RDKit
Open-source cheminformatics and machine learning.
Loading...
Searching...
No Matches
MonomerInfo.h
Go to the documentation of this file.
1//
2// Copyright (C) 2013-2021 Greg Landrum and other RDKit contributors
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/*! \file MonomerInfo.h
11
12 \brief Defines Monomer information classes
13
14*/
15#include <RDGeneral/export.h>
16#ifndef RD_MONOMERINFO_H
17#define RD_MONOMERINFO_H
18
19#include <string>
20#include <utility>
21#include <boost/shared_ptr.hpp>
22
23namespace RDKit {
24
25//! The abstract base class for atom-level monomer info
27 public:
28 typedef enum { UNKNOWN = 0, PDBRESIDUE, OTHER } AtomMonomerType;
29
30 virtual ~AtomMonomerInfo() {}
31
32 AtomMonomerInfo() : d_name("") {}
33 AtomMonomerInfo(AtomMonomerType typ, std::string nm = "")
34 : d_monomerType(typ), d_name(std::move(nm)) {}
36 : d_monomerType(other.d_monomerType), d_name(other.d_name) {}
37
38 const std::string &getName() const { return d_name; }
39 void setName(const std::string &nm) { d_name = nm; }
40 AtomMonomerType getMonomerType() const { return d_monomerType; }
41 void setMonomerType(AtomMonomerType typ) { d_monomerType = typ; }
42
43 virtual AtomMonomerInfo *copy() const { return new AtomMonomerInfo(*this); }
44
45 private:
46 AtomMonomerType d_monomerType{UNKNOWN};
47 std::string d_name;
48};
49
50//! Captures atom-level information about peptide residues
52 public:
55 : AtomMonomerInfo(other),
56 d_serialNumber(other.d_serialNumber),
57 d_altLoc(other.d_altLoc),
58 d_residueName(other.d_residueName),
59 d_residueNumber(other.d_residueNumber),
60 d_chainId(other.d_chainId),
61 d_insertionCode(other.d_insertionCode),
62 d_occupancy(other.d_occupancy),
63 d_tempFactor(other.d_tempFactor),
64 df_heteroAtom(other.df_heteroAtom),
65 d_secondaryStructure(other.d_secondaryStructure),
66 d_segmentNumber(other.d_segmentNumber) {}
67
68 AtomPDBResidueInfo(const std::string &atomName, int serialNumber = 0,
69 std::string altLoc = "", std::string residueName = "",
70 int residueNumber = 0, std::string chainId = "",
71 std::string insertionCode = "", double occupancy = 1.0,
72 double tempFactor = 0.0, bool isHeteroAtom = false,
73 unsigned int secondaryStructure = 0,
74 unsigned int segmentNumber = 0)
75 : AtomMonomerInfo(PDBRESIDUE, atomName),
76 d_serialNumber(serialNumber),
77 d_altLoc(std::move(altLoc)),
78 d_residueName(std::move(residueName)),
79 d_residueNumber(residueNumber),
80 d_chainId(std::move(chainId)),
81 d_insertionCode(std::move(insertionCode)),
82 d_occupancy(occupancy),
83 d_tempFactor(tempFactor),
84 df_heteroAtom(isHeteroAtom),
85 d_secondaryStructure(secondaryStructure),
86 d_segmentNumber(segmentNumber) {}
87
88 int getSerialNumber() const { return d_serialNumber; }
89 void setSerialNumber(int val) { d_serialNumber = val; }
90 const std::string &getAltLoc() const { return d_altLoc; }
91 void setAltLoc(const std::string &val) { d_altLoc = val; }
92 const std::string &getResidueName() const { return d_residueName; }
93 void setResidueName(const std::string &val) { d_residueName = val; }
94 int getResidueNumber() const { return d_residueNumber; }
95 void setResidueNumber(int val) { d_residueNumber = val; }
96 const std::string &getChainId() const { return d_chainId; }
97 void setChainId(const std::string &val) { d_chainId = val; }
98 const std::string &getInsertionCode() const { return d_insertionCode; }
99 void setInsertionCode(const std::string &val) { d_insertionCode = val; }
100 double getOccupancy() const { return d_occupancy; }
101 void setOccupancy(double val) { d_occupancy = val; }
102 double getTempFactor() const { return d_tempFactor; }
103 void setTempFactor(double val) { d_tempFactor = val; }
104 bool getIsHeteroAtom() const { return df_heteroAtom; }
105 void setIsHeteroAtom(bool val) { df_heteroAtom = val; }
106 unsigned int getSecondaryStructure() const { return d_secondaryStructure; }
107 void setSecondaryStructure(unsigned int val) { d_secondaryStructure = val; }
108 unsigned int getSegmentNumber() const { return d_segmentNumber; }
109 void setSegmentNumber(unsigned int val) { d_segmentNumber = val; }
110
111 AtomMonomerInfo *copy() const override {
112 return static_cast<AtomMonomerInfo *>(new AtomPDBResidueInfo(*this));
113 }
114
115 private:
116 // the fields here are from the PDB definition
117 // (http://www.wwpdb.org/documentation/format33/sect9.html#ATOM) [9 Aug, 2013]
118 // element and charge are not present since the atom itself stores that
119 // information
120 unsigned int d_serialNumber = 0;
121 std::string d_altLoc = "";
122 std::string d_residueName = "";
123 int d_residueNumber = 0;
124 std::string d_chainId = "";
125 std::string d_insertionCode = "";
126 double d_occupancy = 1.0;
127 double d_tempFactor = 0.0;
128 // additional, non-PDB fields:
129 bool df_heteroAtom = false; // is this from a HETATM record?
130 unsigned int d_secondaryStructure = 0;
131 unsigned int d_segmentNumber = 0;
132};
133}; // namespace RDKit
134//! allows AtomPDBResidueInfo objects to be dumped to streams
136 std::ostream &target, const RDKit::AtomPDBResidueInfo &apri);
137
138#endif
RDKIT_GRAPHMOL_EXPORT std::ostream & operator<<(std::ostream &target, const RDKit::AtomPDBResidueInfo &apri)
allows AtomPDBResidueInfo objects to be dumped to streams
The abstract base class for atom-level monomer info.
Definition MonomerInfo.h:26
void setName(const std::string &nm)
Definition MonomerInfo.h:39
const std::string & getName() const
Definition MonomerInfo.h:38
AtomMonomerInfo(AtomMonomerType typ, std::string nm="")
Definition MonomerInfo.h:33
virtual AtomMonomerInfo * copy() const
Definition MonomerInfo.h:43
void setMonomerType(AtomMonomerType typ)
Definition MonomerInfo.h:41
AtomMonomerInfo(const AtomMonomerInfo &other)
Definition MonomerInfo.h:35
AtomMonomerType getMonomerType() const
Definition MonomerInfo.h:40
Captures atom-level information about peptide residues.
Definition MonomerInfo.h:51
void setIsHeteroAtom(bool val)
double getTempFactor() const
void setResidueNumber(int val)
Definition MonomerInfo.h:95
void setOccupancy(double val)
AtomMonomerInfo * copy() const override
void setSecondaryStructure(unsigned int val)
double getOccupancy() const
void setInsertionCode(const std::string &val)
Definition MonomerInfo.h:99
void setChainId(const std::string &val)
Definition MonomerInfo.h:97
void setAltLoc(const std::string &val)
Definition MonomerInfo.h:91
const std::string & getInsertionCode() const
Definition MonomerInfo.h:98
const std::string & getChainId() const
Definition MonomerInfo.h:96
void setSerialNumber(int val)
Definition MonomerInfo.h:89
AtomPDBResidueInfo(const AtomPDBResidueInfo &other)
Definition MonomerInfo.h:54
unsigned int getSegmentNumber() const
AtomPDBResidueInfo(const std::string &atomName, int serialNumber=0, std::string altLoc="", std::string residueName="", int residueNumber=0, std::string chainId="", std::string insertionCode="", double occupancy=1.0, double tempFactor=0.0, bool isHeteroAtom=false, unsigned int secondaryStructure=0, unsigned int segmentNumber=0)
Definition MonomerInfo.h:68
void setResidueName(const std::string &val)
Definition MonomerInfo.h:93
const std::string & getResidueName() const
Definition MonomerInfo.h:92
unsigned int getSecondaryStructure() const
void setSegmentNumber(unsigned int val)
const std::string & getAltLoc() const
Definition MonomerInfo.h:90
void setTempFactor(double val)
#define RDKIT_GRAPHMOL_EXPORT
Definition export.h:233
Std stuff.