fhir 1.2.0

//! SubstanceNucleicAcid
//!
//! URL: http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid
//!
//! Version: 4.0.1
//!
//! Nucleic acids are defined by three distinct elements: the base, sugar and
//! linkage. Individual substance/moiety IDs will be created for each of these
//! elements. The nucleotide sequence will be always entered in the 5’-3’
//! direction
//!
//! FHIR R4: <https://hl7.org/fhir/R4/>

// The `types` import is unused by a handful of types that have only primitive fields.
#![allow(unused_imports)]

use crate::r4::types;
use ::serde::{Deserialize, Serialize};
use fhir_derive_macros::{Builder, Validate};

/// Nucleic acids are defined by three distinct elements: the base, sugar and
/// linkage. Individual substance/moiety IDs will be created for each of these
/// elements. The nucleotide sequence will be always entered in the 5’-3’
/// direction.
///
/// # Examples
///
/// ```
/// use fhir::r4::resources::substance_nucleic_acid::SubstanceNucleicAcid;
///
/// let value = SubstanceNucleicAcid::default();
/// let json = ::serde_json::to_value(&value).unwrap();
/// let back: SubstanceNucleicAcid = ::serde_json::from_value(json).unwrap();
/// assert_eq!(value, back);
/// ```
#[serde_with::skip_serializing_none]
#[derive(Debug, Default, Clone, Serialize, Deserialize, PartialEq, Eq, Validate, Builder)]
#[serde(rename_all = "camelCase")]
#[fhir_version("r4")]
pub struct SubstanceNucleicAcid {
    /// Logical id of this artifact
    pub id: Option<types::String>,

    /// Metadata about the resource
    pub meta: Option<types::Meta>,

    /// A set of rules under which this content was created
    pub implicit_rules: Option<types::Uri>,
    /// Primitive extension sibling for [`implicit_rules`](Self::implicit_rules) (FHIR `_implicitRules`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_implicitRules")]
    pub implicit_rules_ext: Option<types::Element>,

    /// Language of the resource content
    pub language: Option<types::Code>,
    /// Primitive extension sibling for [`language`](Self::language) (FHIR `_language`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_language")]
    pub language_ext: Option<types::Element>,

    /// Text summary of the resource, for human interpretation
    pub text: Option<types::Narrative>,

    /// Contained, inline Resources
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub contained: Vec<::serde_json::Value>,

    /// Additional content defined by implementations
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub extension: Vec<types::Extension>,

    /// Extensions that cannot be ignored
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub modifier_extension: Vec<types::Extension>,

    /// The type of the sequence shall be specified based on a controlled
    /// vocabulary
    pub sequence_type: Option<types::CodeableConcept>,

    /// The number of linear sequences of nucleotides linked through
    /// phosphodiester bonds shall be described. Subunits would be strands of
    /// nucleic acids that are tightly associated typically through
    /// Watson-Crick base pairing. NOTE: If not specified in the reference
    /// source, the assumption is that there is 1 subunit
    pub number_of_subunits: Option<types::Integer>,
    /// Primitive extension sibling for [`number_of_subunits`](Self::number_of_subunits) (FHIR `_numberOfSubunits`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_numberOfSubunits")]
    pub number_of_subunits_ext: Option<types::Element>,

    /// The area of hybridisation shall be described if applicable for double
    /// stranded RNA or DNA. The number associated with the subunit followed by
    /// the number associated to the residue shall be specified in increasing
    /// order. The underscore “” shall be used as separator as follows:
    /// “Subunitnumber Residue”
    pub area_of_hybridisation: Option<types::String>,
    /// Primitive extension sibling for [`area_of_hybridisation`](Self::area_of_hybridisation) (FHIR `_areaOfHybridisation`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_areaOfHybridisation")]
    pub area_of_hybridisation_ext: Option<types::Element>,

    /// (TBC)
    pub oligo_nucleotide_type: Option<types::CodeableConcept>,

    /// Subunits are listed in order of decreasing length; sequences of the
    /// same length will be ordered by molecular weight; subunits that have
    /// identical sequences will be repeated multiple times
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub subunit: Vec<SubstanceNucleicAcidSubunit>,
}

/// Subunits are listed in order of decreasing length; sequences of the same
/// length will be ordered by molecular weight; subunits that have identical
/// sequences will be repeated multiple times.
///
/// # Examples
///
/// ```
/// use fhir::r4::resources::substance_nucleic_acid::SubstanceNucleicAcidSubunit;
///
/// let value = SubstanceNucleicAcidSubunit::default();
/// let json = ::serde_json::to_value(&value).unwrap();
/// let back: SubstanceNucleicAcidSubunit = ::serde_json::from_value(json).unwrap();
/// assert_eq!(value, back);
/// ```
#[serde_with::skip_serializing_none]
#[derive(Debug, Default, Clone, Serialize, Deserialize, PartialEq, Eq, Validate)]
#[serde(rename_all = "camelCase")]
#[fhir_version("r4")]
pub struct SubstanceNucleicAcidSubunit {
    /// Unique id for inter-element referencing
    pub id: Option<types::String>,

    /// Additional content defined by implementations
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub extension: Vec<types::Extension>,

    /// Extensions that cannot be ignored even if unrecognized
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub modifier_extension: Vec<types::Extension>,

    /// Index of linear sequences of nucleic acids in order of decreasing
    /// length. Sequences of the same length will be ordered by molecular
    /// weight. Subunits that have identical sequences will be repeated and
    /// have sequential subscripts
    pub subunit: Option<types::Integer>,
    /// Primitive extension sibling for [`subunit`](Self::subunit) (FHIR `_subunit`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_subunit")]
    pub subunit_ext: Option<types::Element>,

    /// Actual nucleotide sequence notation from 5' to 3' end using standard
    /// single letter codes. In addition to the base sequence, sugar and type
    /// of phosphate or non-phosphate linkage should also be captured
    pub sequence: Option<types::String>,
    /// Primitive extension sibling for [`sequence`](Self::sequence) (FHIR `_sequence`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_sequence")]
    pub sequence_ext: Option<types::Element>,

    /// The length of the sequence shall be captured
    pub length: Option<types::Integer>,
    /// Primitive extension sibling for [`length`](Self::length) (FHIR `_length`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_length")]
    pub length_ext: Option<types::Element>,

    /// (TBC)
    pub sequence_attachment: Option<types::Attachment>,

    /// The nucleotide present at the 5’ terminal shall be specified based on a
    /// controlled vocabulary. Since the sequence is represented from the 5' to
    /// the 3' end, the 5’ prime nucleotide is the letter at the first position
    /// in the sequence. A separate representation would be redundant
    pub five_prime: Option<types::CodeableConcept>,

    /// The nucleotide present at the 3’ terminal shall be specified based on a
    /// controlled vocabulary. Since the sequence is represented from the 5' to
    /// the 3' end, the 5’ prime nucleotide is the letter at the last position
    /// in the sequence. A separate representation would be redundant
    pub three_prime: Option<types::CodeableConcept>,

    /// The linkages between sugar residues will also be captured
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub linkage: Vec<SubstanceNucleicAcidSubunitLinkage>,

    /// 5.3.6.8.1 Sugar ID (Mandatory)
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub sugar: Vec<SubstanceNucleicAcidSubunitSugar>,
}

/// The linkages between sugar residues will also be captured.
///
/// # Examples
///
/// ```
/// use fhir::r4::resources::substance_nucleic_acid::SubstanceNucleicAcidSubunitLinkage;
///
/// let value = SubstanceNucleicAcidSubunitLinkage::default();
/// let json = ::serde_json::to_value(&value).unwrap();
/// let back: SubstanceNucleicAcidSubunitLinkage = ::serde_json::from_value(json).unwrap();
/// assert_eq!(value, back);
/// ```
#[serde_with::skip_serializing_none]
#[derive(Debug, Default, Clone, Serialize, Deserialize, PartialEq, Eq, Validate)]
#[serde(rename_all = "camelCase")]
#[fhir_version("r4")]
pub struct SubstanceNucleicAcidSubunitLinkage {
    /// Unique id for inter-element referencing
    pub id: Option<types::String>,

    /// Additional content defined by implementations
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub extension: Vec<types::Extension>,

    /// Extensions that cannot be ignored even if unrecognized
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub modifier_extension: Vec<types::Extension>,

    /// The entity that links the sugar residues together should also be
    /// captured for nearly all naturally occurring nucleic acid the linkage is
    /// a phosphate group. For many synthetic oligonucleotides phosphorothioate
    /// linkages are often seen. Linkage connectivity is assumed to be 3’-5’.
    /// If the linkage is either 3’-3’ or 5’-5’ this should be specified
    pub connectivity: Option<types::String>,
    /// Primitive extension sibling for [`connectivity`](Self::connectivity) (FHIR `_connectivity`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_connectivity")]
    pub connectivity_ext: Option<types::Element>,

    /// Each linkage will be registered as a fragment and have an ID
    pub identifier: Option<types::Identifier>,

    /// Each linkage will be registered as a fragment and have at least one
    /// name. A single name shall be assigned to each linkage
    pub name: Option<types::String>,
    /// Primitive extension sibling for [`name`](Self::name) (FHIR `_name`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_name")]
    pub name_ext: Option<types::Element>,

    /// Residues shall be captured as described in 5.3.6.8.3
    pub residue_site: Option<types::String>,
    /// Primitive extension sibling for [`residue_site`](Self::residue_site) (FHIR `_residueSite`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_residueSite")]
    pub residue_site_ext: Option<types::Element>,
}

/// 5.3.6.8.1 Sugar ID (Mandatory).
///
/// # Examples
///
/// ```
/// use fhir::r4::resources::substance_nucleic_acid::SubstanceNucleicAcidSubunitSugar;
///
/// let value = SubstanceNucleicAcidSubunitSugar::default();
/// let json = ::serde_json::to_value(&value).unwrap();
/// let back: SubstanceNucleicAcidSubunitSugar = ::serde_json::from_value(json).unwrap();
/// assert_eq!(value, back);
/// ```
#[serde_with::skip_serializing_none]
#[derive(Debug, Default, Clone, Serialize, Deserialize, PartialEq, Eq, Validate)]
#[serde(rename_all = "camelCase")]
#[fhir_version("r4")]
pub struct SubstanceNucleicAcidSubunitSugar {
    /// Unique id for inter-element referencing
    pub id: Option<types::String>,

    /// Additional content defined by implementations
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub extension: Vec<types::Extension>,

    /// Extensions that cannot be ignored even if unrecognized
    #[serde(default, skip_serializing_if = "Vec::is_empty")]
    pub modifier_extension: Vec<types::Extension>,

    /// The Substance ID of the sugar or sugar-like component that make up the
    /// nucleotide
    pub identifier: Option<types::Identifier>,

    /// The name of the sugar or sugar-like component that make up the
    /// nucleotide
    pub name: Option<types::String>,
    /// Primitive extension sibling for [`name`](Self::name) (FHIR `_name`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_name")]
    pub name_ext: Option<types::Element>,

    /// The residues that contain a given sugar will be captured. The order of
    /// given residues will be captured in the 5‘-3‘direction consistent with
    /// the base sequences listed above
    pub residue_site: Option<types::String>,
    /// Primitive extension sibling for [`residue_site`](Self::residue_site) (FHIR `_residueSite`):
    /// carries `id` and/or `extension` for the primitive value.
    #[serde(rename = "_residueSite")]
    pub residue_site_ext: Option<types::Element>,
}

#[cfg(test)]
mod tests {
    use super::*;
    type T = SubstanceNucleicAcid;

    #[test]
    fn test_default() {
        let _ = T::default();
    }

    #[test]
    fn test_serde_round_trip() {
        let value = T::default();
        let json = ::serde_json::to_value(&value).expect("to_value");
        let back: T = ::serde_json::from_value(json).expect("from_value");
        assert_eq!(value, back);
    }
}