diff options
Diffstat (limited to 'lib/nanoparticle.rb')
| -rw-r--r-- | lib/nanoparticle.rb | 46 |
1 files changed, 34 insertions, 12 deletions
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb index 23e155c..02d9a89 100644 --- a/lib/nanoparticle.rb +++ b/lib/nanoparticle.rb @@ -3,8 +3,30 @@ module OpenTox class Nanoparticle < Substance include OpenTox - field :core, type: Hash, default: {} - field :coating, type: Array, default: [] + field :core_id, type: String, default: nil + field :coating_ids, type: Array, default: [] + + def core + Compound.find core_id + end + + def coating + coating_ids.collect{|i| Compound.find i } + end + + def fingerprint type=DEFAULT_FINGERPRINT + core_fp = core.fingerprint type + coating_fp = coating.collect{|c| c.fingerprint type}.flatten.uniq.compact + (core_fp.empty? or coating_fp.empty?) ? [] : (core_fp+coating_fp).uniq.compact + end + + def calculate_properties descriptors=PhysChem::OPENBABEL + if core.smiles and !coating.collect{|c| c.smiles}.compact.empty? + core_prop = core.calculate_properties descriptors + coating_prop = coating.collect{|c| c.calculate_properties descriptors if c.smiles} + descriptors.collect_with_index{|d,i| [core_prop[i],coating_prop.collect{|c| c[i] if c}]} + end + end def add_feature feature, value, dataset unless feature.name == "ATOMIC COMPOSITION" or feature.name == "FUNCTIONAL GROUP" # redundand @@ -37,28 +59,28 @@ module OpenTox add_feature feature, v["loValue"], dataset elsif v.keys.size == 2 and v["errorValue"] add_feature feature, v["loValue"], dataset - warn "Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'." + #warn "Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'." elsif v.keys.size == 2 and v["loQualifier"] == "mean" add_feature feature, v["loValue"], dataset - warn "'#{feature.name}' is a mean value. Original data is not available." + #warn "'#{feature.name}' is a mean value. Original data is not available." elsif v.keys.size == 2 and v["loQualifier"] #== ">=" - warn "Only min value available for '#{feature.name}', entry ignored" + #warn "Only min value available for '#{feature.name}', entry ignored" elsif v.keys.size == 2 and v["upQualifier"] #== ">=" - warn "Only max value available for '#{feature.name}', entry ignored" + #warn "Only max value available for '#{feature.name}', entry ignored" elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil? add_feature feature, v["loValue"], dataset - warn "loQualifier and upQualifier are empty." + #warn "loQualifier and upQualifier are empty." elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"] == "" and v["upQualifier"] == "" add_feature feature, v["loValue"], dataset - warn "loQualifier and upQualifier are empty." + #warn "loQualifier and upQualifier are empty." elsif v.keys.size == 4 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil? add_feature feature, v["loValue"], dataset - warn "loQualifier and upQualifier are empty." + #warn "loQualifier and upQualifier are empty." elsif v.size == 4 and v["loQualifier"] and v["upQualifier"] and v["loValue"] and v["upValue"] - add_feature feature, [v["loValue"],v["upValue"]].mean, dataset - warn "Using mean value of range #{v["loValue"]} - #{v["upValue"]} for '#{feature.name}'. Original data is not available." + #add_feature feature, [v["loValue"],v["upValue"]].mean, dataset + #warn "Using mean value of range #{v["loValue"]} - #{v["upValue"]} for '#{feature.name}'. Original data is not available." elsif v.size == 4 and v["loQualifier"] == "mean" and v["errorValue"] - warn "'#{feature.name}' is a mean value. Original data is not available. Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'." + #warn "'#{feature.name}' is a mean value. Original data is not available. Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'." add_feature feature, v["loValue"], dataset elsif v == {} # do nothing else |