source: src/Parser/TremoloParser.hpp@ 4a187d

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Last change on this file since 4a187d was fac58f, checked in by Frederik Heber <heber@…>, 9 years ago

Converted FormatParser::save() to using vector of const atom ptrs.

  • required to change all save() functions in all parsers.
  • Property mode set to 100644
File size: 4.5 KB
Line 
1/*
2 * TremoloParser.hpp
3 *
4 * Created on: Mar 2, 2010
5 * Author: metzler
6 */
7
8#ifndef TREMOLOPARSER_HPP_
9#define TREMOLOPARSER_HPP_
10
11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16#include <boost/function.hpp>
17#include <string>
18
19#include "FormatParser.hpp"
20#include "FormatParserTrait.hpp"
21#include "FormatParserInterface.hpp"
22#include "FormatParser_common.hpp"
23#include "ParserTypes.hpp"
24
25#include "TremoloParser_ElementKeys.hpp"
26#include "TremoloKey.hpp"
27#include "TremoloAtomInfoContainer.hpp"
28
29class molecule;
30class AtomDataValidator;
31
32// declaration of specialized FormatParserTrait
33template<>
34struct FormatParserTrait<tremolo>
35{
36 //!> Name of the parser
37 static const std::string name;
38 //!> suffix of the files the parser understands to read and write
39 static const std::string suffix;
40 //!> ParserTypes enumeration for the parser
41 static const enum ParserTypes type;
42};
43
44/**
45 * Loads a tremolo file into the World and saves the World as a tremolo file.
46 */
47template <>
48class FormatParser< tremolo > : virtual public FormatParserInterface, public FormatParser_common
49{
50 friend class AtomDataValidator;
51public:
52 FormatParser();
53 virtual ~FormatParser();
54 void load(std::istream* file);
55 void save(std::ostream* file, const std::vector<const atom *> &atoms);
56 std::string getAtomData() const;
57 void setAtomData(const std::string &atomdata_string);
58 void resetAtomData(const std::string &atomdata_string);
59
60private:
61 /**
62 * Map to associate element keys with the respective elements.
63 */
64 struct ElementKeys knownTypes;
65
66public:
67
68 void parseKnownTypes(std::istream &file)
69 {
70 knownTypes.parseKnownTypes(file);
71 }
72 void createKnownTypesByIdentity()
73 {
74 knownTypes.createKnownTypesByIdentity();
75 }
76
77 /** Save given \a atoms in tremolo's exttypes file
78 *
79 * \note You should have stored the atoms beforehand to give them unique
80 * and sensible ids.
81 *
82 * @param output output stream
83 * @param atoms vector of atoms whose ids to store
84 * @param id id to given this exttypes group
85 * @return true - all atomic ids are valid, false - one id was not set (-1)
86 */
87 bool saveAtomsInExttypes(
88 std::ostream &output,
89 const std::vector<const atom*> &atoms,
90 const int id) const;
91
92protected:
93 void AtomInserted(atomId_t);
94 void AtomRemoved(atomId_t);
95
96private:
97 //!> typedef for usedFields' vector of strings
98 typedef std::vector<std::string> usedFields_t;
99
100 void readAtomDataLine(const std::string &line, molecule *newmol);
101 void parseAtomDataKeysLine(const std::string &line, const int offset, usedFields_t &fields);
102 static bool testParseAtomDataKeysLine(const std::string &line);
103 void readNeighbors(std::stringstream* line, const int numberOfNeighbors, const int atomId);
104 void processNeighborInformation(const std::vector<atomId_t> &atoms);
105 void adaptImprData(const std::vector<atomId_t> &atoms);
106 void adaptTorsion(const std::vector<atomId_t> &atoms);
107 std::string adaptIdDependentDataString(const std::string &data, const boost::function<int (const int)> &idgetter);
108 bool isUsedField(const usedFields_t &fields, const std::string &fieldName) const;
109 void writeNeighbors(std::ostream* file, const int numberOfNeighbors, const atom* const currentAtom);
110 void saveLine(std::ostream* file, const atom* const currentAtom);
111 void save_AtomDataLine(std::ostream* file) const;
112 void save_BoxLine(std::ostream* file) const;
113 void distributeContinuousIds(const std::vector<const atom *> &AtomList);
114 void makeUsedFieldsUnique(usedFields_t &fields) const;
115
116 /**
117 * Map to associate the known keys with numbers.
118 */
119 static std::map<std::string, TremoloKey::atomDataKey> knownKeys;
120
121 /**
122 * Inverse Map to have a name to each known keys.
123 */
124 std::map<TremoloKey::atomDataKey, std::string> knownKeyNames;
125
126 /**
127 * Fields used globally when storing to a tremolo file.
128 */
129 usedFields_t usedFields_save;
130
131 /**
132 * Fields used locally when parsing in a tremolo file.
133 */
134 usedFields_t usedFields_load;
135
136 /**
137 * Data which is currently not stored in atoms but was provided by the input
138 * file.
139 */
140 std::map<const atomId_t, TremoloAtomInfoContainer> additionalAtomData;
141
142 /**
143 * Default additional atom data.
144 */
145 TremoloAtomInfoContainer defaultAdditionalData;
146
147 //!> bound function to convert id to global id, stored to avoid creation many times
148 const boost::function<int (const int)> idglobalizer;
149
150 //!> bound function to convert id to local id, stored to avoid creation many times
151 const boost::function<int (const int)> idlocalizer;
152};
153
154#endif /* TREMOLOPARSER_HPP_ */
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