From 1581012194f99ff776a23d520a187164df3ee125 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 5 Sep 2018 10:03:33 +0200
Subject: [PATCH] compute 2D coordinates during SMILES to MOL conversion
to enable loading SMILES in MarvinJS (related to #83)
Former-commit-id: f3f0006b98d5bb0f5e303c14e1f7fc8c0bf03f9f
---
ippisite/ippidb/utils.py | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/ippisite/ippidb/utils.py b/ippisite/ippidb/utils.py
index 3927f824..ec26172d 100644
--- a/ippisite/ippidb/utils.py
+++ b/ippisite/ippidb/utils.py
@@ -9,6 +9,11 @@ def mol2smi(mol_string):
def smi2mol(smi_string):
m = pybel.readstring('smi', smi_string)
+ # generate 2D coordinates for MarvinJS layout
+ #NB: the line below should be replaced as soon as the new version of openbabel
+ # is out (>2.4.1), by a call to m.make2D()
+ # (see https://github.com/openbabel/openbabel/blob/06e233e2ca0c6d9f86f74bafe74ffcb75e9d76cd/scripts/python/pybel.py#L577)
+ pybel._operations['gen2D'].Do(m.OBMol)
return m.write(format='mol')
class FingerPrinter(object):
--
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