Package schrodinger :: Package application :: Package matsci :: Module cgforcefield

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Module cgforcefield

Constants, functions and classes for assigning coarse-grained force fields to structures

Classes

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CGFFIOStructure
Manage building a coarse grain structure.

FFIOParam
The base class for FFIO parameters such as bonds, angles, VDW parameters, exclusions, etc.

FFIOBond
The class that handles the FFIO bond block

FFIOAngle
The class that handles the FFIO angle block

FFIODihedral
The class that handles the FFIO dihedral block

FFIOExclusion
The class that handles the FFIO exclusion list block

FFIOVdwType
The class that handles the FFIO VdW type list block

FFIOSite
The class that handles the FFIO site block

FFIOVdwTypesCombined
The class that handles the FFIO combined VdW block

MissingParameterError
Raised if the force field is missing required data for a structure

VDWData
VDWData(vtype, charge)

ShadowData
ShadowData(name1, name2, depth)

ForceField
Reads in force field data and applies it to a structure

Functions

[hide private]

OrderedDict

get_all_force_field_paths()
Get the name and path for all defined CG force fields in FF_PARAMETERS_PATH

add_force_field_to_job_builder(builder, ffname)
Set up the Launch API Job Builder to use the given force field

str

force_field_name_to_file_name(ffname)
Convert the user-facing force field name to a file name - without the full path

str

get_force_field_file_path(force_field_name)
Return the force field file path given the force field name.

str

get_force_field_name(force_field_file_path)
Return the force field name given the force field file path.

dict or None

load_force_field_parameters(path)
Load force field parameters.

str

get_type_name(types)
Get combined name for a parameter based on the given particle names

list

split_type_name(name)
Split a type name up into particle types based on the TYPE_SEPARATOR delimiter

str

get_vdw_type_name(name)
Get the VDW type name based on the given name

schrodinger.application.desmond.cms.Cms

create_cg_system(struct, ff_path, filename=None)
Apply the force field located at ff_path to struct and return the resulting CMS object

Variables

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SITE_MASS_KEY = 'mass/(g/mol)'

SITE_CHARGE_KEY = 'charge'

BOND_EQ_LENGTH_KEY = 'eq_length/Ang.'

BOND_FORCE_CONSTANT_KEY = 'force_constant/(kcal/mol)/Ang.^2'

ANGLE_EQ_ANGLE_KEY = 'eq_angle/deg.'

ANGLE_FORCE_CONSTANT_KEY = 'force_constant/(kcal/mol)/rad.^2'

DIHEDRAL_V1_KEY = 'v1/(kcal/mol)'

DIHEDRAL_V2_KEY = 'v2/(kcal/mol)'

DIHEDRAL_V3_KEY = 'v3/(kcal/mol)'

DIHEDRAL_V4_KEY = 'v4/(kcal/mol)'

VDW_M_PARAMETER_KEY = 'm'

VDW_N_PARAMETER_KEY = 'n'

VDW_EPSILON_KEY = 'epsilon/(kcal/mol)'

VDW_SIGMA_KEY = 'sigma/Ang.'

VDW_A_PARAMETER_KEY = 'a/(kcal/mol)/Ang.^2'

SITES_INTERNAL_KEY = 'sites'

SITES_ATOM_KEY = 'atom'

BONDS_INTERNAL_KEY = 'bonds'

BONDS_HARMONIC_KEY = 'harm'

ANGLES_INTERNAL_KEY = 'angles'

ANGLES_HARMONIC_KEY = 'harm'

DIHEDRALS_INTERNAL_KEY = 'dihedrals'

DIHEDRALS_OPLS_PROPER_KEY = 'opls_proper'

NONBONDS_INTERNAL_KEY = 'nonbonds'

NONBONDS_LENNARD_JONES_KEY = 'Lennard-Jones'

NONBONDS_DISSIPATIVE_PARTICLE_KEY = 'Repulsive harmonic'

EXCLUSIONS_INTERNAL_KEY = 'exclude'

DIELECTRIC_INTERNAL_KEY = 'dielectric_constant'

CUTOFF_INTERNAL_KEY = 'cutoff'

DESCRIPTION_INTERNAL_KEY = 'description'

SHADOWBOND_TYPE_INTERNAL_KEY = 'shadow_bonds'

GAMMA_DISSIPATIVE_PARTICLE_INTERNAL_KEY = 'dpd_reduced_gamma'

FFIO_NAME = 'general'

FFIO_COMBINING_RULE = 'geometric'

FFIO_SITE_TYPE = 'atom'

FFIO_SITE_CHARGE = 0
hash(x)

FFIO_BOND_FUNCT = 'harm'

FFIO_ANGLE_FUNCT = 'harm'

FFIO_DIHEDRAL_FUNCT = 'opls_proper'

FFIO_VDW_FUNCT = 'polynomial_cij'

FFIO_VDW_NTERMS = 16

FFIO_VDW_TYPE_NAME_BASE = 'general_vdw_%s'

FFIO_VDW_COMBINED_FUNCT = 'polynomial_cij'

FFIO_VDW_COMBINED_T1 = 1

FFIO_PROPERTY_KEY = 'r_ffio_c%s'

FFIO_CT_TYPE_KEY = 's_ffio_ct_type'

FFIO_FULL_SYSTEM = 'full_system'

FFIO_SOLUTE = 'solute'

TYPE_SEPARATOR = ','
hash(x)

EWALD_EPSILON = 1e-09

EWALD_REF_CUTOFF_1 = 12.0

EWALD_FIT = {12.0: [(1, 0, -60.2944774726), (3, -2, 756.484695...

FF_PARAMETERS_DIR = 'coarse_grain_force_field_parameters'

FF_PARAMETERS_PATH = '/home/buildbot/.schrodinger/matsci_templ...

FORCE_FIELD_FILE_EXT = '_cgff.json'

DESCRIPTION_KEY = 's_matsci_ff_description'

DPD_REDUCED_GAMMA = 4.5

DPD_REDUCED_GAMMA_PROP_KEY = 'r_matsci_dpd_gamma'

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

get_all_force_field_paths()

Get the name and path for all defined CG force fields in FF_PARAMETERS_PATH

Returns: OrderedDict: Keys are force field names, values are the absolute path to that force field file. Items are sorted in the sort order of the keys.

add_force_field_to_job_builder(builder, ffname)

Set up the Launch API Job Builder to use the given force field

Parameters:

builder (schrodinger.job.launchapi.JobSpecificationArgsBuilder) - The job builder to use for setting the FF as an input file
ffname (str) - The name of the force field to use (should be the user-facing name, not the force field file name)

force_field_name_to_file_name(ffname)

Convert the user-facing force field name to a file name - without the full path

Parameters:

ffname (str) - The name of the force field

Returns: str

The name of the force field file

get_force_field_file_path(force_field_name)

Return the force field file path given the force field name.

Parameters:

force_field_name (str) - the force field name

Returns: str

the force field file path

get_force_field_name(force_field_file_path)

Return the force field name given the force field file path.

Parameters:

force_field_file_path (str) - the force field file path

Returns: str

the force field name

load_force_field_parameters(path)

Load force field parameters.

Parameters:

path (str) - The path to the force field file to read

Returns: dict or None

the force field parameters dictionary or None if there isn't one

get_type_name(types)

Get combined name for a parameter based on the given particle names

Parameters:

types (tuple) - A tuple of particle names that should be joined together for form the type name

Returns: str

The particle names in types joined by the TYPE_SEPARATOR character

split_type_name(name)

Split a type name up into particle types based on the TYPE_SEPARATOR delimiter

Parameters:

name (str) - A string with the particle type names joined by the TYPE_SEPARATOR delimiter

Returns: list

The list of particle type names that formed name

get_vdw_type_name(name)

Get the VDW type name based on the given name

Parameters:

name (str) - The name of the site for this vdw type

Returns: str

The VDW type name for this particle name

create_cg_system(struct, ff_path, filename=None)

Apply the force field located at ff_path to struct and return the resulting CMS object

Parameters:

struct (schrodinger.structure.Structure) - The structure to apply the forcefield to
ff_path (str) - The path to the force field file
filename (str) - If given, the CMS structure will be written to this file

Returns: schrodinger.application.desmond.cms.Cms

The Cms object that results from applying the force field to the structure

Variables Details

[hide private]

EWALD_FIT

Value:

{12.0: [(1, 0, -60.2944774726),
        (3, -2, 756.484695192),
        (5, -4, -1668.18483484),
        (7, -6, 3347.27774486),
        (9, -8, -4185.97700152),
        (11, -10, 2823.83598188),
        (13, -12, -780.261684567),
        (14, 1, 10.9568283029),
...

FF_PARAMETERS_PATH

Value:

'/home/buildbot/.schrodinger/matsci_templates/coarse_grain_force_field
_parameters'