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
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: PDB2discover.C,v 1.9 2004/05/27 19:49:57 oliver Exp $
//
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/FORMAT/PDBFile.h>
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
// check for command line arguments
if (argc != 3)
{
Log.error() << argv[0] << " <PDB file> <new PDB file>" << endl;
Log.error() << " read a PDB file from <PDB file>, add hydrogen atoms where needed" << endl;
Log.error() << " convert the atom names to the Discover naming scheme, and write" << endl;
Log.error() << " everything to <new PDB file>." << endl << endl;
return 1;
}
PDBFile in_file(argv[1]);
if (in_file.bad())
{
Log.error() << "cannot read PDB file " << argv[1] << endl;
return 2;
}
// read the contents of the file into a System
Log << "reading file " << argv[1] << endl;
System S;
in_file >> S;
in_file.close();
Log << "opening fragment database" << endl;
FragmentDB db("");
Log << "adding hydrogens..." << endl;
S.apply(db.add_hydrogens);
Log << "normalizing atom names" << endl;
db.normalize_names.setNamingStandard("Discover");
S.apply(db.normalize_names);
Log << "writing file " << argv[2] << endl;
PDBFile out_file(argv[2], ios::out);
out_file << S;
out_file.close();
return 0;
}
|
