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UFF/Builder.h
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1 //
2 // Copyright (C) 2004-2006 Rational Discovery LLC
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 #ifndef _RD_UFFBUILDER_H_
11 #define _RD_UFFBUILDER_H_
12
13 #include <vector>
14 #include <string>
15 #include <boost/shared_array.hpp>
16
17 namespace ForceFields {
18 class ForceField;
19 namespace UFF {
20 class AtomicParams;
21 }
22 }
23
24 namespace RDKit {
25 class ROMol;
26 namespace UFF {
27 typedef std::vector<const ForceFields::UFF::AtomicParams *> AtomicParamVect;
28
29 //! Builds and returns a UFF force field for a molecule
30 /*!
31
32 \param mol the molecule to use
33 \param vdwThresh the threshold to be used in adding van der Waals terms
34 to the force field. Any non-bonded contact whose current
35 distance is greater than \c vdwThresh * the minimum value
36 for that contact will not be included.
37 \param confId the optional conformer id, if this isn't provided, the
38 molecule's
39 default confId will be used.
40 \param ignoreInterfragInteractions if true, nonbonded terms will not be added
41 between
42 fragments
43
44 \return the new force field. The client is responsible for free'ing this.
45 */
46 ForceFields::ForceField *constructForceField(
47 ROMol &mol, double vdwThresh = 100.0, int confId = -1,
48 bool ignoreInterfragInteractions = true);
49
50 //! Builds and returns a UFF force field for a molecule
51 /*!
52
53 \param mol the molecule to use
54 \param params a vector with pointers to the ForceFields::UFF::AtomicParams
55 structures to be used
56 \param vdwThresh the threshold to be used in adding van der Waals terms
57 to the force field. Any non-bonded contact whose current
58 distance is greater than \c vdwThresh * the minimum value
59 for that contact will not be included.
60 \param confId the optional conformer id, if this isn't provided, the
61 molecule's
62 default confId will be used.
63 \param ignoreInterfragInteractions if true, nonbonded terms will not be added
64 between
65 fragments
66
67 \return the new force field. The client is responsible for free'ing this.
68 */
69 ForceFields::ForceField *constructForceField(
70 ROMol &mol, const AtomicParamVect &params, double vdwThresh = 100.0,
71 int confId = -1, bool ignoreInterfragInteractions = true);
72
73 namespace Tools {
74 enum { RELATION_1_2 = 0, RELATION_1_3 = 1, RELATION_1_4 = 2, RELATION_1_X = 3 };
75 // these functions are primarily exposed so they can be tested.
76 void setTwoBitCell(boost::shared_array<boost::uint8_t> &res, unsigned int pos,
77 boost::uint8_t value);
78 boost::uint8_t getTwoBitCell(boost::shared_array<boost::uint8_t> &res,
79 unsigned int pos);
80 boost::shared_array<boost::uint8_t> buildNeighborMatrix(const ROMol &mol);
81 void addBonds(const ROMol &mol, const AtomicParamVect &params,
82 ForceFields::ForceField *field);
83 void addAngles(const ROMol &mol, const AtomicParamVect &params,
84 ForceFields::ForceField *field);
85 void addNonbonded(const ROMol &mol, int confId, const AtomicParamVect &params,
86 ForceFields::ForceField *field,
87 boost::shared_array<boost::uint8_t> neighborMatrix,
88 double vdwThresh = 100.0,
89 bool ignoreInterfragInteractions = true);
90 void addTorsions(const ROMol &mol, const AtomicParamVect &params,
91 ForceFields::ForceField *field,
92 std::string torsionBondSmarts = "[!$(*#*)&!D1]~[!$(*#*)&!D1]");
93 void addInversions(const ROMol &mol, const AtomicParamVect &params,
94 ForceFields::ForceField *field);
95 }
96 }
97 }
98
99 #endif
RDKit::UFF::Tools::RELATION_1_X
Definition: UFF/Builder.h:74
RDKit::UFF::Tools::addInversions
void addInversions(const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)
RDKit::UFF::Tools::buildNeighborMatrix
boost::shared_array< boost::uint8_t > buildNeighborMatrix(const ROMol &mol)
RDKit::UFF::Tools::RELATION_1_3
Definition: UFF/Builder.h:74
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:102
RDKit::UFF::Tools::getTwoBitCell
boost::uint8_t getTwoBitCell(boost::shared_array< boost::uint8_t > &res, unsigned int pos)
RDKit::UFF::Tools::addBonds
void addBonds(const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)
ForceFields
Definition: TorsionAngleM6.h:23
RDKit::UFF::Tools::RELATION_1_2
Definition: UFF/Builder.h:74
RDKit::UFF::Tools::addTorsions
void addTorsions(const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field, std::string torsionBondSmarts="[!$(*#*)&!D1]~[!$(*#*)&!D1]")
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::UFF::Tools::addNonbonded
void addNonbonded(const ROMol &mol, int confId, const AtomicParamVect &params, ForceFields::ForceField *field, boost::shared_array< boost::uint8_t > neighborMatrix, double vdwThresh=100.0, bool ignoreInterfragInteractions=true)
RDKit::UFF::AtomicParamVect
std::vector< const ForceFields::UFF::AtomicParams * > AtomicParamVect
Definition: UFF/AtomTyper.h:27
RDKit::UFF::Tools::setTwoBitCell
void setTwoBitCell(boost::shared_array< boost::uint8_t > &res, unsigned int pos, boost::uint8_t value)
RDKit::UFF::constructForceField
ForceFields::ForceField * constructForceField(ROMol &mol, double vdwThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
Builds and returns a UFF force field for a molecule.
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition: ForceField.h:56
RDKit::UFF::Tools::addAngles
void addAngles(const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)
RDKit::UFF::Tools::RELATION_1_4
Definition: UFF/Builder.h:74