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
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/MOPACOutputFile.h>
#include <BALL/DATATYPE/regularExpression.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/PDBAtom.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/PTE.h>
namespace BALL
{
MOPACOutputFile::MOPACOutputFile()
: GenericMolFile()
{
}
MOPACOutputFile::MOPACOutputFile(const String& name, File::OpenMode open_mode)
: GenericMolFile()
{
open(name, open_mode);
}
MOPACOutputFile::~MOPACOutputFile()
{
}
void MOPACOutputFile::clear()
{
atoms_.clear();
type_counts_.clear();
}
bool MOPACOutputFile::read(System& system)
{
Molecule* mol = read();
if (mol)
{
system.insert(*mol);
if (system.getName() == "")
system.setName(mol->getName());
}
else
{
return false;
}
return true;
}
Molecule* MOPACOutputFile::read()
{
clear();
Molecule* result = new Molecule;
// read until we find the cartesian coordinates
bool found_coords = false;
while (!found_coords && readLine())
{
getLine().toUpper();
found_coords = getLine().hasSubstring("CARTESIAN COORDINATES");
}
if (!found_coords)
{
Log.error() << "Could not find cartesian coordinates in MOPAC output file" << std::endl;
delete(result);
return NULL;
}
// try to find the first coordinate line
RegularExpression coord_reg_exp("\\s*[0-9]+\\s+[A-Z]+\\s+-?[0-9.]+\\s+-?[0-9.]+\\s+-?[0-9.]+");
bool first_coord_found = false;
while (!first_coord_found && readLine())
{
first_coord_found =coord_reg_exp.match(getLine());
}
if (!first_coord_found)
{
Log.error() << "Could not find cartesian coordinates in MOPAC output file" << std::endl;
delete(result);
return NULL;
}
addAtom_(getLine(), result);
while (readLine() && coord_reg_exp.match(getLine()))
addAtom_(getLine(), result);
// TODO: handle bonds
// ok, now try to find the charges
bool found_charges = false;
while (!found_charges && readLine())
{
found_charges = getLine().hasSubstring("NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS");
}
if (found_charges)
{
bool first_charge_found = false;
RegularExpression charge_reg_exp("\\s*[0-9]+\\s+[A-Z]+\\s+-?[0-9.]+\\s+[0-9.]+");
while (!first_charge_found && readLine())
{
first_charge_found = charge_reg_exp.match(getLine());
}
if (first_charge_found)
{
std::vector<String> split;
getLine().split(split);
atoms_[split[0].toInt()-1]->setCharge(split[2].toFloat());
while (readLine() && charge_reg_exp.match(getLine()))
{
getLine().split(split);
atoms_[split[0].toInt()-1]->setCharge(split[2].toFloat());
}
}
}
return result;
}
void MOPACOutputFile::addAtom_(const String& line, Molecule* mol)
{
std::vector<String> split;
line.split(split);
if (type_counts_.find(split[1]) == type_counts_.end())
type_counts_[split[1]] = 1;
else
type_counts_[split[1]]++;
atoms_.push_back(new Atom(PTE[split[1]], split[1]+String(type_counts_[split[1]])));
Vector3 position(split[2].toFloat(), split[3].toFloat(), split[4].toFloat());
atoms_.back()->setPosition(position);
mol->insert(*(atoms_.back()));
}
}
|
