Calculation input file section (required)
This required section is denoted by the keyword calculate
and includes a list of objects of the type apbs.input_file.calculate.Calculate
.
Calculation types
Calculate API
These classes provide input syntax for APBS calculations.
- class apbs.input_file.calculate.Calculate(dict_=None, yaml=None, json=None)[source]
Bases:
InputFile
Specify parameters for APBS calculations.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
alias
: A string that allows the output from the calculation to be referenced later.type
: A string that indicates the type of calculation to be performed. Seecalculation_type()
for list.parameters
: Object with parameters for calculation. See calculation types above for details.
- property alias: str
Alias string to refer to this calculation elsewhere.
- Raises:
TypeError – if not string.
- property calculation_type: str
Calculation type.
One of the following:
nonpolar
: A nonpolar solvation energy calculation using grid-based integrals. Seenonpolar.Nonpolar
.
- Raises:
TypeError – if not a string
ValueError – if not a recognized calculation type
- from_dict(input_)[source]
Load dictionary input into object.
- Parameters:
input (dict) – data to load into object
- Raises:
KeyError – if input contents are not found
- from_json(input_)
Parse JSON-format input string into this object.
- Parameters:
input (str) – JSON-format input string
- from_yaml(input_)
Parse YAML-format input string into this object.
- Parameters:
input (str) – YAML-format input string
- property parameters: InputFile
Parameter object, dependent on calculation type, sub-classed from
apbs.input_file.InputFile
.The format of this object is based on the calculation type; see
calculation_type()
.- Raises:
TypeError – if object is not derived from
apbs.input_file.InputFile
.
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
Generic objects for polar solvation calculations.
This only contains common properties that are complex objects (e.g., not strings, lists, etc.)
- class apbs.input_file.calculate.generic.Ion(dict_=None, json=None, yaml=None)[source]
Bases:
InputFile
Description of a single mobile ion species.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
charge
: charge of ion; seecharge()
radius
: radius of ion; seeradius()
concentration
: concentration of ion species; seeconcentration()
- property charge: float
The charge (in electrons) of the ion.
- Raises:
TypeError – if set to something that is not a number
- property concentration: float
Concentration (in M) of ion species.
- Raises:
TypeError – if not a positive number or zero
- from_dict(dict_)[source]
Populate object from dictionary.
- Raises:
KeyError – if dictionary missing information
- from_json(input_)
Parse JSON-format input string into this object.
- Parameters:
input (str) – JSON-format input string
- from_yaml(input_)
Parse YAML-format input string into this object.
- Parameters:
input (str) – YAML-format input string
- property radius: float
The radius (in Å) of the ion.
- Raises:
TypeError – if set to something that is not a positive number
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- class apbs.input_file.calculate.generic.MobileIons(dict_=None, json=None, yaml=None)[source]
Bases:
InputFile
Provide information about mobile ion species in system.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
species
: list of ion species; seespecies()
- from_dict(dict_)[source]
Parse dictionary-format input into this object.
- Parameters:
input (dict) – input dictionary
- Raises:
KeyError – when input is missing
- from_json(input_)
Parse JSON-format input string into this object.
- Parameters:
input (str) – JSON-format input string
- from_yaml(input_)
Parse YAML-format input string into this object.
- Parameters:
input (str) – YAML-format input string
- property species: list
List of mobile ion species.
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- class apbs.input_file.calculate.generic.UseMap(dict_=None, yaml=None, json=None)[source]
Bases:
InputFile
Use a previously read in map.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
property
: what property being loaded from the map; seeproperty()
alias
: alias assigned when reading in map; seealias()
- from_json(input_)
Parse JSON-format input string into this object.
- Parameters:
input (str) – JSON-format input string
- from_yaml(input_)
Parse YAML-format input string into this object.
- Parameters:
input (str) – YAML-format input string
- property property: str
Specify the property being read from the map.
One of the following values:
dielectric
: Dielectric function map (as read in Data loading input file section (required)); this causes theFiniteDifference.solute_dielectric()
,FiniteDifference.solvent_dielectric()
,FiniteDifference.solvent_radius()
,FiniteDifference.surface_method()
, andFiniteDifference.surface spline window()
properties to be ignored, along with the radii of the solute atoms. Note thatFiniteDifference.solute_dielectric()
andFiniteDifference.solvent_dielectric()
are still used for some boundary condition calculations (seeFiniteDifference.boundary_condition()
)ion accessibility
: Mobile ion-accessibility function map (as read in Data loading input file section (required)); this causes theFiniteDifference.surface_method()
, andFiniteDifference.surface spline window()
properties to be ignored, along with the radii of the solute atoms. TheFiniteDifference.ions()
property is not ignored and will still be used.charge density
: Charge distribution map (as read in Data loading input file section (required)); this causes thecharge discretization()
parameter and the charges of the biomolecular atoms to be ignored when assembling the fixed charge distribution for the Poisson-Boltzmann equation.potential
: Potential map (as read in Data loading input file section (required)); this is used to set the boundary condition and causes theboundary_condition()
property to be ignored.
- Raises:
TypeError – if not string
ValueError – if not valid value
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- class apbs.input_file.calculate.generic.WriteMap(dict_=None, yaml=None, json=None)[source]
Bases:
InputFile
Write the specified property to a map.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
property
: what property is being written to the map; seeproperty()
format
: output format; seeformat()
path
: a suggested path and file name for the map; seepath()
- property format: str
Format for writing output.
Allowed formats (see documentation for details) include:
dx
: OpenDX-format data. This is the preferred format for APBS input/output.dx.gz
: GZipped OpenDX-format data.flat
: Write out data as a plain text file.uhbd
: UHBD-format data.
- Raises:
TypeError – if not set to a strinng
ValueError – if invalid format specified
- from_dict(input_)[source]
Parse dictionary-format input into this object.
- Parameters:
input (dict) – input dictionary
- Raises:
KeyError – when input is missing
- from_json(input_)
Parse JSON-format input string into this object.
- Parameters:
input (str) – JSON-format input string
- from_yaml(input_)
Parse YAML-format input string into this object.
- Parameters:
input (str) – YAML-format input string
- property path: str
Suggested path for writing results.
This path is only a suggestion; if parallel calculations are performed, then the filename will be modified to include the processor number for the output.
- Raises:
TypeError – if not set to string.
- property property: str
Property to write to map.
See the documentation for a discussion of units for these properties.
One of:
charge density
: Write out the biomolecular charge distribution in units of \(e_c\) (electron charge) per Å3.potential
: Write out the electrostatic potential over the entire problem domain in units of \(k_b \, T \, e_c^{-1}\).solvent accessibility
: Write out the solvent accessibility defined by the molecular surface definition (seeFiniteDifference.surface_definition()
). Values are unitless and range from 0 (inaccessible) to 1 (accessible).ion accessibility
: Write out the inflated van der Waals-based ion accessibility (seeFiniteDifference.surface_definition()
). Values are unitless and range from 0 (inaccessible) to 1 (accessible).laplacian
: Write out the Laplacian of the potential \(\nabla^2 \phi\) in units of kB T ec-1 Å-2.energy density
: Write out the “energy density” \(-\nabla \cdot \epsilon \nabla \phi\) in units of kB T ec-1 Å-2.ion number density
: Write out the total mobile ion number density for all ion species in units of M. The output is calculated according to the formula (for nonlinear PB calculations): \(\rho(x) = \sum_i^N {\bar{\rho}_i e^{-q_i\phi(x) - V_i (x)}}\), where \(N\) is the number of ion species, \(\bar{\rho}_i\) is the bulk density of ion species \(i\), \(q_i\) is the charge of ion species \(i\), \(\phi(x)\) is the electrostatic potential, and \(V_i\) is the solute-ion interaction potential for species \(i\).ion charge density
: Write out the total mobile ion charge density for all ion species in units of ec M. The output is calculated according to the formula (for nonlinear PB calculations): \(\rho(x) = \sum_i^N {\bar{\rho}_i q_i e^{-q_i\phi(x) - V_i(x)}}\), where \(N\) is the number of ion species, \(\bar{\rho}_i\) is the bulk density of ion species \(i\), \(q_i\) is the charge of ion species \(i\), \(\phi(x)\) is the electrostatic potential, and \(V_i\) is the solute-ion interaction potential for species \(i\).dielectric x
ordielectric y
ordielectric z
: Write out the dielectric map shifted by 1/2 grid spacing in the {x
,y
,z
}-direction. The values are unitless.
- Raises:
TypeError – if not a string
ValueError – if invalid value
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.