Struct AnalysisPolicy 

pub struct AnalysisPolicy {

    pub assembly: AssemblyChoice,
    pub model: ModelChoice,
    pub altloc: AltlocPolicy,
    pub identifiers: Namespace,
    pub missing_atoms: MissingPolicy,
    pub hydrogens: HydrogenPolicy,
    pub atom_equivalence: EquivalencePolicy,
    pub symmetry: SymmetryPolicy,
    pub alignment: AlignmentPolicy,
    pub precision: Precision,
    pub periodic: PeriodicPolicy,
    pub vdw_radii: RadiiSet,
    pub contact_def: ContactDefinition,
    pub float_tolerance: Tolerance,
}

Every semantic decision an analysis depends on.

Examples

use molframe_core::contract::{AnalysisPolicy, Namespace, ProfileId};

let policy = AnalysisPolicy::default();
assert_eq!(policy.profile(), Some(ProfileId::DEFAULT));
assert_eq!(policy.identifiers, Namespace::Auth);

let explicit = AnalysisPolicy::default().with_identifiers(Namespace::Explicit);
assert_eq!(explicit.profile(), None, "no longer the named profile");
assert_ne!(explicit.fingerprint(), policy.fingerprint());

Fields

assembly: AssemblyChoice

Which arrangement of the contents to analyse.

model: ModelChoice

Which model.

altloc: AltlocPolicy

How alternate conformations resolve.

identifiers: Namespace

Which identifier namespace an unqualified selector means.

missing_atoms: MissingPolicy

What to do about atoms that were not modelled.

hydrogens: HydrogenPolicy

How hydrogens enter.

atom_equivalence: EquivalencePolicy

How atoms are matched between structures.

symmetry: SymmetryPolicy

Whether symmetry copies participate.

alignment: AlignmentPolicy

How structures are put into correspondence.

precision: Precision

The width accumulation runs at.

periodic: PeriodicPolicy

How periodic boundaries are handled.

vdw_radii: RadiiSet

Which radii set.

contact_def: ContactDefinition

What counts as a contact.

float_tolerance: Tolerance

How close two floating-point values must be to count as equal.

Implementations

impl AnalysisPolicy

pub fn check_consistency(&self) -> Result<(), Diagnostic>

Checks that the decisions describe one runnable system.

The rules, each a statement about what the copies are:

• the asymmetric unit has no copies, so it goes with SymmetryPolicy::None;
• a biological assembly’s copies are the assembly’s, so it goes with None (the assembly alone) or BiologicalAssembly;
• crystal contacts are crystallographic copies within a radius, so they go with None (the radius alone names them) or Crystallographic, and the radius must be positive and finite.

Errors

Returns Code::E6004 naming the two contradictory fields, or Code::E6016 for a crystal radius that is not a positive finite number.

impl AnalysisPolicy

pub fn profile(&self) -> Option<ProfileId>

The named profile this policy is, if it has not been altered.

A result recording a profile name is reproducible by someone who has only the name. A result recording “the defaults” is not.

pub fn fingerprint(&self) -> Fingerprint

A stable fingerprint of every field.

Two policies that differ anywhere differ here, and the same policy always fingerprints the same way, within and across runs. It is a fingerprint for telling policies apart, not a cryptographic commitment.

pub fn with_identifiers(self, namespace: Namespace) -> Self

Returns this policy with a different identifier namespace.

pub fn with_altloc(self, altloc: AltlocPolicy) -> Self

Returns this policy with a different alternate-conformation rule.

pub fn with_model(self, model: ModelChoice) -> Self

Returns this policy with a different model choice.

pub fn with_assembly(self, assembly: AssemblyChoice) -> Self

Returns this policy with a different assembly choice.

pub fn with_missing_atoms(self, missing: MissingPolicy) -> Self

Returns this policy with a different rule for unmodelled atoms.

Trait Implementations

impl Clone for AnalysisPolicy

fn clone(&self) -> Self

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for AnalysisPolicy

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for AnalysisPolicy

fn default() -> Self

Returns the “default value” for a type.

impl Display for AnalysisPolicy

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Writes the policy as one field per line, which is what the command line prints and what a written record contains.

impl PartialEq for AnalysisPolicy

fn eq(&self, other: &Self) -> bool

Equality operator ==.

fn ne(&self, other: &Rhs) -> bool

Inequality operator !=.

impl StructuralPartialEq for AnalysisPolicy