Package schrodinger :: Package application :: Package matsci :: Module coarsegrain

[frames] | no frames]

Module coarsegrain

Classes

[hide private]

Internals
Manage the internal coordinates of a structure.

Functions

[hide private]

bool

is_coarse_grain(struct)
Check if struct is a coarse grain structure

set_as_coarse_grain(struct)
Mark struct as a coarse grain structure

set_nonbond_potential_type(struct, nbtype)
Mark the structure with the non-bond pontential type

str or None

get_nonbond_potential_type(struct)
Return the type of non-bond potential for this structure

bool

is_lennard_jones(struct)
Check if this is a Lennard-Jones coarse grain structure

bool

is_repulsive_harmonic(struct)
Check if this is a repulsive harmonic coarse grain structure

float

vdw_radius(atom)
Get the proper VDW radius for an atom.

set_atom_coarse_grain_properties(struct, atom, name, rgb=(100, 100, 100), atom_type=400, formal_charge=0.0, partial_charge=0.0, radius=10.0, mass=12.0)
Set the properties required for a coarse grain particle atom

Variables

[hide private]

_doc__ = '\nUtilities for working with coarse grain structures...

CG_REP_TYPE = 'CG'

REP_TYPE_KEY = 's_matsci_rep_type'

NB_TYPE_KEY = 's_matsci_cg_non-bond_type'

FF_CUTOFF_PROPERTY = 'r_matsci_cg_ff_cutoff_(Ang)'

LENNARD_JONES = 'Lennard-Jones'

DISSIPATIVE_PARTICLE = 'Repulsive harmonic'

NONBOND_POTENTIALS = ['Lennard-Jones', 'Repulsive harmonic']

CG_UNIQUE_BOND_PARTICLE_1_LABEL_KEY = 's_matsci_cg_particle_1_...

CG_UNIQUE_BOND_PARTICLE_2_LABEL_KEY = 's_matsci_cg_particle_2_...

CG_UNIQUE_PARTICLE_LABEL_KEY = 's_matsci_cg_particle_label'

CG_ELEMENT_SYMBOL = 'H'

CG_ATOMIC_NUMBER = 1

DEFAULT_MMOD_ATOM_TYPE = 400

DEFAULT_RADIUS = 10.0

DEFAULT_MASS = 12.0

DEFAULT_RGB = (100, 100, 100)

CG_PARTICLE_COLOR_NAME_KEY = 's_matsci_cg_particle_color_name'

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

is_coarse_grain(struct)

Check if struct is a coarse grain structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to check

Returns: bool

True if it is a coarse grain structure, False if not

set_as_coarse_grain(struct)

Mark struct as a coarse grain structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to mark

set_nonbond_potential_type(struct, nbtype)

Mark the structure with the non-bond pontential type

Parameters:

struct (schrodinger.structure.Structure) - The structure to mark
nbtype (str) - Should be a module constant in the NONBOND_POTENTIALS list

Raises:

ValueError - if nbtype is not in NONBOND_POTENTIALS
TypeError - if struct is not a coarse grain system

get_nonbond_potential_type(struct)

Return the type of non-bond potential for this structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to check

Returns: str or None

The value of the NB_TYPE_KEY property on the structure, or None if the structure is not a coarse grain structure or does not have this property set

is_lennard_jones(struct)

Check if this is a Lennard-Jones coarse grain structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to check

Returns: bool

True if this is a coarse grain Lennard-Jones structure, False if not

is_repulsive_harmonic(struct)

Check if this is a repulsive harmonic coarse grain structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to check

Returns: bool

True if this is a coarse grain repulsive harmoic structure, False if not

vdw_radius(atom)

Get the proper VDW radius for an atom. This works for coarse grain and non-coarse grain atoms.

Parameters:

atom (schrodinger.structure._StructureAtom) - The atom to get the radius for

Returns: float

The proper VDW radius to use

set_atom_coarse_grain_properties(struct, atom, name, rgb=`(`100`,` 100`,` 100`)`, atom_type=400, formal_charge=0.0, partial_charge=0.0, radius=10.0, mass=12.0)

Set the properties required for a coarse grain particle atom

Parameters:

structure (schrodinger.structure.Structure) - The structure containing the atom
atom (schrodinger.structure._StructureAtom) - The atom to set properties on
name (str) - The name of the coarse grain particle.
rgb (tuple) - The 0-255 tuple of red, green and blue that defines the atom color
atom_type (int) - The mmod atom type
formal_charge (int) - The formal charge
partial_charge (float) - The partial charge
radius (float) - The particle radius, in Angstrom
mass (float) - The particle mass

Variables Details

[hide private]

_doc__

Value:

'''
Utilities for working with coarse grain structures

Copyright Schrodinger, LLC. All rights reserved.
'''

CG_UNIQUE_BOND_PARTICLE_1_LABEL_KEY

Value:

's_matsci_cg_particle_1_label'

CG_UNIQUE_BOND_PARTICLE_2_LABEL_KEY

Value:

's_matsci_cg_particle_2_label'

Module coarsegrain

is_coarse_grain(struct)

set_as_coarse_grain(struct)

set_nonbond_potential_type(struct, nbtype)

get_nonbond_potential_type(struct)

is_lennard_jones(struct)

is_repulsive_harmonic(struct)

vdw_radius(atom)

set_atom_coarse_grain_properties(struct, atom, name, rgb=(100, 100, 100), atom_type=400, formal_charge=0.0, partial_charge=0.0, radius=10.0, mass=12.0)

_doc__

CG_UNIQUE_BOND_PARTICLE_1_LABEL_KEY

CG_UNIQUE_BOND_PARTICLE_2_LABEL_KEY

set_atom_coarse_grain_properties(struct, atom, name, rgb=`(`100`,` 100`,` 100`)`, atom_type=400, formal_charge=0.0, partial_charge=0.0, radius=10.0, mass=12.0)