molsysmt.build.define_new_chain#

molsysmt.build.define_new_chain(molecular_system, selection='all', chain_id=None, chain_name=None, syntax='MolSysMT', skip_digestion=False)[source]#

Defining a new chain from selected atoms.

This function creates a new chain by assigning a unique chain_id and/or chain_name to a selection of atoms in a molecular system. The selected atoms are grouped into a new chain, which is appended to the existing list of chains in the system. This does not alter or remove any of the existing chains.

molecular_systemmolecular system

Molecular system in any of the supported forms to be modified.

selectionindex, tuple, list, numpy.ndarray or str, default ‘all’

Selection of atoms to assign to the new chain. The selection can be given as a list, tuple, or NumPy array of atom indices (0-based integers), or as a string following one of the supported selection syntaxes.

chain_idstr, optional

Identifier of the new chain (e.g., ‘A’, ‘B’, ‘C’). If not provided, a unique string chain_id will be automatically generated. Numeric inputs are converted to strings internally.

chain_namestr, optional

Descriptive name for the new chain. If not provided, the name will be left empty or automatically assigned.

syntaxstr, default ‘MolSysMT’

Supported syntax used in the selection argument (in case it is a string).

molecular system

A modified molecular system with the selected atoms grouped into a newly defined chain.

NotSupportedFormError

Raised if the molecular system has a non-supported form.

ArgumentError

Raised if any of the input values is invalid or incompatible.

  • This function is useful when merging multiple molecules, redefining topology, or recovering proper chain segmentation after structural edits.

  • Chains are identified by their chain_id (unique identifier) and chain_name (optional descriptive label).

molsysmt.basic.set()

Setting attribute values in a molecular system.

molsysmt.basic.info()

Displaying a summary of elements and chain structure.

molsysmt.build.merge()

Merging multiple molecular systems, often requiring reassignment of chains.

>>> import molsysmt as msm
>>> molsys = msm.convert('1TCD')
>>> msm.build.define_new_chain(molsys, selection='molecule_type=="water"', chain_name='C')
    >>> msm.get(molsys, element='chain', chain_name=True)
    ['A', 'B', 'C']

User guide

Follow this link for a tutorial on how to work with this function: User Guide > Tools > Build > Define new chain

Added in version 1.0.0.

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