1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
|
require 'digest/md5'
ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk"
module OpenTox
module Algorithm
class Descriptor
include OpenTox
JAVA_DIR = File.join(File.dirname(__FILE__),"..","java")
CDK_JAR = Dir[File.join(JAVA_DIR,"cdk-*jar")].last
JOELIB_JAR = File.join(JAVA_DIR,"joelib2.jar")
LOG4J_JAR = File.join(JAVA_DIR,"log4j.jar")
JMOL_JAR = File.join(JAVA_DIR,"Jmol.jar")
obexclude = ["cansmi","cansmiNS","formula","InChI","InChIKey","s","smarts","title"]
OBDESCRIPTORS = Hash[OpenBabel::OBDescriptor.list_as_string("descriptors").split("\n").collect do |d|
name,description = d.split(/\s+/,2)
["Openbabel."+name,description] unless obexclude.include? name
end.compact.sort{|a,b| a[0] <=> b[0]}]
CDKDESCRIPTORS = Hash[YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR} CdkDescriptorInfo`).collect { |d| ["Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,''), d[:description]] }.sort{|a,b| a[0] <=> b[0]}]
# exclude Hashcode (not a physchem property) and GlobalTopologicalChargeIndex (Joelib bug)
joelibexclude = ["MoleculeHashcode","GlobalTopologicalChargeIndex"]
# strip Joelib messages from stdout
JOELIBDESCRIPTORS = Hash[YAML.load(`java -classpath #{JOELIB_JAR}:#{LOG4J_JAR}:#{JAVA_DIR} JoelibDescriptorInfo | sed '0,/---/d'`).collect do |d|
name = d[:java_class].sub(/^joelib2.feature.types./,'')
# impossible to obtain meaningful descriptions from JOELIb, see java/JoelibDescriptors.java
["Joelib."+name, "no description available"] unless joelibexclude.include? name
end.compact.sort{|a,b| a[0] <=> b[0]}]
DESCRIPTORS = OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS))
require_relative "unique_descriptors.rb"
def self.description descriptor
lib = descriptor.split('.').first
case lib
when "Openbabel"
OBDESCRIPTORS[descriptor]
when "Cdk"
name = descriptor.split('.')[0..-2].join('.')
CDKDESCRIPTORS[name]
when "Joelib"
JOELIBDESCRIPTORS[descriptor]
when "lookup"
"Read feature values from a dataset"
end
end
def self.smarts_match compounds, smarts, count=false
obconversion = OpenBabel::OBConversion.new
obmol = OpenBabel::OBMol.new
obconversion.set_in_format('inchi')
smarts_pattern = OpenBabel::OBSmartsPattern.new
fingerprint = {}
compounds = [compounds] unless compounds.is_a? Array
smarts = [smarts] unless smarts.is_a? Array
compounds.each do |compound|
obconversion.read_string(obmol,compound.inchi)
fingerprint[compound] = {}
smarts.each do |smart|
smarts_pattern.init(smart)
if smarts_pattern.match(obmol)
count ? value = smarts_pattern.get_map_list.to_a.size : value = 1
else
value = 0
end
fingerprint[compound][smart] = value
end
end
fingerprint
end
def self.smarts_count compounds, smarts
smarts_match compounds,smarts,true
end
def self.physchem compounds, descriptors
des = {}
descriptors.each do |d|
lib, descriptor = d.split(".",2)
lib = lib.downcase.to_sym
des[lib] ||= []
des[lib] << descriptor
end
result = {}
des.each do |lib,d|
send(lib, compounds, d).each do |compound,values|
result[compound] ||= {}
result[compound].merge! values
end
end
result
end
def self.openbabel compounds, descriptors
obdescriptors = descriptors.collect{|d| OpenBabel::OBDescriptor.find_type d}
obmol = OpenBabel::OBMol.new
obconversion = OpenBabel::OBConversion.new
obconversion.set_in_format 'inchi'
fingerprint = {}
compounds.each do |compound|
obconversion.read_string obmol, compound.inchi
fingerprint[compound] = {}
obdescriptors.each_with_index do |descriptor,i|
fingerprint[compound]["Openbabel."+descriptors[i]] = fix_value(descriptor.predict(obmol))
end
end
fingerprint
end
def self.cdk compounds, descriptors
sdf = sdf_3d compounds
# use java system call (rjb blocks within tasks)
# use Tempfiles to avoid "Argument list too long" error
`java -classpath #{CDK_JAR}:#{JAVA_DIR} CdkDescriptors #{sdf} #{descriptors.join(" ")}`
fingerprint = {}
YAML.load_file(sdf+"cdk.yaml").each_with_index do |calculation,i|
$logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
descriptors.each do |descriptor|
fingerprint[compounds[i]] = calculation
end
end
FileUtils.rm sdf+"cdk.yaml"
fingerprint
end
def self.joelib compounds, descriptors
# use java system call (rjb blocks within tasks)
# use Tempfiles to avoid "Argument list too long" error
sdf = sdf_3d compounds
`java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR} JoelibDescriptors #{sdf} #{descriptors.join(' ')}`
fingerprint = {}
YAML.load_file(sdf+"joelib.yaml").each_with_index do |calculation,i|
$logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
descriptors.each do |descriptor|
fingerprint[compounds[i]] = calculation
end
end
FileUtils.rm sdf+"joelib.yaml"
fingerprint
end
def self.lookup compounds, features, dataset
fingerprint = []
compounds.each do |compound|
fingerprint << []
features.each do |feature|
end
end
end
def self.sdf_3d compounds
obconversion = OpenBabel::OBConversion.new
obmol = OpenBabel::OBMol.new
obconversion.set_in_format 'inchi'
obconversion.set_out_format 'sdf'
digest = Digest::MD5.hexdigest compounds.inspect
sdf_file = "/tmp/#{digest}.sdf"
unless File.exists? sdf_file # do not recreate existing 3d sdfs
sdf = File.open sdf_file,"w+"
# create 3d sdf file (faster in Openbabel than in CDK)
compounds.each do |compound|
obconversion.read_string obmol, compound.inchi
sdf_2d = obconversion.write_string(obmol)
OpenBabel::OBOp.find_type("Gen3D").do(obmol)
sdf_3d = obconversion.write_string(obmol)
if sdf_3d.match(/.nan/)
warning = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure."
$logger.warn warning
# TODO
#@feature_dataset[RDF::OT.Warnings] ? @feature_dataset[RDF::OT.Warnings] << warning : @feature_dataset[RDF::OT.Warnings] = warning
sdf.puts sdf_2d
else
sdf.puts sdf_3d
end
end
sdf.close
end
sdf_file
end
def self.fix_value val
val = val.first if val.is_a? Array and val.size == 1
if val.numeric?
val = Float(val)
val = nil if val.nan? or val.infinite?
else
val = nil if val == "NaN"
end
val
end
private_class_method :sdf_3d, :fix_value
end
end
end
|