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
|
/**********************************************************************
Copyright (C) 2000 by Geoffrey Hutchison
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
#include "mol.h"
#define BOHR_TO_ANGSTROM 0.529177249
#define ANGSTROM_TO_BOHR 1.889725989
using namespace std;
namespace OpenBabel {
bool ReadDMol(istream &ifs,OBMol &mol,char *title)
{
char buffer[BUFF_SIZE];
string str;
float x,y,z;
OBAtom *atom;
vector<string> vs;
ifs.getline(buffer,BUFF_SIZE);
while (strstr(buffer,"$coordinates") == NULL)
ifs.getline(buffer,BUFF_SIZE);
// ifs.getline(buffer,BUFF_SIZE);
while (strstr(buffer,"$end") == NULL)
{
if (!ifs.getline(buffer,BUFF_SIZE)) break;
tokenize(vs,buffer);
if (vs.size() != 4) break;
atom = mol.NewAtom();
//set atomic number
atom->SetAtomicNum(etab.GetAtomicNum(vs[0].c_str()));
x = atof((char*)vs[1].c_str()) * BOHR_TO_ANGSTROM;
y = atof((char*)vs[2].c_str()) * BOHR_TO_ANGSTROM;
z = atof((char*)vs[3].c_str()) * BOHR_TO_ANGSTROM;
atom->SetVector(x,y,z); //set coordinates
}
mol.ConnectTheDots();
mol.PerceiveBondOrders();
mol.SetTitle(title);
return(true);
}
bool WriteDMol(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
ofs << "$coordinates" << endl;
OBAtom *atom;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%-3s% 27.14f% 20.14f% 20.14f",
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetX() * ANGSTROM_TO_BOHR,
atom->GetY() * ANGSTROM_TO_BOHR,
atom->GetZ() * ANGSTROM_TO_BOHR);
ofs << buffer << endl;
}
ofs << "$end" << endl;
return(true);
}
}
|
