File: set_chi1.c

package info (click to toggle)
garlic 1.6-3
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, buster, sid
  • size: 4,516 kB
  • sloc: ansic: 52,465; makefile: 2,254
file content (212 lines) | stat: -rw-r--r-- 5,966 bytes parent folder | download | duplicates (5)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
/* Copyright (C) 2001, 2002 Damir Zucic */

/*=============================================================================

				  set_chi1.c

Purpose:
	Set the chi1 angle for each selected residue in  the given complex.
	A residue is treated as selected  if the first atom of this residue
	is selected. For proteins, this is typically the N atom (nitrogen).

Input:
	(1) Pointer to MolComplexS structure.
	(2) Pointer to ConfigS structure.
	(3) The chi1 angle in degrees.

Output:
	(1) Chi1 set for each selected residue in each caught complex.
	(2) Return value.

Return value:
	(1) Positive always (trivial).

Notes:
	(1) This function ignores ALA, GLY and PRO.

========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:=================================================*/

int		IsStandard_ (char *);
double		Chi1FromNCACBCG_ (AtomS *, size_t, size_t);
double		Chi1FromNCACBSG_ (AtomS *, size_t, size_t);
double		Chi1FromNCACBCG1_ (AtomS *, size_t, size_t);
double		Chi1FromNCACBOG_ (AtomS *, size_t, size_t);
double		Chi1FromNCACBOG1_ (AtomS *, size_t, size_t);
int		ExtractCACB_ (VectorS *, VectorS *, AtomS *, size_t, size_t);
int		RotateAtom_ (AtomS *, VectorS *, VectorS *, double);
int		DihedralAngles_ (MolComplexS *, ConfigS *);

/*======set chi1:============================================================*/

int SetChi1_ (MolComplexS *mol_complexSP, ConfigS *configSP, double chi1_new)
{
int			residuesN, residueI;
size_t			atomsN, atomI;
ResidueS		*current_residueSP;
AtomS			*first_atomSP;
char			*residue_nameP;
size_t			current_startI, current_endI;
int			residue_typeI;
double			chi1_old, delta_chi1;
int			n;
static VectorS		CA_vectorS, CB_vectorS;
AtomS			*atomSP;
char			*atom_nameP;

/* Copy the number of residues in the specified complex: */
residuesN = mol_complexSP->residuesN;

/* Copy the number of atoms in the specified complex: */
atomsN = mol_complexSP->atomsN;

/* Scan the residues: */
for (residueI = 0; residueI < residuesN; residueI++)
	{
	/* Pointer to the current residue: */
	current_residueSP = mol_complexSP->residueSP + residueI;

	/* Pointer to the first atom of this residue: */
	first_atomSP = mol_complexSP->atomSP +
		       current_residueSP->residue_startI;

	/* If the first atom of this residue is not */
	/* selected,  the residue  is not selected: */
	if (first_atomSP->selectedF == 0) continue;

	/* The name of the current residue: */
	residue_nameP = first_atomSP->raw_atomS.pure_residue_nameA;

	/* The range of atomic indices for the current residue: */
	current_startI = current_residueSP->residue_startI;
	current_endI   = current_residueSP->residue_endI;

	/* Check is the current residue from */
	/* the set of  20 standard residues: */
	residue_typeI = IsStandard_ (residue_nameP);

	/* Do nothing for ALA, GLY and PRO: */
	if ((residue_typeI ==  0) || (residue_typeI == 7) ||
	    (residue_typeI == 14)) continue;

	/* Now calculate and check the old chi1 value. */

	/* Initialize the old chi1: */
	chi1_old = BADDIHEDANGLE;

	/* Calculate the chi1_old: */
	switch (residue_typeI)
		{
		/* Use N, CA, CB and CG for ARG, ASN, ASP, GLN, */
		/* GLU, HIS, LEU, LYS, MET, PHE, TRP  and  TYR: */
		case  1:	/* ARG */ 
		case  2:	/* ASN */
		case  3:	/* ASP */
		case  5:	/* GLN */
		case  6:	/* GLU */
		case  8:	/* HIS */
		case 10:	/* LEU */
		case 11:	/* LYS */
		case 12:	/* MET */
		case 13:	/* PHE */
		case 17:	/* TRP */
		case 18:	/* TYR */
			chi1_old = Chi1FromNCACBCG_ (mol_complexSP->atomSP,
						     current_startI,
						     current_endI);
			break;

		/* Use N, CA, CB and SG for CYS: */
		case 4:		/* CYS */
			chi1_old = Chi1FromNCACBSG_ (mol_complexSP->atomSP,
						     current_startI,
						     current_endI);
			break;

		/* Use N, CA, CB and CG1 for ILE and VAL: */
		case  9:	/* ILE */
		case 19:	/* VAL */
			chi1_old = Chi1FromNCACBCG1_ (mol_complexSP->atomSP,
						      current_startI,
						      current_endI);
			break;

		/* Use N, CA, CB and OG for SER: */
		case 15:	/* SER */
			chi1_old = Chi1FromNCACBOG_ (mol_complexSP->atomSP,
						     current_startI,
						     current_endI);
			break;

		/* Use N, CA, CB and OG1 for THR: */
		case 16:	/* THR */
			chi1_old = Chi1FromNCACBOG1_ (mol_complexSP->atomSP,
						      current_startI,
						      current_endI);
			break;

		/* At present, exotic residues are ignored: */
		default:
			;
		}

	/* Check the value: */
	if (chi1_old == BADDIHEDANGLE) continue;

	/* Calculate the difference: */
	delta_chi1 = chi1_new - chi1_old;

	/* Extract CA and CB coordinates: */
	n = ExtractCACB_ (&CA_vectorS, &CB_vectorS,
			  mol_complexSP->atomSP, current_startI, current_endI);
	if (n < 2) continue;

	/* Change the chi1 angle: */
	for (atomI = current_startI; atomI <= current_endI; atomI++)
		{
		/* Pointer to the current atom: */
		atomSP = mol_complexSP->atomSP + atomI;

		/* Pointer to the purified atom name: */
		atom_nameP = atomSP->raw_atomS.pure_atom_nameA;

		/* Do not rotate H, N, CA, HA, C, O and CB: */
		if (strcmp (atom_nameP, "H" ) == 0) continue;
		if (strcmp (atom_nameP, "N" ) == 0) continue;
		if (strcmp (atom_nameP, "CA") == 0) continue;
		if (strcmp (atom_nameP, "HA") == 0) continue;
		if (strcmp (atom_nameP, "C" ) == 0) continue;
		if (strcmp (atom_nameP, "O" ) == 0) continue;
		if (strcmp (atom_nameP, "CB") == 0) continue;

		/* Rotate the current atom about CA-CB bond: */
		RotateAtom_ (atomSP, &CA_vectorS, &CB_vectorS, delta_chi1);
                }
	}

/* Update dihedral angles and cis-trans flags: */
DihedralAngles_ (mol_complexSP, configSP);

/* Set the position_changedF: */
mol_complexSP->position_changedF = 1;

/* Return positive value (trivial): */
return 1;
}

/*===========================================================================*/