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
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
/* CrystalGenerator.C
* 2012 Stefan Nickels
*/
// ----------------------------------------------------
// $Maintainer: Stefan Nickels $
// $Authors: Stefan Nickels $
// ----------------------------------------------------
#include <BALL/XRAY/crystalGenerator.h>
#include <BALL/XRAY/crystalInfo.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/KERNEL/system.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/FORMAT/parameters.h>
#include <BALL/FORMAT/parameterSection.h>
#include <BALL/SYSTEM/path.h>
#include "version.h"
using namespace std;
using namespace BALL;
int main(int argc, char* argv[])
{
// instantiate CommandlineParser object supplying
// - tool name
// - short description
// - version string
// - build date
// - category
CommandlineParser parpars("CrystalGenerator", "creates crystals", "VERSION", String(__DATE__), "Structure Creation");
parpars.registerMandatoryInputFile("i", "input pdb file");
parpars.registerMandatoryOutputFile("o", "output pdb file");
// the space group
parpars.registerMandatoryStringParameter("sg", "space group symbol in Herman-Mauguin notation");
CrystalGenerator generator;
// Fill the space group symbol list
generator.getSpaceGroupFilename();
Path path;
String filename = generator.getSpaceGroupFilename();
String filepath = path.find(filename);
if (filepath == "")
{
throw Exception::FileNotFound(__FILE__, __LINE__, filename);
}
Parameters* param = new Parameters(filepath);
if (!param->isValid()) return false;
ParameterSection* pms = new ParameterSection();
pms->extractSection(*param, "SpacegroupList");
if (!pms->isValid()) return false;
delete param;
list<String> space_groups;
for (Position i = 0; i < pms->getNumberOfKeys(); i++)
{
space_groups.push_back(pms->getValue(i,0).c_str());
}
delete pms;
parpars.setParameterRestrictions("sg", space_groups);
// the cell axes
parpars.registerOptionalDoubleParameter("axis_a", "cell axis a");
parpars.registerOptionalDoubleParameter("axis_b", "cell axis b");
parpars.registerOptionalDoubleParameter("axis_c", "cell axis c");
// the cell angles
parpars.registerOptionalDoubleParameter("angle_alpha", "cell angle alpha");
parpars.setParameterRestrictions("angle_alpha", 0.0, 359.0);
parpars.registerOptionalDoubleParameter("angle_beta", "cell angle beta");
parpars.setParameterRestrictions("angle_beta", 0.0, 359.0);
parpars.registerOptionalDoubleParameter("angle_gamma", "cell angle gamma");
parpars.setParameterRestrictions("angle_gamma", 0.0, 359.0);
// the unit cell indices to create
parpars.registerMandatoryIntegerParameter("from_uc_a", "from unit cell index a");
parpars.setParameterRestrictions("from_uc_a", 0, 9);
parpars.registerMandatoryIntegerParameter("from_uc_b", "from unit cell index b");
parpars.setParameterRestrictions("from_uc_b", 0, 9);
parpars.registerMandatoryIntegerParameter("from_uc_c", "from unit cell index c");
parpars.setParameterRestrictions("from_uc_c", 0, 9);
parpars.registerMandatoryIntegerParameter("to_uc_a", "to unit cell index a");
parpars.setParameterRestrictions("from_uc_a", 0, 9);
parpars.registerMandatoryIntegerParameter("to_uc_b", "to unit cell index b");
parpars.setParameterRestrictions("from_uc_b", 0, 9);
parpars.registerMandatoryIntegerParameter("to_uc_c", "to unit cell index c");
parpars.setParameterRestrictions("from_uc_c", 0, 9);
String man = "TODO: Manual";
parpars.setToolManual(man);
parpars.setSupportedFormats("i","pdb");
parpars.setSupportedFormats("o","pdb");
parpars.parse(argc, argv);
PDBFile file;
file.open(parpars.get("i"));
System system;
file >> system;
generator.setSystem(&system);
boost::shared_ptr<CrystalInfo> ci_ptr(new CrystalInfo());
ci_ptr->setSpaceGroup(parpars.get("sg"));
ci_ptr->setCellEdgeLengthA(parpars.get("axis_a").toDouble());
ci_ptr->setCellEdgeLengthB(parpars.get("axis_b").toDouble());
ci_ptr->setCellEdgeLengthC(parpars.get("axis_c").toDouble());
ci_ptr->setCellAngleAlpha(Angle(parpars.get("angle_alpha").toDouble(), false));
ci_ptr->setCellAngleBeta(Angle(parpars.get("angle_beta").toDouble(), false));
ci_ptr->setCellAngleGamma(Angle(parpars.get("angle_gamma").toDouble(), false));
generator.setCrystalInfo(ci_ptr);
System* output = 0;
std::list<System*> crystal = generator.generatePacking(parpars.get("from_uc_a").toInt(), parpars.get("to_uc_a").toInt(),
parpars.get("from_uc_b").toInt(), parpars.get("to_uc_b").toInt(),
parpars.get("from_uc_c").toInt(), parpars.get("to_uc_c").toInt());
output = new System();
output->setName(system.getName());
std::list<System*>::iterator it_c = crystal.begin();
for(;it_c != crystal.end(); it_c++)
{
output->spliceAfter(**it_c);
}
PDBFile outfile(parpars.get("o"), ios::out);
outfile << *output;
outfile.close();
Log << "seems to be done." << endl;
}
|
