LOOS  v2.3.2
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  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
 

Functions

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

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

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...

Definition at line 31 of file KernelValue.cpp.

Variable Documentation

OutputTrajectoryNameBindingType loos::internal::output_trajectory_name_bindings[]
Initial value:
= {
{ "dcd", "NAMD DCD", &DCDWriter::create},
{ "xtc", "Gromacs XTC (compressed trajectory)", &XTCWriter::create},
{ "", "", 0}
}

Definition at line 203 of file sfactories.cpp.

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 },
{ "", "", 0}
}

Definition at line 68 of file sfactories.cpp.

TrajectoryNameBindingType loos::internal::trajectory_name_bindings[]
Initial value:
= {
{ "crd", "Amber Traj", &AmberTraj::create},
{ "mdcrd", "Amber Traj", &AmberTraj::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},
{ "", "", 0}
}

Definition at line 131 of file sfactories.cpp.