loos::internal Namespace Reference

Loos esoterica. More...

Classes
class	Action
	Base class for all commands... More...
class	AtomicNumberDeducer
class	Backbone
	Shortcut for checking for backbone atoms... More...
struct	BasicMatrixFormatter
class	drop
	Drop the top item from the stack. More...
class	dup
	Duplicate the top item on the stack. More...
class	equals
	Test for equality: ARG1 ARG ==. More...
class	extractNumber
	Extracts a number for a string on the stack using a regular expression: ARG1 regexp(S) More...
class	greaterThan
	ARG1 ARG2 > More...
class	greaterThanEquals
	ARG1 ARG2 >=. More...
class	Hydrogen
	Shortcut for checking for hydrogens... More...
class	lessThan
	Relation operators...: ARG1 ARG2 <. More...
class	lessThanEquals
	ARG1 ARG2 <=. More...
class	logicalAnd
	ARG1 ARG2 &&. More...
class	logicalNot
	ARG1 ! More...
class	logicalOr
	ARG1 ARG2 ||. More...
class	logicalTrue
	Always returns true... More...
class	matchRegex
	Regular expression matching: ARG1 regexp(S) More...
class	matchStringAsRegex
	Regular expression matching: ARG1 regexp(ARG2) More...
struct	OutputTrajectoryNameBindingType
class	pushAtomChainId
	Push atom's chain ID onto the stack. More...
class	pushAtomId
	Push atom id onto the stack. More...
class	pushAtomIndex
	Push atom index onto the stack. More...
class	pushAtomName
	Push atom name onto the stack. More...
class	pushAtomResid
	Push atom's residue id onto the stack. More...
class	pushAtomResname
	Push atom'ss residue name onto the stack. More...
class	pushAtomSegid
	Push atom's segid onto the stack. More...
class	pushFloat
	Push a float onto the data stack. More...
class	pushInt
	Push an integer onto the data stack. More...
class	pushString
	Push a std::string onto the data stack. More...
struct	RangeItem
struct	RangeParser
struct	SystemNameBindingType
struct	TrajectoryNameBindingType
struct	Value
	Value class for the LOOS Kernel (virtual machine) More...
class	ValueStack
class	XDRReader
	This class provides some facility for handling XDR data. More...
class	XDRWriter

Typedefs
typedef vector< RangeItem * >	RangeList
typedef RangeItem *	RangeItemPointer

Functions
std::ostream &	operator<< (std::ostream &os, const ValueStack &s)
int	compare (const Value &, const Value &)
	Compare two Value objects, depending on their types.

Variables
const float	FLT_THRESHOLD = 1e-10
SystemNameBindingType	system_name_bindings []
TrajectoryNameBindingType	trajectory_name_bindings []
OutputTrajectoryNameBindingType	output_trajectory_name_bindings []

Detailed Description

Loos esoterica.

You probably don't want to look in here unless you want to program with the virtual machine for atom selections, but I'd advise against that...

Function Documentation

compare()

int loos::internal::compare	(	const Value &	,
		const Value &	)

Compare two Value objects, depending on their types.

Returns -1 if x < y 0 if x = y 1 if x > y

For strings, this is based on the lexical value... For floats, the equality is determined by the FLT_THRESHOLD constant...

Comparison of non-like types is an error...

Variable Documentation

output_trajectory_name_bindings

OutputTrajectoryNameBindingType loos::internal::output_trajectory_name_bindings[]

Initial value:

= {
      { "dcd", "NAMD DCD", &DCDWriter::create},
      { "xtc", "Gromacs XTC (compressed trajectory)", &XTCWriter::create},
      { "", "", 0}
    }

system_name_bindings

SystemNameBindingType loos::internal::system_name_bindings[]

Initial value:

= {
      { "prmtop", "Amber", &Amber::create },
      { "crd", "CHARMM CRD", &CHARMM::create },
      { "pdb", "CHARMM/NAMD PDB", &PDB::create },
      { "psf", "CHARMM/NAMD PSF", &PSF::create },
      { "gro", "Gromacs", &Gromacs::create },
      { "xyz", "Tinker", &TinkerXYZ::create },
      { "cif", "PDBx/mmcif", &MMCIF::create },
      { "h5", "MDTraj HDF5", &MDTraj::create },
      { "", "", 0}
    }

trajectory_name_bindings

TrajectoryNameBindingType loos::internal::trajectory_name_bindings[]

Initial value:

= {
      { "crd", "Amber Traj (NetCDF/Amber)", &AmberNetcdf::create},
      { "mdcrd", "Amber Traj (NetCDF/Amber)", &AmberNetcdf::create},
      { "nc", "Amber Traj (NetCDF)", &AmberNetcdf::create},
      { "netcdf", "Amber Traj (NetCDF)", &AmberNetcdf::create},
      { "inpcrd", "Amber Restart", &AmberRst::create},
      { "rst", "Amber Restart", &AmberRst::create},
      { "rst7", "Amber Restart", &AmberRst::create},
      { "dcd", "CHARMM/NAMD DCD", &DCD::create},
      { "pdb", "Concatenated PDB", &CCPDB::create},
      { "trr", "Gromacs TRR", &TRR::create},
      { "xtc", "Gromacs XTC", &XTC::create},
      { "arc", "Tinker ARC", &TinkerArc::create},
      { "h5", "MDTraj HDF5", &MDTrajTraj::create},
      { "", "", 0}
    }