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
|
/**********************************************************************
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
{
static bool FirstTime = true;
static int MolCount = 1;
static void WriteSize(int,ostream&);
static char *PadString(char*,int);
static void WriteCSRHeader(ostream&,OBMol&);
static void WriteCSRCoords(ostream&,OBMol&);
bool WriteCSR(ostream &ofs,OBMol &mol)
{
if (FirstTime)
{
WriteCSRHeader(ofs,mol);
FirstTime = false;
}
WriteCSRCoords(ofs,mol);
MolCount++;
return(true);
}
void WriteCSRHeader(ostream &ofs,OBMol &mol)
{
char *molnames;
int nmol, natom;
molnames = PadString((char*)mol.GetTitle(),100);
nmol = 1;
natom = mol.NumAtoms();
WriteSize(4*sizeof(char),ofs);
ofs.write("V33 ",strlen("V33 ")*sizeof(char));
WriteSize(4*sizeof(char),ofs);
WriteSize(2*sizeof(int),ofs);
ofs.write((char*)&natom,sizeof(int));
ofs.write((char*)&nmol,sizeof(int));
WriteSize(2*sizeof(int),ofs);
WriteSize(100*sizeof(char),ofs);
ofs.write(molnames,100*sizeof(char));
WriteSize(100*sizeof(char),ofs);
WriteSize(sizeof(int),ofs);
ofs.write((char*)&natom,sizeof(int));
WriteSize(sizeof(int),ofs);
delete [] molnames;
}
void WriteCSRCoords(ostream &ofs,OBMol &mol)
{
int the_size,jconf;
float x,y,z,energy;
char title[100];
char *tag;
the_size = sizeof(int) + sizeof(float) + (80 * sizeof(char));
jconf = 1;
energy = -2.584565f;
sprintf(title,"%s:%d",mol.GetTitle(),MolCount);
tag = PadString(title,80);
WriteSize(the_size,ofs);
ofs.write((char*)&jconf,sizeof(int));
ofs.write((char*)&energy,sizeof(float));
ofs.write(tag,80*sizeof(char));
WriteSize(the_size,ofs);
WriteSize(mol.NumAtoms()*sizeof(float),ofs);
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
x = atom->x();
ofs.write((char*)&x,sizeof(float));
}
WriteSize(mol.NumAtoms()*sizeof(float),ofs);
WriteSize(mol.NumAtoms()*sizeof(float),ofs);
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
y = atom->y();
ofs.write((char*)&y,sizeof(float));
}
WriteSize(mol.NumAtoms()*sizeof(float),ofs);
WriteSize(mol.NumAtoms()*sizeof(float),ofs);
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
z = atom->z();
ofs.write((char*)&z,sizeof(float));
}
WriteSize(mol.NumAtoms()*sizeof(float),ofs);
delete [] tag;
}
void WriteSize(int size,ostream &ofs)
{
ofs.write((char*)&size,sizeof(int));
}
char *PadString(char *input, int size)
{
unsigned int i;
char *output;
output = new char [size];
for (i = 0; i < (unsigned)size; i++)
output[i] = ' ';
for (i = 0; i < strlen(input); i++)
output[i] = input[i];
return(output);
}
}
|
