IndigoRender rotate image

[twall]

Are there any options to force a rotation of a rendered molecule? I'd like the option to request rendering of an arbitrary rotation of the structure, leaving the labels in the correct orientation. If I'm looking at two molecules side by side I'd like to be able to orient them in a way that highlights similarity.

Ketcher allows rotation of selected molecules.

[AlexanderSavelyev]

Hi @twall . It is not clear what exactly is required. It seems like not rendering but re-layout a molecule with appropriate angle and center of the rotation. Is it correct? If you want to highlight substructure, one can use highlightedTarget

match = indigo.substructureMatcher(mol).match(query)

if match:
   match.highlightedTarget().saveMolfile("highlighted.mol")

[twall]

Suppose I’m displaying two identical molecules but for whatever reason one is rendered upside down. How do I correct that? I can do a CSS transform, but that leaves the labels inverted. Ideally I would be able to automatically align and highlight similarities of two molecules, but I don’t think that’s possible currently without some extra input. So my starting point is to just enable the user to rotate one or the other images.

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On Wed, Apr 10, 2024 at 4:59 AM Aleksandr Savelev ***@***.***> wrote: Hi @twall <https://github.com/twall> . It is not clear what exactly is required. It seems like not rendering but re-layout a molecule with appropriate angle and center of the rotation. Is it correct? If you want to highlight substructure, one can use highlightedTarget match = indigo.substructureMatcher(mol).match(query) if match: match.highlightedTarget().saveMolfile("highlighted.mol") — Reply to this email directly, view it on GitHub <#1906 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFYZLM3QBYB7UECZ2ZYJYLY4T5N5AVCNFSM6AAAAABF5N2S7OVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TANRYGQZDG> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[twall]

Thank you for the highlighting tip, though, I was not aware of that functionality (the docs, particularly for nosql, are rather thin).

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On Wed, Apr 10, 2024 at 4:59 AM Aleksandr Savelev ***@***.***> wrote: Hi @twall <https://github.com/twall> . It is not clear what exactly is required. It seems like not rendering but re-layout a molecule with appropriate angle and center of the rotation. Is it correct? If you want to highlight substructure, one can use highlightedTarget match = indigo.substructureMatcher(mol).match(query) if match: match.highlightedTarget().saveMolfile("highlighted.mol") — Reply to this email directly, view it on GitHub <#1906 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFYZLM3QBYB7UECZ2ZYJYLY4T5N5AVCNFSM6AAAAABF5N2S7OVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TANRYGQZDG> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[AlexanderSavelyev]

As a solution we can suggest to use XYZ function for atoms and rotate using standard rotation matrix. See the following code as an example

def rotate(x, y, angle):
    xn = x * math.cos(angle) - y * math.sin(angle)
    yn = x * math.sin(angle) + y * math.cos(angle)
    return xn, yn


m = indigo.loadMolecule('C1([H])C=CC=C1')
m.layout()

indigoRenderer.renderToFile(m, 'result1.png')

angle = 3.14159
for a in m.iterateAtoms():
    xyz = a.xyz()
    xn, yn = rotate(xyz[0], xyz[1], angle)
    a.setXYZ(xn, yn, 0)

indigoRenderer.renderToFile(m, 'result2.png')