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author | helma@in-silico.ch <helma@in-silico.ch> | 2018-11-06 19:01:58 +0100 |
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committer | helma@in-silico.ch <helma@in-silico.ch> | 2018-11-06 19:01:58 +0100 |
commit | cf80ed17102a0368df8d65037d113b521cdf6f0c (patch) | |
tree | f2930939673d7e5b28021351d32d92750875992b /lib/dataset.rb | |
parent | 3a9c9332b660d35720ad4fa1f55ee0883e53aecd (diff) |
sdf export fixed
Diffstat (limited to 'lib/dataset.rb')
-rw-r--r-- | lib/dataset.rb | 19 |
1 files changed, 11 insertions, 8 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index 42733e4..b09d7bf 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -199,7 +199,6 @@ module OpenTox end dataset.parse_table table end - dataset.save dataset end @@ -290,7 +289,7 @@ module OpenTox all_substances = [] table.each_with_index do |vals,i| - original_id.name.match(/LineID$/) ? original_id_value = i+1 : original_id_value = vals.shift.strip + original_id.name.match(/LineID$/) ? original_id_value = i+1 : original_id_value = vals.shift.to_s.strip identifier = vals.shift.strip begin case compound_format @@ -368,13 +367,17 @@ module OpenTox # @return [String] SDF string def to_sdf sdf = "" - substances.each do |substance| - sdf_lines = substance.sdf.sub(/\$\$\$\$\n/,"").split("\n") - sdf_lines[0] = substance.smiles + compounds.each do |compound| + sdf_lines = compound.sdf.sub(/\$\$\$\$\n/,"").split("\n") + sdf_lines[0] = compound.smiles sdf += sdf_lines.join("\n") - features.each do |f| - sdf += "\n> <#{f.name}>\n" - sdf += values(substance,f).uniq.join "," + bioactivity_features.each do |f| + v = values(compound,f) + unless v.empty? + sdf += "\n> <#{f.name}>\n" + sdf += v.uniq.join "," + sdf += "\n" + end end sdf += "\n$$$$\n" end |