The majorobj Command

This command provides simple, generic versions of some commonly used major objects (ensembles, reactions, datasets, molfiles, tables, networks) commands. The difference to the object-specific commands is that any major object handle is accepted as object identifier, not just the type of handle associated with the associated specialized object command. Specialized object commands generally implement more powerful commands with additional, usually class-specific options. This command is generally used when different types of objects (such as ensembles and reactions) share a common simple processing path and code duplication for each type of object would be tedious.

It is not possible to create generic major objects without specialization - this is an abstraction.

majorobj delete

majorobj delete ?handle?...
Majorobj.Delete(?mrefsequence/mref/handle?,...)

Delete major objects.

The command returns the number of deleted objects.

Example:

majorobj delete $ehandle $xhandle

majorobj dget

majorobj dget handle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The difference between majorobj get and majorobj dget is that the latter does not attempt computation of property data, but rather initializes the property values to the default and return that default if the data is not yet available. For data already present, majorobj get and majorobj dget are equivalent.

A Python implementation would not be useful because every major object has a dget() method, which can be invoked without exact knowledge of the object class.

majorobj dup

majorobj dup handle ?dataset? ?position?

Duplicate a major object.

The duplicate object is placed into the same dataset as the source, if it is a member of a dataset. Specifying an explicitly empty dataset argument places the duplicate outside any dataset, regardless of the dataset membership of the source object.

If the duplicate is moved to a dataset, it is appended to the dataset end by default. This happens also if the position parameter is explicitly specified as end or an empty string. Otherwise, the object is inserted at the given position, starting with 0. If the requested position is larger than the current size of the dataset, the object is appended.

A Python implementation would not be useful because every major object has a dup() method, which can be invoked without exact knowledge of the object class.

Example:

majorobj dup $handle

The command returns a new object handle or reference.

majorobj exists

majorobj exists handle ?filterlist?

Check whether a handle is valid. The command returns boolean 0 or 1. Optionally, the object may be filtered by a standard filter list, and if it does not pass the filter, it is reported as not valid.

A Python implementation would not be useful because every major object has a exists() method, which can be invoked without exact knowledge of the object class.

Example:

majorobj exists $handle

majorobj get

majorobj get handle propertylist ?filterset? ?parameterdict?
majorobj get handle attribute

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For the use of the optional property parameter list argument, refer to the documentation of the ens get command.

Variants of the majorobj get command are majorobj new, majorobj dget, majorobj jget, majorobj jnew, majorobj jshow, majorobj nget, majorobj show, majorobj sqldget, majorobj sqlget, majorobj sqlnew, and majorobj sqlshow .

In addition to property data, all major objects possess a few common attributes, which can be retrieved with the get command (but not by its related sister subcommands like dget, sqlget, etc.). Object-specific attributes can only be retrieved via the object-specific access commands. The common attributes are:

A Python implementation would not be useful because every major object has a get() method, which can be invoked without exact knowledge of the object class.

majorobj hadd

majorobj hadd handle

Add a standard set of hydrogens to the object, if applicable (ensembles, reaction, datasets). The command returns the total number of hydrogens added. This command version has less options than the class-specific variants.

A Python implementation would not be useful because all applicable major objects have a hadd() method, which can be invoked without exact knowledge of the object class.

majorobj hdup

majorobj hdup handle ?dataset? ?position?

This command is the same as majorobj dup , except that a full set of hydrogens is added to the duplicated objects if applicable (ensembles, reactions, datasets).

A Python implementation would not be useful because all applicable major objects have a hdup() method, which can be invoked without exact knowledge of the object class.

majorobj hstrip

majorobj hstrip handle ?flags?

This command removes hydrogens from all applicable objects (ensembles, reactions, datasets). By default, all hydrogen atoms on the object are removed.

The flags parameter can be used to make the operation more selective. It may be a list of the following flags:

If the flags parameter is an empty string, or none , it is ignored. The default flag value is wedgetransfer - but the default value is overridden if any flags are set!

The return value is the total number of hydrogens deleted.

A Python implementation would not be useful because all applicable major objects have a hstrip() method, which can be invoked without exact knowledge of the object class.

majorobj jget

majorobj jget handle propertylist ?filterset? ?parameterdict?

This is a variant of majorobj get which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects. The command is usable only for property data, not attribute retrieval.

A Python implementation would not be useful because every major object has a jget() method, which can be invoked without exact knowledge of the object class.

majorobj jnew

majorobj jnew handle propertylist ?filterset? ?parameterdict?

This is a variant of majorobj new which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

A Python implementation would not be useful because every major object has a jnew() method, which can be invoked without exact knowledge of the object class.

majorobj jshow

majorobj jshow handle propertylist ?filterset? ?parameterdict?

This is a variant of majorobj show which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

A Python implementation would not be useful because every major object has a jshow() method, which can be invoked without exact knowledge of the object class.

majorobj ldup

majorobj ldup ?handlelist?...
Majorobj.ldup(?mref/mrefsequence/handle?,...)

Duplicate all objects in the handle list(s) in default mode.

The return value is a single list (even if multiple source lists are used) of the duplicated object handles or references. If an argument list element is an empty string (or None for Python ), it indicates a missing object, and the output list also receives an empty string (or None ) element at its position, without raising an error.

majorobj lhdup

majorobj lhdup ?handlelist?...
Majorobj.lhdup(?mref/mrefsequence/handle?,...)

Duplicate all objects in the handle list(s) in default mode, and add hydrogens if applicable (ensembles, reactions, datasets).

The return value is a single list (even if multiple source lists are used) of the duplicated object handles. If an argument list element is an empty string (or None for Python ), it indicates a missing object, and the output list also receives an empty string (or None ) element at its position, without raising an error.

majorobj new

majorobj new handle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The difference between majorobj get and majorobj new is that the latter forces the re-computation of the property data, regardless whether it is present and valid, or not.

A Python implementation would not be useful because every major object has a new() method, which can be invoked without exact knowledge of the object class.

majorobj nget

majorobj nget handle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The difference between majorobj get and majorobj nget is that the latter always returns numeric data, even if symbolic names for the values are available.

A Python implementation would not be useful because every major object has a nget() method, which can be invoked without exact knowledge of the object class.

majorobj nnew

majorobj nget handle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The difference between majorobj get and majorobj nget is that the latter always returns numeric data, even if symbolic names for the values are available.

For examples, see the majorobj get command. The difference between majorobj get and majorobj nnew is that the latter always returns numeric data, even if symbolic names for the values are available, and that property data re-computation is enforced.

A Python implementation would not be useful because every major object has a nnew() method, which can be invoked without exact knowledge of the object class.

majorobj show

majorobj show handle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The difference between majorobnj get and majorobj show is that the latter does not attempt computation of property data, but raises an error if the data is not present and valid. For data already present, majorobj get and majorobj show are equivalent.

A Python implementation would not be useful because every major object has a show() method, which can be invoked without exact knowledge of the object class.

majorobj sqldget

majorobj sqldget nhandle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The differences between majorobj get and majorobj sqldget are that the latter does not attempt computation of property data, but initializes the property value to the default and returns that default, if the data is not present and valid; and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

A Python implementation would not be useful because every major object has a sqldget() method, which can be invoked without exact knowledge of the object class.

majorobj sqlget

majorobj sqlget nhandle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The difference between majorobj get and majorobj sqlget is that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

A Python implementation would not be useful because every major object has a sqlget() method, which can be invoked without exact knowledge of the object class.

majorobj sqlnew

majorobj sqlnew nhandle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The differences between majorobj get and majorobj sqlnew are that the latter forces re-computation of the property data, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

A Python implementation would not be useful because every major object has a sqlnew() method, which can be invoked without exact knowledge of the object class.

majorobj sqlshow

majorobj sqlshow nhandle propertylist ?filterset? ?parameterdict?

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the majorobj get command. The differences between majorobj get and majorobj sqlshow are that the latter does not attempt computation of property data, but raises an error if the data is not present and valid, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

A Python implementation would not be useful because every major object has a sqlshow() method, which can be invoked without exact knowledge of the object class.

majorobj subcommands

majorobj subcommands
dir(Majorobj)

List all currently implemented subcommands of this command.

The Python version is somewhat misleading, because it also lists methods which are implemented in a generic fashion for all major objects and then inherited by specialized classes.

majorobj valid

majorobj valid handle propertylist

Returns a list of boolean values indicating whether values for the named properties are currently set for the object. No attempt at computation is made.

majorobj has is an alias to this command.

A Python implementation would not be useful because every major object has a valid() method, which can be invoked without exact knowledge of the object class.