Here is a list of all documented namespaces with brief descriptions:
[detail level 123]
| Nadd_bonds | |
| Nall_contacts | |
| ►Nall_stacking | |
| CFullHelp | |
| Naxis_with_membrane | |
| Ncenter_molecule | |
| Ncluster | -structures |
| Ncluster_pops | |
| Ncontact_distance | |
| Ncylindrical | -density |
| ►NENM | Namespace to encapsulate Elastic Network Model routines |
| CANM | Anisotropic network model |
| CBadSpringFunction | Bad spring function was requested |
| CBadSpringParameter | Unspecified problem with parameters in SpringFunction |
| CBoundSuperBlock | Decorator for switching spring functions based on a matrix of flags |
| CConstBonded | Use a spring function that is a constant weight regardless of distance |
| CDistanceCutoff | Basic distance cutoff for "traditional" ENM |
| CDistanceWeight | Distance weighting (i.e.  |
| CElasticNetworkModel | Interface for all ENMs |
| CExponentialDistance | Exponential distance weighting (i.e.  |
| CHCA | HCA method (bimodal distance-based function) |
| CSpringFunction | Interface for ENM spring functions |
| CSuperBlock | This class creates superblocks in a hessian |
| CSuperBlockDecorator | SuperBlock decorator base class |
| CUniformSpringFunction | Spring functions that are uniform in all directions (ie return a single value) |
| CVSA | Vibrational subsystem analysis ENM |
| Nflip_chirality | |
| Nframe | -picker |
| Nhierarchical | -cluster |
| Ninside_helices | |
| ►Nloos | Namespace for most things not already encapsulated within a class |
| ►NDensityTools | Namespace for Density package |
| CBulkedWaterFilter | Add bulk water back into the mask/map |
| CBulkEstimator | |
| CDensityGrid | A simple 3D grid class of arbitrary types |
| CDensityGridIterator | Random access iterator using the BOOST facade |
| CDensityGridPlane | Encapsulates an i,j-plane from an DensityGrid |
| CDensityGridRow | Encapsulates a j-row from an DensityGrid |
| CNonzeroDensity | Functor that is true for any non-zero density |
| CNullEstimator | |
| CSimpleMeta | Simple class for handling metadata |
| CThreshold | Functor that is true if value is greater than or equal to threshold |
| CThresholdRange | Functor that is true if value is between low and hi, inclusive |
| CWaterFilterAxis | Pick waters that are within a radius of the principal axis for a molecule |
| CWaterFilterBase | Base interface for water filter/picker |
| CWaterFilterBlob | Pick waters based on a grid-mask |
| CWaterFilterBox | Pick waters inside a bounding box |
| CWaterFilterContacts | Pick waters with a minimum number of contacts to protein atoms |
| CWaterFilterCore | Pick waters that are within a radius of the core axis for a molecule |
| CWaterFilterDecorator | Decorator base class for "decorating" the core water filters.. |
| CWaterFilterRadius | Pick waters within a given radius of a group of atoms |
| CWaterHistogrammer | |
| CXEDMWriter | Functor for writing out ASCII formatted X-Plor electron density maps |
| CZClipEstimator | |
| CZClippedWaterFilter | Restrict waters to be within a given z-range |
| CZSliceEstimator | |
| ►Ninternal | Loos esoterica |
| CAction | Base class for all commands.. |
| CAtomicNumberDeducer | |
| CBackbone | Shortcut for checking for backbone atoms.. |
| CBasicMatrixFormatter | |
| Cdrop | Drop the top item from the stack |
| Cdup | Duplicate the top item on the stack |
| Cequals | Test for equality: ARG1 ARG == |
| CextractNumber | Extracts a number for a string on the stack using a regular expression: ARG1 regexp(S) |
| CgreaterThan | ARG1 ARG2 > |
| CgreaterThanEquals | ARG1 ARG2 >= |
| CHydrogen | Shortcut for checking for hydrogens.. |
| ClessThan | Relation operators...: ARG1 ARG2 < |
| ClessThanEquals | ARG1 ARG2 <= |
| ClogicalAnd | ARG1 ARG2 && |
| ClogicalNot | ARG1 ! |
| ClogicalOr | ARG1 ARG2 || |
| ClogicalTrue | Always returns true.. |
| CmatchRegex | Regular expression matching: ARG1 regexp(S) |
| CmatchStringAsRegex | Regular expression matching: ARG1 regexp(ARG2) |
| COutputTrajectoryNameBindingType | |
| CpushAtomChainId | Push atom's chain ID onto the stack |
| CpushAtomId | Push atom id onto the stack |
| CpushAtomIndex | Push atom index onto the stack |
| CpushAtomName | Push atom name onto the stack |
| CpushAtomResid | Push atom's residue id onto the stack |
| CpushAtomResname | Push atom'ss residue name onto the stack |
| CpushAtomSegid | Push atom's segid onto the stack |
| CpushFloat | Push a float onto the data stack |
| CpushInt | Push an integer onto the data stack |
| CpushString | Push a std::string onto the data stack |
| CRangeItem | |
| CRangeParser | |
| CSystemNameBindingType | |
| CTrajectoryNameBindingType | |
| CValue | Value class for the LOOS Kernel (virtual machine) |
| CValueStack | |
| CXDRReader | This class provides some facility for handling XDR data |
| CXDRWriter | |
| ►NMath | Namespace for math and math-related things in loos |
| CColMajor | Class for storing a matrix in column-major order |
| CMatrix | Simple matrix template class using policy classes to determine behavior |
| CRowMajor | Class for storing a matrix in row-major order.. |
| CSharedArray | Storage policy for a block of memory wrapped in a boost::shared_array pointer |
| CSparseArray | Storage policy for a sparse matrix (see important note in the detailed documentation) |
| CTriangular | Class for storing a symmetric triangular matrix |
| ►NOptionsFramework | Namespace for encapsulating options processing |
| CAggregateOptions | Combines a set of OptionsPackages |
| CBasicConvergence | |
| CBasicOptions | Options common to all tools (including –fullhelp) |
| CBasicSelection | Provides a single LOOS selection (–selection) |
| CBasicSplitBy | Provides a mechanism for controlling how to split an AtomicGroup |
| CBasicTrajectory | Basic trajectory with a –skip option |
| CBasicWater | Options specific to tools that work with water/internal-water |
| CModelWithCoords | Request a model with coordinates |
| CMultiTrajOptions | Multiple trajectories as one trajectory via MultiTrajectory |
| COptionsPackage | Base class for options |
| COutputPrefix | Gets a string as prefix for output files (–prefix) |
| COutputTrajectoryOptions | |
| COutputTrajectoryTypeOptions | |
| CRequiredArguments | Provides simple way to add command-line arguments (required options) |
| CTrajectoryWithFrameIndices | Trajectory with either a –range or –skip |
| CTwoModelsWithCoords | Request Two models with coordinates |
| CWeightsOptions | |
| CAbstractObserver | |
| CAmber | Class for reading in AMBER parmtop/coord files.. |
| CAmberNetcdf | Class for reading Amber Trajectories in NetCDF format |
| CAmberRst | Class for reading amber restart files as a single-frame trajectory |
| CAmberTraj | Class for reading amber coordinate trajectories |
| CAndSelector | Combines two selectors with a logical "and" |
| CAscendingSort | Policy class for sorting in ascending sequence |
| ►CAtom | Basic Atom class for handling atom properties |
| CUnsetProperty | DEPRECATED exception class...use loos::UnsetProperty instead |
| CAtomCoordsEquals | Compares two atoms based on name, id, resid, resname, segid, and coords |
| CAtomEquals | Compares two atoms based solely on name, id, resid, resname, and segid |
| ►CAtomicGroup | Class for handling groups of Atoms (pAtoms, actually) |
| CIterator | Our own simple iterator for stepping over all managed atoms |
| CAtomNameSelector | Predicate for selecting atoms based on explicit name matching |
| CAtomSelector | Virtual base-class for selecting atoms from a group |
| CBackboneSelector | Predicate for selecting backbone |
| CBasicProgress | |
| CBoundFmt | Internal helper class to bind formatting state |
| CCAlphaSelector | Predicate for selecting CA atoms |
| CCCPDB | Class for interpreting concatenated PDB files as a Trajectory |
| CCHARMM | Class for reading a CHARMM coordinate file |
| CCoord | Basic 3-D coordinates class |
| ►CDCD | Class for reading DCD files |
| CEndOfFile | |
| CDCDWriter | A very lightweight class for writing simple DCDs |
| CDescendingSort | Policy class for sorting in descending sequence |
| CEstimatingCounter | A progress counter that can estimate how much time is left |
| CFileError | Errors related to File I/O |
| CFileOpenError | Error while opening a file |
| CFileReadError | Errors that occur while reading a file |
| CFileReadErrorWithLine | Errors that occur while reading a text file (where lines are tracked) |
| CFileWriteError | Errors while writing to files |
| CFmt | Output formatter class, adapted from Stroustrup's book |
| CFormFactor | |
| CFormFactorSet | |
| CGromacs | Implements a GROMACS model file (.gro) |
| CHBondDetector | Class for detecting hydrogen bonds |
| CHeavyAtomSelector | Select non-hydrogen atoms |
| CHeavySolventSelector | Select only heavy solvent atoms |
| CHydrogenSelector | Select hydrogen atoms |
| CIndexSelector | Predicate for selecting atoms based on index |
| CKernel | The Kernel (virtual machine) for compiling and executing user-defined atom selections |
| CKernelSelector | Selection predicate that executes a compiled Kernel |
| CLineReader | Class for reading line-by-line from a file while tracking line numbers and stripping comments |
| CLOOSError | Generic LOOS exception |
| CMatrix44 | Specialized 4x4 Matrix class for handling coordinate transforms |
| CMatrixReadError | Generic reading error class |
| CMatrixReadImpl | |
| CMatrixReadImpl< T, Math::Triangular, S > | Special handling for triangular matrices |
| CMatrixReadImpl< T, P, Math::SparseArray > | Special handling for sparse matrices |
| CMatrixWriteImpl | |
| CMatrixWriteImpl< T, Math::Triangular, S, F > | Write out a triangular matrix |
| CMatrixWriteImpl< T, P, Math::SparseArray, F > | Write out a sparse matrix |
| CMDTraj | Class for reading a MDTraj HDF5 file |
| CMDTrajTraj | Class for reading MDTraj HDF5 coordinate trajectories |
| CMMCIF | Class to read pdbx/mmcif files |
| CMultiTrajectory | Combine multiple trajectories (pTraj's) into one large virtual trajectory |
| CNotSelector | Negates a selection predicate |
| CNumericalError | Exception caused by a blas/atlas error |
| COptionsError | Exception in options |
| COrSelector | Combines two selectors with a logical "or" |
| CParseError | Exception when parsing input data |
| CParser | Front-end to the Bison/Flex parser |
| CParserDriver | |
| CPDB | PDB reading/writing class |
| CPDBTraj | Class for intepreting separate PDB files as a single trajectory |
| CPercentProgress | Provide feedback by percent-complete |
| CPercentProgressWithTime | |
| CPercentTrigger | Trigger whenever at least frac percent more iterations have happened |
| CPeriodicBox | Class for managing periodic box information |
| CPreciseMatrixFormatter | Generic matrix element formatter allowing setting of width and precision |
| CProgressCounter | The progress counter front-end |
| CPSF | Class for reading a subset of the PSF format |
| CRemarks | Class for handling PDB Remarks |
| CResidRangeSelector | Predicate for selecting atoms from a range of resid's |
| CRnaSuite | Class for assigning backbone suites to an RNA |
| CScientificMatrixFormatter | Generic matrix element formatter using scientific notation.. |
| CSegidSelector | Predicate for selecting atoms based on the passed segid string |
| CSharedPeriodicBox | This class manages a shared Periodicbox |
| CSimpleCounter | Basic progress counter object, defining the interface.. |
| CSolventSelector | Predicate for selecting solvent based on common solvent SEGIDs |
| CStreamWrapper | Simple wrapper class for caching stream pointers |
| CTimer | Class for tracking time |
| CTimeSeries | Time Series Class |
| CTinkerArc | Class for handling Tinker ARC files (concatenation of .xyz files) |
| CTinkerXYZ | Class for reading a subset of the TinkerXYZ format |
| CTrajectory | Base-class for polymorphic trajectories |
| CTrajectoryError | Errors related to trajectory reading and writing |
| CTrajectoryWriter | Base class for writing trajectories |
| CTriggerAlways | This is a simple "trigger" for use as a default |
| CTriggerEvery | Trigger every i-iterations |
| CTRR | Class representing the GROMACS TRR trajectory files |
| CUniformWeight | |
| CUniqueStrings | Class for uniquifying strings.. |
| CUnitCell | This class encapsulates crystallographic unit cell data |
| Cunordered_pair_eq | Test equality of unordered pair. typename T must have == operator |
| Cunordered_pair_hash | |
| CUnsetProperty | Exception when trying to use an unset Atom property |
| CUserTimer | Policy class for tracking only user process time |
| CWallTimer | Policy class for tracking wall-time |
| CWeights | |
| CWeightsFromFile | |
| CXDRDataSizeError | Exception indicating internal XDR error |
| CXForm | Matrix class for handling coordinate transforms.. |
| CXTC | Class representing GROMACS reduced precision, compressed trajectories |
| CXTCWriter | Class for writing Gromacs XTC trajectories |
| CZSliceSelector | Predicate for selecting atoms in a specific range of z values |
| ►Npacking_score_per_res | |
| CFullHelp | |
| Nrare | -event-detection |
| Nrenum | -by-mol |
| Nrmsd_to_average | |
| ►Nscattering | |
| CFullHelp | |
| ►Nset_segids | |
| CFullHelp | |
| Nsimple_model_calc | |
| Nsimple_model_transform | |
| Nsimple_traj_calc | |
| Nsimple_traj_transform | |
| Nsysinfo |
