CCP4i Documentation for Programmers: Core Documentation

Contents

The Procedures

Initialisation and Utilities (system.tcl and utils.tcl)

Initialisation and Utilities

Def Files

Def Files

InitialiseArray Initialise an array with data from a def file

reserved_prefix Check whether a parameter name has a reserved prefix

WriteIdentifier Write header to CCP4i file (mainly used for def files)

SaveArray Save the data in an array to a def file

WriteDefLine Create a text line for the def file to define one parameter

WriteDefLine1 Create a text line for the def file to define one parameter including it's data type

Preferences Files

Preferences Files

InitialisePreferences Initialise the parameters from preferences configure and directories def files

MakeLock Test if a LOCK file exists and query user how to proceed

LockStatus Return status of lock file

DeleteLock Delete lock file if it belongs to the current process

CreateLock Create a lock file

SavePreferences Save a directories/preferences/configure/status.def file to user's directory

SaveInstallPreferences Save the preferences to the CCP4i installation area

update_defdir_menu Update the project/alias menus that appears in file selection

CCP4i Startup Utilities

ElementExists Test if a given element name exists in an array

autoconf_UNIX_configure Attempt to configure the configure parameters for a UNIX system

autoconf_WINDOWS_configure Attempt to configure the configure parameters for a WINDOWS system

autoconf_WINDOWS_system Attempt to configure the system parameters for a WINDOWS system

set_configured_menus Create menus which are based on data in the configure def file.

set_typedef_menu Use a list of values from indexed array element(s) to define a menu data type

set_default_mapviewer (Re)set the default mapviewer

set_default_pdbviewer (Re)set the default PDB viewer

set_default_mtzviewer (Re)set the default MTZ viewer

set_default_viewer Set the default viewer for a particular file type

SetDefaultMapFormat Return the default map format set by the user in preferences

SetMapConversionMenu Update a menu to only include possible map format conversions

TestEnvVariables Test CCP4 environment variables set - used at ccp4i startup.

InitialiseDotCCP4 Create/update the $HOME/.CCP4 directory

SetDomain Unused. Part of project to support multiple machine domains

CreateSessionLog Open a session log file which is written to by the Report

Report Write diagnostics to the session log file

WarningMessage Minimal WarningMessage proc to output diagnostic from WindowsNT

Saving Global Parameters

Saving Global Parameters

GetSystemVar Get a global parameter from array system_save

SetSystemVar Save a global parameter in array system_save

Querying the Operating System

Querying the Operating System

GetHostname Return the name of the machine running the process

GetUserId Return the user's id.

GetVersion Return the CCP4i version.

GetPid Return the process id of the current process

GetCurrentDir Return the name of directory from which current process was started

GetDate Return the date/time appropriately formatted

BinPath Return path name for an executable

FindExecutable Return the full path for the program named

Execute Execute a program with a command script and some error trapping

Handling File Names

GetEnvPath Get operating system environment variable

GetFullDirName Return full path name for given directory alias

GetFullFileName Return full path name for given file name and directory alias.

GetFullFileName1 GetFullFileName version used in ExecuteScript

GetFullFileName0 Return the full path name of a file which is defined in an array.

SetCurrentProject Set the project alias for the currently open user project.

GetCurrentProject Return the project alias for the currently open user project.

GetCurrentProjectDir Return the directory path for the currently open user project.

GetDefaultDirPath Return the full path name for an input project/directory alias.

GetDbDirPath Return the project database directory

SearchPath Return full path name for a CCP4i code or data file.

datapath Return the full path name for a configure file in the user's home directory.

GetTmpFileName Return a unique name for a temporary file

GetFileFormat Return the file type as inferred from the file extension

FileJoin Concatenates file names using the correct path separator for platform.

FileRootName Return file base name - i.e. remove the file extension and path name.

Manipulating Files

OpenFile Open a file

CloseFile Close a file

ReadFile Read contents of file into a text variable

ReadEndOfFile Return specified number of lines from the end of a file.

WriteFile Write text to a file

DeleteFile Delete a file or directory

DeleteFiles Delete multiple files.

FileWritable Return flag to say if file is writable

MoveFile Move (i.e. rename) a file.

CopyFile Copy file - i.e. make a new version and keep existing file

TranscribeFile Append contents from one file to the end of another file

CompressFile Compress file using gzip

UnCompressFile Uncompress file using gzip

UnTarFile Apply 'tar -xf' to a file

CompressExtension Return the expected extension for compressed file

Handling Directories

CreateDir Create a directory

CopyDir Copy a directory

ChangeDirectory Change working directory

Parsing Files

Parsing Files

ExtractFromFile 'grep' text from a file

GetWords Return selected words in a line as a Tcl list

ExtractTextLine Extract words from a line of text

ExtractFromText 'Grep' for a line in text and return specified fields from line.

StringSame String comparison - is the first argument the same as any of the other arguments.

Socket Handling

Socket Handling

OpenClientSocket Open a client side socket

ListenClientSocket Listen for input from a server socket.

TestSocket Test if a socket is open - return true (1) is socket responds

PutsSocket Write to a socket

Handling Data Types

Handling Data Types

GetType Returns the data type for an input array element

Indxv Generate the element name for multi-dimensional data

GetIndx Parse the name of a dimensioned element

Indxv0 For indexed element names (eg root,4) return the zero index (eg root,0)

Indxv0 name Name of an array element

GetTypeInfo Return some information which is a property of the data type of an element

get_type_list Get the full list of properties of the data type of an array element

get_type_info_error Output warning message when fail to find type information

get_type_info_error Get the full list of properties of the data type of an array element

GetWidget Return the Tk id of the widget representing an array element

DefineVariable Define the data type and initial value of a variable

DefineMenu Define a data type which is of class menu

GetMenuValue Return the alias for the value of an array element which is a menu

GetMenuText Return the text which appears on the menu for given value of parameter

Handling Arrays

GetIndexedElements Return all the indexed elements in an array with a given root

GetIndexedElements0 Return all the indexed elements in an array with a given root

ArrayToList Copy data values from all the instaces of an indexed element to a list

CopyArray Copy all elements of arrayname in array(PARAM_LIST) to arrayname1

SimpleCopyArray Copy all elements of arrayname to arrayname1

CheckUnique Check that all instances of an indexed variable are unique

CreateNewArray Create new unique global array with name $root_$n

ArraySearch Return the name of an indexed element with a value of 'text'

DeleteArray Delete an array

Simple Mathematical Functions

max Return the maximum value of the values in the argument list

min Return the minimum value of the values in the argument list

iremainder Return the mod of n and m

push Push a parameter onto a stack (i.e. append to list)

pop Pop a parameter off a stack (i.e. append to list)

maxdecimal Round an input number to given number of decimal places

sortorder Sort a list using Tcl lsort and return a list of offsets to position in input list

String Handling

IfSet Test if input argument(s) are not blank strings

StringSame String comparison - is the first argument the same as any of the other arguments

RemoveMetaChars Return text string with non-alphanumeric characters & leading/trailing spaces removed

ResolveUnixFileSymbols Interpret tilde or environment variable, or a relative path

FeedListbox Colourise the entries of a listbox

get_job_display_colours Return the colours to display the job with

Handling Data Harvesting "Central Deposit" Location

SetCentralDeposit Set the CENTRAL_DEPOSIT location for data harvesting

GetCentralDeposit Fetch the current CENTRAL_DEPOSIT location for data harvesting

The Task Mode (src/task.tcl)

The Task Mode

task Initialisation to run CCP4i in task mode.

The Taskbrowser (src/taskbrowser.tcl)

The Taskbrowser

taskbrowser Initialise CCP4i to run the taskbrowser

Utilities for CCP4i Main Window (src/browser_utils.tcl)

update_module_menu Populate the menu of available modules

update_module_menu This creates entries in a menu corresponding to the modules loaded in to a data structure. Any existing entries are first deleted from the menu.

GetTaskFile Get the Tcl file associated with a task

GetRunCmd Return the command for running a task

ReadTaskList Read the etc/$OPSYS/modules and $USER/.CCP4/$OPSYS/modules files

UpdateModulesList Update the lists of modules and tasks

CreateTaskBrowser Draw the main graphical window of ccp4i

module_help Handle user clicking for help on the Module menu

update_module Update task menu when user changes modules

open_module_folder Open a module folder by (re)packing it

close_module_folder Collapse a module folder by unpacking it

update_module_scroll Update the scrolling region of the tasklist

check_task_prereq Check for prerequisites for a task

MailHandler Create mail window for interface

MailtoDev Define the 'Mail CCP4' dialog box

send_mail Handler for MailtoDev 'Send Mail' command

SwitchProject Switch the main window to another project

build_project_shortcut_menu Build the menu of project shortcuts on the main window

ReloadTasklists Reload the data for the modules and tasklists, and redraw

Utilities for building CCP4i modules data structure (src/modules_utils.tcl)

BuildModulesDataStruct Build a data structure for the modules and tasklists

SortProgramList Sort the tasks in the program list module into alphabetical order

compare_task_titles Internal - compare the titles of two tasks given their ids

SetModuleProject Set the project name and title within the data structure

NewModuleSeparator Add a "separator" into the module list

NewFolder Add a new folder to the data structure

NewTask Add a new task to the data structure

SetFolderVisibility Set the visibility of the folder contents

GetFolderVisibility Return the visibility of the folder contents

ListModules List the modules in the data structure

GetModuleDesc Return the description string for the module name

ReverseLookupModuleName Given the module description, find the matching name

ListModuleContents Return a list of the module contents

ListFolderContents Return a list of the module contents

GetContentType Return the type (FOLDER or TASK) for the module content

GetFolderTitle Return the title string for a folder in a module

GetFolderDesc Return the description string for a folder in a module

GetTaskName Return the taskname for a task id

GetTaskTitle Return the title string for a task

GetTaskDesc Return the description string for a task

Utilities for manipulating CCP4i modules.def files (src/modules_utils.tcl)

InitialiseModulesArray Initialise an array with the data in a modules.def file

GetModuleList Return a list of the modules in the specified modules def file

GetTaskList Return a list of the tasks in the specified module of a modules def file

GetModuleContentList Return a list of the items (tasks and folders) in the specified module

GetFolderContentList Return a list of the tasks in the specified folder of a module

AddModule Add a new module reference to the specified modules def file

GetModule Fetch the attributes of a particular module reference

UpdateModule Change the module title text

DeleteModule Remove a module reference from the specified modules def file

AddTaskReference Add a new task reference to the specified modules file

AddModuleFolder Add a new folder to the specified modules file

GetFolderReference Fetch the attributes of a particular folder reference

UpdateFolderReference Update the attributes of a particular task reference

DeleteModuleFolder Remove a folder from the specified modules def file

UpdateTaskReference Update the attributes of a particular task reference

DeleteTaskReference Remove a task reference from the specified modules def file

Handling CCP4-Specific File Formats

InitialiseProject The place for CCP4 specific initialisation

InitialiseProject Load data from file CCP4/lib/data/symop.lib & CCP4/ccp4i/etc/crystal.lib

ReadCrystalData Read etc/crystal.lib file and extract crystallographic info

MTZ Column Selection

MTZ Column Selection

CreateLabinLine Draw task interface line for selecting input MTZ column labels

CreateLabinLine4 Draw task interface line for selecting input MTZ column labels

add_labinline_command Internal function used in CreateLabinLine

invoke_labinline_command Internal function used in CreateLabinLine

SetLabin An updated version of SetLabin ...

SetLabin Handler to update Labin menu after user has selected MTZ file

add_label_menu_extras Internal procedure called from SetLabin

extract_label_data Internal procedure called from SetLabin

SetLabinUnassigned Set labin menu to 'Unassigned' if the user has deselected an MTZ file

UpdateDependentLabin Update the second labin column in a line when user selects the first labin#d_desc This procedure is called when the user selects a new item from the labin menu

SetLabelList Save a list of allowed column labels and types a labin array element

GetLabelList Return the list of allowed column labels and types for a labin array element

ListAllLabels List all column labels in MTZ file to support the 'List all Labels' option on column label menu

handle_list_labels handler to update column label when it is selected from 'List all Columns'

EnterLabel Window for user to type column label to support 'Enter Label' option on columns menu

CreateCadLabinLine Display the MTZ label selection line used in the Cad task interface

cad_update_labin Handler for CreateCadLabinLine to create menu of input column names

CreateLaboutLine Draw a task interface line for user to specify output MTZ column name

CheckLabout Procedure to be called before running a task to check uniqueness of output MTZ column names

PackLabinLine Pack, i.e. set the layout, of the task interface line to select MTZ columns

Extracting Data from Map Files

InitialiseMAPData Initialise the MAP_file_data array with header info from the last selected input CCP4 map file.

ReadCCP4Map Read a CCP4 map file using mapdump and return program output

ExtractMAPData Read header info from a CCP4 map file and save to MAP_file_data array

Extracting Data from PDB Files

InitialisePDBData Initialise the PDB_file_data array which holds header parameters from the last selected input PDB file.

ExtractPDBData Read header from PDB file and load params into global array PDB_file_data

GetCCP4SpaceGroup Return space group in CCP4 format

Extracting Data from MTZ Files

SetMtzParamField Put data value from MTZ header into an array element

GetMtzParam Return a specified data item from specified MTZ file

GetMtzParamFromDataset Return a specified data item from specified MTZ file

GetMtzColumnResolution Return the maximum and minimum resolution for an MTZ column.

GetMtzDatasetFromLabel Return the parent dataset for the specified label

GetMtzXtals Return list of crystal names in an MTZ file

GetMtzDatasetsInXtal Return a list of the datasets associated with a crystal in an MTZ file

GetMtzColsInDataset Return a list of the columns in a dataset in an MTZ file

MtzColSameDataset Determine whether two columns belong to the same dataset

GetMtzAllCols List all column labels in an MTZ file

GetMtzColType Return MTZ column type corresponding to a specific label

GroupMtzCols Group a list of MTZ columns by type

InitialiseMTZData Initialise the MTZ_file_data array with header info from the last selected input MTZ file

ReadMTZ Read an MTZ file using mtzdump and return program output

ExtractMTZData Read header info from an MTZ file and save to MTZ_file_data array

InitialiseParamFromFile Initialise the *_file_data arrays containing data from map/pdb/mtz file headers

GetMtzColumnList Return the labelled columns of a specified type and one default

GetMtzColumnByType Return the labelled columns of a specified type found in an MTZ file

GetMtzGroupByType Return groups of MTZ columns based on the requested types

Accessing Standard Crystallographic Data

GetSpaceGroupNumber Return space group number from input space group code

GetSpaceGroupCode Return CCP4 space group code from input space group number

GetSpaceGroupStdCode Return PDB standard space group code from input space group number

GetSpaceGroupNops Return the number of symmetry ops for a space group

GetSpaceGroupLattice Return the crystal lattice for a space group

GetSpaceGroupSymops Return the symmetry ops for a space group as a list

GetAsymUnit Return the CCP4 standard asymmetric unit

GetLaueGroupNumber Return an identifier for the laue group

GetLaueGroup Return a list of space groups in given Laue group

GetPattersonSpaceGroup Return the Patterson space group for given space group

GetHarkerSections Return the Harker sections for given space group (as Tcl list)

GetFFTSpaceGroups Get a list of space groups supported by FFT program

GetChangeHandData Get resultant space group and transformations fro changing hand of data

GetTwinData Get the transformation(s) for twinned data

GetLatticeFromSpaceGp Return the lattice type from space group name ('cos shelx can not!)

Interaction with Operating System & Local Packages(src/local.tcl)

Interaction with Operating System & Local Packages(src/local.tcl)

SendMail Send email using system Mail utility

Interaction with Netscape

Interaction with Netscape

start_netscape Start the Netscape program

start_hypertext_viewer Start the hypertext viewer program defined in configure

open_url Open a specified file in a browser window

warning_no_netscape Output warning message when fail to open page in Netscape

warning_no_hypertext_viewer Output warning message when there is a failure to open a URL

poll_netscape Make repeat attempts to load page into Netscape

Running Program Scripts

Running Program Scripts

RunBatchJob Submit a job to a local batch queue

RunRemote Start a job on a remote machine

RunServer Procedure not fully implemented. Start a job on a server

CreateBatchCom Create a command file to start a job on a remote machine or batch queue

KillScript Kill a non-graphical ccp4i process

GetProcessList Return the process information from the Unix ps command

get_process_list Execute and return the output of Unix command ps ...

KillProcess Kill a system process

KillChildProcesses Kill a system process id and all its child processes

KillRemoteScript Kill a ccp4i non-graphical script running on a remote machine

ReadLogPid Read log file header to get process id

Server-Side Socket Handling

Server Side Socket Handling

OpenServerPort Open a port in the CCP4i server i.e. the main graphical process

ServerAcceptSocket Accept a socket connection from a client

ServerAcceptInput Accept input from a client

Database Utilities (src/database.tcl)

Database Utilities

DbInterrogateLock Obtain the status of the lock for the given project database

APIs to Access the Database

APIs to Access the Database

DbRegisterJob Register a new job with the project database.

DbUnregisterJob Unregister job at some stage in job startup

DbGetJobFileRoot Return the root name for files such as script and log files

GetLogFileName Return the full file name for the log file

GetLogFileFormat Return the full file name for the log file and its format

DbGetJobFiles Return a list of either INPUT/OUTPUT files

Database GUI

Database GUI

ssdb_setup Create the window containing the tools for searching and sorting

ssdb_handler Handle action when user clicks "Execute" or "Refine" buttons

update_ssdb_list update the list from jobs inside the search/sort tool

db_sort_handler Handle a simple or advanced sorting triggered by the search/sort tool

ssdb_reordering_array Reorder the entries of an array.

db_search_handler Handles a simple or advanced search triggered by the sort/search tool

ScheduleDbUpdateList Schedule an update of the job list.

DbUpdateList Update the list of jobs displayed and save data to file.

db_update_list Draw any generic list of parameters from database to the job list window.

db_handle_selection Handler for user picking a job from list

db_update_selection Update the internal array elements for the current job selection

db_context_menu Handler for user right-clicking on job window

db_handle_doubleclick Handler for user double-clicking on job window

db_handle_shiftdoubleclick Handler for user double-clicking on job window while pressing shift

db_command_handler Handle a user pick of the utility menu

DbDrawUtilityMenu Draw the utility menu

db_draw_utilities Draw a utility menu on the right side of main window.

DbViewJobMenu Update "View Job File" menu to list the in/output files for selected job

dbviewjobmenu_cascade_dirs Append cascading menus for subdirectory contents

Initialising, Loading & Saving the Database

DbGetCurrentProject Return the project alias and database directory for the current project.

DbInitialise Initialise project database.

DbOpen Open a project database within CCP4i

DbClose Close the currently open project database within CCP4i

DbChangeFile Change the project database

Handling Input from Running Jobs

Handling Input from Running Jobs

DbReceive Update database parameters after receiving status report from external job

DbAddOutputFile Update list of job output files after receiving command from external job.

DbUpdateOutFiles Check the existence of the listed output files for a job

DbCheckOutputFiles Look through all jobs and check uniqueness of output file name

DbUpdateStatus For any job with status RUNNING check log file to see it it has finished

ReportJobFinish Read end of logfile to find termination status

DbHandleOverwrite Remove filename from database for file that user has opted to overwrite

Database Utility GUIs

db_archive_window Draw the window with archive/delete options

db_archive_window_update Update archive/delete window if user changes default

db_archive_handler Delete/archive output files & log file as specified in archive window

db_removeoutput_handler Delete all output files for the selected job

db_cleanup_handler Apply the defined cleanup after a job

db_lock_and_archive Perform archive/delete operations while the interface is locked

db_restore_window Draw the window with file restore options

db_select_warning Write warning message if user picks utility menu without selecting job(s)

db_rerun Draw interface for rerunning a selected job

db_edit_info Edit the information stored for a job

db_load_taskinfo Load database data for job into a task array

DefFileName Return the full path name of a def file in project database directory

DbArchiveExists Look if there is archive file for filename

DbArchiveFile Archive or restore a file

ArchiveFileName Return the appropriate name for an archive file

db_job_has_notebook Check for existance of notebook entry for a job

db_edit_notebook Display & allow edit of the notebook for one job

DbMergeComFiles Merge com files for a job so they can be displayed

db_sort_tmpfiles Comparison command for lsort in DbMergeComFiles

DbKillJob Kill a job whose current status is REMOTE or RUNNING

DbStopJob Not implemented - stop job cleanly after next program finish

db_view_session_log Display the session log file

db_config_window Present a window for the user to configure the connection to the db

db_update_startup Update the user preference for database access mode on startup

db_monitor_connection Check and update the status of the connection in the db config window

Autotest Utilities

DbAutotest Handle command line running of autotest

db_autotest Interface to automatic regression testing - rerun jobs in project

db_autotest_handler Automatic regression testing - rerun jobs in project

AutotestRunjob Check status of automatic test jobs and start new job

UpdateAutoTestDef Update the def file when running regression tests

db_query_lock Create a dialogue window for overriding database lock

DbFlushCommandBuffer Flush the command buffer and execute the commands

Handling Delayed Execution of Buffered Commands

DbGetBufferFile Return the name of the database command buffer file

Starting Jobs (src/runjob.tcl)

Starting Jobs

run_command Create a def file, add new job to database and run a job

RunScript Run a job - start a new ccp4i process and pass it the def file name

RunFileCheck Before running a task check input files exist and output files do not.

InputFileCheck Check task input file exists and warn user if not

OutputFileCheck Check if task output file does not exist and offer to delete or abort

RunParameterCheck

RunAborted Invoke the cleanup handler to deal with an aborted job

RunCompleted Trigger post-run operations once a running job has finished

SetDefaultTitle Set a task title if user has not entered one

ChooseRunMode Present 'Remote' window for user to choose remote/batch mode

handle_chooserunmode Run remote/batch after user clicks 'Run' in 'Remote' window

Project Directory Utilities (src/projectdirs.tcl)

Project Directory Utilities

Core Project Directory Functions

Core Project Directory Functions

InitialiseDirectories Initialise the directories data

Accessing Project Directory Data

Accessing Project Directory Data

ListProjects Return a list of project aliases

AddProject Add a new project to list of projects

DeleteProject Remove an existing project from list of projects

GetProjectPath Return the project directory corresponding to a project alias

GetProjectDBPath Return the database directory corresponding to a project alias

SetProjectPath (Re)set the directory for the specified project.

get_indx_project Internal: get an index value for a project name

Accessing DefDir Data

Accessing DefDir Data

ListDefdirs Return a list of defdir aliases

AddDefdir Add a new defdir to list of default directories

DeleteDefdir Remove an existing def dir from list of def dirs

GetDefdirPath Return the directory corresponding to a defdir alias

SetDefdirPath (Re)set the directory for the specified defdir.

get_indx_defdir Internal: get an index value for a defdir name

Project and DefDir Utility Functions

Project and DefDir Utility Functions

ProjectIsDefined Check if a project is defined

ProjectIsDefined Return 1 if the project name is already defined, 0 if not.

DirIsProject Check whether a directory is a project directory

Functions for handing default dir menus

Functions for handing default dir menus

SetDefdirMenu Set the value of the DEFDIR_MENU internal parameter

GetDefdirMenu Return the value of the DEFDIR_MENU internal parameter

Functions for handling database specifics

Functions for handling database specifics

CreateNewProjectDb Create new database file

DirectoriesRegisterCallback Specify a procedure that will be invoked on save

Commands for Handling Automatic Directories Saves

Commands for Handling Automatic Directories Saves

DirectoriesModified Register that the directories data has been modified.

SaveDirectories Save the directories data

Internal functions for dealing with the state of CCP4i

Internal functions for dealing with the state of CCP4i

SetProjectDatabase Set the value of the PROJECT_DATABASE internal parameter

GetProjectDatabase Fetch the value of the PROJECT_DATABASE internal parameter

Commands for switching the database access mode

Commands for switching the database access mode

switch_to_direct_db Switch to CCP4i accessing the database directly

switch_to_remote_db Switch to using a database handler on a remote machine

switch_to_local_db Switch to using a database handler on the local machine

InitialiseDatabaseOptions Reset database configuration options after startup.

Internal functions for interacting with the database handler

Internal functions for interacting with the database handler

using_dbccp4i Determine if we're using the db handler as the database backend

connect_to_dbccp4i Initialise the connection to the database handler

handle_dbccp4i_broadcast Receive a broadcast from the handler and determine how to react

dbccp4i_verify_connection Check there is a working connection to the database handler

dbccp4i_list_projects Return a list of projects from the database handler

dbccp4i_add_project Add a project to the list of projects in the handler.

dbccp4i_delete_project Remove a project from the list of projects in the handler.

dbccp4i_get_project_path Return the directory path for a project.

dbccp4i_get_project_db_path Return the directory path for a project database directory.

dbccp4i_list_defdirs Return a list of "default" (data) directories from the db handler

dbccp4i_add_defdir Add a "default" (data) directory to the list in the handler.

dbccp4i_delete_defdir Remove a "default" (data) directory from the handler.

dbccp4i_get_defdir_path Return the directory path for a "default" (data) directory.

dbccp4i_dir_is_project Check whether a directory path is a project or data directory

dbccp4i_project_is_defined Check whether a project name is already defined in the handler

DbReport Handle reporting diagnostic messages for database code

Database cache for database handler

Database cache for database handler

dbccp4i_populate_dirs_cache Initialise the directories data in the cache

dbccp4i_dirs_is_cached Check whether the directories data has been cached

dbccp4i_update_dirs_cache Update the directories cache in response to a handler broadcast

dbccp4i_cache_addproject Add the data for a new project into the cache

dbccp4i_cache_deleteproject Remove a project from the cache

dbccp4i_cache_adddefdir Add the data for a new def dir into the cache

dbccp4i_cache_deletedefdir Remove a def dir from the cache

Core Database Functions (src/projectdb.tcl)

Core Database Functions

Commands for Handling Database Files

Commands for Handling Database Files

DbLoadFile Load a database.def file into the database array

DbSaveFile Save the current contents of the database to database.def

Commands for handling messages and callbacks

Commands for handling messages and callbacks

DbSetMessage (Re)set the internal message from the core database functions.

DbGetMessage Fetch and clear the last internal message from the core db functions.

DbRegisterCallback Specify a procedure that will be invoked on save

Commands for Handling Automatic Database Saves

Commands for Handling Automatic Database Saves

DbModified Register that the database has been modified.

DbSave Save the currently open project database within CCP4i

Commands for Handling Database Locking

Commands for Handling Database Locking

DbLockFileName Return the lock file name

DbLockStatus Return status of lock file

DbCreateLock Create a lock file

DbDeleteLock Delete lock file for specified project database

Commands for Opening and Closing the Job Database

Commands for Opening and Closing the Job Database

DbOpenDatabase Open a project database

DbCloseDatabase Close the current database

Core Database Functions

Core Database Functions

DbNewRecord Creates a new record in the database and returns handle (=job id)

DbJobExists Check whether a job exists in the database

DbItemExists Check whether a data item is defined in the database

DbSetJobData Assign a value to database item(s)

DbGetNJOBS Return the value of the NJOBS parameter

DbGetJobData Return a data item from the database

DbJobHasSubjobs Check if a job has any associated subjobs

DbGetNotebookFile Return the filename for the notebook file associated with a job

DbSelectJobs Return list of jobs based on selection criteria

DbJobDescription Append all database information for one job into one string for display

DbDeleteJob Remove the record of a job from the database

DbVerifyLock Verify that the current process owns the lock on the database

Internal functions for interacting with the database handler

Internal functions for interacting with the database handler

dbccp4i_open_project Open an existing project via the database handler.

dbccp4i_close_project Close access to an open project.

dbccp4i_project_is_writable Check whether write access is available for a project.

dbccp4i_new_job Create a new job record in a project.

dbccp4i_item_exists Check whether a data item is defined for a given job.

dbccp4i_set_data Set the value of one or more data items for a job.

dbccp4i_get_njobs Return the highest job id number for the project.

dbccp4i_get_data Fetch the value of one or more data items associated with a job.

dbccp4i_job_has_subjobs Check if a job has associated subjobs

dbccp4i_select_jobs Return a list of jobs where data items match a regular expression.

dbccp4i_job_description Return a formatted description of a list of jobs.

dbccp4i_delete_job Deletes the specified job record from the project.

Database cache for database handler

Database cache for database handler

dbccp4i_populate_cache Initialise the job data in the database cache

dbccp4i_update_cache Update the cache in response to a broadcast from the handler

dbccp4i_cache_updatejob Update the data for a single job in the cache

dbccp4i_cache_addjob Add a new job to the database cache

dbccp4i_cache_deletejob Delete a job from the database cache

Creating Windows (src/window.tcl)

Creating Windows

OpenWindow Open a graphical window

OpenGridWindow Similar to OpenWindow but uses grid geometry manager

CloseWindow Close a window opened by OpenWindow, OpenGridWindow or OpenTaskWindow

CreateFrame Set up a frame structure (i.e. folders) in a window opened by OpenWindow

CloseFrame End the definition of a frame.

OpenFolder Begin the definition of a folder in a task window

update_folder Update visibility of folder dependent on protocol defined by OpenFolder

update_folder_display Switch on or off the display of folders dependent on the value of the switch parameter

OpenSubFrame Open a sub frame within the context of OpenWindow/CreateFrame or CreateTaskWindow

CloseSubFrame Close a sub frame

toggle_frame_display Set up a trace command for handler controlling visibility of a line or subframe

update_frame_display Handler controlling visibility of a line or subframe

update_table_row Toggle the display of a line in the table dependent on value of some varaible

toggle_button_disabled Set up a trace command for handler controlling greying of a varbutton

update_button_disabled Handler controlling greying out of a varbutton

scrolled_frame Create a scrollable frame

update_main_scroll Update the scrollable extent of a task window.

UnsetArrayExtras Delete the 'extra' elements from a task window array

run_update_script After defining a new window tidy up the extending frames

GetNewWindowName Return a unique name for an array root_$n

Help, Message Line and Wait Commands

SetProgramHelpFile Set the name of the help file for the current window

KeywordHelp Open a web browser to display a help document.

SetMessage Bind cursor entering a widget to display help textline

ShowHelp Show inline help text message

CancelHelp Cancel display of inline help text message

InitialiseBubbleHelp Initialise bubble help functionality

bubblehelp_pending Initiate display of help text via bubble help

bubblehelp_show Display help text in a help bubble.

bubblehelp_cancel Cancel display of help text via bubble help

set_message Display the given text in the message line

PleaseWait Display a 'Please wait' message

TkBusy' Iteratively set the cursor for all child windows to a watch/arrow

TkBusy Set the cursor style for a window and all of it's children

File Selection Widgets

CreateInputFileLine Draw a line to select an input file

CreateOutputFileLine Draw a line to select an output file

FileViewer0 Extracts file name from a data array and passes to FileViewer

FileDialog Open a file selection dialog box associated with one file input line

DirBrowser Present a 'file' browser for user to select a directory

CheckFileInput Check user input to file selection and return 1 if OK, 0 otherwise

IsPathADefaultDir Check if explicitly entered path corresponds to a project or aliased directory.

ResolveDirInput Expand user input directory path

CheckDirInput Validate user input of directory path

update_default_dir Update the path to file name in file selection line when user changes default directory

MoveFileNameLeft For long file name move position of file name in widget

UpdateOutputFilename Derive an output file name from an input file name

add_file_command Bind a command to be issued after user has selected a file

SetParamFromFile Handler for the -setfileparam argument to CreateInputLine

GetParamFromFile Get specified type of data from a specified file header

The Generic Line Widget

CreateLine Draw a line in a window

CreateCheckbutton Create a checkbutton

CreateLineTemplate Define a template for the layout of a line

PackByTemplate Apply the template defined by CreateLineTemplate to pack a line

UpdateDependentParams Callback afer user selects item from menu update the array element

initialise_menu Create a menu or reinitiallise an existing one

UpdateVarLabel Update a variable label to an explicitly entered value

update_varlabel Update a variable label when the associated variable is changed

add_command Bind a command to a widget which may be a menu or an entry widget

paste_into_entries Paste into multiple fields

continue_paste Handler for user input for paste GUI

toggle_on Handler to toggle on a checkbutton when user inputs anywhere on a line

check_input Check entry widget input is consistent with data type

set_field_colour Set the colour of an input widget dependent on validity of user input

Other Complex Widgets

CreateButton Create an action button in the 'button' frame of a window created by 'CreateFrame'

CreateText Create a Tk text widget, optionally scrollable.

AppendTextWindow Append text to CreateText widget

add_modalDialog_safeguard Add the modalDialog bindtag to a window

break_menu_column Internal procedure to set the -columnbreak value for items in a menu

Task Window Utilities (src/taskwindow.tcl)

Task Window Utilities (src/taskwindow.tcl)

RunTask Initialise parameters for task and draw task window

draw_task_window Procedure called at end of RunTask to actually put the window on the screen

RerenderTask Redraw an existing task window

CreateTaskWindow Called from taskname_run to define general appearance of task window

DrawRunButton Draw the 'Run' button for task windows

UnsetProjectDefault Handle 'Unset Project default' option on Save or Restore menubutton

task_display_log Handle option to 'Display Log Files' which is presented to user in 'task' mode of running ccp4i.

redraw_task_window_title Redraw task window title with information on the origin of the initial parameters

SaveUserDefinedDef Handler to save current parameters to user specified file

SaveProjectDef Handler to save current parameters to the user or the project default file.

RedrawTaskWindow Redraw a task window from scratch after destroying existing window.

ReCreateTaskWindow Load parameters from a def file and redraw the task window.

DeleteTaskWindow Close a task window cleanly.

SaveOnProgramExit Specify a task array which will be saved to a def file if the user exits the interface.

LockInterface "Lock" the interface to prevent it from exiting

UnlockInterface Unlock the interface after a call to LockInterface

InterfaceIsLocked Check whether the interface is locked and prevented from exiting

ConfirmExitInterface Prompt for user confirmation before exiting the interface

ExitInterface On exiting the interface save the status file and database file

CreateTitleLine Draw the title line which is standard at top of task window.

check_title_line Hander when user enters title line test to remove 'bad' characters

WriteCredits Write author credits at bottom of task window

WriteImage Write an image into a task window

RunUtility Start up a utility using the specified command

Extending and Toggle Frames (src/exframe.tcl)

Extending and Toggle Frames

CreateToggleFrame Create a toggle frame widget

create_toggle_button Create the title line for the toggle frame

SetToggleTitle Reset the title for a toggle frame

update_subframe_display Update the visibility of a toggle frame.

UpdateExtendingFrame Explicit programmer command to add or remove lines from an extending frame

set_open_frame Save information on the currently open frame (i.e. the one currently being drawn) to the systemvar array.

create_addline_command Draw the Edit menubutton and the increment button for toggle frames and extending frames.

exframe_select Update the edit menu button after the user has selected a row for editing

exframe_edit Handle mouse click tied to editing extending frames

delete_frame Delete a frame

delete_frame_data Delete the data when a frame is deleted

unset_child_indexed_params Unset the array variables for all the child frames of def_proc

copy_frame Copy the data in one row to another row

copy_frame_c1 Copy parameters of a child frame from one parent (from) to another (to)

append_extend_frame Add another frame to the bottom of extending frame

append_toggle_frame Add another frame to the bottom of a toggle frame widget

append_frame_c1 Draw child frames when called from append_*_frame

bind_edit_select Add the edit function right-mouse button bindings

SetIndexedParam Assign values to a group of indexed elements with the same index

UnsetIndexedParam Unset the elements of array for a parameter, its data type and widget

Using the BLT Table Widget

Using the BLT Table Widget

CreateTable Create a table using the BLT table function

CreateTableTitle Draw column titles in table

table_edit_buttons Draw the edit menu button and increment button under the table

TableDrawRow Draw one row of a table

TableAddRow Add an extra row to the table to support the edit functions

TableDeleteRow Delete a row from the table

TableDeleteContents Delete the entire contents of the table but keep the column titles.

TableGetExtent Return the Cnumber of rows in the table

get_table_extent Return the Cnumber of rows in the table

TableUpdateScroll Update the scrollable area of the table.

Variable Menus (src/varmenu.tcl)

Variable Menus

create_varmenu Called from CreateLine procedure to update array(DEPVARS_$deflistVar)

UpdateVariableMenu Invoked by user to update the variable menu

update_varmenu Handler to update one item of variable menu

update_menu Called from UpdateVariableMenu to redraw the menu(s) associated with one variable.

update_menu0 Update each individual instance of a variable menu

General Utility Windows (src/util_windows.tcl)

General Utility Windows

WarningMessage Output a 'warning' message to the user - the one default action is 'Dismiss' to close the window.

warning_message_command Handler for exit button on the warning message window

ChooseOptionDialog Give user multiple choice with one button per option

choose_opt_command Handler for action buttons on the choose option window

choose_opt_sel handler for listbox selection in ChooseOptionDialog listbox mode

InputParamDialog Present user dialog box with simple list of variables to edit

EditComFile Display a program command script and command line for user to edit

handle_edit_com_file Handler for action button in EditComFile

Code for Uniqueify, Harvesting and HKL Rejects

UniqueifyFrame1 Uniqueify interface - a fragment of several task interfaces

UniqueifyFrame2 Uniqueify interface - a fragment of several task interfaces

SetHarvestParams Initialise parameters for tasks which interface to harvesting mechanism

util_set_harvesthome Set the HARVESTHOME environmental variable

util_fix_harvestnames Call RemoveMetaChars to ensure valid project/crystal/dataset names.

CreateHarvestLine Draw the three line interface to dataset/harvesting commands

UpdateHarvestMTZ Fill in default project and dataset name when the user selects MTZ

HklRejects Define one line of extending frame for rejects in combat/scalepack2mtz/d*trek

File Selection Window (src/fileselect.tcl)

File Selection Window

SelectFile Open a file selection window

fileselectDefdir Update file list when user changes the default directory alias

fileselectFilter Handle user changing the filetype selection filter

fileselectViewers Set up the menu to allow user to select a viewer for a given file type.

fileselectList Update list of directories and files visible to user

fileselectOK Handle user selection of a file or directory

fileselectCancel Handle user clicking the cancel button.

fileselectClick Take the file item the user clicked on in listbox

dirselectClick Take the directory item the user clicked on

fileselectTake Take the currently selected list item

fileselectComplete Do file name completion for the file name in the input text widget

up_directory Handle user selection of the 'go up a directory' widget

sort_files Sort list of files by criteria of date or name

compare_date The sorting procedure for the Tcl lsort command sorting by date

display_file_list Put list of files into display listbox

fileselectIsDirectory Check if file is a directory by looking it up in the cache

fileselectFileMtime Get the mtime attribute of a file

Projects and Directories Interface (src/directories.tcl)

Projects and Directories Interface

directories Initialise interface if user open the 'Directories' window stand alone.

check_directory_alias Check that user input project or directory alias is unique

DefineDirectory Create the graphics for defining one directory

DefineProject Create the graphics for defining one project

undo_DefineProject Handler when user removes project definition from the extending frame list

Directories Draw the 'Projects and Directories' window

populate_directories_window Populate the parameters of the Directories window

InitialiseCCP4ITemp Initialise the CCP4i TEMPORARY data directory

apply_directories Handle updates on applying the changes in the window

apply_directories_init Apply user changes to the projects for a new user

directories_update_window Update, redraw or exit the directories window

make_one_word Force all project and directory aliases to be one word

init_mg_directories Invoked on MG startup to ensure MG_CURRENT_PROJECT parameter exists

File Viewer (src/fileviewer.tcl)

File Viewer

fileviewer Setup procedure called if file viewer is run stand-alone

ExitFileViewer Called on exiting file viewer - will terminate process in stand-alone mode

FileViewer Display a file

fileviewer0 Display a file

LOGViewer Display a log file

LogGraph_graph Use loggraph to display data from a 'graph' file

LogGraph Display files using ccp4i loggraph

PDBViewer Display PDB file as text

MAPViewer Use mapdump to read map header and display this

MTZViewer Use mtzdump to read mtz header and display this

mtzviewer_info pass-thru to set up new global array

mtzviewer_info0 Handle option for Extra Information when displaying MTZ files

mtzviewer_info_handler Handle the 'Run' command for mtz_info - Run mtzdmp or sftools

mtz_info_review Review and display the output from the mtz_info task

PSViewer Display a postscript file

XMGRViewer Display xmgr file - as output by scala

PLOT84Viewer Use xplot84driver to display a plot84 file

PLOT84PSViewer Convert plot84 format file to PostScript and display with PSViewer

MRViewer Display (and edit) a mr (molecular replacement) file

HAViewer Display (and edit) a ha (heavy atom) file

mr_ha_viewer Pass-thru to mr_edit task which will display & edit mr and ha files

RunRasMol Run RasMol to display coordinates

RunPyMol Run PyMol lto display coordinates

RunMapslicer Run the mapslicer program

RunCoot Run the Coot program

RunCCP4mg Run the CCP4mg program

RunDbviewer Launch the Dbviewer application

DisplayTextFile Display a text file

LoadTextWindow Load the text into the window set up by DisplayTextFile

display_next_frame handle the display of the next frame of text if displaying a very large file

display_read_frame Read a frame from a log file into memory so it can be displayed

display_skip_frame Read through a frame from a log file and discard it

display_text_update_case Handle user changing the respect/ignore case option

display_text_close Handle user clicking Close button.

display_text_save Handle user opting to save contents when using 'edit' mode

display_text_find Handle user hitting Find or 'Close Find' button

display_text_find_string Find and highlight given string in the text

display_links Dispaly links in log file

MonitorFile Read and display a file that is still being written

display_text_summary Handle the 'Show Summary' option

display_text_full Handle the 'Show Full Text' option

ExtractLogSummary Extract the text tagged as 'summary' from a log file

HilightLogSummary Highlight the sections of log file which are tagged as 'summary'

GetViewerList Extract the list of file formats, viewers and full viewer commands from the typedef array

Plugin Utilities (src/plugins.tcl)

Plugin Utilities

GetPlugins Return available plugins for a specific task

get_plugin_executable Helper function: verify and return the executable name

Plugin Command Generation Functions

Plugin Command Generation Functions

Utilities called from Run Scripts (src/execute.tcl)

Utilities called from Run Scripts

ExecuteScript Read the def file and source the run script.

GetJobid Return the job id

SetOutputFileRoot Return a root file name which identifies the job that created the file

Execute Execute a command and handle editting of command script and program failure.

ResetDatabaseAccess Reset the database access mode for running jobs

AppendCommand Append the command line as a comment to input script

TerminateScript Cleanly terminate a run script process and notify the main CCP4i process

InitialiseLog Write ccp4i header to the log file for the job

WriteTerminationToLog Write ccp4i footer to the log file

WriteToLog Write comments to log file with wrappers to indicate that comments are from ccp4i script.

WriteHtml Write an html tag to log file

WriteTable Write a neatly formatted table to log file or other summary file

Creating the Program Command Script

CreateComScript Create the program command script using a template.

UpsetVar Set a variable at a higher level in the procedure calling stack

set_at_filename Handle the AT command in a com file - save the name of a file to be sourced

get_at_filename Return the name of the 'AT' file

set_label_stack Handling the LABELLINE keyword for MTZ LABIN/LABOUT

getcomline Read the next line from the 'com' template file

Automatic Test Mode

ExecuteAutoTest Execute a script in autotest mode

UpdateAutoTestDef Copy def file to working test directory and update the def file header and file names

Procedures for Communications to the Database

NotifyDatabase Communicate with the job database

dbccp4i_notify_database Communicate with the job database via the database handler

Procedures for Communications with the Main CCP4i Process

NotifyEditComFile Send command script to main CCP4i process for user to inspect/edit

NotifyRunAborted Notify main CCP4i process that the run has been aborted

NotifyRunCompleted Notify main CCP4i process that the run has completed

RunNotification Send message to main CCP4i process to say this process is running

FailNotification Send message to main graphical CCP4i process to say this process has failed

AddOutputDir Notify the main CCP4i process of additional output dirs

AddOutputFile Notify the main CCP4i process of additional output files

Communication between Script not written in Tcl and CCP4i

ExecuteSocket Use ccp4ish to communicate to CCP4i main process from a non-Tcl script

BufferSocketCommand Add a command to the buffer for execution later

GetBufferFile Return the name of the database command buffer file

OpenSocket Open a client side socket to connect to the server in the main CCP4i process

GetServerPort Return server port for CCP4i process associated with current project

Helper commands for CCP4i jobs (utils/job_utils.tcl)

Helper commands for CCP4i jobs

CreateAnnotatedLogfile Run the baubles program to generate an annotated logfile

Map Handling Utilities (utils/map_utils.tcl)

ExtendMap Interface to mapmask program to extend map to cover molecule

ConvertMapAsu Run mapmask convert map to cover the standard CCP4 asymmetric unit

ConvertMapFormat Convert from CCP4 to alternative map formats

CreateMap Create a map of optional type in various formats

MakeOMapMacro Create a macro for O to display map(s)

MakeXtalMacro Create a macro and crystal file for xtalview to display map(s)

GetCellfromMtz Extract header information from an MTZ file

GetMapHeader Extract header information from a map file

ConvertMapCell Extend map to cover unit cell

WatPeak UNTESTED Search input differnce map for water peaks

AddXtalMapFom Add an extra column of dummy FOMS to an XtalView phases file

CalcCellVolume Calculate the cell volume

Coordinate Handling Utilities (utils/pdb_utils.tcl)

CalcCellVolume Get the atomic contents of PDB file

AtomType Return the Element name for a given atomic number

GetAminoInfo Return some information for a given input amino acid type

ParsePDBId Extract the cards relevant to the atom id from a PDB ATOM line

ParsePDBIz Extract atomic number from PDB atom card (or element type from name)

PDBRemoveZeroOcc Remove atoms with zero occupancy from PDB file

ExtractPdbColumns Extract columns from the ATOM records of a PDB file

MergePdbFiles Merge 2 or more PDB files

PdbGetChains Get a list of the chains and the first & last residue ids in a PDB file

HandleHarvestFile Add the output harvest file to the output file list for a job

FindNCSTransforms For multi-chain PDB find the inter-chain transformations using Lsqkab program

Mol Procedures for Handling Coordinate Data

MolReadPDB Read some or all atoms from a PDB file into the Mol array

MolReadCif Read atoms from a CIF file into the Mol array

read_cif_name Strip the inverted commas (quotes) from a cif atom name

MolReadSybyl Read some or all atoms from a Sybyl file into the Mol array

MolConvertSybylType placemarker for code to convert Sybyl atom types

MolConvertSybylBond placemarker for code to convert Sybyl bond types

MolBoundingBox Find centre of mass and bounding box for coordinates in Mol

MolTranslate Apply a translation to all coordinates in Mol array

MolWriteCifCoords Write out a CIF coordinate format file

write_cif_name Put quotes about name if it contains a quote character

MolReadPdbRestraints Read MODRES/SSBOND/LINK/CISPEP cards from pdb file

MolCheckPdbRestraints Not implemented - should check sensible restraints defined

MolCheckReadFile Not implemented - should check sensible atom name input etc.

MolFindFragments Find all the separate non-bonded fragments in Mol array

MolChiralVolume Find the chiral volume of four atoms in the Mol array

MolSaveParam Make a backup of Mol array values

Utilities for Phasing Tasks (utils/phasing_utils.tcl)

ExtractShelxLog UNTESTED - Extract info from the Shelx log file

MakeShelxDismat Convert the distance list from shelx log file into a neat distance matrix

NpoMapScale Devise scale for NPO plots with orthogonal sections on same scale

FindScaleitDiff Run scaleit to find optimal value for exclude cutoff for Patterson

scaleit_analysis Extract date from scaleit log file for correlation analysis

scaleit_write_tab Write the summary of the scaleit log file(s) to the table file

Uniqueify Run the Tcl version of 'uniqueify' script to standardise MTZ and add FreeR column

AMoRe Utilities (utils/amore_utils.tcl)

amore_get_tabling_data Extract data from the amore tabling log file

amore_calc_model_cell Use the model extent and radius to calculate reasonable model cell

amore_get_log_solution Extract solutions from log file

amore_update_database Update the mr_database.def file

amore_get_solution Extract solutions from an 'mr' file and write in input format for Amore

amore_block_mr_database send command to main ccp4i to block update of the mr database

amore_extract_mr_header Extract information from the header of an mr file

Utilities for managing task installation (src/CCP4i_packages_utils.tcl)

Utilities for managing task installation

InstallTaskPackage Driver procedure to perform installation of a new task

ImportTaskPackage Driver procedure to import a task package from another CCP4 installation

ImportAllTaskPackages Driver procedure to import all task packages from another CCP4 installation

ExportTaskPackage Driver procedure to create a task package archive file

UninstallTaskPackage Driver procedure to uninstall a previously installed task package

ExamineTaskArchive Examine the contents of a task archive package file

MakeTmpTaskInstallDir Create a temporary directory in which to unpack an archive file

GetTaskInstallDir Return the root path for the installation area

GetTaskInstallFileDir Return the root path for the installation modules and packages files

UnpackTaskArchive Unpack a CCP4i task package archive file.

GetPackageList Return a list of CCP4i package names from a ccp4i_packages.def file

GetPackageFiles Return a list of files for a package registered in a CCP4i subdirectory

GetPackageReferences Return a list of associated task references registered with a package

GetPackageVersion Return the version string of a CCP4i task package in the ccp4i_packages.def file

UpdatePackagesEntry Update an entry in a ccp4i_packages.def file

RemovePackagesEntry Remove an existing entry from a ccp4i_packages.def file

CreateTarFile Apply 'tar cf' to dir to create a tar file

ValidatePackageName Check that the supplied package name is valid

ComparePackageVersions Compare version strings for CCP4i task packages

InstallReport Report a message from the install procedures.

Utilities used for reading XML files (src/xml_utils.tcl)

Utilities used for reading XML files

XmlStatus Query/return status of XML switch in CCP4i preferences

XmlDataLoaded Check whether data from an XML file has been loaded into xmldata

XmlDataReset Reset the status of xmldata force rereading of XML files

GetXmlAttributeValue Return the value of an XML attribute

GetCCP4XmlData Return data extracted from a CCP4 XML file

ccp4_parse_xmlfile Extract information from CCP4 XML files

HandleStartCCP4Xml Internal parsing procedure for processing CCP4 XML files

HandleEndCCP4Xml Internal parsing procedure for processing CCP4 XML files.

GetAlmnReindexOp Return a reindexing operator from an ALMN XML output file

GetMolrepNMonomers Return the ideal number of monomers from Matthews XML output

GetMolrepPseudoTransPeak Return peak number of pseudotranslation from mr_analyse XML file

GetMolrepPseudoTrans Return pseudotranslation vector from mr_analyse XML file

Vector and Matrix Arithmetic (src/vector.tcl)

vmult return vector (a list) which is vector a multiplied by factor b

vdotp return the dot product of two vectors

vlen return the magnitude of the vector

vdist return the distance between two points

vadd return the sum of two vectors

vsub return the difference of two vectors

vcent return the average coordinate of a list of 2D coordinates

vscal return vector (a list) which is vector v scaled by factor s

vrot Apply a rotation to a 2D coordinate

vmatmult apply rotation matrix rmat to vector a

vmirror apply a mirror transformation in x or y axis