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/* Copyright (C) 2000 Damir Zucic */
/*=============================================================================
check_dist.c
Purpose:
Try to recognize the atomic pair. If pair is recognized, check
the distance between two atoms. If this distance fits into the
bond length range which corresponds to given atomic pair,
return positive value. Otherwise return negative value. See
bellow for a list of pairs this routine recognizes. This array
is called known_pairAA. Add more to the list, but don't forget
to update the array size. Changes in PDB format may require
the modification of this function. It is assumed that chemical
symbol is right justified and that exactly two characters are
used for representation. Pairs like " C N" and " N C" etc. are
treated as equivalent and thus should have equal ID's. The
array with pair ID's is called known_pairsIDA. Unrecognized
pairs are also checked, using generic bond length limits.
Input:
(1) Pointer to inter-atomic distance.
(2) Pointer to AtomS structure with data about one atom.
(3) Pointer to AtomS structure with data about another atom.
(4) Pointer to ConfigS structure, with configuration data,
Output:
(1) Bond length, if bond is recognized.
(2) Return value.
Return value:
(1) If atomic pair is recognized and the distance corresponds
to a valid bond length, atomic pair ID is returned.
(2) Negative if inter-atomic distance is bad.
Notes:
(1) The pair identifier value of zero is reserved for hydrogen
bonds.
========includes:============================================================*/
#include <stdio.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"
/*======check inter-atomic distance:=========================================*/
short int CheckDistance_ (double *distanceP,
AtomS *atom1SP, AtomS *atom2SP, ConfigS *configSP)
{
char atomic_pairA[40];
char known_pairAA[KNOWNPAIRS][PAIRSIZE] =
{" C C", " C C", " C N", " N C", " C O", " O C",
" C S", " S C", " C H", " H C", " N H", " H N",
" O H", " H O", " S H", " H S", " O P", " P O",
" S S", " S S"};
short int known_pairIDA[KNOWNPAIRS] = {1, 1, 2, 2, 3, 3,
4, 4, 5, 5, 6, 6,
7, 7, 8, 8, 9, 9,
10, 10};
int pair_string_len;
int i;
short int pairID;
double delta_x, delta_y, delta_z;
double distance_squared;
/* Auxiliary integer: */
pair_string_len = PAIRSIZE - 1;
/* Prepare the string which will contain both chemical symbols: */
strcpy (atomic_pairA, atom1SP->raw_atomS.chemical_symbolA);
strncat (atomic_pairA, atom2SP->raw_atomS.chemical_symbolA, 2);
atomic_pairA[pair_string_len] = '\0';
/* Hydrogen to hydrogen bond is not allowed in garlic: */
/* (Note: H_TO_H_BOND must be negative, see defines.h!) */
if (strncmp (" H H", atomic_pairA, pair_string_len) == 0) return H_TO_H_BOND;
/* Try to recognize the atomic pair: */
pairID = GENERICID; /* The initial value */
for (i = 0; i < KNOWNPAIRS; i++)
{
if (strncmp (known_pairAA[i], atomic_pairA, pair_string_len) == 0)
{
pairID = known_pairIDA[i];
break;
}
}
/* Calculate the squared distance: */
delta_x = atom1SP->raw_atomS.x[0] - atom2SP->raw_atomS.x[0];
delta_y = atom1SP->raw_atomS.y - atom2SP->raw_atomS.y;
delta_z = atom1SP->raw_atomS.z[0] - atom2SP->raw_atomS.z[0];
distance_squared = delta_x * delta_x + delta_y * delta_y + delta_z * delta_z;
/* Check the squared distance: if it doesn't fit into */
/* the range for a given pair, return negative value: */
switch (pairID)
{
/* C-C: */
case 1:
if (distance_squared > configSP->C_C_max_squared) return -1;
if (distance_squared < configSP->C_C_min_squared) return -2;
break;
/* C-N: */
case 2:
if (distance_squared > configSP->C_N_max_squared) return -3;
if (distance_squared < configSP->C_N_min_squared) return -4;
break;
/* C-O: */
case 3:
if (distance_squared > configSP->C_O_max_squared) return -5;
if (distance_squared < configSP->C_O_min_squared) return -6;
break;
/* C-S: */
case 4:
if (distance_squared > configSP->C_S_max_squared) return -7;
if (distance_squared < configSP->C_S_min_squared) return -8;
break;
/* C-H: */
case 5:
if (distance_squared > configSP->C_H_max_squared) return -9;
if (distance_squared < configSP->C_H_min_squared) return -10;
break;
/* N-H: */
case 6:
if (distance_squared > configSP->N_H_max_squared) return -11;
if (distance_squared < configSP->N_H_min_squared) return -12;
break;
/* O-H: */
case 7:
if (distance_squared > configSP->O_H_max_squared) return -13;
if (distance_squared < configSP->O_H_min_squared) return -14;
break;
/* S-H: */
case 8:
if (distance_squared > configSP->S_H_max_squared) return -15;
if (distance_squared < configSP->S_H_min_squared) return -16;
break;
/* O-P: */
case 9:
if (distance_squared > configSP->O_P_max_squared) return -17;
if (distance_squared < configSP->O_P_min_squared) return -18;
break;
/* S-S (disulphide bond): */
case 10:
if (distance_squared > configSP->S_S_max_squared) return -19;
if (distance_squared < configSP->S_S_min_squared) return -20;
break;
/* If this happens, pair was not recognized: */
case GENERICID:
if (distance_squared > configSP->generic_max_squared)
return -21;
if (distance_squared < configSP->generic_min_squared)
return -22;
break;
/* The impossible option: */
default:
return -9999;
}
/* If this point is reached, the bond fits */
/* into the range; calculate the distance: */
*distanceP = sqrt (distance_squared);
/* Return pair ID on success: */
return pairID;
}
/*===========================================================================*/
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