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
|
/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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"
using namespace std;
namespace OpenBabel
{
bool ReadBallAndStick(istream &ifs,OBMol &mol,char *title)
{
int i,natoms;
char buffer[BUFF_SIZE];
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
sscanf(buffer,"%d",&natoms);
mol.ReserveAtoms(natoms);
float x,y,z;
OBAtom *atom;
vector<string> vs;
vector<string>::iterator j;
for (i = 1; i <= natoms;i ++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
tokenize(vs,buffer);
if (vs.size() < 4) return(false);
if (vs[0].size() > 1) vs[0][1] = tolower(vs[0][1]);
atom = mol.NewAtom();
x = atof((char*)vs[1].c_str());
y = atof((char*)vs[2].c_str());
z = atof((char*)vs[3].c_str());
atom->SetVector(x,y,z); //set coordinates
atom->SetAtomicNum(etab.GetAtomicNum(vs[0].c_str()));
for (j = vs.begin()+4;j != vs.end();j++)
mol.AddBond(atom->GetIdx(),atoi((char*)j->c_str()),1);
}
mol.SetTitle(title);
return(true);
}
bool WriteBallAndStick(ostream &ofs,OBMol &mol)
{
char tmptype[10];
char buffer[BUFF_SIZE];
if (strlen(mol.GetTitle()) > 0) ofs << mol.GetTitle() << endl;
else ofs << "Untitled" << endl;
snprintf(buffer,BUFF_SIZE,"%d",mol.NumAtoms()); ofs << buffer << endl;
OBAtom *atom,*nbr;
vector<OBNodeBase*>::iterator i;
vector<OBEdgeBase*>::iterator j;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
strcpy(tmptype,etab.GetSymbol(atom->GetAtomicNum()));
if (strlen(tmptype) > 1) tmptype[1] = toupper(tmptype[1]);
snprintf(buffer,BUFF_SIZE,"%-3s %8.4f %8.4f %8.4f",
tmptype,
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer;
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
{
sprintf(buffer,"%6d",nbr->GetIdx());
ofs << buffer;
}
ofs << endl;
}
return(true);
}
}
|
