From 05386e748270c337c66f6f379317ea4b25905236 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 4 May 2016 19:24:42 +0200 Subject: first reasonable results for nanoparticle crossvalidation --- scripts/import-enm.rb | 6 ++++++ scripts/mg2mmol.rb | 17 +++++++++++++++++ scripts/mmol2-log10.rb | 17 +++++++++++++++++ 3 files changed, 40 insertions(+) create mode 100644 scripts/import-enm.rb create mode 100644 scripts/mg2mmol.rb create mode 100644 scripts/mmol2-log10.rb (limited to 'scripts') diff --git a/scripts/import-enm.rb b/scripts/import-enm.rb new file mode 100644 index 0000000..9cbe5d4 --- /dev/null +++ b/scripts/import-enm.rb @@ -0,0 +1,6 @@ +require_relative '../lib/lazar' +include OpenTox +$mongo.database.drop +$gridfs = $mongo.database.fs # recreate GridFS indexes +Import::Enanomapper.import +`mongodump -h 127.0.0.1 -d production` diff --git a/scripts/mg2mmol.rb b/scripts/mg2mmol.rb new file mode 100644 index 0000000..dc6b953 --- /dev/null +++ b/scripts/mg2mmol.rb @@ -0,0 +1,17 @@ +#!/usr/bin/env ruby +require_relative '../lazar/lib/lazar' +include OpenTox +newfile = ARGV[0].sub(/.csv/,"_mmol.csv") +p newfile +CSV.open(newfile, "wb") do |csv| + CSV.read(ARGV[0]).each do |line| + smi,mg = line + if mg.numeric? + c = Compound.from_smiles smi + mmol = c.mg_to_mmol mg.to_f + csv << [smi, mmol] + else + csv << [smi, mg.gsub(/mg/,'mmol')] + end + end +end diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb new file mode 100644 index 0000000..0c99a0b --- /dev/null +++ b/scripts/mmol2-log10.rb @@ -0,0 +1,17 @@ +#!/usr/bin/env ruby +require_relative '../lib/lazar' +include OpenTox +newfile = ARGV[0].sub(/.csv/,"_log10.csv") +p newfile +CSV.open(newfile, "wb") do |csv| + CSV.read(ARGV[0]).each do |line| + smi,mmol = line + if mmol.numeric? + c = Compound.from_smiles smi + mmol = -Math.log10(mmol.to_f) + csv << [smi, mmol] + else + csv << [smi, "-log10(#{mmol})"] + end + end +end -- cgit v1.2.3 From 48234554ea99b972a01718ac36c4e8332dd9159b Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sat, 7 May 2016 10:34:03 +0200 Subject: -log10 for regression datasets, test cleanups --- scripts/import-enm.rb | 1 + scripts/mg2mmol.rb | 0 scripts/mmol2-log10.rb | 0 3 files changed, 1 insertion(+) mode change 100644 => 100755 scripts/import-enm.rb mode change 100644 => 100755 scripts/mg2mmol.rb mode change 100644 => 100755 scripts/mmol2-log10.rb (limited to 'scripts') diff --git a/scripts/import-enm.rb b/scripts/import-enm.rb old mode 100644 new mode 100755 index 9cbe5d4..4fb414b --- a/scripts/import-enm.rb +++ b/scripts/import-enm.rb @@ -1,3 +1,4 @@ +#!/usr/bin/env ruby require_relative '../lib/lazar' include OpenTox $mongo.database.drop diff --git a/scripts/mg2mmol.rb b/scripts/mg2mmol.rb old mode 100644 new mode 100755 diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb old mode 100644 new mode 100755 -- cgit v1.2.3 From 06fc914653face2c58fd4e6c47161cb03e217582 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sun, 8 May 2016 12:22:58 +0200 Subject: default validations fixed --- scripts/mmol2-log10.rb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'scripts') diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb index 0c99a0b..f28ff8f 100755 --- a/scripts/mmol2-log10.rb +++ b/scripts/mmol2-log10.rb @@ -3,6 +3,7 @@ require_relative '../lib/lazar' include OpenTox newfile = ARGV[0].sub(/.csv/,"_log10.csv") p newfile +i = 1 CSV.open(newfile, "wb") do |csv| CSV.read(ARGV[0]).each do |line| smi,mmol = line @@ -11,7 +12,10 @@ CSV.open(newfile, "wb") do |csv| mmol = -Math.log10(mmol.to_f) csv << [smi, mmol] else - csv << [smi, "-log10(#{mmol})"] + #csv << [smi, "-log10(#{mmol})"] + p "Line #{i}: '#{mmol}' is not a numeric value." + csv << [smi, ""] end + i += 1 end end -- cgit v1.2.3 From 611bac891177f8d9185d45486dd574b6ef4d1912 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Mon, 9 May 2016 15:11:46 +0200 Subject: nanoparticle models fixed --- scripts/import-enm.rb | 7 ------- scripts/mirror-enm2test.rb | 4 ++++ 2 files changed, 4 insertions(+), 7 deletions(-) delete mode 100755 scripts/import-enm.rb create mode 100755 scripts/mirror-enm2test.rb (limited to 'scripts') diff --git a/scripts/import-enm.rb b/scripts/import-enm.rb deleted file mode 100755 index 4fb414b..0000000 --- a/scripts/import-enm.rb +++ /dev/null @@ -1,7 +0,0 @@ -#!/usr/bin/env ruby -require_relative '../lib/lazar' -include OpenTox -$mongo.database.drop -$gridfs = $mongo.database.fs # recreate GridFS indexes -Import::Enanomapper.import -`mongodump -h 127.0.0.1 -d production` diff --git a/scripts/mirror-enm2test.rb b/scripts/mirror-enm2test.rb new file mode 100755 index 0000000..f6638bc --- /dev/null +++ b/scripts/mirror-enm2test.rb @@ -0,0 +1,4 @@ +#!/usr/bin/env ruby +require_relative '../lib/lazar' +include OpenTox +Import::Enanomapper.mirror File.join(File.dirname(__FILE__),"..","test","data","enm") -- cgit v1.2.3 From b8bb12c8a163c238d7d4387c1914e2100bb660df Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 12 May 2016 15:23:01 +0200 Subject: enm study import fixed --- scripts/mmol2-log10.rb | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) (limited to 'scripts') diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb index f28ff8f..ec0fdf5 100755 --- a/scripts/mmol2-log10.rb +++ b/scripts/mmol2-log10.rb @@ -3,18 +3,21 @@ require_relative '../lib/lazar' include OpenTox newfile = ARGV[0].sub(/.csv/,"_log10.csv") p newfile -i = 1 CSV.open(newfile, "wb") do |csv| + i = 1 CSV.read(ARGV[0]).each do |line| smi,mmol = line - if mmol.numeric? - c = Compound.from_smiles smi - mmol = -Math.log10(mmol.to_f) - csv << [smi, mmol] + if i == 1 + csv << [smi, "-log10(#{mmol})"] else - #csv << [smi, "-log10(#{mmol})"] - p "Line #{i}: '#{mmol}' is not a numeric value." - csv << [smi, ""] + if mmol.numeric? + c = Compound.from_smiles smi + mmol = -Math.log10(mmol.to_f) + csv << [smi, mmol] + else + p "Line #{i}: '#{mmol}' is not a numeric value." + #csv << [smi, ""] + end end i += 1 end -- cgit v1.2.3 From 0ddd04c32280e6fd166a52fa6da653df24aabf99 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 23 Nov 2016 15:10:58 +0000 Subject: added delog10;generalized mmol2-log10 --- scripts/mmol2-log10.rb | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) (limited to 'scripts') diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb index ec0fdf5..188d8cb 100755 --- a/scripts/mmol2-log10.rb +++ b/scripts/mmol2-log10.rb @@ -1,22 +1,29 @@ #!/usr/bin/env ruby require_relative '../lib/lazar' include OpenTox -newfile = ARGV[0].sub(/.csv/,"_log10.csv") + +newfile = ARGV[0].sub(/.csv/,"_log10.csv") p newfile CSV.open(newfile, "wb") do |csv| i = 1 CSV.read(ARGV[0]).each do |line| - smi,mmol = line + type,mmol = line if i == 1 - csv << [smi, "-log10(#{mmol})"] + csv << [type, "-log10(#{mmol})"] + @type = type else if mmol.numeric? - c = Compound.from_smiles smi + if @type =~ /smiles/i + c = Compound.from_smiles type + elsif @type =~ /inchi/i + c = Compound.from_inchi type + else + p "Unknown type '#{@type}' at line #{i}." + end mmol = -Math.log10(mmol.to_f) - csv << [smi, mmol] + csv << [type, mmol] else p "Line #{i}: '#{mmol}' is not a numeric value." - #csv << [smi, ""] end end i += 1 -- cgit v1.2.3 From e111369ce5564f159b3f5f85c92afdd22352eaa1 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 24 Nov 2016 07:16:54 +0000 Subject: always convert to SMILES --- scripts/mmol2-log10.rb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'scripts') diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb index 188d8cb..ff4af2a 100755 --- a/scripts/mmol2-log10.rb +++ b/scripts/mmol2-log10.rb @@ -9,16 +9,17 @@ CSV.open(newfile, "wb") do |csv| CSV.read(ARGV[0]).each do |line| type,mmol = line if i == 1 - csv << [type, "-log10(#{mmol})"] @type = type + csv << ["SMILES", "-log10(#{mmol})"] else if mmol.numeric? if @type =~ /smiles/i c = Compound.from_smiles type elsif @type =~ /inchi/i c = Compound.from_inchi type + type = c.smiles else - p "Unknown type '#{@type}' at line #{i}." + p "Unknown type '#{type}' at line 1." end mmol = -Math.log10(mmol.to_f) csv << [type, mmol] -- cgit v1.2.3