molsysmt.form package#

Subpackages#

Submodules#

molsysmt.form.get_attributes module#

molsysmt.form.get_attributes.get_attributes(form, output_type='dictionary', skip_digestion=False)[source]#

Getting the list of attributes of a molecular system’s form.

The function returns a dictionary with all attribute names as keys and True or False as values reporting whether or not the attribute is in the molecular system’s form.

Parameters:

  • form (str, list or tuple of str) – Any of the supported forms by MolSysMT, or a list of them.

  • output_type ({'dictionary', 'list'}, default 'dictionary')

Returns:

If output_type=='dictionary' a dictionary is returned with all attribute names as keys and booleans as values: True if the attribute is in the input molecular system’s form, False otherwise. If output_type=='list' a list is returned with all attribute names in the molecular system’s form.

Return type:

dict, list

Raises:

NotSupportedFormError – The function raises a NotSupportedFormError in case a molecular system is introduced with a not supported form.

Added in version 0.8.3.

Notes

The list of supported molecular systems’ forms is detailed in the documentation section User Guide > Introduction > Molecular systems > Forms.

Examples

The following example illustrates the use of the function.

>>> import molsysmt as msm
>>> dict_attributes = msm.form.get_attributes('file:mmtf')
>>> dict_attributes['box']
True
>>> dict_attributes['forcefield']
False
>>> dict_attributes = msm.form.get_attributes(['file:mmtf','molsysmt.MolecularMechanicsDict'])
>>> dict_attributes['box']
True
>>> dict_attributes['forcefield']
True

User guide

Follow this link for a tutorial on how to work with this function: User Guide > Tools > Form > Get attributes.

molsysmt.form.has_attribute module#

molsysmt.form.has_attribute.has_attribute(form, attribute, skip_digestion=False)[source]#

Checking if a molecular systems’form has a certain attribute.

The function returns True if the attribute is found in the molecular system’s form, and False otherwise.

Parameters:

  • form (str, list or tuple of str) – Any of the supported forms by MolSysMT, or a list of them.

  • attribute (str) – The attribute name to be checked in the molecular system.

Returns:

The function returns a boolean value reporting whether or not the attribute is found in the molecular system.

Return type:

bool

Added in version 0.8.3.

Notes

The list of supported molecular systems’ forms is detailed in the documentation section User Guide > Introduction > Molecular systems > Forms.

See also

molsysmt.form.get_attributes()

Getting the list of attributes of a molecular system’s for’s form.

molsysmt.basic.get_attributes()

Getting the list of attributes of a molecular system.

molsysmt.basic.has_attribute()

Checking if a molecular system has a certain attribute.

Examples

The following example illustrates the use of the function.

>>> import molsysmt as msm
>>> msm.form.has_attribute('file:mmtf', 'box')
True
>>> msm.form.has_attribute('file:mmtf', 'forcefield')
False
>>> msm.form.has_attribute(['file:mmtf','molsysmt.MoleculeMechanicsDict'], 'forcefield')
True

User guide

Follow this link for a tutorial on how to work with this function: User Guide > Tools > Form > Has attribute.

molsysmt.form.is_file module#

molsysmt.form.is_file.is_file(item_or_form)[source]#

molsysmt.form.is_item module#

molsysmt.form.is_item.is_item(item)[source]#

molsysmt.form.is_string module#

molsysmt.form.is_string.is_string(form)[source]#

molsysmt.form.iterators module#

class molsysmt.form.iterators.StructuresIterator(molecular_system, atom_indices='all', start=0, interval=1, stop=None, chunk=1, structure_indices=None)[source]#

Bases: object

class molsysmt.form.iterators.TopologyIterator(molecular_system)[source]#

Bases: object

Module contents#