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MMFF/Builder.h
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1 //
2 // Copyright (C) 2013 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 #ifndef _RD_MMFFBUILDER_H_
13 #define _RD_MMFFBUILDER_H_
14
15 #include <vector>
16 #include <string>
17 #include <boost/shared_array.hpp>
18 #include <boost/scoped_ptr.hpp>
19 #include <boost/thread/once.hpp>
20 #include <boost/noncopyable.hpp>
21 #include <boost/tuple/tuple.hpp>
22 #include <boost/cstdint.hpp>
23
24 namespace ForceFields {
25 class ForceField;
26 }
27
28 namespace RDKit {
29 class ROMol;
30 namespace MMFF {
31 class MMFFMolProperties;
32
33 //! Builds and returns a MMFF force field for a molecule
34 /*!
35
36 \param mol the molecule to use
37 \param nonBondedThresh the threshold to be used in adding non-bonded terms
38 to the force field. Any non-bonded contact whose
39 current
40 distance is greater than \c nonBondedThresh * the minimum
41 value
42 for that contact will not be included.
43 \param confId the optional conformer id, if this isn't provided, the
44 molecule's
45 default confId will be used.
46 \param ignoreInterfragInteractions if true, nonbonded terms will not be added
47 between
48 fragments
49
50 \return the new force field. The client is responsible for free'ing this.
51 */
52 ForceFields::ForceField *constructForceField(
53 ROMol &mol, double nonBondedThresh = 100.0, int confId = -1,
54 bool ignoreInterfragInteractions = true);
55
56 //! Builds and returns a MMFF force field for a molecule
57 /*!
58
59 \param mol the molecule to use
60 \param mmffMolProperties pointer to a MMFFMolProperties object
61 \param nonBondedThresh the threshold to be used in adding non-bonded terms
62 to the force field. Any non-bonded contact whose current
63 distance is greater than \c nonBondedThresh * the minimum
64 value
65 for that contact will not be included.
66 \param confId the optional conformer id, if this isn't provided, the
67 molecule's
68 default confId will be used.
69 \param ignoreInterfragInteractions if true, nonbonded terms will not be added
70 between
71 fragments
72
73 \return the new force field. The client is responsible for free'ing this.
74 */
75 ForceFields::ForceField *constructForceField(
76 ROMol &mol, MMFFMolProperties *mmffMolProperties,
77 double nonBondedThresh = 100.0, int confId = -1,
78 bool ignoreInterfragInteractions = true);
79
80 namespace Tools {
81 class DefaultTorsionBondSmarts : private boost::noncopyable
82 {
83 public:
84 static const std::string &string() {
85 return ds_string;
86 }
87 static const ROMol *query();
88 private:
89 DefaultTorsionBondSmarts() {}
90 static void create();
91 static const std::string ds_string;
92 static boost::scoped_ptr<const ROMol> ds_instance;
93 static boost::once_flag ds_flag;
94 };
95
96 enum { RELATION_1_2 = 0, RELATION_1_3 = 1, RELATION_1_4 = 2, RELATION_1_X = 3 };
97 // these functions are primarily exposed so they can be tested.
98 unsigned int twoBitCellPos(unsigned int nAtoms, int i, int j);
99 void setTwoBitCell(boost::shared_array<boost::uint8_t> &res, unsigned int pos,
100 boost::uint8_t value);
101 boost::uint8_t getTwoBitCell(boost::shared_array<boost::uint8_t> &res,
102 unsigned int pos);
103 boost::shared_array<boost::uint8_t> buildNeighborMatrix(const ROMol &mol);
104 void addBonds(const ROMol &mol, MMFFMolProperties *mmffMolProperties,
105 ForceFields::ForceField *field);
106 void addAngles(const ROMol &mol, MMFFMolProperties *mmffMolProperties,
107 ForceFields::ForceField *field);
108 void addStretchBend(const ROMol &mol, MMFFMolProperties *mmffMolProperties,
109 ForceFields::ForceField *field);
110 void addOop(const ROMol &mol, MMFFMolProperties *mmffMolProperties,
111 ForceFields::ForceField *field);
112 void addTorsions(const ROMol &mol, MMFFMolProperties *mmffMolProperties,
113 ForceFields::ForceField *field,
114 const std::string &torsionBondSmarts =
115 DefaultTorsionBondSmarts::string());
116 void addVdW(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties,
117 ForceFields::ForceField *field,
118 boost::shared_array<boost::uint8_t> neighborMatrix,
119 double nonBondedThresh = 100.0,
120 bool ignoreInterfragInteractions = true);
121 void addEle(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties,
122 ForceFields::ForceField *field,
123 boost::shared_array<boost::uint8_t> neighborMatrix,
124 double nonBondedThresh = 100.0,
125 bool ignoreInterfragInteractions = true);
126 }
127 }
128 }
129
130 #endif
RDKit::MMFF::Tools::getTwoBitCell
boost::uint8_t getTwoBitCell(boost::shared_array< boost::uint8_t > &res, unsigned int pos)
RDKit::MMFF::Tools::addOop
void addOop(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
RDKit::MMFF::Tools::RELATION_1_2
Definition: MMFF/Builder.h:96
RDKit::MMFF::Tools::RELATION_1_3
Definition: MMFF/Builder.h:96
RDKit::MMFF::Tools::twoBitCellPos
unsigned int twoBitCellPos(unsigned int nAtoms, int i, int j)
RDKit::MMFF::Tools::setTwoBitCell
void setTwoBitCell(boost::shared_array< boost::uint8_t > &res, unsigned int pos, boost::uint8_t value)
RDKit::MMFF::Tools::addStretchBend
void addStretchBend(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
RDKit::MMFF::Tools::RELATION_1_4
Definition: MMFF/Builder.h:96
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
RDKit::MMFF::Tools::buildNeighborMatrix
boost::shared_array< boost::uint8_t > buildNeighborMatrix(const ROMol &mol)
ForceFields
Definition: TorsionAngleM6.h:23
RDKit::MMFF::Tools::DefaultTorsionBondSmarts
Definition: MMFF/Builder.h:81
RDKit::MMFF::Tools::RELATION_1_X
Definition: MMFF/Builder.h:96
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::MMFF::Tools::addAngles
void addAngles(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
RDKit::MMFF::Tools::addTorsions
void addTorsions(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, const std::string &torsionBondSmarts=DefaultTorsionBondSmarts::string())
RDKit::MMFF::Tools::addEle
void addEle(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, boost::shared_array< boost::uint8_t > neighborMatrix, double nonBondedThresh=100.0, bool ignoreInterfragInteractions=true)
RDKit::MMFF::constructForceField
ForceFields::ForceField * constructForceField(ROMol &mol, MMFFMolProperties *mmffMolProperties, double nonBondedThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
Builds and returns a MMFF force field for a molecule.
RDKit::MMFF::MMFFMolProperties
Definition: MMFF/AtomTyper.h:47
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition: ForceField.h:57
RDKit::MMFF::Tools::addVdW
void addVdW(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, boost::shared_array< boost::uint8_t > neighborMatrix, double nonBondedThresh=100.0, bool ignoreInterfragInteractions=true)
RDKit::MMFF::Tools::DefaultTorsionBondSmarts::string
static const std::string & string()
Definition: MMFF/Builder.h:84
RDKit::MMFF::Tools::addBonds
void addBonds(const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)