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
|
/*****************************************************************************
*
* Copyright (c) 2000 - 2010, Lawrence Livermore National Security, LLC
* Produced at the Lawrence Livermore National Laboratory
* LLNL-CODE-400124
* All rights reserved.
*
* This file is part of VisIt. For details, see https://visit.llnl.gov/. The
* full copyright notice is contained in the file COPYRIGHT located at the root
* of the VisIt distribution or at http://www.llnl.gov/visit/copyright.html.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* - Redistributions of source code must retain the above copyright notice,
* this list of conditions and the disclaimer below.
* - Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the disclaimer (as noted below) in the
* documentation and/or other materials provided with the distribution.
* - Neither the name of the LLNS/LLNL nor the names of its contributors may
* be used to endorse or promote products derived from this software without
* specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY,
* LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
* DAMAGE.
*
*****************************************************************************/
// ************************************************************************* //
// avtProteinDataBankFileFormat.h //
// ************************************************************************* //
#ifndef AVT_ProteinDataBank_FILE_FORMAT_H
#define AVT_ProteinDataBank_FILE_FORMAT_H
#include <avtSTSDFileFormat.h>
#include <vector>
#include <map>
#include <string>
#include <utility>
class DBOptionsAttributes;
// ****************************************************************************
// Struct: Atom
//
// Purpose:
// Encapsulates an Atom for a PDB file.
//
// Programmer: Jeremy Meredith
// Creation: March 23, 2006
//
// Modifications:
// Jeremy Meredith, Wed Oct 17 11:27:10 EDT 2007
// Added compound support.
//
// ****************************************************************************
//This namespace needs to exist on each merge, or the compiler
//will choose the struct inside avtCTRLFileFormat causing
//me to waste hours of my life as I can't figure out why the copy constructor fails
namespace avtProteinDataBankNamespace
{
struct Atom
{
int serial;
char name[5];
char altloc;
char resname[4];
char chainid;
int resseq;
char icode;
float x;
float y;
float z;
float occupancy;
float tempfactor;
char segid[5];
char element[3];
char charge[3];
int atomicnumber;
int residuenumber;
bool backbone;
int compound;
Atom(const char *line, int compound=0);
void Print(ostream &out);
};
}
struct ConnectRecord
{
int a;
int b[4];
ConnectRecord(const char *line);
void Print(ostream &out);
};
// ****************************************************************************
// Class: avtProteinDataBankFileFormat
//
// Purpose:
// Reads in ProteinDataBank files as a plugin to VisIt.
//
// Programmer: Jeremy Meredith
// Creation: March 23, 2006
//
// Modifications:
// Brad Whitlock, Thu Mar 23 11:45:32 PDT 2006
// Added support for PDB title information.
//
// Jeremy Meredith, Mon Aug 28 17:42:26 EDT 2006
// Changed to a STSD file format; models are now exposed through
// directories, and times require multiple grouped files.
// Changed molecular data model so that bonds are line elements, not
// a 4-component array.
//
// Jeremy Meredith, Wed Oct 17 11:27:10 EDT 2007
// Added compound support.
//
// ****************************************************************************
class avtProteinDataBankFileFormat : public avtSTSDFileFormat
{
public:
avtProteinDataBankFileFormat(const char *, DBOptionsAttributes *);
virtual ~avtProteinDataBankFileFormat() {;};
virtual const char *GetType(void) { return "ProteinDataBank"; };
virtual void FreeUpResources(void);
virtual vtkDataSet *GetMesh(const char *);
virtual vtkDataArray *GetVar(const char *);
virtual vtkDataArray *GetVectorVar(const char *);
protected:
virtual void PopulateDatabaseMetaData(avtDatabaseMetaData *);
ifstream in;
bool metadata_read;
int nmodels;
std::vector< std::vector<avtProteinDataBankNamespace::Atom> > allatoms;
std::vector< std::pair<int, int> > bonds;
std::vector<ConnectRecord> connect;
std::vector<std::string> compoundNames;
std::string filename;
std::string dbTitle;
void OpenFileAtBeginning();
void ReadAllMetaData();
void ReadAtomsForModel(int);
void CreateBondsFromModel(int);
void CreateBondsFromModel_Slow(int);
void CreateBondsFromModel_Fast(int);
};
#endif
|
