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
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: solventParameter.C,v 1.11 2003/08/26 09:18:26 oliver Exp $
//
#include <BALL/SOLVATION/solventParameter.h>
#include <BALL/SYSTEM/path.h>
using namespace std;
namespace BALL
{
SolventParameter::SolventParameter()
: ParameterSection(),
name_(),
number_density_(0.0),
solvent_atoms_(),
solvent_descriptor_(),
atom_types_()
{
}
SolventParameter::SolventParameter(const SolventParameter& param)
: ParameterSection(param),
name_(param.name_),
number_density_(param.number_density_),
solvent_atoms_(param.solvent_atoms_),
solvent_descriptor_(param.solvent_descriptor_),
atom_types_(param.atom_types_)
{
}
SolventParameter::SolventParameter(const AtomTypes& atom_types)
: ParameterSection(),
name_(),
number_density_(),
solvent_atoms_(),
solvent_descriptor_(),
atom_types_(atom_types)
{
}
SolventParameter::~SolventParameter()
{
clear();
valid_ = false;
}
void SolventParameter::clear()
{
ParameterSection::clear();
name_ = "";
number_density_ = 0.0;
solvent_descriptor_.clear();
solvent_atoms_.clear();
atom_types_.clear();
}
const SolventParameter& SolventParameter::operator =
(const SolventParameter& param)
{
ParameterSection::operator = (param);
name_ = param.name_;
number_density_ = param.number_density_;
solvent_atoms_ = param.solvent_atoms_;
solvent_descriptor_ = param.solvent_descriptor_;
atom_types_ = param.atom_types_;
return *this;
}
bool SolventParameter::operator == (const SolventParameter& param) const
{
// ?????
return ((ParameterSection::operator == (param))
&& (name_ == param.name_)
&& (number_density_ == param.number_density_));
// && (solvent_atoms_ == param.solvent_atoms_)
// && (solvent_descriptor_ == param.solvent_descriptor_));
}
SolventDescriptor& SolventParameter::getSolventDescriptor()
{
return solvent_descriptor_;
}
const SolventDescriptor& SolventParameter::getSolventDescriptor() const
{
return solvent_descriptor_;
}
const String& SolventParameter::getSolventName() const
{
return name_;
}
const std::vector<SolventAtomDescriptor>& SolventParameter::getSolventDescription() const
{
return solvent_atoms_;
}
const float& SolventParameter::getSolventDensity() const
{
return number_density_;
}
bool SolventParameter::extractSection(Parameters& parameters,
const String& section_name)
{
// ?????
if (!parameters.isValid())
{
return false;
}
// extract the basis information
ParameterSection::extractSection(parameters, section_name);
// check whether all variables we need are defined, terminate otherwi
if (!hasVariable("radius") || !hasVariable("number_of_atoms") || !hasVariable("element_symbol"))
{
Log.error() << "SolventParameter::extractSection(): Variable missing." << endl;
return false;
}
else
{
if (options.has("name"))
{
name_ = options.get("name");
}
else
{
Log.warn() << "SolventParameter::extractSection(): no name given." << endl;
}
if (options.has("number_density"))
{
number_density_ = options.getReal("number_density");
}
else
{
Log.warn() << "SolventParameter::extractSection(): " << "no number density given." << endl;
}
if (!atom_types_.isValid())
{
if (options.has("force_field"))
{
Path path;
String force_field_file = path.find(options.get("force_field"));
if (force_field_file == "")
{
force_field_file = options.get("force_field");
}
Parameters tmp_ffp(force_field_file);
tmp_ffp.init();
atom_types_.extractSection(tmp_ffp, "AtomTypes");
}
else
{
Log.error() << "SolventParameter::extractSection(): "
<< "did not find atom types, aborting." << endl;
return(false);
}
}
Size number_of_keys = getNumberOfKeys();
solvent_atoms_.resize(number_of_keys);
Size index_element_symbol = getColumnIndex("element_symbol");
Size index_radius = getColumnIndex("radius");
Size index_number_of_atoms = getColumnIndex("number_of_atoms");
for (Size i = 0; i < number_of_keys; ++i)
{
String type_name = getKey(i);
if (atom_types_.has(type_name))
{
solvent_atoms_[i].type = atom_types_.getType(type_name);
solvent_atoms_[i].element_symbol = getValue(i, index_element_symbol);
solvent_atoms_[i].radius = getValue(i, index_radius).toFloat();
solvent_atoms_[i].number_of_atoms = getValue(i, index_number_of_atoms).toInt();
}
else
{
Log.error() << "SolventParameter::extractSection(): " << "Cannot assign atom type." << endl;
return(false);
}
}
// build descriptor
solvent_descriptor_ = SolventDescriptor(name_, number_density_, solvent_atoms_);
return true;
}
}
}
|
