RDKit
Open-source cheminformatics and machine learning.
MMFF/Builder.h
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1//
2// Copyright (C) 2013-2018 Paolo Tosco
3//
4// Copyright (C) 2004-2006 Rational Discovery LLC
5//
6// @@ All Rights Reserved @@
7// This file is part of the RDKit.
8// The contents are covered by the terms of the BSD license
9// which is included in the file license.txt, found at the root
10// of the RDKit source tree.
11//
12#include <RDGeneral/export.h>
13#ifndef RD_MMFFBUILDER_H
14#define RD_MMFFBUILDER_H
15
16#include <vector>
17#include <string>
18#include <boost/shared_array.hpp>
19#include <boost/scoped_ptr.hpp>
20#ifdef RDK_THREADSAFE_SSS
21#include <mutex>
22#endif
23#include <boost/noncopyable.hpp>
24#include <boost/tuple/tuple.hpp>
25#include <cstdint>
26
27namespace ForceFields {
28class ForceField;
29}
30
31namespace RDKit {
32class ROMol;
33namespace MMFF {
34class MMFFMolProperties;
35
36//! Builds and returns a MMFF force field for a molecule
37/*!
38
39 \param mol the molecule to use
40 \param nonBondedThresh the threshold to be used in adding non-bonded terms
41 to the force field. Any non-bonded contact whose
42 current
43 distance is greater than \c nonBondedThresh * the minimum
44 value
45 for that contact will not be included.
46 \param confId the optional conformer id, if this isn't provided, the
47 molecule's
48 default confId will be used.
49 \param ignoreInterfragInteractions if true, nonbonded terms will not be added
50 between
51 fragments
52
53 \return the new force field. The client is responsible for free'ing this.
54*/
56 ROMol &mol, double nonBondedThresh = 100.0, int confId = -1,
57 bool ignoreInterfragInteractions = true);
58
59//! Builds and returns a MMFF force field for a molecule
60/*!
61
62 \param mol the molecule to use
63 \param mmffMolProperties pointer to a MMFFMolProperties object
64 \param nonBondedThresh the threshold to be used in adding non-bonded terms
65 to the force field. Any non-bonded contact whose current
66 distance is greater than \c nonBondedThresh * the minimum
67 value
68 for that contact will not be included.
69 \param confId the optional conformer id, if this isn't provided, the
70 molecule's
71 default confId will be used.
72 \param ignoreInterfragInteractions if true, nonbonded terms will not be added
73 between
74 fragments
75
76 \return the new force field. The client is responsible for free'ing this.
77*/
79 ROMol &mol, MMFFMolProperties *mmffMolProperties,
80 double nonBondedThresh = 100.0, int confId = -1,
81 bool ignoreInterfragInteractions = true);
82
83namespace Tools {
85 : private boost::noncopyable {
86 public:
87 static const std::string &string() { return ds_string; }
88 static const ROMol *query();
89
90 private:
92 static void create();
93 static const std::string ds_string;
94 static boost::scoped_ptr<const ROMol> ds_instance;
95#ifdef RDK_THREADSAFE_SSS
96 static std::once_flag ds_flag;
97#endif
98};
99
101// these functions are primarily exposed so they can be tested.
102RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int twoBitCellPos(unsigned int nAtoms,
103 int i, int j);
105 boost::shared_array<std::uint8_t> &res, unsigned int pos,
106 std::uint8_t value);
108 boost::shared_array<std::uint8_t> &res, unsigned int pos);
109RDKIT_FORCEFIELDHELPERS_EXPORT boost::shared_array<std::uint8_t>
112 const ROMol &mol, MMFFMolProperties *mmffMolProperties,
115 const ROMol &mol, MMFFMolProperties *mmffMolProperties,
118 const ROMol &mol, MMFFMolProperties *mmffMolProperties,
121 MMFFMolProperties *mmffMolProperties,
124 const ROMol &mol, MMFFMolProperties *mmffMolProperties,
126 const std::string &torsionBondSmarts = DefaultTorsionBondSmarts::string());
128 const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties,
130 boost::shared_array<std::uint8_t> neighborMatrix,
131 double nonBondedThresh = 100.0, bool ignoreInterfragInteractions = true);
133 const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties,
135 boost::shared_array<std::uint8_t> neighborMatrix,
136 double nonBondedThresh = 100.0, bool ignoreInterfragInteractions = true);
137} // namespace Tools
138} // namespace MMFF
139} // namespace RDKit
140
141#endif
A class to store forcefields and handle minimization.
Definition: ForceField.h:79
static const std::string & string()
Definition: MMFF/Builder.h:87
#define RDKIT_FORCEFIELDHELPERS_EXPORT
Definition: export.h:185
RDKIT_FORCEFIELDHELPERS_EXPORT void setTwoBitCell(boost::shared_array< std::uint8_t > &res, unsigned int pos, std::uint8_t value)
RDKIT_FORCEFIELDHELPERS_EXPORT void addStretchBend(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
RDKIT_FORCEFIELDHELPERS_EXPORT void addTorsions(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, const std::string &torsionBondSmarts=DefaultTorsionBondSmarts::string())
RDKIT_FORCEFIELDHELPERS_EXPORT void addBonds(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
RDKIT_FORCEFIELDHELPERS_EXPORT std::uint8_t getTwoBitCell(boost::shared_array< std::uint8_t > &res, unsigned int pos)
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int twoBitCellPos(unsigned int nAtoms, int i, int j)
RDKIT_FORCEFIELDHELPERS_EXPORT void addOop(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
RDKIT_FORCEFIELDHELPERS_EXPORT void addAngles(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
RDKIT_FORCEFIELDHELPERS_EXPORT void addVdW(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, boost::shared_array< std::uint8_t > neighborMatrix, double nonBondedThresh=100.0, bool ignoreInterfragInteractions=true)
RDKIT_FORCEFIELDHELPERS_EXPORT void addEle(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, boost::shared_array< std::uint8_t > neighborMatrix, double nonBondedThresh=100.0, bool ignoreInterfragInteractions=true)
RDKIT_FORCEFIELDHELPERS_EXPORT boost::shared_array< std::uint8_t > buildNeighborMatrix(const ROMol &mol)
RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField * constructForceField(ROMol &mol, double nonBondedThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
Builds and returns a MMFF force field for a molecule.
Std stuff.
Definition: Abbreviations.h:18