Public API

View Module Index

class sire.system.ForceFieldInfo(val, map=None)

class sire.system.System(system=None)

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.

angle(*args, **kwargs)

Return the angle that matches the passed index/search

angles(*args, **kwargs)

Return all angles in this System (or those that match the passed index, if supplied)

apply(*args, **kwargs)

Apply (perform / map) the passed function (with associated arguments) on all of the molecules in this System

apply_reduce(*args, **kwargs)

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

atom(*args, **kwargs)

Return the atom that matches the passed index/search

atoms(*args, **kwargs)

Return all atoms in this System (or those that match the passed index, if supplied)

bond(*args, **kwargs)

Return the bond that matches the passed index/search

bonds(*args, **kwargs)

Return all bonds in this System (or those that match the passed index, if supplied)

chain(*args, **kwargs)

Return the chain that matches the passed index/search

chains(*args, **kwargs)

Return all chains in this System (or those that match the passed index, if supplied)

charge(*args, **kwargs)

Return the total charge of this System (or of the matching index/search subset of this System)

clone()

Return a copy (clone) of this System

coordinates(*args, **kwargs)

Return the center of geometry of this System (or of the matching index/search subset of this System)

count()

Return the number of items in this System

cursor()

Return a sire.mol.Cursor that can be used to edit the molecules in this System

delete_frame(i)

Delete the ith frame from the trajectory

dihedral(*args, **kwargs)

Return the dihedral that matches the passed index/search

dihedrals(*args, **kwargs)

Return all dihedrals in this System (or those that match the passed index, if supplied)

dynamics(*args, **kwargs)

Return a Dynamics object that can be used to perform dynamics of the molecule(s) in this view

energies(*args, **kwargs)

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)

Calculate and return the energy of this System (or of the matching index/search subset of this System)

evaluate(*args, **kwargs)

Return an evaluator for this Systme (or of the matching index/search subset of this System)

find(views)

Return the index(es) of the molecule(s) that are in views

improper(*args, **kwargs)

Return the improper that matches the passed index/search

impropers(*args, **kwargs)

Return all impropers in this System (or those that match the passed index, if supplied)

static is_system(obj)

Return whether the passed object is a System class (either a new or legacy System)

load_frame(i)

Load the ith frame into this System

mass(*args, **kwargs)

Return the total mass of this System (or of the matching index/search subset of this System)

minimisation(map=None)

Return a Minimisation object that can be used to minimise the energy of the molecule(s) in this view.

molecule(*args, **kwargs)

Return the molecule that matches the passed index/search

molecules(*args, **kwargs)

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.

names()

Return the names of all of the molecules in this System

num_atoms()

Return the number of atoms in this System

num_chains()

Return the number of chains in this System

num_frames()

Return the number of trajectory frames for this System

num_molecules()

Return the number of molecules in this System

num_residues()

Return the number of residues in this System

num_segments()

Return the number of segments in this System

numbers()

Return the numbers of all of the molecules in this System

properties()

Return all of the System-level properties of this System

property(*args, **kwargs)

Return the System property that matches the passed key/arguments

property_keys()

Return the keys (IDs) of all of the System-level properties of this System

residue(*args, **kwargs)

Return the residue that matches the passed index/search

residues(*args, **kwargs)

Return all residues in this System (or those that match the passed index, if supplied)

save_frame(i=None, map=None)

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

segment(*args, **kwargs)

Return the segment that matches the passed index/search

segments(*args, **kwargs)

Return all segments in this System (or those that match the passed index, if supplied)

set_property(*args, **kwargs)

Set the System property according to the passed arguments

size()

Return the number of items in this System

smiles(*args, **kwargs)

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

to_molecule_group()

Return this System converted to a sire.mol.MoleculeGroup

trajectory()

Return an iterator over the trajectory of frames for this System

update(value)

Update the molecules in this system so that they have the same versions and data as the new molecules contained in ‘value’

view(*args, **kwargs)

View this System (or the matching index/search subset) via a nglview viewer. Only works in an interactive notebook session, e.g. in a Jupyter notebook

view2d(*args, **kwargs)

Create a 2D representation of the molecules in this system. If ‘filename’ is set then this will be written to that file. Otherwise this will be returned for visualisation in a jupyter notebook.