10 #ifndef _RD_UFFBUILDER_H_ 11 #define _RD_UFFBUILDER_H_ 15 #include <boost/shared_array.hpp> 27 typedef std::vector<const ForceFields::UFF::AtomicParams *>
AtomicParamVect;
47 ROMol &mol,
double vdwThresh = 100.0,
int confId = -1,
48 bool ignoreInterfragInteractions =
true);
70 ROMol &mol,
const AtomicParamVect ¶ms,
double vdwThresh = 100.0,
71 int confId = -1,
bool ignoreInterfragInteractions =
true);
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,
81 void addBonds(
const ROMol &mol,
const AtomicParamVect ¶ms,
87 boost::shared_array<boost::uint8_t> neighborMatrix,
88 double vdwThresh = 100.0,
89 bool ignoreInterfragInteractions =
true);
92 std::string torsionBondSmarts =
"[!$(*#*)&!D1]~[!$(*#*)&!D1]");
ForceFields::ForceField * constructForceField(ROMol &mol, const AtomicParamVect ¶ms, double vdwThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
Builds and returns a UFF force field for a molecule.
ROMol is a molecule class that is intended to have a fixed topology.
Includes a bunch of functionality for handling Atom and Bond queries.
std::vector< const ForceFields::UFF::AtomicParams * > AtomicParamVect
A class to store forcefields and handle minimization.