chemicalml 0.2.1 → 0.3.0

data/lib/chemicalml/cml/base/atom_array.rb

@@ -3,10 +3,21 @@
 module Chemicalml
   module Cml
     module Base
+      # Container for a list of atoms. Two equivalent serialisations:
+      #
+      #   <atomArray><atom id="a1" elementType="C"/></atomArray>
+      #
+      #   <atomArray atomID="a1 a2" elementType="C O" x3="0.0 1.0"/>
+      #
+      # The parallel-array form uses the *same* XML attribute names as
+      # the singular `<atom>` (e.g. `elementType`, `x3`), NOT names
+      # like `elementTypeArray`. The XSD names the attribute *groups*
+      # `elementTypeArray` etc., but the wire attribute is `elementType`.
       module AtomArray
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::AtomArray
+
             attribute :atoms, :atom, collection: true
 
             attribute :title, :string
@@ -14,8 +25,13 @@ module Chemicalml
             attribute :convention, :string
             attribute :dict_ref, :string
             attribute :ref, :string
-            attribute :element_type_array, :string
+
+            # Parallel-array attributes. Wire names match the singular
+            # <atom> attributes; the Ruby names use _array suffix for
+            # clarity at the call site.
+            attribute :atom_id_array, :string
             attribute :count_array, :string
+            attribute :element_type_array, :string
             attribute :formal_charge_array, :string
             attribute :hydrogen_count_array, :string
             attribute :occupancy_array, :string
@@ -27,30 +43,51 @@ module Chemicalml
             attribute :x_fract_array, :string
             attribute :y_fract_array, :string
             attribute :z_fract_array, :string
-            attribute :atom_i_d_array, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "atomArray"
-              map_element "atom", to: :atoms
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "ref", to: :ref
-              map_attribute "elementTypeArray", to: :element_type_array
-              map_attribute "countArray", to: :count_array
-              map_attribute "formalChargeArray", to: :formal_charge_array
-              map_attribute "hydrogenCountArray", to: :hydrogen_count_array
-              map_attribute "occupancyArray", to: :occupancy_array
-              map_attribute "x2Array", to: :x2_array
-              map_attribute "y2Array", to: :y2_array
-              map_attribute "x3Array", to: :x3_array
-              map_attribute "y3Array", to: :y3_array
-              map_attribute "z3Array", to: :z3_array
-              map_attribute "xFractArray", to: :x_fract_array
-              map_attribute "yFractArray", to: :y_fract_array
-              map_attribute "zFractArray", to: :z_fract_array
-              map_attribute "atomIDArray", to: :atom_i_d_array
+              root 'atomArray'
+              map_element 'atom', to: :atoms
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'ref', to: :ref
+              map_attribute 'atomID', to: :atom_id_array
+              map_attribute 'count', to: :count_array
+              map_attribute 'elementType', to: :element_type_array
+              map_attribute 'formalCharge', to: :formal_charge_array
+              map_attribute 'hydrogenCount', to: :hydrogen_count_array
+              map_attribute 'occupancy', to: :occupancy_array
+              map_attribute 'x2', to: :x2_array
+              map_attribute 'y2', to: :y2_array
+              map_attribute 'x3', to: :x3_array
+              map_attribute 'y3', to: :y3_array
+              map_attribute 'z3', to: :z3_array
+              map_attribute 'xFract', to: :x_fract_array
+              map_attribute 'yFract', to: :y_fract_array
+              map_attribute 'zFract', to: :z_fract_array
+            end
+            key_value do
+              map 'atom', to: :atoms
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'ref', to: :ref
+              map 'atomID', to: :atom_id_array
+              map 'count', to: :count_array
+              map 'elementType', to: :element_type_array
+              map 'formalCharge', to: :formal_charge_array
+              map 'hydrogenCount', to: :hydrogen_count_array
+              map 'occupancy', to: :occupancy_array
+              map 'x2', to: :x2_array
+              map 'y2', to: :y2_array
+              map 'x3', to: :x3_array
+              map 'y3', to: :y3_array
+              map 'z3', to: :z3_array
+              map 'xFract', to: :x_fract_array
+              map 'yFract', to: :y_fract_array
+              map 'zFract', to: :z_fract_array
             end
           end
         end

data/lib/chemicalml/cml/base/atom_parity.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::AtomParity
+
             attribute :atom_refs4, :string
             attribute :content, :string
 
@@ -16,13 +17,20 @@ module Chemicalml
             attribute :dict_ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "atomParity"
-              map_attribute "atomRefs4", to: :atom_refs4
+              root 'atomParity'
+              map_attribute 'atomRefs4', to: :atom_refs4
               map_content to: :content
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+            end
+            key_value do
+              map 'atomRefs4', to: :atom_refs4
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
             end
           end
         end

data/lib/chemicalml/cml/base/atom_set.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::AtomSet
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,12 +16,19 @@ module Chemicalml
             attribute :size, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "atomSet"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "size", to: :size
+              root 'atomSet'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'size', to: :size
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'size', to: :size
             end
           end
         end

data/lib/chemicalml/cml/base/atom_type.rb

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::AtomType
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -18,15 +20,29 @@ module Chemicalml
             attribute :atom_ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "atomType"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "elementType", to: :elementType
-              map_attribute "ref", to: :ref
-              map_attribute "name", to: :name
-              map_attribute "atomRef", to: :atom_ref
+              root 'atomType'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'elementType', to: :elementType
+              map_attribute 'ref', to: :ref
+              map_attribute 'name', to: :name
+              map_attribute 'atomRef', to: :atom_ref
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'elementType', to: :elementType
+              map 'ref', to: :ref
+              map 'name', to: :name
+              map 'atomRef', to: :atom_ref
             end
           end
         end

data/lib/chemicalml/cml/base/atom_type_list.rb

@@ -7,23 +7,37 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::AtomTypeList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :atom_types, :atomType, collection: true
+            attribute :atom_types, :atomType, collection: true
 
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "atomType", to: :atom_types
-              root "atomTypeList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "ref", to: :ref
+              map_element 'atomType', to: :atom_types
+              root 'atomTypeList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'ref', to: :ref
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'atomType', to: :atom_types
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
             end
           end
         end

data/lib/chemicalml/cml/base/atomic_basis_function.rb

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::AtomicBasisFunction
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -22,19 +24,37 @@ module Chemicalml
             attribute :lm, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "atomicBasisFunction"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRef", to: :atomRef
-              map_attribute "n", to: :n
-              map_attribute "l", to: :l
-              map_attribute "m", to: :m
-              map_attribute "ms", to: :ms
-              map_attribute "type", to: :type
-              map_attribute "symbol", to: :symbol
-              map_attribute "lm", to: :lm
+              root 'atomicBasisFunction'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'atomRef', to: :atomRef
+              map_attribute 'n', to: :n
+              map_attribute 'l', to: :l
+              map_attribute 'm', to: :m
+              map_attribute 'ms', to: :ms
+              map_attribute 'type', to: :type
+              map_attribute 'symbol', to: :symbol
+              map_attribute 'lm', to: :lm
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'atomRef', to: :atomRef
+              map 'n', to: :n
+              map 'l', to: :l
+              map 'm', to: :m
+              map 'ms', to: :ms
+              map 'type', to: :type
+              map 'symbol', to: :symbol
+              map 'lm', to: :lm
             end
           end
         end

data/lib/chemicalml/cml/base/band.rb

@@ -7,24 +7,37 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Band
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :kpointRef, :string
+            attribute :kpoint, :string
             attribute :weight, :string
 
             attribute :label, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "band"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "kpointRef", to: :kpointRef
-              map_attribute "weight", to: :weight
-              map_attribute "label", to: :label
+              root 'band'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'kpointRef', to: :kpointRef
+              map_attribute 'kpoint', to: :kpoint
+              map_attribute 'weight', to: :weight
+              map_attribute 'label', to: :label
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'kpointRef', to: :kpointRef
+              map 'kpoint', to: :kpoint
+              map 'weight', to: :weight
+              map 'label', to: :label
             end
           end
         end

data/lib/chemicalml/cml/base/band_list.rb

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BandList
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :bands, :band, collection: true
+            attribute :bands, :band, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "band", to: :bands
-              root "bandList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'band', to: :bands
+              root 'bandList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+            end
+            key_value do
+              map 'band', to: :bands
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end

data/lib/chemicalml/cml/base/basis_set.rb

@@ -7,25 +7,40 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BasisSet
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :atomic_basis_functions, :atomicBasisFunction, collection: true
+            attribute :atomic_basis_functions, :atomicBasisFunction, collection: true
 
             attribute :ref, :string
             attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "atomicBasisFunction", to: :atomic_basis_functions
-              root "basisSet"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "ref", to: :ref
-              map_attribute "role", to: :role
+              map_element 'atomicBasisFunction', to: :atomic_basis_functions
+              root 'basisSet'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'ref', to: :ref
+              map_attribute 'role', to: :role
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'atomicBasisFunction', to: :atomic_basis_functions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'role', to: :role
             end
           end
         end

data/lib/chemicalml/cml/base/bond.rb

@@ -7,28 +7,54 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Bond
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :atom_refs2, :string
+            attribute :atom_refs, :string
             attribute :order, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :bond_stereo, :bondStereo
+            attribute :bond_type, :bondType
+            attribute :electrons, :electron, collection: true
 
             attribute :convention, :string
             attribute :ref, :string
             attribute :bond_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bond"
-              map_attribute "id", to: :id
-              map_attribute "atomRefs2", to: :atom_refs2
-              map_attribute "order", to: :order
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_element "bondStereo", to: :bond_stereo
-              map_attribute "convention", to: :convention
-              map_attribute "ref", to: :ref
-              map_attribute "bondRefs", to: :bond_refs
+              root 'bond'
+              map_attribute 'id', to: :id
+              map_attribute 'atomRefs2', to: :atom_refs2
+              map_attribute 'atomRefs', to: :atom_refs
+              map_attribute 'order', to: :order
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_element 'bondStereo', to: :bond_stereo
+              map_element 'bondType', to: :bond_type
+              map_element 'electron', to: :electrons
+              map_attribute 'convention', to: :convention
+              map_attribute 'ref', to: :ref
+              map_attribute 'bondRefs', to: :bond_refs
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'bondStereo', to: :bond_stereo
+              map 'bondType', to: :bond_type
+              map 'electron', to: :electrons
+              map 'id', to: :id
+              map 'atomRefs2', to: :atom_refs2
+              map 'atomRefs', to: :atom_refs
+              map 'order', to: :order
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'bondRefs', to: :bond_refs
             end
           end
         end

data/lib/chemicalml/cml/base/bond_array.rb

@@ -3,32 +3,55 @@
 module Chemicalml
   module Cml
     module Base
+      # Container for a list of bonds. Two equivalent serialisations:
+      #
+      #   <bondArray><bond atomRefs2="a1 a2" order="1"/></bondArray>
+      #
+      #   <bondArray atomRef1="a1 a2" atomRef2="a2 a3" order="1 2"/>
+      #
+      # The parallel-array form uses the wire attribute names
+      # `atomRef1`, `atomRef2`, `bondID`, `order` — the XSD attribute
+      # *group* is named `atomRef1Array` etc., but the wire attribute
+      # is `atomRef1`.
       module BondArray
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BondArray
+
             attribute :bonds, :bond, collection: true
 
             attribute :title, :string
             attribute :id, :string
             attribute :convention, :string
             attribute :dict_ref, :string
-            attribute :bond_i_d_array, :string
+
+            attribute :bond_id_array, :string
             attribute :atom_ref1_array, :string
             attribute :atom_ref2_array, :string
             attribute :order_array, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bondArray"
-              map_element "bond", to: :bonds
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "bondIDArray", to: :bond_i_d_array
-              map_attribute "atomRef1Array", to: :atom_ref1_array
-              map_attribute "atomRef2Array", to: :atom_ref2_array
-              map_attribute "orderArray", to: :order_array
+              root 'bondArray'
+              map_element 'bond', to: :bonds
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'bondID', to: :bond_id_array
+              map_attribute 'atomRef1', to: :atom_ref1_array
+              map_attribute 'atomRef2', to: :atom_ref2_array
+              map_attribute 'order', to: :order_array
+            end
+            key_value do
+              map 'bond', to: :bonds
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'bondID', to: :bond_id_array
+              map 'atomRef1', to: :atom_ref1_array
+              map 'atomRef2', to: :atom_ref2_array
+              map 'order', to: :order_array
             end
           end
         end

data/lib/chemicalml/cml/base/bond_set.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BondSet
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,12 +16,19 @@ module Chemicalml
             attribute :size, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bondSet"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "size", to: :size
+              root 'bondSet'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'size', to: :size
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'size', to: :size
             end
           end
         end