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../example/awtype.c
1: /* This program is a minor derivative of the amw.c program distributed with
2: * the CEX distribution. It has been changed to compute an awtype property for
3: * each atom which included the average atomic weight for the atom and all
4: * attached hydrogens. This is attached to each atom and output as a tuple
5: * for use in the DockIt example scoring function program. This program
6: * illustrates, in a simple way, the atom type assignment which must be
7: * done for each ligand and receptor atom in the CEX input stream, prior
8: * to DockIt being run.
9: */
11: /* The original header for the program follows: */
12: /*****************************************************************************
13: * amw.c -- CEX average molecular weight generator
14: *----------------------------------------------------------------------------
15: * Contributing author and institution: Dave Weininger, Daylight CIS, Inc.
16: *
17: * This source code is contributed to the public domain and may be freely
18: * copied and redistributed for research, profit, fun or any other reason,
19: * with these restrictions: (1) unmodified or functionally equivalent code
20: * derived from CX code must contain this notice, (2) all derived code must
21: * acknowledge the author and institution, and (3) the functional definition
22: * of symbols starting CX_ or cx_ may not be changed (if you need to change
23: * a function, CHANGE THE NAME: prefixes CU_ and cu_ are suggested).
24: *****************************************************************************/
26:
27: #include <string.h>
28: #include <stdlib.h>
29: #include <stdio.h>
30:
31: #include "cx.h"
32: #include "cx_molecule.h"
33:
34: #define MX_ELEM 105
35:
36: /*** aaw -- average atomic weight data ***/
37:
38: static double aaw[MX_ELEM + 1] = {
39: 0.000, 1.008, 4.0026, 6.94, 9.01218, 10.81, 12.011, 14.0067, 15.9994,
40: 18.99846, 20.17, 22.98977, 24.305, 26.9815, 28.086, 30.9738, 32.06,
41: 35.453, 39.948, 39.1, 40.08, 44.9559, 47.9, 50.941, 51.996, 54.938,
42: 55.847, 58.9332, 58.71, 63.543, 65.38, 69.72, 72.59, 74.9216, 78.96,
43: 79.904, 83.8, 85.467, 87.62, 88.9059, 91.22, 92.9064, 95.94, 98.9062,
44: 101.07, 102.9055, 106.4, 107.868, 112.4, 114.82, 118.69, 121.75, 127.6,
45: 126.9045, 131.3, 132.9055, 137.34, 138.9055, 140.12, 140.9077, 144.24,
46: 145., 150.4, 151.96, 157.25, 158.9254, 162.5, 164.9303, 167.26, 168.9342,
47: 173.04, 174.97, 178.49, 180.947, 183.85, 186.2, 190.2, 192.22, 195.09,
48: 196.9665, 200.59, 204.37, 207.2, 208.9806, 209., 210., 222., 223., 226.,
49: 227., 232.0381, 231.0359, 238.029, 237.0408, 244., 243., 247., 247.,
50: 251., 254.09, 257.08, 258.098, 259.10, 260.1, 261.1, 262.11
51: };
52:
53: /*** prec -- precision, as places past decimal point ***/
54:
55: static int prec[MX_ELEM + 1] = { 6,
56: 3,4,2,5,2,3,4,4,5,2,5,3,4,3,4,2,3,3,1,2,4,1,3,3,3,3,4,2,3,2,2,2,4,2,3,
57: 1,3,2,4,2,4,2,4,2,4,1,3,1,2,2,2,1,4,1,4,2,4,2,4,2,0,1,2,2,4,1,4,2,4,2,
58: 2,2,3,2,1,1,2,2,4,2,2,1,4,0,0,0,0,0,0,4,4,3,4,0,0,0,0,0,2,2,3,2,1,1,2
59: };
60:
61: /*** Handy macro. ***/
62:
63: #define NOTE(msg) cx_error_save(msg, CX_ERR_NOTE, *argv)
64: #define FATAL(msg) cx_error_save(msg, CX_ERR_FATAL, *argv)
65:
66: /*============================================================================
67: * amwof() -- calculate average molecular weight of molecule
68: *
69: * This function ignores atomic mass and accounts for implicit hydrogens.
70: */
72:
73: static void amwof(cx_Object mol)
74: {
75: static char buf[20];
76: int atno, imph, p = 6;
77: double amw = 0.0;
78: cx_Object atom, atoms = cx_stream(mol, CX_OB_ATOM);
79:
80: /*** Loop over atoms, adding up molecular weight. ***/
81:
82: while (NULL != (atom = cx_next(atoms))) {
83: atno = cx_iprop(atom, "atomic number");
84:
85: /*** Get atomic weight of each heavy atom, track precision. ***/
86:
87: if (0 < atno && MX_ELEM >= atno) {
88: amw = aaw[atno];
89: p = CX_MIN(p, prec[atno]);
90: }
91:
92: /*** Add atomic weight of non-explicit hydrogens. ***/
93:
94: if (0 < (imph = cx_iprop(atom, "implicit hcount"))) {
95: amw += imph * aaw[1];
96: p = CX_MIN(p, prec[1]);
97: }
98: sprintf(buf, "%.*f", p, amw);
99: cx_set_sprop(atom, "awtype", buf);
100: }
101: cx_destroy(atoms);
102:
103: /*** Write ave mol wt to correct precision and return it. ***/
104:
105: return ;
106: }
107:
108: /*============================================================================
109: * main() for amw
110: */
112:
113: int main(int argc, char **argv)
114: {
115: cx_Object ob, ins, outs;
116: cx_Object dt, atuple;
117:
118: /*** This program takes no options -- show usage if any specified. ***/
119:
120: if (1 < argc) {
121: FATAL("This program doesn't accept options or arguments.");
122: NOTE ("usage: cex input | awtype | cex output" );
123: NOTE ("Adds awtype (ave atomic wt) to atoms in molecules on cex stream" );
124: cx_error_spew(stderr, NULL);
125: exit(0);
126: }
127:
128: /*** Initialize molecule package. ***/
129:
130: cx_molecule_pkg();
131:
132: /*** Create AMW datatype in default datatype table. ***/
133: if (NULL == (dt = cx_tag2datatype(NULL, "AWTYPE")))
134: dt = cx_create_datatype(NULL, "AWTYPE", "awtype",
135: "AW ligand atom type", "1A", "STRING",
136: "AW ligand atom type");
137:
138: /*** Create input and output streams. ***/
139:
140: ins = cx_create_iostream("-", CX_IO_READ );
141: outs = cx_create_iostream("-", CX_IO_WRITE);
142:
143: /*** Loop over objects on standard input and output streams. ***/
144:
145: while (NULL != (ob = cx_next(ins))) {
146:
147: /*** Calculate AMW for molecules, add as property. ***/
148:
149: if (CX_OB_MOLECULE == cx_type(ob)) {
150: atuple = cx_create_atomtuple(ob, "awtype");
151: cx_set_datatype(atuple, cx_tag2datatype(NULL, "AWTYPE"));
152:
153: amwof(ob);
154: }
155:
156: /*** Send object to stdout. ***/
157:
158: cx_append(outs, ob);
159:
160: /*** Clean up. ***/
161:
162: cx_error_spew(stderr, NULL);
163: cx_destroy(ob);
164: }
165:
166: /*** DON'T: Transmit remaining datatypes. (This was only a test!) ***/
167:
168: /* cx_append(outs, cx_default_datatypetable()); */
169:
170: /*** Clean up, close files, and exit with 0. ***/
171:
172: cx_error_spew(stderr, NULL);
173: cx_destroy(outs);
174: cx_cleanup();
175: return 0;
176: }
177: