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module OpenTox
# Small molecules with defined chemical structures
class Compound < Substance
require_relative "unique_descriptors.rb"
DEFAULT_FINGERPRINT = "MP2D"
field :inchi, type: String
field :smiles, type: String
field :inchikey, type: String
field :names, type: Array
field :cid, type: String
#field :chemblid, type: String
field :png_id, type: BSON::ObjectId
field :svg_id, type: BSON::ObjectId
field :sdf_id, type: BSON::ObjectId
field :fingerprints, type: Hash, default: {}
field :default_fingerprint_size, type: Integer
index({smiles: 1}, {unique: true})
# Overwrites standard Mongoid method to create fingerprints before database insertion
def self.find_or_create_by params
compound = self.find_or_initialize_by params
compound.default_fingerprint_size = compound.fingerprint(DEFAULT_FINGERPRINT).size
compound.save
compound
end
# Create chemical fingerprint
# @param [String] fingerprint type
# @return [Array<String>]
def fingerprint type=DEFAULT_FINGERPRINT
unless fingerprints[type]
return [] unless self.smiles
if type == "MP2D" # http://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html#molprint2d-format
fp = obconversion(smiles,"smi","mpd").strip.split("\t")
name = fp.shift # remove Title
fingerprints[type] = fp.uniq # no fingerprint counts
elsif type== "MNA" # http://openbabel.org/docs/dev/FileFormats/Multilevel_Neighborhoods_of_Atoms_(MNA).html
level = 2 # TODO: level as parameter, evaluate level 1, see paper
fp = obconversion(smiles,"smi","mna","xL\"#{level}\"").split("\n")
fp.shift # remove Title
fingerprints[type] = fp
else # standard fingerprints
fp = OpenBabel::OBFingerprint.find_fingerprint(type)
obmol = OpenBabel::OBMol.new
obconversion = OpenBabel::OBConversion.new
obconversion.set_in_format "smi"
obconversion.read_string obmol, self.smiles
result = OpenBabel::VectorUnsignedInt.new
fp.get_fingerprint(obmol,result)
# TODO: %ignore *::DescribeBits @ line 163 openbabel/scripts/openbabel-ruby.i
#p OpenBabel::OBFingerprint.describe_bits(result)
# convert result to a list of the bits that are set
# from openbabel/scripts/python/pybel.py line 830
# see also http://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html#fingerprints
result = result.to_a
bitsperint = OpenBabel::OBFingerprint.getbitsperint()
bits_set = []
start = 1
result.each do |x|
i = start
while x > 0 do
bits_set << i if (x % 2) == 1
x >>= 1
i += 1
end
start += bitsperint
end
fingerprints[type] = bits_set
end
save
end
fingerprints[type]
end
# Calculate physchem properties
# @param [Array<Hash>] list of descriptors
# @return [Array<Float>]
def calculate_properties descriptors=PhysChem::OPENBABEL
calculated_ids = properties.keys
# BSON::ObjectId instances are not allowed as keys in a BSON document.
new_ids = descriptors.collect{|d| d.id.to_s} - calculated_ids
descs = {}
algos = {}
new_ids.each do |id|
descriptor = PhysChem.find id
descs[[descriptor.library, descriptor.descriptor]] = descriptor
algos[descriptor.name] = descriptor
end
# avoid recalculating Cdk features with multiple values
descs.keys.uniq.each do |k|
descs[k].send(k[0].downcase,k[1],self).each do |n,v|
properties[algos[n].id.to_s] = v # BSON::ObjectId instances are not allowed as keys in a BSON document.
end
end
save
descriptors.collect{|d| properties[d.id.to_s]}
end
# Match a SMARTS substructure
# @param [String] smarts
# @param [TrueClass,FalseClass] count matches or return true/false
# @return [TrueClass,FalseClass,Fixnum]
def smarts_match smarts, count=false
obconversion = OpenBabel::OBConversion.new
obmol = OpenBabel::OBMol.new
obconversion.set_in_format('smi')
obconversion.read_string(obmol,self.smiles)
smarts_pattern = OpenBabel::OBSmartsPattern.new
smarts.collect do |sma|
smarts_pattern.init(sma.smarts)
if smarts_pattern.match(obmol)
count ? value = smarts_pattern.get_map_list.to_a.size : value = 1
else
value = 0
end
value
end
end
# Create a compound from smiles string
# @example
# compound = OpenTox::Compound.from_smiles("c1ccccc1")
# @param [String] smiles
# @return [OpenTox::Compound]
def self.from_smiles smiles
return nil if smiles.match(/\s/) # spaces seem to confuse obconversion and may lead to invalid smiles
smiles = obconversion(smiles,"smi","can") # test if SMILES is correct and return canonical smiles (for compound comparisons)
smiles.empty? ? nil : Compound.find_or_create_by(:smiles => smiles)
end
# Create a compound from InChI string
# @param [String] InChI
# @return [OpenTox::Compound]
def self.from_inchi inchi
smiles = obconversion(inchi,"inchi","can")
smiles.empty? ? nil : Compound.find_or_create_by(:smiles => smiles)
end
# Create a compound from SDF
# @param [String] SDF
# @return [OpenTox::Compound]
def self.from_sdf sdf
# do not store sdf because it might be 2D
Compound.from_smiles obconversion(sdf,"sdf","can")
end
# Create a compound from name. Relies on an external service for name lookups.
# @example
# compound = OpenTox::Compound.from_name("Benzene")
# @param [String] name, can be also an InChI/InChiKey, CAS number, etc
# @return [OpenTox::Compound]
def self.from_name name
Compound.from_smiles RestClientWrapper.get(File.join(PUBCHEM_URI,"compound","name",URI.escape(name),"property","CanonicalSMILES","TXT")).chomp
end
# Get InChI
# @return [String]
def inchi
unless self["inchi"]
result = obconversion(smiles,"smi","inchi")
update(:inchi => result.chomp) if result and !result.empty?
end
self["inchi"]
end
# Get InChIKey
# @return [String]
def inchikey
update(:inchikey => obconversion(smiles,"smi","inchikey")) unless self["inchikey"]
self["inchikey"]
end
# Get (canonical) smiles
# @return [String]
def smiles
update(:smiles => obconversion(self["smiles"],"smi","can")) unless self["smiles"]
self["smiles"]
end
# Get SDF
# @return [String]
def sdf
if self.sdf_id.nil?
sdf = obconversion(smiles,"smi","sdf")
file = Mongo::Grid::File.new(sdf, :filename => "#{id}.sdf",:content_type => "chemical/x-mdl-sdfile")
sdf_id = $gridfs.insert_one file
update :sdf_id => sdf_id
end
$gridfs.find_one(_id: self.sdf_id).data
end
# Get SVG image
# @return [image/svg] Image data
def svg
if self.svg_id.nil?
svg = obconversion(smiles,"smi","svg")
file = Mongo::Grid::File.new(svg, :filename => "#{id}.svg", :content_type => "image/svg")
update(:svg_id => $gridfs.insert_one(file))
end
$gridfs.find_one(_id: self.svg_id).data
end
# Get png image
# @example
# image = compound.png
# @return [image/png] Image data
def png
if self.png_id.nil?
png = obconversion(smiles,"smi","_png2")
file = Mongo::Grid::File.new(Base64.encode64(png), :filename => "#{id}.png", :content_type => "image/png")
update(:png_id => $gridfs.insert_one(file))
end
Base64.decode64($gridfs.find_one(_id: self.png_id).data)
end
# Get all known compound names. Relies on an external service for name lookups.
# @example
# names = compound.names
# @return [Array<String>]
def names
update(:names => RestClientWrapper.get(File.join(PUBCHEM_URI,"compound","smiles",URI.escape(smiles),"synonyms","TXT")).split("\n")) #unless self["names"]
self["names"]
end
# Get PubChem Compound Identifier (CID), obtained via REST call to PubChem
# @return [String]
def cid
update(:cid => RestClientWrapper.post(File.join(PUBCHEM_URI, "compound", "inchi", "cids", "TXT"),{:inchi => inchi}).strip) unless self["cid"]
self["cid"]
end
=begin
# Get ChEMBL database compound id, obtained via REST call to ChEMBL
# @return [String]
def chemblid
update(:chemblid => JSON.parse(RestClientWrapper.get(File.join CHEMBL_URI,URI.escape(smiles)+".json"))["molecule_chembl_id"])
self["chemblid"]
end
=end
def db_neighbors min_sim: 0.2, dataset_id:
#p fingerprints[DEFAULT_FINGERPRINT]
# from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb
#qn = default_fingerprint_size
#qmin = qn * threshold
#qmax = qn / threshold
#not sure if it is worth the effort of keeping feature counts up to date (compound deletions, additions, ...)
#reqbits = [count['_id'] for count in db.mfp_counts.find({'_id': {'$in': qfp}}).sort('count', 1).limit(qn - qmin + 1)]
aggregate = [
#{'$match': {'mfp.count': {'$gte': qmin, '$lte': qmax}, 'mfp.bits': {'$in': reqbits}}},
#{'$match' => {'_id' => {'$ne' => self.id}}}, # remove self
{'$project' => {
'similarity' => {'$let' => {
'vars' => {'common' => {'$size' => {'$setIntersection' => ["$fingerprints.#{DEFAULT_FINGERPRINT}", fingerprints[DEFAULT_FINGERPRINT]]}}},
'in' => {'$divide' => ['$$common', {'$subtract' => [{'$add' => [default_fingerprint_size, '$default_fingerprint_size']}, '$$common']}]}
}},
'_id' => 1,
#'measurements' => 1,
'dataset_ids' => 1
}},
{'$match' => {'similarity' => {'$gte' => min_sim}}},
{'$sort' => {'similarity' => -1}}
]
# TODO move into aggregate pipeline, see http://stackoverflow.com/questions/30537317/mongodb-aggregation-match-if-value-in-array
$mongo["substances"].aggregate(aggregate).select{|r| r["dataset_ids"].include? dataset_id}
end
# Convert mmol to mg
# @return [Float] value in mg
def mmol_to_mg mmol
mmol.to_f*molecular_weight
end
# Convert mg to mmol
# @return [Float] value in mmol
def mg_to_mmol mg
mg.to_f/molecular_weight
end
# Calculate molecular weight of Compound with OB and store it in compound object
# @return [Float] molecular weight
def molecular_weight
mw_feature = PhysChem.find_or_create_by(:name => "Openbabel.MW")
calculate_properties([mw_feature]).first
end
private
def self.obconversion(identifier,input_format,output_format,option=nil)
obconversion = OpenBabel::OBConversion.new
obconversion.set_options(option, OpenBabel::OBConversion::OUTOPTIONS) if option
obmol = OpenBabel::OBMol.new
obconversion.set_in_and_out_formats input_format, output_format
return nil if identifier.nil?
obconversion.read_string obmol, identifier
case output_format
when /smi|can|inchi/
obconversion.write_string(obmol).split(/\s/).first
when /sdf/
# TODO: find disconnected structures
# strip_salts
# separate
obmol.add_hydrogens
builder = OpenBabel::OBBuilder.new
builder.build(obmol)
sdf = obconversion.write_string(obmol)
print sdf
if sdf.match(/.nan/)
#warn "3D generation failed for compound #{identifier}, trying to calculate 2D structure"
obconversion.set_options("gen2D", OpenBabel::OBConversion::GENOPTIONS)
sdf = obconversion.write_string(obmol)
if sdf.match(/.nan/)
#warn "2D generation failed for compound #{identifier}, rendering without coordinates."
obconversion.remove_option("gen2D", OpenBabel::OBConversion::GENOPTIONS)
sdf = obconversion.write_string(obmol)
end
end
sdf
else
obconversion.write_string(obmol)
end
end
def obconversion(identifier,input_format,output_format,option=nil)
self.class.obconversion(identifier,input_format,output_format,option)
end
end
end
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