Indigo 1.1.12

Date:23 Dec 2013

Summary

New features and improvements:

  • Bold bonds detection in the rendering procedure (details)
  • Transformation method do not change molecule layout for simple transformations.
  • Timeout option works for layout and transformation methods [5]
  • Build process and dependencies update (details)
  • Smiles includes cis-trans marks in rings including in canonical smiles (details)
  • checkBadValance, checkAmbiguousH methods try to find number of implicit hydrogens for aromatic molecules first. If molecule is aromatic then there is no need to dearomatize it first to check ambiguous hydrogens. See unique-dearomatization option that contains examples.
  • cdxml format: text width estimation
  • indigo-python: createSaver method to render or save into buffers (details)
  • Rendering module supports multiline comments and titles. See render-comment and render-grid-title-property options.
  • Linux distributive do not depend on GLIBC_2.14. Binary files can be used even on old versions of Linux.
  • Multiline properties, empty properties are loaded from SDF file. rawData method includes properties too.
  • SDF reader can read sdf.gz and files

Bugfixes:

  • Various fixes in the transformation procedure [2]
  • Fixed canvas estimation in the rendering methods.
  • Indigo finalization method could affect other Indigo instances as well in Java [1]
  • foldHydrogens method mark other bond if that bond were marked
  • Fixed issues in deserialization method if molecule cis-trans configuration was invalid
  • Substructure matcher matches N[C@H](O)S on C[C@@](N)(O)S
  • Normalize method validates cis-trans after doing normalization
  • Molfile with ISISHOST header are supported. Such molecules has empty molfile version.
  • Layout did not respect cis-trans configuration in rare cases
  • Memory leak in InChI to molecule conversion
  • Monoisotpic mass computation fix [3]
  • SMARTS expressions can have multiple atom constraints for a single atom without explicit and operation. For example [!#1!#6]. [4]
  • Fixed collapse option value for render-superatom-mode option.
  • Complete Python 3 compatibility

Details

Smiles cis-trans flags

Cis-trans bonds in rings are saved using SMILES extension with “c” and “t” fields.

m = indigo.loadMoleculeFromFile('data/macro.mol')

indigoRenderer.renderToFile(m, "result.png")

print(m.canonicalSmiles())
../../../_images/indigorenderer_183a4eab0bd10c4ab060ccb44b71ce55909e3fa1.svg

Output:
C1C=CC=CCC=CC=CC=CC=C1 |c:1,3,8,12,t:6,10|

Bold bonds detection and rendering

To depict Sugars Indigo can automatically detect where bold bond should be drawn:

m = indigo.loadMoleculeFromFile('data/bold-bond2.mol')

indigo.setOption("render-comment", "With bold bonds")
indigoRenderer.renderToFile(m, "result_1.png")

indigo.setOption('render-bold-bond-detection', False)

indigo.setOption("render-comment", "Original")
indigoRenderer.renderToFile(m, "result_2.png")
Input: data/bold-bond2.mol

../../../_images/indigorenderer_b785e84c4c703e4bfa2242fbc7675e5869a6eea11.svg ../../../_images/indigorenderer_b785e84c4c703e4bfa2242fbc7675e5869a6eea12.svg

Generic saver

Python bindings has a new method createSaver that can be used to save chemical structures into buffers.

# Create molecules and set their names
m1 = indigo.loadMolecule('[H][C@](C)(N)O')
m1.setName("Molecule 1")
m2 = indigo.loadMolecule('C1=CC=CC=C1')
m2.setName("Molecule 2")

# Create string stream and save molecules in SMILES format into it
buffer = indigo.writeBuffer()
# Instead of "smi" one can use "sdf", "cml", "rdf"
saver = indigo.createSaver(buffer, "smi")
saver.append(m1)
saver.append(m2)

print(buffer.toString())

Output:
[H][C@@](O)(N)C
C1C=CC=CC=1

Build Process

  • Visual Studio 2013 and OS X Mavericks support added.
  • Indigo-java: source and target compatibility versions set to Java 1.5.
  • Third party libraries: Cairo updated to 1.126; Pixman updated to 0.30.2; Cairo can be built with cairo-gl, cairo-vg, cairo-egl and cairo-glesv2 support.

Footnotes

[1]Bug report by Joos: https://groups.google.com/d/msg/indigo-bugs/Vdzp0B26KsA/DehJm2QhW34J
[2]Bug report by Ken: https://groups.google.com/d/msg/indigo-general/6B-LlLR0Ppw/fvI1RM7CzWUJ
[3]Bug report by Oliver Kohlbacher: https://groups.google.com/d/msg/indigo-general/h6p9QxMuI_Q/4x2TckxWProJ
[4]Bug report by Oleg: https://groups.google.com/d/msg/indigo-general/D3P-TbZBnL0/oJEOM82i1lwJ
[5]Feature request by Ken: https://groups.google.com/d/msg/indigo-general/wK4eDGiOzJc/kgwc0mAH89YJ