RDKit
Open-source cheminformatics and machine learning.
MolSGroupWriting.h
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1 //
2 // Copyright (C) 2002-2021 Greg Landrum and T5 Informatics GmbH
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 
11 #pragma once
12 
13 #include <boost/algorithm/string/trim.hpp>
14 #include <boost/format.hpp>
16 
17 namespace RDKit {
18 namespace SGroupWriting {
19 typedef std::unordered_map<int, SubstanceGroup> IDX_TO_SGROUP_MAP;
20 
21 /* ------------------ Inlined Formatters ------------------ */
22 
23 inline std::string FormatV2000IntField(int value) {
24  auto fmt = boost::format(" %3d") % value;
25  return fmt.str();
26 }
27 
28 inline std::string FormatV2000NumEntriesField(int value) {
29  auto fmt = boost::format(" %2d") % value;
30  return fmt.str();
31 }
32 
33 inline std::string FormatV2000DoubleField(double value) {
34  auto fmt = boost::format("%10.4f") % value;
35  return fmt.str();
36 }
37 
38 inline std::string FormatV2000StringField(const std::string &value,
39  unsigned int fieldSize, bool pad,
40  bool addSeparator) {
41  std::ostringstream os;
42  if (addSeparator) {
43  os << ' ';
44  }
45  if (value.size() >= fieldSize) {
46  os << value.substr(0, fieldSize);
47  } else if (pad) {
48  os << std::setw(fieldSize) << std::left << value;
49  } else {
50  os << value;
51  }
52  return os.str();
53 }
54 
55 inline std::string FormatV3000DoubleField(double value) {
56  return boost::trim_copy(FormatV2000DoubleField(value));
57 }
58 
59 /* ------------------ V2000 Utils ------------------ */
60 
61 std::string BuildV2000STYLines(const ROMol &mol);
62 
63 std::string BuildV2000StringPropLines(const unsigned int entriesPerLine,
64  const ROMol &mol,
65  const std::string &propName,
66  const std::string &propCode,
67  const unsigned int fieldWitdh);
68 
69 std::string BuildV2000SLBLines(const ROMol &mol);
70 
71 std::string BuildV2000SDSLines(const ROMol &mol);
72 
73 std::string BuildV2000SPLLines(const ROMol &mol);
74 
75 std::string BuildV2000SNCLines(const ROMol &mol);
76 
77 std::string BuildV2000SBTLines(const ROMol &mol);
78 
79 template <class T>
80 std::string BuildV2000IdxVectorDataLines(const unsigned int entriesPerLine,
81  const unsigned int sGroupId,
82  const std::string &code,
83  const T &dataVector);
84 
85 std::string BuildV2000SMTLine(const int idx, const SubstanceGroup *sgroup);
86 
87 std::string BuildV2000SDILine(const int idx, const SubstanceGroup *sgroup);
88 
89 std::string BuildV2000SBVLine(const int idx, const SubstanceGroup *sgroup);
90 
91 std::string BuildV2000SDTLine(const int idx, const SubstanceGroup *sgroup);
92 
93 std::string BuildV2000SDDLine(const int idx, const SubstanceGroup *sgroup);
94 
95 std::string BuildV2000SCDSEDLines(const int idx, const SubstanceGroup *sgroup);
96 
97 std::string BuildV2000SAPLines(const int idx, const SubstanceGroup *sgroup);
98 
99 std::string BuildV2000SCLLine(const int idx, const SubstanceGroup *sgroup);
100 const std::string GetMolFileSGroupInfo(const RWMol &mol);
101 
102 /* ------------------ V3000 Utils ------------------ */
103 
104 template <class T>
105 std::string BuildV3000IdxVectorDataBlock(const std::string &key,
106  const std::vector<T *> &dataVector);
107 
108 template <class Iterator>
109 std::string BuildV3000IdxVectorDataBlock(const std::string &key,
110  const Iterator &dataVectorBegin,
111  const Iterator &dataVectorEnd);
112 
113 /* Classify bonds between XBONDS and CBOfindP work on a copy of
114  * bonds vector to prevent reordering of original vector */
115 std::string BuildV3000BondsBlock(const SubstanceGroup &sgroup);
116 
117 std::string FormatV3000StringPropertyBlock(const std::string &prop,
118  const SubstanceGroup &sgroup);
119 
120 std::string FormatV3000ParentBlock(const SubstanceGroup &sgroup);
121 
122 std::string FormatV3000CompNoBlock(const SubstanceGroup &sgroup);
123 
125  const std::vector<SubstanceGroup::Bracket> brackets);
126 
128  const std::vector<SubstanceGroup::CState> &cstates);
129 
130 const std::string GetV3000MolFileSGroupLines(const unsigned int idx,
131  const SubstanceGroup &sgroup);
132 } // namespace SGroupWriting
133 } // namespace RDKit
Defines the SubstanceGroup class.
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
The class for representing SubstanceGroups.
std::string BuildV2000SBTLines(const ROMol &mol)
std::string BuildV2000StringPropLines(const unsigned int entriesPerLine, const ROMol &mol, const std::string &propName, const std::string &propCode, const unsigned int fieldWitdh)
std::string FormatV3000CompNoBlock(const SubstanceGroup &sgroup)
std::string BuildV2000SCDSEDLines(const int idx, const SubstanceGroup *sgroup)
std::string BuildV2000STYLines(const ROMol &mol)
const std::string GetMolFileSGroupInfo(const RWMol &mol)
std::string BuildV2000SNCLines(const ROMol &mol)
const std::string GetV3000MolFileSGroupLines(const unsigned int idx, const SubstanceGroup &sgroup)
std::string BuildV2000SPLLines(const ROMol &mol)
std::string BuildV2000SLBLines(const ROMol &mol)
std::string FormatV3000CStateBlock(const std::vector< SubstanceGroup::CState > &cstates)
std::string FormatV3000BracketBlock(const std::vector< SubstanceGroup::Bracket > brackets)
std::string BuildV3000BondsBlock(const SubstanceGroup &sgroup)
std::string BuildV2000SDTLine(const int idx, const SubstanceGroup *sgroup)
std::string FormatV3000DoubleField(double value)
std::string BuildV2000SCLLine(const int idx, const SubstanceGroup *sgroup)
std::string BuildV2000SMTLine(const int idx, const SubstanceGroup *sgroup)
std::string BuildV2000SBVLine(const int idx, const SubstanceGroup *sgroup)
std::string BuildV2000SAPLines(const int idx, const SubstanceGroup *sgroup)
std::string FormatV3000StringPropertyBlock(const std::string &prop, const SubstanceGroup &sgroup)
std::string FormatV2000NumEntriesField(int value)
std::string FormatV2000StringField(const std::string &value, unsigned int fieldSize, bool pad, bool addSeparator)
std::string FormatV3000ParentBlock(const SubstanceGroup &sgroup)
std::string BuildV2000SDDLine(const int idx, const SubstanceGroup *sgroup)
std::unordered_map< int, SubstanceGroup > IDX_TO_SGROUP_MAP
std::string BuildV2000SDILine(const int idx, const SubstanceGroup *sgroup)
std::string FormatV2000DoubleField(double value)
std::string BuildV3000IdxVectorDataBlock(const std::string &key, const std::vector< T * > &dataVector)
std::string BuildV2000SDSLines(const ROMol &mol)
std::string FormatV2000IntField(int value)
std::string BuildV2000IdxVectorDataLines(const unsigned int entriesPerLine, const unsigned int sGroupId, const std::string &code, const T &dataVector)
Std stuff.
Definition: Abbreviations.h:18