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/* Copyright (C) 2002 Damir Zucic */
/*=============================================================================
donor_dipole.c
Purpose:
Prepare two vectors which define the hydrogen bond donor dipole.
The first vector is the position of the dipole center. The second
vector is the unit vector which defines the dipole direction. If
the donor atom is an oxygen, try to find the hydrogen atom bound
to oxygen. If it is nitrogen, try to find one or two carbon atoms
bound to this nitrogen atom (see the table below for details).
Input:
(1) Pointer to VectorS structure, where the position of the dipole
center will be stored.
(2) Pointer to VectorS, where the unit vector which defines the
direction of dipole will be stored.
(3) The expected number of carbon atoms bound to the hydrogen bond
donor atom. This number is positive if the hydrogen bond donor
is nitrogen and negative if hydrogen bond donor is oxygen. The
value of -1 is assigned to OG atom from SER, -2 to OG1 atom
from THR and -3 to OH atom from TYR.
(4) Half of N-H bond length, in angstroms.
(5) Pointer to AtomS structure, with data about the hydrogen bond
donor.
(6) Pointer to MolComplexS structure, which contains the data
about the macromolecular complex to which the hydrogen bond
donor belongs.
(7) The array index of the macromolecular complex to which the
hydrogen bond donor belongs.
Output:
(1) The vector which defines the dipole center.
(2) The unit vector which defines the dipole direction.
(3) Return value.
Return value:
(1) Positive on success.
(2) Negative on failure.
Notes:
(1) Here is the list of hydrogen bond donors for twenty standard
residues. For most of these atoms, the donor dipole may be
constructed without the coordinates of hydrogen atom. The
exceptions are OG from SER, OG1 from THR and OH from TYR.
o---------o------o-------------------------------------------o
| RESIDUE | ATOM | Number of carbon atoms bound to this atom |
|---------|------|-------------------------------------------|
| every | N | 2 (the main chain nitrogen atom) |
| ARG | NE | 2 |
| ARG | NH1 | 1 |
| ARG | NH2 | 1 |
| ASN | ND2 | 1 |
| GLN | NE2 | 1 |
| HIS | ND1 | 2 |
| LYS | NZ | 1 |
| SER | OG | 1 (the coordinates of H atom required) |
| THR | OG1 | 1 (the coordinates of H atom required) |
| TRP | NE1 | 2 |
| TYR | OH | 1 (the coordinates of H atom required) |
|_________|______|___________________________________________|
========includes:============================================================*/
#include <stdio.h>
#include <string.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:=================================================*/
double AbsoluteValue_ (VectorS *);
/*======prepare vectors which define the donor dipole:=======================*/
int DonorDipole_ (VectorS *center_vectorSP, VectorS *unit_vectorSP,
int expected_bound_carbonsN, double half_NH_bond_length,
AtomS *donor_atomSP,
MolComplexS *current_mol_complexSP, int mol_complexI)
{
ResidueS *current_residueSP;
size_t first_atomI, last_atomI;
char hydrogen_nameA[10];
int bondI;
TrueBondS *current_bondSP;
char alt_location;
AtomS *partner_atomSP;
double x1, y1, z1, x2, y2, z2;
double absolute_value, reciprocal_abs_value;
double carbon_x, carbon_y, carbon_z;
int bound_carbonsN;
/* Prepare the pointer to the residue to which the hydrogen */
/* bond donor belongs. Only this residue should be scanned: */
current_residueSP = current_mol_complexSP->residueSP +
donor_atomSP->residue_arrayI;
/* The range of atomic array indices which define this residue: */
first_atomI = current_residueSP->residue_startI;
last_atomI = current_residueSP->residue_endI;
/*---------------------------------------------------------------------------*/
/* If the hydrogen bond donor is an oxygen atom, it is not possible */
/* to reconstruct the position of the hydrogen atom using only the */
/* coordinates of this oxygen atom and of the carbon atoms bound to */
/* the oxygen. Thus, try to find the hydrogen atom, if available. */
if (expected_bound_carbonsN < 0)
{
/* OG atom from SER: */
if (expected_bound_carbonsN == -1) strcpy (hydrogen_nameA, "HG");
/* OG1 atom from THR: */
else if (expected_bound_carbonsN == -2) strcpy (hydrogen_nameA, "HG1");
/* OH atom from TYR: */
else if (expected_bound_carbonsN == -3) strcpy (hydrogen_nameA, "HH");
/* Check all bonds of the donor atom to find the hydrogen atom: */
for (bondI = 0; bondI < donor_atomSP->bondsN; bondI++)
{
/* Pointer to the current bond: */
current_bondSP = donor_atomSP->true_bondSA + bondI;
/* Only covalently bound partners are valid candidates: */
if (current_bondSP->bond_typeI != 1) continue;
/* The bond partner should belong to the same complex: */
if (current_bondSP->neighbor_mol_complexI != mol_complexI)
{
continue;
}
/* The bond partner should belong to the same residue: */
if (current_bondSP->neighbor_arrayI < first_atomI) continue;
if (current_bondSP->neighbor_arrayI > last_atomI) continue;
/* The bond partner should be the hydrogen */
/* atom (see check_dist.c for pair ID's): */
if (current_bondSP->pairID != 8) continue;
/* Prepare the pointer to the bond partner (carbon atom): */
partner_atomSP = current_mol_complexSP->atomSP +
current_bondSP->neighbor_arrayI;
/* Ignore atoms at alternate positions: */
alt_location = partner_atomSP->raw_atomS.alt_location;
if ((alt_location != ' ') && (alt_location != 'A')) continue;
/* If this point is reached, the hydrogen */
/* atom bound to the oxygen atom is found. */
/* Copy atomic coordinates: */
x1 = donor_atomSP->raw_atomS.x[0];
y1 = donor_atomSP->raw_atomS.y;
z1 = donor_atomSP->raw_atomS.z[0];
x2 = partner_atomSP->raw_atomS.x[0];
y2 = partner_atomSP->raw_atomS.y;
z2 = partner_atomSP->raw_atomS.z[0];
/* Prepare and store the position of dipole center: */
center_vectorSP->x = 0.5 * (x1 + x2);
center_vectorSP->y = 0.5 * (y1 + y2);
center_vectorSP->z = 0.5 * (z1 + z2);
/* Prepare and store the unit vector */
/* pointing from oxygen to hydrogen */
/* atom (don't forget normalization!): */
unit_vectorSP->x = x2 - x1;
unit_vectorSP->y = y2 - y1;
unit_vectorSP->z = z2 - z1;
absolute_value = AbsoluteValue_ (unit_vectorSP);
if (absolute_value <= 0.0) return -1;
reciprocal_abs_value = 1.0 / absolute_value;
unit_vectorSP->x *= reciprocal_abs_value;
unit_vectorSP->y *= reciprocal_abs_value;
unit_vectorSP->z *= reciprocal_abs_value;
/* Return the success indicator: */
return 1;
}
/* If this point is reached, the hydrogen atom */
/* was not found. Return the failure indicator: */
return -2;
}
/*---------------------------------------------------------------------------*/
/* If the hydrogen bond donor is a nitrogen atom, find and use the */
/* coordinates of carbon atoms bound to this nitrogen to construct */
/* the position of hydrogen atom. If the hydrogen atoms bound to */
/* nitrogen are present in PDB file, they will be ignored anyway. */
else if ((expected_bound_carbonsN == 1) || (expected_bound_carbonsN == 2))
{
/* If there is only one carbon atom bound to nitrogen, */
/* initialize the position of this carbon atom. If there */
/* are two carbon atoms bound to nitrogen, initialize the */
/* position which lays between these two carbon atoms. */
carbon_x = 0.0;
carbon_y = 0.0;
carbon_z = 0.0;
/* Initialize the number of carbon atoms bound to nitrogen: */
bound_carbonsN = 0;
/* Check all bonds of the acceptor atom to find one or */
/* two partners which form the dipole with the acceptor: */
for (bondI = 0; bondI < donor_atomSP->bondsN; bondI++)
{
/* Pointer to the current bond: */
current_bondSP = donor_atomSP->true_bondSA + bondI;
/* Only covalently bound partners are valid candidates: */
if (current_bondSP->bond_typeI != 1) continue;
/* The bond partner should belong to the same complex: */
if (current_bondSP->neighbor_mol_complexI != mol_complexI)
{
continue;
}
/* Note: one of two carbon atoms which are usually bound to */
/* the nitrogen atom does not belong to the same residue! */
/* The bond partner should be the carbon */
/* atom (see check_dist.c for pair ID's): */
if (current_bondSP->pairID != 2) continue;
/* Prepare the pointer to the bond partner (carbon atom): */
partner_atomSP = current_mol_complexSP->atomSP +
current_bondSP->neighbor_arrayI;
/* Ignore atoms at alternate positions: */
alt_location = partner_atomSP->raw_atomS.alt_location;
if ((alt_location != ' ') && (alt_location != 'A')) continue;
/* If this point is reached, one of the carbon */
/* atoms bound to the nitrogen atom is found. */
/* Add the coordinates of this carbon atom */
/* to the coordinates of the point which lays */
/* in the middle between two carbon atoms: */
carbon_x += partner_atomSP->raw_atomS.x[0];
carbon_y += partner_atomSP->raw_atomS.y;
carbon_z += partner_atomSP->raw_atomS.z[0];
/* Increment the counter which counts the */
/* carbon atoms bound to the nitrogen atom: */
bound_carbonsN++;
}
/* The true number of carbon atoms bound to */
/* nitrogen should match the expected number: */
if (bound_carbonsN != expected_bound_carbonsN) return -3;
/* If there are two carbon atoms bound to donor nitrogen, */
/* fix the position of the point between these two atoms: */
if (bound_carbonsN == 2)
{
carbon_x *= 0.5;
carbon_y *= 0.5;
carbon_z *= 0.5;
}
/* Copy the coordinates of the nitrogen atom: */
x1 = donor_atomSP->raw_atomS.x[0];
y1 = donor_atomSP->raw_atomS.y;
z1 = donor_atomSP->raw_atomS.z[0];
/* Prepare the unit vector pointing from the carbon */
/* position (or from the combined position obtained for */
/* two carbons) to the nitrogen atom. This vector will */
/* be used as the vector pointing from nitrogen to */
/* hydrogen. Don't forget to normalize this vector! */
unit_vectorSP->x = x1 - carbon_x;
unit_vectorSP->y = y1 - carbon_y;
unit_vectorSP->z = z1 - carbon_z;
absolute_value = AbsoluteValue_ (unit_vectorSP);
if (absolute_value <= 0.0) return -4;
reciprocal_abs_value = 1.0 / absolute_value;
unit_vectorSP->x *= reciprocal_abs_value;
unit_vectorSP->y *= reciprocal_abs_value;
unit_vectorSP->z *= reciprocal_abs_value;
/* Prepare and store the position of dipole center: */
center_vectorSP->x = x1 + half_NH_bond_length * unit_vectorSP->x;
center_vectorSP->y = y1 + half_NH_bond_length * unit_vectorSP->y;
center_vectorSP->z = z1 + half_NH_bond_length * unit_vectorSP->z;
/* Return the success indicator: */
return 2;
}
/*---------------------------------------------------------------------------*/
/* If this point is reached, the donor atom was */
/* not recognized - return the failure indicator: */
return -5;
}
/*===========================================================================*/
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