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
|
//
// Copyright (C) 2020 Brian P Kelley, Joann Prescott-Roy
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef RDK_DEPROTECT_LIBRARY
#define RDK_DEPROTECT_LIBRARY
#include <RDGeneral/export.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <string>
#include <memory>
namespace RDKit {
namespace Deprotect {
/*! Data for Deprotecting molecules
Deprotects are described as reactions that remove the protecting
group and leave behind the group being protected.
Each DeprotectData has the following attributes:
- <b>deprotection_class</b> functional group being protected (i.e. amine,
alcohol, ...)
- <b>reaction_smarts</b> the reaction smarts pattern for removing the
protecting group
- <b>abbreviation</b> common abbreviation for the protecting group (Boc,
Fmoc)
- <b>full_name</b> full name for the protecting group
- <b> rxn </b> the reaction itself.
*/
struct RDKIT_DEPROTECT_EXPORT DeprotectData {
std::string deprotection_class;
std::string reaction_smarts;
std::string abbreviation;
std::string full_name;
std::string example;
std::shared_ptr<ChemicalReaction>
rxn; // so much easier than unique_ptr, sigh...
DeprotectData(const std::string &deprotection_class,
const std::string &reaction_smarts,
const std::string &abbrevition,
const std::string &full_name,
const std::string &example="");
bool operator==(const DeprotectData &other) const {
return (deprotection_class == other.deprotection_class &&
full_name == other.full_name &&
abbreviation == other.abbreviation &&
reaction_smarts == other.reaction_smarts &&
isValid() == other.isValid());
}
//! Returns true if the deprotection is valid
bool isValid() const {
return rxn.get() != nullptr && rxn->getNumProductTemplates() == 1;
}
};
//! Retrieves the built in list of common deprotections
RDKIT_DEPROTECT_EXPORT const std::vector<DeprotectData> &getDeprotections();
//! Deprotect a molecule
/*!
The resulting molecule is annotated with the deprotections used (property
DEPROTECTIONS) and the number of deprotections applied (property
DEPROTECTIION_COUNT)
\param mol the molecule to deprotect
\param deprotections - a vector of deprotections to use, defaults to the
built in deprotections.
\return The deprotected form of the input molecule
*/
RDKIT_DEPROTECT_EXPORT std::unique_ptr<ROMol> deprotect(
const ROMol &mol,
const std::vector<DeprotectData> &deprotections = getDeprotections());
} // namspace Deprotect
} // namespace RDKit
#endif
|
