Public API#
- class sire.system.System(system=None)[source]#
This class holds a complete system of molecules. This is normally created by reading in molecules from an input file.
This provides a “MoleculeView”-style interface to the molecules, acting very similarly to a sire.mol.SelectorMol object.
You can convert this to a sire.mol.SelectorMol object by calling the System.molecules() function.
- angles(*args, **kwargs)[source]#
Return all angles in this System (or those that match the passed index, if supplied)
- apply(*args, **kwargs)[source]#
Apply (perform / map) the passed function (with associated arguments) on all of the molecules in this System
- apply_reduce(*args, **kwargs)[source]#
Apply (perform / map) the passed function (with associated arguments) on all of the molecules in this System, reducing the result using the passed reduction function
- atoms(*args, **kwargs)[source]#
Return all atoms in this System (or those that match the passed index, if supplied)
- bonds(*args, **kwargs)[source]#
Return all bonds in this System (or those that match the passed index, if supplied)
- chains(*args, **kwargs)[source]#
Return all chains in this System (or those that match the passed index, if supplied)
- charge(*args, **kwargs)[source]#
Return the total charge of this System (or of the matching index/search subset of this System)
- coordinates(*args, **kwargs)[source]#
Return the center of geometry of this System (or of the matching index/search subset of this System)
- dihedrals(*args, **kwargs)[source]#
Return all dihedrals in this System (or those that match the passed index, if supplied)
- dynamics(*args, **kwargs)[source]#
Return a Dynamics object that can be used to perform dynamics of the molecule(s) in this view
- energies(*args, **kwargs)[source]#
Calculate and return the individual energies of the contents of this System (or of the matching index/search subset of this System)
- energy(*args, **kwargs)[source]#
Calculate and return the energy of this System (or of the matching index/search subset of this System)
- evaluate(*args, **kwargs)[source]#
Return an evaluator for this Systme (or of the matching index/search subset of this System)
- impropers(*args, **kwargs)[source]#
Return all impropers in this System (or those that match the passed index, if supplied)
- static is_system(obj)[source]#
Return whether the passed object is a System class (either a new or legacy System)
- mass(*args, **kwargs)[source]#
Return the total mass of this System (or of the matching index/search subset of this System)
- minimisation(map=None)[source]#
Return a Minimisation object that can be used to minimise the energy of the molecule(s) in this view.
- molecules(*args, **kwargs)[source]#
Return this System converted to a sire.mol.SelectorMol. You can pass in arguments to search or index so that you limit the number of molecules returned.
- residues(*args, **kwargs)[source]#
Return all residues in this System (or those that match the passed index, if supplied)
- save_frame(i=None, map=None)[source]#
Save the current coordinates to the ith frame of this System. If i is not specfied then this adds the frame onto the end of the trajectory
- segments(*args, **kwargs)[source]#
Return all segments in this System (or those that match the passed index, if supplied)
- smiles(*args, **kwargs)[source]#
Return the molecule views in this container as smiles strings. Include hydrogens in ‘include_hydrogens’ is True. This returns a list of smiles strings, in the same order as the views in the container
- update(value)[source]#
Update the molecules in this system so that they have the same versions and data as the new molecules contained in ‘value’