Gromacs
5.1
|
Generic GROMACS namespace.
Namespaces | |
test | |
Testing utilities namespace. | |
Classes | |
class | AbstractAnalysisData |
Abstract base class for all objects that provide data. More... | |
class | AnalysisData |
Parallelizable data container for raw data. More... | |
class | AnalysisDataHandle |
Handle for inserting data into AnalysisData. More... | |
class | AbstractAnalysisArrayData |
Abstract base class for data objects that present in-memory data. More... | |
class | AnalysisArrayData |
Simple in-memory data array. More... | |
class | AnalysisDataValue |
Value type for representing a single value in analysis data objects. More... | |
class | AnalysisDataFrameHeader |
Value type for storing frame-level information for analysis data. More... | |
class | AnalysisDataPointSetRef |
Value type wrapper for non-mutable access to a set of data column values. More... | |
class | AnalysisDataFrameRef |
Value type wrapper for non-mutable access to a data frame. More... | |
class | AnalysisDataModuleInterface |
Interface for a module that gets notified whenever data is added. More... | |
class | AnalysisDataModuleSerial |
Convenience base class for serial analysis data modules. More... | |
class | AnalysisDataModuleParallel |
Convenience base class for parallel analysis data modules. More... | |
class | AnalysisDataModuleManager |
Encapsulates handling of data modules attached to AbstractAnalysisData. More... | |
class | AnalysisDataStorageFrame |
Allows assigning values for a data frame in AnalysisDataStorage. More... | |
class | AnalysisDataStorage |
Helper class that implements storage of data. More... | |
class | AnalysisDataAverageModule |
Data module for independently averaging each column in input data. More... | |
class | AnalysisDataFrameAverageModule |
Data module for averaging of columns for each frame. More... | |
class | AnalysisDataDisplacementModule |
Data module for calculating displacements. More... | |
class | AnalysisHistogramSettingsInitializer |
Provides "named parameter" idiom for constructing histograms. More... | |
class | AnalysisHistogramSettings |
Contains parameters that specify histogram bin locations. More... | |
class | AbstractAverageHistogram |
Base class for representing histograms averaged over frames. More... | |
class | AnalysisDataSimpleHistogramModule |
Data module for per-frame histograms. More... | |
class | AnalysisDataWeightedHistogramModule |
Data module for per-frame weighted histograms. More... | |
class | AnalysisDataBinAverageModule |
Data module for bin averages. More... | |
class | AnalysisDataLifetimeModule |
Data module for computing lifetime histograms for columns in input data. More... | |
class | AnalysisDataPlotSettings |
Common settings for data plots. More... | |
class | AbstractPlotModule |
Abstract data module for writing data into a file. More... | |
class | AnalysisDataPlotModule |
Plotting module for straightforward plotting of data. More... | |
class | AnalysisDataVectorPlotModule |
Plotting module specifically for data consisting of vectors. More... | |
class | AnalysisDataParallelOptions |
Parallelization options for analysis data objects. More... | |
class | CommandLineHelpContext |
Context information for writing out command-line help. More... | |
class | GlobalCommandLineHelpContext |
Helper for passing CommandLineHelpContext into parse_common_args(). More... | |
class | ConstArrayRef |
STL-like container for non-mutable interface to a C array (or part of a std::vector). More... | |
class | CommandLineHelpWriter |
Writes help information for Options in ascii format. More... | |
class | CommandLineModuleSettings |
Settings to pass information between a module and the general runner. More... | |
class | CommandLineModuleInterface |
Module that can be run from command line using CommandLineModuleManager. More... | |
class | CommandLineModuleManager |
Implements a wrapper command-line interface for multiple modules. More... | |
class | CommandLineModuleGroup |
Handle to add content to a group added with CommandLineModuleManager::addModuleGroup(). More... | |
class | CommandLineOptionsModuleInterface |
Module that can be run from a command line and uses gmx::Options for argument processing. More... | |
class | CommandLineParser |
Implements command-line parsing for Options objects. More... | |
class | ExecutableEnvironmentInterface |
Allows customization of the way various directories are found by CommandLineProgramContext. More... | |
class | CommandLineProgramContext |
Program context implementation for command line programs. More... | |
class | BinaryInformationSettings |
Settings for printBinaryInformation(). More... | |
class | BasicVector |
C++ class for 3D vectors. More... | |
class | ArrayRef |
STL-like container for an interface to a C array (or part of a std::vector). More... | |
class | TextTableFormatter |
Formats rows of a table for text output. More... | |
class | HelpManager |
Helper for providing interactive online help. More... | |
class | AbstractSimpleHelpTopic |
Abstract base class for help topics that have simple text and no subtopics. More... | |
class | AbstractCompositeHelpTopic |
Abstract base class for help topics that have simple text and subtopics. More... | |
class | SimpleHelpTopic |
Template for simple implementation of AbstractSimpleHelpTopic. More... | |
class | CompositeHelpTopic |
Template for simple implementation of AbstractCompositeHelpTopic. More... | |
class | HelpTopicInterface |
Provides a single online help topic. More... | |
class | HelpLinks |
Hyperlink data for writing out help. More... | |
class | HelpWriterContext |
Context information for writing out help. More... | |
class | OptionStorageTemplate |
Templated base class for constructing option value storage classes. More... | |
class | AbstractOption |
Abstract base class for specifying option properties. More... | |
class | OptionTemplate |
Templated base class for constructing concrete option settings classes. More... | |
class | OptionInfo |
Gives information and allows modifications to an option after creation. More... | |
class | AbstractOptionStorage |
Abstract base class for converting, validating, and storing option values. More... | |
class | BooleanOption |
Specifies an option that provides boolean values. More... | |
class | IntegerOption |
Specifies an option that provides integer values. More... | |
class | Int64Option |
Specifies an option that provides 64-bit integer values. More... | |
class | DoubleOption |
Specifies an option that provides floating-point (double) values. More... | |
class | FloatOption |
Specifies an option that provides floating-point (float) values. More... | |
class | StringOption |
Specifies an option that provides string values. More... | |
class | BooleanOptionInfo |
Wrapper class for accessing boolean option information. More... | |
class | IntegerOptionInfo |
Wrapper class for accessing integer option information. More... | |
class | Int64OptionInfo |
Wrapper class for accessing 64-bit integer option information. More... | |
class | DoubleOptionInfo |
Wrapper class for accessing floating-point option information. More... | |
class | FloatOptionInfo |
Wrapper class for accessing floating-point option information. More... | |
class | StringOptionInfo |
Wrapper class for accessing string option information. More... | |
class | FileNameOption |
Specifies an option that provides file names. More... | |
class | FileNameOptionInfo |
Wrapper class for accessing file name option information. More... | |
class | FileNameOptionManager |
Handles interaction of file name options with global options. More... | |
class | OptionManagerContainer |
Container to keep managers added with Options::addManager() and pass them to options. More... | |
class | OptionManagerInterface |
Base class for option managers. More... | |
class | Options |
Collection of options. More... | |
class | OptionsAssigner |
Decorator class for assigning values to Options. More... | |
class | OptionsVisitor |
Pure interface for visiting options in a Options object. More... | |
class | OptionsTypeVisitor |
Abstract base class for visiting options of a particular type. More... | |
class | OptionsIterator |
Decorator class for visiting options in a Options object. More... | |
class | OptionsModifyingVisitor |
Pure interface for visiting options in a Options object, allowing modifications. More... | |
class | OptionsModifyingTypeVisitor |
Abstract base class for visiting options of a particular type, allowing modifications. More... | |
class | OptionsModifyingIterator |
Decorator class for visiting options in a Options object, allowing changes. More... | |
class | TimeUnitManager |
Provides common functionality for time unit conversions. More... | |
class | AnalysisNeighborhoodPositions |
Input positions for neighborhood searching. More... | |
class | AnalysisNeighborhood |
Neighborhood searching for analysis tools. More... | |
class | AnalysisNeighborhoodPair |
Value type to represent a pair of positions found in neighborhood searching. More... | |
class | AnalysisNeighborhoodSearch |
Initialized neighborhood search with a fixed set of reference positions. More... | |
class | AnalysisNeighborhoodPairSearch |
Initialized neighborhood pair search with a fixed set of positions. More... | |
class | Selection |
Provides access to a single selection. More... | |
class | SelectionPosition |
Provides access to information about a single selected position. More... | |
class | SelectionCollection |
Collection of selections. More... | |
class | SelectionFileOption |
Specifies a special option that provides selections from a file. More... | |
class | SelectionFileOptionInfo |
Wrapper class for accessing and modifying selection file option information. More... | |
class | SelectionOption |
Specifies an option that provides selection(s). More... | |
class | SelectionOptionInfo |
Wrapper class for accessing and modifying selection option information. More... | |
class | SelectionOptionManager |
Handles interaction of selection options with other options and user input. More... | |
class | TrajectoryAnalysisModuleData |
Base class for thread-local data storage during trajectory analysis. More... | |
class | TrajectoryAnalysisModule |
Base class for trajectory analysis modules. More... | |
class | TrajectoryAnalysisSettings |
Trajectory analysis module configuration object. More... | |
class | TopologyInformation |
Topology information passed to a trajectory analysis module. More... | |
class | TrajectoryAnalysisCommandLineRunner |
Runner class for command-line analysis tools. More... | |
struct | EmptyArrayRef |
Tag type to initialize empty array references. More... | |
class | PrivateImplPointer |
Helper class to manage a pointer to a private implementation class. More... | |
class | DataFileOptions |
Search parameters for DataFileFinder. More... | |
struct | DataFileInfo |
Information about a data file found by DataFileFinder::enumerateFiles(). More... | |
class | DataFileFinder |
Searches data files from a set of paths. More... | |
class | DirectoryEnumerator |
Lists files in a directory. More... | |
class | ExceptionInitializer |
Provides information for Gromacs exception constructors. More... | |
class | GromacsException |
Base class for all exception objects in Gromacs. More... | |
class | FileIOError |
Exception class for file I/O errors. More... | |
class | UserInputError |
Exception class for user input errors. More... | |
class | InvalidInputError |
Exception class for situations where user input cannot be parsed/understood. More... | |
class | InconsistentInputError |
Exception class for situations where user input is inconsistent. More... | |
class | SimulationInstabilityError |
Exception class for simulation instabilities. More... | |
class | InternalError |
Exception class for internal errors. More... | |
class | APIError |
Exception class for incorrect use of an API. More... | |
class | NotImplementedError |
Exception class for use of an unimplemented feature. More... | |
class | FileInitializer |
Parameters for creating a File object. More... | |
class | File |
Basic file object. More... | |
class | FileInputRedirectorInterface |
Allows overriding file existence checks from code that supports it. More... | |
class | FileOutputRedirectorInterface |
Allows capturing stdout and file output from code that supports it. More... | |
class | FlagsTemplate |
Template class for typesafe handling of combination of flags. More... | |
class | Regex |
Represents a regular expression. More... | |
class | MessageStringCollector |
Helper class for collecting message strings, optionally with context. More... | |
class | MessageStringContext |
Convenience class for creating a message context. More... | |
struct | InstallationPrefixInfo |
Provides information about installation prefix (see ProgramContextInterface::installationPrefix()). More... | |
class | ProgramContextInterface |
Provides context information about the program that is calling the library. More... | |
class | scoped_cptr |
Stripped-down version of scoped_ptr that uses sfree() or custom deleter. More... | |
class | StringFormatter |
Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms. More... | |
class | IdentityFormatter |
Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further. More... | |
class | TextLineWrapperSettings |
Stores settings for line wrapping. More... | |
class | TextLineWrapper |
Wraps lines to a predefined length. More... | |
class | gmx_unique_ptr |
Smart pointer for unique ownership. More... | |
Typedefs | |
typedef boost::shared_ptr < AnalysisDataModuleInterface > | AnalysisDataModulePointer |
Smart pointer for managing a generic analysis data module. | |
typedef ConstArrayRef < AnalysisDataValue > | AnalysisDataValuesRef |
Shorthand for reference to an array of data values. | |
typedef boost::shared_ptr < AnalysisDataAverageModule > | AnalysisDataAverageModulePointer |
Smart pointer to manage an AnalysisDataAverageModule object. | |
typedef boost::shared_ptr < AnalysisDataFrameAverageModule > | AnalysisDataFrameAverageModulePointer |
Smart pointer to manage an AnalysisDataFrameAverageModule object. | |
typedef boost::shared_ptr < AnalysisDataDisplacementModule > | AnalysisDataDisplacementModulePointer |
Smart pointer to manage an AnalysisDataDisplacementModule object. | |
typedef boost::shared_ptr < AbstractAverageHistogram > | AverageHistogramPointer |
Smart pointer to manage an AbstractAverageHistogram object. | |
typedef boost::shared_ptr < AnalysisDataSimpleHistogramModule > | AnalysisDataSimpleHistogramModulePointer |
Smart pointer to manage an AnalysisDataSimpleHistogramModule object. | |
typedef boost::shared_ptr < AnalysisDataWeightedHistogramModule > | AnalysisDataWeightedHistogramModulePointer |
Smart pointer to manage an AnalysisDataWeightedHistogramModule object. | |
typedef boost::shared_ptr < AnalysisDataBinAverageModule > | AnalysisDataBinAverageModulePointer |
Smart pointer to manage an AnalysisDataBinAverageModule object. | |
typedef boost::shared_ptr < AnalysisDataLifetimeModule > | AnalysisDataLifetimeModulePointer |
Smart pointer to manage an AnalysisDataLifetimeModule object. | |
typedef boost::shared_ptr < AnalysisDataPlotModule > | AnalysisDataPlotModulePointer |
Smart pointer to manage an AnalysisDataPlotModule object. | |
typedef boost::shared_ptr < AnalysisDataVectorPlotModule > | AnalysisDataVectorPlotModulePointer |
Smart pointer to manage an AnalysisDataVectorPlotModule object. | |
typedef std::map< std::string, CommandLineModulePointer > | CommandLineModuleMap |
Container type for mapping module names to module objects. | |
typedef gmx_unique_ptr < CommandLineModuleGroupData > ::type | CommandLineModuleGroupDataPointer |
Smart pointer type for managing a CommandLineModuleGroup. | |
typedef std::vector < CommandLineModuleGroupDataPointer > | CommandLineModuleGroupList |
Container type for keeping a list of module groups. | |
typedef gmx_unique_ptr < CommandLineModuleInterface > ::type | CommandLineModulePointer |
Smart pointer type for managing a CommandLineModuleInterface. | |
typedef boost::shared_ptr < ExecutableEnvironmentInterface > | ExecutableEnvironmentPointer |
Shorthand for a smart pointer to ExecutableEnvironmentInterface. | |
typedef BasicVector< real > | RVec |
Shorthand for C++ rvec -equivalent type. | |
typedef gmx_unique_ptr < AbstractCompositeHelpTopic > ::type | CompositeHelpTopicPointer |
Smart pointer type to manage a AbstractCompositeHelpTopic object. | |
typedef gmx_unique_ptr < HelpTopicInterface >::type | HelpTopicPointer |
Smart pointer type to manage a HelpTopicInterface object. | |
typedef FloatOption | RealOption |
Typedef for either DoubleOption or FloatOption, depending on precision. More... | |
typedef FloatOptionInfo | RealOptionInfo |
Typedef for either DoubleOptionInfo or FloatOptionInfo, depending on precision. More... | |
typedef FlagsTemplate< OptionFlag > | OptionFlags |
Holds a combination of OptionFlag values. | |
typedef std::list < SelectionParserValue > | SelectionParserValueList |
Container for a list of SelectionParserValue objects. | |
typedef gmx::gmx_unique_ptr < SelectionParserValueList > ::type | SelectionParserValueListPointer |
Smart pointer type for managing a SelectionParserValueList. | |
typedef std::list < SelectionParserParameter > | SelectionParserParameterList |
Container for a list of SelectionParserParameter objects. | |
typedef gmx::gmx_unique_ptr < SelectionParserParameterList > ::type | SelectionParserParameterListPointer |
Smart pointer type for managing a SelectionParserParameterList. | |
typedef std::vector< Selection > | SelectionList |
Container of selections used in public selection interfaces. | |
typedef gmx_unique_ptr < internal::SelectionData > ::type | SelectionDataPointer |
Smart pointer for managing an internal selection data object. | |
typedef std::vector < SelectionDataPointer > | SelectionDataList |
Container for storing a list of selections internally. | |
typedef boost::shared_ptr < SelectionTreeElement > | SelectionTreeElementPointer |
Smart pointer type for selection tree element pointers. | |
typedef boost::shared_ptr < TrajectoryAnalysisModuleData > | TrajectoryAnalysisModuleDataPointer |
Smart pointer to manage a TrajectoryAnalysisModuleData object. | |
typedef boost::shared_ptr < TrajectoryAnalysisModule > | TrajectoryAnalysisModulePointer |
Smart pointer to manage a TrajectoryAnalysisModule. | |
typedef void(* | ErrorHandlerFunc )(int retcode, const char *msg, const char *file, int line) |
Callback function pointer type for error handlers. More... | |
typedef scoped_cptr< void > | scoped_guard_sfree |
Simple guard which calls sfree. See scoped_cptr for details. | |
Functions | |
AnalysisHistogramSettingsInitializer | histogramFromRange (real min, real max) |
Initializes a histogram using a range and a bin width. More... | |
AnalysisHistogramSettingsInitializer | histogramFromBins (real start, int nbins, real binwidth) |
Initializes a histogram using bin width and the number of bins. More... | |
CommandLineProgramContext & | initForCommandLine (int *argc, char ***argv) |
Initializes the GROMACS library for command-line use. More... | |
void | finalizeForCommandLine () |
Deinitializes the GROMACS library after initForCommandLine(). More... | |
int | processExceptionAtExitForCommandLine (const std::exception &ex) |
Handles an exception and deinitializes after initForCommandLine. More... | |
int | runCommandLineModule (int argc, char *argv[], CommandLineModuleInterface *module) |
Implements a main() method that runs a single module. More... | |
int | runCommandLineModule (int argc, char *argv[], const char *name, const char *description, CommandLineOptionsModuleInterface *(*factory)()) |
Implements a main() method that runs a single module. More... | |
void | writeCommandLineHelpCMain (const CommandLineHelpContext &context, const char *name, int(*mainFunction)(int argc, char *argv[])) |
Helper to implement CommandLineModuleInterface::writeHelp() with a C-like main() function that calls parse_common_args(). More... | |
void | printBinaryInformation (FILE *fp, const ProgramContextInterface &programContext) |
Print basic information about the executable. More... | |
void | printBinaryInformation (FILE *fp, const ProgramContextInterface &programContext, const BinaryInformationSettings &settings) |
Print basic information about the executable with custom settings. More... | |
template<typename ValueType > | |
static BasicVector< ValueType > ::RawArray * | as_vec_array (BasicVector< ValueType > *x) |
Casts a gmx::BasicVector array into an equivalent raw C array. | |
template<typename ValueType > | |
static const BasicVector < ValueType >::RawArray * | as_vec_array (const BasicVector< ValueType > *x) |
Casts a gmx::BasicVector array into an equivalent raw C array. | |
static rvec * | as_rvec_array (RVec *x) |
Casts a gmx::RVec array into an rvec array. | |
static const rvec * | as_rvec_array (const RVec *x) |
Casts a gmx::RVec array into an rvec array. | |
HelpTopicPointer | createSelectionHelpTopic () |
*/ More... | |
void | registerTrajectoryAnalysisModules (CommandLineModuleManager *manager) |
Registers all trajectory analysis command-line modules. More... | |
template<typename T > | |
void | swap (ArrayRef< T > &a, ArrayRef< T > &b) |
Simple swap method for ArrayRef objects. More... | |
template<typename T > | |
void | swap (ConstArrayRef< T > &a, ConstArrayRef< T > &b) |
Simple swap method for ConstArrayRef objects. More... | |
const char * | getErrorCodeString (int errorcode) |
Returns a short string description of an error code. More... | |
ErrorHandlerFunc | setFatalErrorHandler (ErrorHandlerFunc handler) |
Sets callback function for handling errors. More... | |
void | printFatalErrorMessage (FILE *fp, const std::exception &ex) |
Formats a standard fatal error message for reporting an exception. More... | |
std::string | formatExceptionMessageToString (const std::exception &ex) |
Formats an error message for reporting an exception. More... | |
void | formatExceptionMessageToFile (FILE *fp, const std::exception &ex) |
Formats an error message for reporting an exception. More... | |
int | processExceptionAtExit (const std::exception &ex) |
Handles an exception that is causing the program to terminate. More... | |
int | translateException (const std::exception &ex) |
Converts an exception into a return code. | |
FileInputRedirectorInterface & | defaultFileInputRedirector () |
Returns default implementation for FileInputRedirectorInterface. More... | |
FileOutputRedirectorInterface & | defaultFileOutputRedirector () |
Returns default implementation for FileOutputRedirectorInterface. More... | |
const DataFileFinder & | getLibraryFileFinder () |
Gets a finder for locating data files from share/top/. More... | |
void | setLibraryFileFinder (const DataFileFinder *finder) |
Sets a finder for location data files from share/top/. More... | |
bool | regexMatch (const char *str, const Regex ®ex) |
Matches a string with a regular expression. More... | |
bool | regexMatch (const std::string &str, const Regex ®ex) |
Matches a string with a regular expression. More... | |
void | init (int *argc, char ***argv) |
Initializes the GROMACS library. More... | |
void | finalize () |
Deinitializes the GROMACS library. More... | |
const ProgramContextInterface & | getProgramContext () |
Returns the global ProgramContextInterface instance. More... | |
void | setProgramContext (const ProgramContextInterface *context) |
Sets the global ProgramContextInterface instance. More... | |
template<class T > | |
void | sfree_wrapper (T *p) |
sfree wrapper to be used as scoped_cptr deleter | |
bool | endsWith (const std::string &str, const char *suffix) |
Tests whether a string ends with another string. More... | |
std::string | stripSuffixIfPresent (const std::string &str, const char *suffix) |
Removes a suffix from a string. More... | |
std::string | stripString (const std::string &str) |
Removes leading and trailing whitespace from a string. More... | |
std::string | formatString (const char *fmt,...) |
Formats a string (snprintf() wrapper). More... | |
std::vector< std::string > | splitString (const std::string &str) |
Splits a string to whitespace separated tokens. More... | |
std::string | replaceAll (const std::string &input, const char *from, const char *to) |
Replace all occurrences of a string with another string. More... | |
std::string | replaceAll (const std::string &input, const std::string &from, const std::string &to) |
Replace all occurrences of a string with another string. More... | |
std::string | replaceAllWords (const std::string &input, const char *from, const char *to) |
Replace whole words with others. More... | |
std::string | replaceAllWords (const std::string &input, const std::string &from, const std::string &to) |
Replace whole words with others. More... | |
bool | isNullOrEmpty (const char *str) |
Tests whether a string is null or empty. More... | |
bool | startsWith (const std::string &str, const std::string &prefix) |
Tests whether a string starts with another string. More... | |
bool | startsWith (const char *str, const char *prefix) |
Tests whether a string starts with another string. More... | |
template<typename InputIterator , typename FormatterType > | |
std::string | formatAndJoin (InputIterator begin, InputIterator end, const char *separator, const FormatterType &formatter) |
Formats all the range as strings, and then joins them with a separator in between. More... | |
template<typename ContainerType , typename FormatterType > | |
std::string | formatAndJoin (const ContainerType &container, const char *separator, const FormatterType &formatter) |
Formats all elements of the container as strings, and then joins them with a separator in between. More... | |
template<typename InputIterator > | |
std::string | joinStrings (InputIterator begin, InputIterator end, const char *separator) |
Joins strings from a range with a separator in between. More... | |
template<typename ContainerType > | |
std::string | joinStrings (const ContainerType &container, const char *separator) |
Joins strings from a container with a separator in between. More... | |
template<size_t count> | |
std::string | joinStrings (const char *const (&array)[count], const char *separator) |
Joins strings from an array with a separator in between. More... | |
template<typename T > | |
boost::shared_ptr< T > & | move (boost::shared_ptr< T > &ptr) |
Moves gmx::gmx_unique_ptr type pointers. More... | |
enum gmx::OptionFlag |
Flags for options.
These flags are not part of the public interface, even though they are in an installed header. They are needed in a few template class implementations.
Enumerator | |
---|---|
efOption_Set |
Option has been set. |
efOption_HasDefaultValue |
The current value of the option is a programmatic default value. |
efOption_ExplicitDefaultValue |
An explicit default value has been provided for the option. |
efOption_ClearOnNextSet |
Next assignment to the option clears old values. This flag is set when a new option source starts, such that values from the new source will overwrite old ones. |
efOption_Required |
Option is required to be set. |
efOption_MultipleTimes |
Option can be specified multiple times. |
efOption_Hidden |
Option is hidden from standard help. |
efOption_Vector |
Option value is a vector, but a single value is also accepted.
|
efOption_DefaultValueIfSetExists |
Option has a defaultValueIfSet() specified. |
efOption_NoDefaultValue |
Option does not support default values. |
efOption_DontCheckMinimumCount |
Storage object does its custom checking for minimum value count. If this flag is set, the class derived from OptionStorageTemplate should implement processSetValues(), processAll(), and possible other functions it provides such that it always fails if not enough values are provided. This is useful to override the default check, which is done in OptionStorageTemplate::processSet(). |
void gmx::printBinaryInformation | ( | FILE * | fp, |
const ProgramContextInterface & | programContext | ||
) |
Print basic information about the executable.
fp | Where to print the information to. | |
[in] | programContext | Program information object to use. |
void gmx::printBinaryInformation | ( | FILE * | fp, |
const ProgramContextInterface & | programContext, | ||
const BinaryInformationSettings & | settings | ||
) |
Print basic information about the executable with custom settings.
Needed to read the members without otherwise unnecessary accessors.
fp | Where to print the information to. | |
[in] | programContext | Program information object to use. |
[in] | settings | Specifies what to print. |
int gmx::processExceptionAtExitForCommandLine | ( | const std::exception & | ex | ) |
Handles an exception and deinitializes after initForCommandLine.
[in] | ex | Exception that is the cause for terminating the program. |
This method should be called as the last thing before terminating the program because of an exception. See processExceptionAtExit() for details. Additionally this method undoes the work done by initForCommandLine.
Does not throw.
bool gmx::regexMatch | ( | const std::string & | str, |
const Regex & | regex | ||
) |
Matches a string with a regular expression.
[in] | str | String to match. |
[in] | regex | Regular expression to match. |
regex
matches the whole str
.Does not throw currently, but this is subject to change if/when better error handling is implemented (currently, it returns false if the matching fails, e.g., because of out-of-memory).
int gmx::runCommandLineModule | ( | int | argc, |
char * | argv[], | ||
CommandLineModuleInterface * | module | ||
) |
Implements a main() method that runs a single module.
This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).
The signature assumes that module
construction does not throw (because otherwise the caller would need to duplicate all the exception handling code). It is possible to move the construction inside the try/catch in this method using an indirection similar to TrajectoryAnalysisCommandLineRunner::runAsMain(), but until that is necessary, the current approach leads to simpler code.
Usage:
Does not throw. All exceptions are caught and handled internally.
int gmx::runCommandLineModule | ( | int | argc, |
char * | argv[], | ||
const char * | name, | ||
const char * | description, | ||
CommandLineOptionsModuleInterface *(*)() | factory | ||
) |
Implements a main() method that runs a single module.
argc | argc passed to main(). | |
argv | argv passed to main(). | |
[in] | name | Name for the module. |
[in] | description | Short description for the module. |
factory | Factory method that creates the module to run. |
This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).
Usage:
Does not throw. All exceptions are caught and handled internally.
void gmx::setLibraryFileFinder | ( | const DataFileFinder * | finder | ) |
Sets a finder for location data files from share/top/.
[in] | finder | finder to set (can be NULL to restore the default finder). |
The library does not take ownership of finder
. The provided object must remain valid until the global instance is changed by another call to setLibraryFileFinder().
The global instance is used by gmxlibfn() and libopen().
This method is not thread-safe. See setProgramContext(); the same constraints apply here as well.
Does not throw.