (&vector1S);
if (abs_value == 0.0) continue;
reciprocal_abs_value = 1.0 / abs_value;
unit_vector1S.x = reciprocal_abs_value * vector1S.x;
unit_vector1S.y = reciprocal_abs_value * vector1S.y;
unit_vector1S.z = reciprocal_abs_value * vector1S.z;
/* Prepare the vector parallel to CA-N bond of the previous residue: */
vector1S.x = N_old_vectorS.x - CA_old_vectorS.x;
vector1S.y = N_old_vectorS.y - CA_old_vectorS.y;
vector1S.z = N_old_vectorS.z - CA_old_vectorS.z;
/* Prepare the vector perpendicular to the first unit */
/* vector and to the CA-N bond of the previous residue: */
VectorProduct_ (&vector2S, &unit_vector1S, &vector1S);
/* Prepare the vector in the N-CA-C plane of the previous residue: */
VectorProduct_ (&vector1S, &unit_vector1S, &vector2S);
/* Prepare the second unit vector, required to set N atom: */
abs_value = AbsoluteValue_ (&vector1S);
if (abs_value == 0.0) continue;
reciprocal_abs_value = 1.0 / abs_value;
unit_vector2S.x = reciprocal_abs_value * vector1S.x;
unit_vector2S.y = reciprocal_abs_value * vector1S.y;
unit_vector2S.z = reciprocal_abs_value * vector1S.z;
/* Prepare the position where N atom should be moved: */
x = cn1 * unit_vector1S.x + cn2 * unit_vector2S.x + C_old_vectorS.x;
y = cn1 * unit_vector1S.y + cn2 * unit_vector2S.y + C_old_vectorS.y;
z = cn1 * unit_vector1S.z + cn2 * unit_vector2S.z + C_old_vectorS.z;
/* Prepare the shift for the entire residue: */
delta_x = x - N_vectorS.x;
delta_y = y - N_vectorS.y;
delta_z = z - N_vectorS.z;
/* Translate all atoms which belong to the current residue: */
TranslateRange_ (mol_complexSP->atomSP, atom_startI, atom_endI,
delta_x, delta_y, delta_z);
/*------the first rotation:------------------------------------------*/
/* Extract new N, CA and C coordinates: */
n = ExtractNCAC_ (&N_vectorS, &CA_vectorS, &C_vectorS,
mol_complexSP->atomSP, atom_startI, atom_endI);
/* Three atoms are required to properly rotate the current residue: */
if (n < 3) continue;
/* Prepare the vector parallel to C-N bond (the C atom */
/* which belongs to the previous residue should be used): */
vector1S.x = N_vectorS.x - C_old_vectorS.x;
vector1S.y = N_vectorS.y - C_old_vectorS.y;
vector1S.z = N_vectorS.z - C_old_vectorS.z;
/* Prepare the first unit vector, required to place the CA atom: */
abs_value = AbsoluteValue_ (&vector1S);
if (abs_value == 0.0) continue;
reciprocal_abs_value = 1.0 / abs_value;
unit_vector1S.x = reciprocal_abs_value * vector1S.x;
unit_vector1S.y = reciprocal_abs_value * vector1S.y;
unit_vector1S.z = reciprocal_abs_value * vector1S.z;
/* Prepare the vector parallel to C-CA bond of the previous residue: */
vector1S.x = CA_old_vectorS.x - C_old_vectorS.x;
vector1S.y = CA_old_vectorS.y - C_old_vectorS.y;
vector1S.z = CA_old_vectorS.z - C_old_vectorS.z;
/* Prepare the vector perpendicular to the first unit */
/* vector and to the C-CA bond of the previous residue: */
VectorProduct_ (&vector2S, &unit_vector1S, &vector1S);
/* Prepare the vector in the peptide unit plane: */
VectorProduct_ (&vector1S, &unit_vector1S, &vector2S);
/* Prepare the second unit vector, */
/* required to calculate CA position: */
abs_value = AbsoluteValue_ (&vector1S);
if (abs_value == 0.0) continue;
reciprocal_abs_value = 1.0 / abs_value;
unit_vector2S.x = reciprocal_abs_value * vector1S.x;
unit_vector2S.y = reciprocal_abs_value * vector1S.y;
unit_vector2S.z = reciprocal_abs_value * vector1S.z;
/* Prepare the position where CA atom should be moved: */
x = nca1 * unit_vector1S.x + nca2 * unit_vector2S.x + N_vectorS.x;
y = nca1 * unit_vector1S.y + nca2 * unit_vector2S.y + N_vectorS.y;
z = nca1 * unit_vector1S.z + nca2 * unit_vector2S.z + N_vectorS.z;
/* The vector parallel to the current (bad) N-CA bond: */
vector1S.x = CA_vectorS.x - N_vectorS.x;
vector1S.y = CA_vectorS.y - N_vectorS.y;
vector1S.z = CA_vectorS.z - N_vectorS.z;
/* The vector parallel to the future (correct) N-CA bond: */
vector2S.x = x - N_vectorS.x;
vector2S.y = y - N_vectorS.y;
vector2S.z = z - N_vectorS.z;
/* The vector which defines the rotation axis: */
VectorProduct_ (&axis_vectorS, &vector1S, &vector2S);
/* Calculate the rotation angle, but remember that arc */
/* cosine is very sensitive to floating point errors: */
denominator = AbsoluteValue_ (&vector1S) * AbsoluteValue_ (&vector2S);
if (denominator == 0.0) continue;
ratio = ScalarProduct_ (&vector1S, &vector2S) / denominator;
if (ratio <= -1.0) angle = 3.1415927;
else if (ratio >= 1.0) angle = 0.0;
else angle = acos (ratio);
/* Rotate all atoms which belong to the current residue: */
RotateRange_ (mol_complexSP->atomSP, atom_startI, atom_endI,
&N_vectorS, &axis_vectorS, angle);
/*------the second rotation:-----------------------------------------*/
/* Extract new N, CA and C coordinates: */
n = ExtractNCAC_ (&N_vectorS, &CA_vectorS, &C_vectorS,
mol_complexSP->atomSP, atom_startI, atom_endI);
/* Three atoms are required to properly rotate the current residue: */
if (n < 3) continue;
/* Prepare the rotation axis vector (parallel to N-CA bond): */
axis_vectorS.x = CA_vectorS.x - N_vectorS.x;
axis_vectorS.y = CA_vectorS.y - N_vectorS.y;
axis_vectorS.z = CA_vectorS.z - N_vectorS.z;
/* Prepare the first unit vector, required to place the C atom: */
abs_value = AbsoluteValue_ (&axis_vectorS);
if (abs_value == 0.0) continue;
reciprocal_abs_value = 1.0 / abs_value;
unit_vector1S.x = reciprocal_abs_value * axis_vectorS.x;
unit_vector1S.y = reciprocal_abs_value * axis_vectorS.y;
unit_vector1S.z = reciprocal_abs_value * axis_vectorS.z;
/* Prepare the vector parallel to N-C bond (the C atom */
/* which belongs to the previous residue should be used): */
vector1S.x = C_old_vectorS.x - N_vectorS.x;
vector1S.y = C_old_vectorS.y - N_vectorS.y;
vector1S.z = C_old_vectorS.z - N_vectorS.z;
/* Prepare the vector perpendicular to the */
/* first unit vector and to the N-C bond: */
VectorProduct_ (&vector2S, &unit_vector1S, &vector1S);
/* Prepare the vector in the peptide unit plane: */
VectorProduct_ (&vector1S, &unit_vector1S, &vector2S);
/* Prepare the second unit vector, */
/* required to calculate C position: */
abs_value = AbsoluteValue_ (&vector1S);
if (abs_value == 0.0) continue;
reciprocal_abs_value = 1.0 / abs_value;
unit_vector2S.x = reciprocal_abs_value * vector1S.x;
unit_vector2S.y = reciprocal_abs_value * vector1S.y;
unit_vector2S.z = reciprocal_abs_value * vector1S.z;
/* Prepare the third unit vector, required to */
/* calculate the sign of the rotation angle: */
VectorProduct_ (&unit_vector3S, &unit_vector1S, &unit_vector2S);
/* The current (bad) CA-C vector: */
vector1S.x = C_vectorS.x - CA_vectorS.x;
vector1S.y = C_vectorS.y - CA_vectorS.y;
vector1S.z = C_vectorS.z - CA_vectorS.z;
/* The parallel part of CA-C vector: */
n = ParallelPart_ (¶llel_vectorS, &axis_vectorS, &vector1S);
if (n < 0) continue;
/* The perpendicular part of CA-C vector: */
perpendicular_vectorS.x = vector1S.x - parallel_vectorS.x;
perpendicular_vectorS.y = vector1S.y - parallel_vectorS.y;
perpendicular_vectorS.z = vector1S.z - parallel_vectorS.z;
/* Calculate the rotation angle, but remember that arc */
/* cosine is very sensitive to floating point errors: */
denominator = AbsoluteValue_ (&perpendicular_vectorS);
if (denominator == 0.0) continue;
ratio = ScalarProduct_ (&perpendicular_vectorS, &unit_vector2S) /
denominator;
if (ratio < -1.0) angle = 3.1415927;
else if (ratio > 1.0) angle = 0.0;
else angle = acos (ratio);
if (ScalarProduct_ (&perpendicular_vectorS, &unit_vector3S) > 0.0)
{
angle *= -1;
}
/* Rotate all atoms which belong to the current residue: */
RotateRange_ (mol_complexSP->atomSP, atom_startI, atom_endI,
&CA_vectorS, &axis_vectorS, angle);
/*------copy N, CA and C coordinates:--------------------------------*/
/* Copy the N, CA and C coordinates for later use. If it */
/* worked eighty lines above, it should work again here. */
/* Therefore, I believe it is not necessary to check n. */
n = ExtractNCAC_ (&N_old_vectorS, &CA_old_vectorS, &C_old_vectorS,
mol_complexSP->atomSP, atom_startI, atom_endI);
}
/* Return positive value on success: */
return 2;
}
/*===========================================================================*/
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