PREFIX ontorxn: <http://www.semanticweb.com/OntoRxn#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

<http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#GaussianCalculation> a rdfs:Class ;
  rdfs:subClassOf <http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#BaseCalculation> .

<http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#hasUniqueSpecies> a rdf:Property ;
  rdfs:domain <http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#BaseCalculation> ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#hasEnvironment> a rdf:Property ;
  rdfs:domain <http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#BaseCalculation> ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#hasInitialization> a rdf:Property ;
  rdfs:domain <http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#BaseCalculation> ;
  rdfs:range <https://w3id.org/linkml/Any> .

ontorxn:CompCalculation a rdfs:Class ;
  rdfs:label "computational calculation" ;
  rdfs:comment "Collection of computational data from an electronic structure calculation."@en .

ontorxn:hasInChI a rdf:Property ;
  rdfs:label "has InChI" ;
  rdfs:domain ontorxn:CompCalculation ;
  rdfs:range <https://w3id.org/linkml/Any> .

ontorxn:hasMolecularFormula a rdf:Property ;
  rdfs:label "has molecular formula" ;
  rdfs:range <https://w3id.org/linkml/Any> .

ontorxn:hasSymmetryNumber a rdf:Property ;
  rdfs:domain ontorxn:CompCalculation ;
  rdfs:range xsd:integer .

ontorxn:hasXYZGeometry a rdf:Property ;
  rdfs:label "has XYZ geometry" ;
  rdfs:comment "Property defining the string corresponding to the XYZ coordinates of a calculation."@en ;
  rdfs:domain ontorxn:CompCalculation ;
  rdfs:range xsd:string .

ontorxn:hasThermoConditions a rdf:Property ;
  rdfs:label "has thermodynamic conditions" ;
  rdfs:comment "Property to link calculations with the corresponding thermodynamic conditions" ;
  rdfs:domain ontorxn:CompCalculation ;
  rdfs:range ontorxn:ThermoCondition .

ontorxn:hasSolvent a rdf:Property ;
  rdfs:label "has solvent" ;
  rdfs:comment "Property defining the solvent modelled for a calculation."@en ;
  rdfs:domain ontorxn:CompCalculation ;
  rdfs:range xsd:string .

<http://purl.org/gc/FloatValue> a rdfs:Class .

ontorxn:ChemSpecies a rdfs:Class ;
  rdfs:label "chemical species" ;
  rdfs:comment "Individual molecular entity participating at some point of a reaction network."@en .

ontorxn:hasStgSetIdentifier a rdf:Property ;
  rdfs:comment "Associates an identifier depending on the NetworkStage to which the ChemSpecies is related, to map chemically related mechanisms mapped to different chemical entities" ;
  rdfs:domain ontorxn:ChemSpecies ;
  rdfs:range xsd:string .

ontorxn:hasCalculation a rdf:Property ;
  rdfs:label "has calculation" ;
  rdfs:comment "Links a given chemical entity in the reaction network to the calculation(s) defined for that entity."@en ;
  rdfs:domain ontorxn:ChemSpecies ;
  rdfs:range ontorxn:CompCalculation .

ontorxn:StoichReference a rdfs:Class ;
  rdfs:label "stoichiometry reference" ;
  rdfs:comment "Stoichiometry of a given stage related to a given species" .

ontorxn:toSpecies a rdf:Property ;
  rdfs:label "to species" ;
  rdfs:comment "Links a StoichReference with the corresponding ChemSpecies, to complete the mapping of the NetworkStage" ;
  rdfs:domain ontorxn:StoichReference ;
  rdfs:range ontorxn:ChemSpecies .

<http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#BaseCalculation> a rdfs:Class ;
  rdfs:label "base calculation" ;
  rdfs:comment "General class for computational chemistry calculations" .

ontorxn:ThermoCondition a rdfs:Class ;
  rdfs:label "thermodynamic condition" ;
  rdfs:comment "A class representing the thermodynamic conditions for a calculation" ;
  rdfs:subClassOf <http://purl.org/gc/AuxiliaryConcept> .

ontorxn:hasTemperature a rdf:Property ;
  rdfs:label "has temperature" ;
  rdfs:comment "Property defining the temperature for determining thermodynamic properties" ;
  rdfs:domain ontorxn:ThermoCondition ;
  rdfs:range <http://purl.org/gc/FloatValue> .

ontorxn:hasPressure a rdf:Property ;
  rdfs:label "has pressure" ;
  rdfs:comment "Property defining the pressure for determining thermodynamic properties" ;
  rdfs:domain ontorxn:ThermoCondition ;
  rdfs:range <http://purl.org/gc/FloatValue> .

<http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#GenericCalculation> a rdfs:Class ;
  rdfs:label "generic calculation" ;
  rdfs:comment "Calculations performed by unspecified software." ;
  rdfs:subClassOf <http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#BaseCalculation> .

<http://purl.obolibrary.org/obo/MOP_0000543> a rdfs:Class .

<http://purl.org/gc/VectorValue> a rdfs:Class ;
  rdfs:subClassOf <http://purl.org/gc/Value> .

<http://purl.org/gc/AuxiliaryConcept> a rdfs:Class .

<http://purl.org/gc/CalculationResult> a rdfs:Class .

ontorxn:hasFreqList a rdf:Property ;
  rdfs:label "has freqlist" ;
  rdfs:comment "Property defining the list of frequencies (in cm-1) for a calculation." ;
  rdfs:domain <http://purl.org/gc/CalculationResult> ;
  rdfs:range <http://purl.org/gc/VectorValue> .

ontorxn:hasSolventPolarity a rdf:Property ;
  rdfs:label "has solvent polarity" ;
  rdfs:domain <http://purl.org/gc/CalculationResult> ;
  rdfs:range <http://purl.org/gc/FloatValue> .

ontorxn:hasMomentInertia a rdf:Property ;
  rdfs:domain <http://purl.org/gc/CalculationResult> ;
  rdfs:range <http://purl.org/gc/VectorValue> .

ontorxn:hasMolMass a rdf:Property ;
  rdfs:domain <http://purl.org/gc/CalculationResult> ;
  rdfs:range <http://purl.org/gc/FloatValue> .

ontorxn:hasVibrationalDispl a rdf:Property ;
  rdfs:domain <http://purl.org/gc/CalculationResult> ;
  rdfs:range <http://purl.org/gc/VectorValue> .

ontorxn:hasRotTemps a rdf:Property ;
  rdfs:domain <http://purl.org/gc/CalculationResult> ;
  rdfs:range <http://purl.org/gc/VectorValue> .

ontorxn:hasEnergy a rdf:Property ;
  rdfs:label "has energy" ;
  rdfs:comment "Parent property for energies in a calculation." ;
  rdfs:domain <http://purl.org/gc/CalculationResult> ;
  rdfs:range <http://purl.org/gc/FloatValue> .

<http://purl.org/gc/Value> a rdfs:Class .

ontorxn:ReactionStep a rdfs:Class ;
  rdfs:label "reaction step" ;
  rdfs:comment "Non-directed step in a reaction network containing two intermediates and (possibly) the corresponding transition state between them."@en .

ontorxn:isConnectedWith a rdf:Property ;
  rdfs:label "is connected with" ;
  rdfs:comment "Links two reaction steps having some common intermediate."@en ;
  rdfs:domain ontorxn:ReactionStep ;
  rdfs:range ontorxn:ReactionStep .

ontorxn:hasTS a rdf:Property ;
  rdfs:label "has TS" ;
  rdfs:comment "Links a reaction step in the reaction network with the stage corresponding to a transition state."@en ;
  rdfs:domain ontorxn:ReactionStep ;
  rdfs:range ontorxn:NetworkStage .

ontorxn:hasReactionType a rdf:Property ;
  rdfs:label "has reaction type" ;
  rdfs:comment "Property that links a named molecular process to a ReactionStep entity" ;
  rdfs:domain ontorxn:ReactionStep ;
  rdfs:range <http://purl.obolibrary.org/obo/MOP_0000543> .

ontorxn:hasNode a rdf:Property ;
  rdfs:label "has node" ;
  rdfs:comment "Links a reaction step in the reaction network with the stage corresponding to an intermediate."@en ;
  rdfs:domain ontorxn:ReactionStep ;
  rdfs:range ontorxn:NetworkStage .

<https://w3id.org/linkml/Any> a rdfs:Class ;
  rdfs:comment "An unconstrained type or object" .

ontorxn:NetworkStage a rdfs:Class ;
  rdfs:label "network stage" ;
  rdfs:comment "Collection of structures that must be combined to define a point in a reaction network, so as the corresponding energy of the molecule set matches the chosen reference state."@en .

ontorxn:hasStoichiometry a rdf:Property ;
  rdfs:label "has stoichiometry" ;
  rdfs:comment "Links a NetworkStage with the corresponding StoichReference that will be linked to a ChemSpecies and to the integer value of the coefficient" ;
  rdfs:domain ontorxn:NetworkStage ;
  rdfs:range ontorxn:StoichReference .

ontorxn:hasSpecies a rdf:Property ;
  rdfs:label "has species" ;
  rdfs:comment "Links a given stage in the reaction network to the chemical entities collected by that stage."@en ;
  rdfs:domain ontorxn:NetworkStage ;
  rdfs:range ontorxn:ChemSpecies .

ontorxn:hasAnnotation a rdf:Property ;
  rdfs:label "has annotation" ;
  rdfs:comment "Property defining string annotations"@en ;
  rdfs:range xsd:string .

ontorxn:hasElecEnergy a rdf:Property ;
  rdfs:label "has electronic energy" ;
  rdfs:comment "Property defining the electronic energy of a calculation" ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf ontorxn:hasEnergy .

ontorxn:hasGibbsFreeEnergy a rdf:Property ;
  rdfs:label "has Gibbs free energy" ;
  rdfs:comment "Property defining the Gibbs free energy of a calculation." ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf ontorxn:hasEnergy .

ontorxn:isCalculationOf a rdf:Property ;
  rdfs:label "is calculation of" ;
  rdfs:comment "Links a calculation to the chemical entity to which it refers."@en ;
  rdfs:range <https://w3id.org/linkml/Any> .

ontorxn:isNodeOf a rdf:Property ;
  rdfs:label "is node of" ;
  rdfs:comment "Links the stage corresponding to an intermediate in the reaction network to the reaction step(s) it participates in."@en ;
  rdfs:range <https://w3id.org/linkml/Any> .

ontorxn:isSpeciesOf a rdf:Property ;
  rdfs:label "is species of" ;
  rdfs:comment "Links a given chemical entity in the reaction network to the stage(s) in which it is contained."@en ;
  rdfs:range <https://w3id.org/linkml/Any> .

ontorxn:isTSOf a rdf:Property ;
  rdfs:label "is TS of" ;
  rdfs:comment "Links the stage corresponding to a transition state in the reaction network to the reaction step it participates in."@en ;
  rdfs:range <https://w3id.org/linkml/Any> .