Re: [Rdkit-discuss] sanitization removes Hs - is this expected?
Hi, I have a question, directly related to this topic: I would like to achieve the following behavior from RDKit: 1. If input molfile has explicit hydrogens defined, then perform only partial sanitization and keep hydrogens. 2. Otherwise perform full sanitization as usual. Will that happen automatically or do I need to check if the molfile has explicit hydrogens? If the latter, how can I check this using RDKit without writing my own SDF parser? Michał Nowotka On Tue, Apr 7, 2015 at 11:50 AM, Greg Landrum greg.land...@gmail.com wrote: On Tue, Apr 7, 2015 at 12:13 PM, Michal Krompiec michal.kromp...@gmail.com wrote: Thanks a lot! Glad it works. By the way, it would be useful to have this feature (MergeQueryHs) also in the substructure search KNIME node. Indeed. :-) We already have a version of the MolToRDKit node ready to allow this; it just hasn't made it into the open-source version of the KNIME nodes yet (we forgot to include this the last time we updated those nodes). It's coming soon. -greg -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] out-of-plane bends
Dear Michal,
please find attached a small script which accomplishes what you describe
by a different approach, i.e. it minimizes only the methyl group in
2-methylthiophene while keeping the rest fixed, effectively pushing it
back in plane. Would that work for you?
Best,
Paolo
On 04/15/2015 10:57 AM, Michal Krompiec wrote:
Hello,
I'm trying to manipulate out-of-plane bends of substituents attached
to aromatic rings. Obviously, they should lie in the plane of the
ring, but sometimes (after constrained optimization) they come
slightly out of plane and there doesn't seem to be a way to
push/rotate them back to the ring plane. Adding constraints to the
forcefield (which seems to work for out-of-plane bends as well) is not
a perfect solution.
For example, there is no way to manipulate the out-of-plane bend
(dihedral angle) of the methyl group in the 2-methylthiophene molecule
c1cc(C)sc1, defined by the first four atoms c1cc(C). If you try to use
rdMolTransforms.SetDihedralDeg, it will raise an exception because the
bond around it tries to rotate is part of a ring (line 375 in
MolTransforms.cpp) - and for a good reason, because what I wanted to
do is to rotate just the methyl group (atom l as defined in
setDihedralRad, and everything attached to it), not all atoms
connected to atom k being on the right hand side of the j-k bond.
Would it make sense to make a modified version of setDihedralRad():
setOutOfPlaneBendRad(), with the following modifications:
* omit line 375: if(queryIsBondInRing(bondJK)) throw
ValueErrorException(bond (j,k) must not belong to a ring); instead
perhaps check if bond k,l belongs to a ring
* change line 401: _toBeMovedIdxList(mol, jAtomId, kAtomId, alist); to
_toBeMovedIdxList(mol, kAtomId, lAtomId, alist); (we want to rotate
the tree rooted in atom l, not atom k)
Best regards,
Michal
--
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Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
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#!/usr/bin/env python
import rdkit
from rdkit import Chem
from rdkit.Chem import ChemicalForceFields, rdForceFieldHelpers
oopThiophene = \
oopThiophene
3D
21 21 0 0 0 0 0 0 0 0999 V2000
-3.73161.23670.7532 S 0 0 0 0 0 0 0 0 0 0 0 0
-2.67580.5095 -0.4904 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.41760.8536 -0.3142 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.20021.72110.8189 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.29992.01451.4780 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.37542.07483.1288 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1713 -0.4058 -1.5990 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.41160.0803 -2.3745 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.7054 -0.1744 -1.5816 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.61960.5172 -0.9595 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.22622.09411.0990 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.40912.08633.4416 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.88341.20763.5436 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.88332.97013.4792 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.3665 -0.5309 -2.3083 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.4122 -1.3608 -1.1559 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.31651.1398 -2.5607 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.4667 -0.4472 -3.3153 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.55920.0279 -2.2113 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.73260.4748 -0.7189 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.7325 -1.2044 -1.2581 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
3 4 1 0
4 5 2 0
5 1 1 0
5 6 1 0
2 7 1 0
7 8 1 0
8 9 1 0
3 10 1 0
4 11 1 0
6 12 1 0
6 13 1 0
6 14 1 0
7 15 1 0
7 16 1 0
8 17 1 0
8 18 1 0
9 19 1 0
9 20 1 0
9 21 1 0
M END
mol = Chem.MolFromMolBlock(oopThiophene, sanitize = True, removeHs = False)
methyl = Chem.MolFromSmarts('C([H])([H])([H])')
match = mol.GetSubstructMatch(methyl)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(mol)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(mol, mp)
for i in range(mol.GetNumAtoms()):
if (not (i in match)):
ff.AddFixedPoint(i)
ff.Minimize()
w = Chem.SDWriter('minOopThiophene.sdf')
w.write(mol)
w.close()
--
BPM Camp - Free Virtual Workshop May
[Rdkit-discuss] out-of-plane bends
Hello, I'm trying to manipulate out-of-plane bends of substituents attached to aromatic rings. Obviously, they should lie in the plane of the ring, but sometimes (after constrained optimization) they come slightly out of plane and there doesn't seem to be a way to push/rotate them back to the ring plane. Adding constraints to the forcefield (which seems to work for out-of-plane bends as well) is not a perfect solution. For example, there is no way to manipulate the out-of-plane bend (dihedral angle) of the methyl group in the 2-methylthiophene molecule c1cc(C)sc1, defined by the first four atoms c1cc(C). If you try to use rdMolTransforms.SetDihedralDeg, it will raise an exception because the bond around it tries to rotate is part of a ring (line 375 in MolTransforms.cpp) - and for a good reason, because what I wanted to do is to rotate just the methyl group (atom l as defined in setDihedralRad, and everything attached to it), not all atoms connected to atom k being on the right hand side of the j-k bond. Would it make sense to make a modified version of setDihedralRad(): setOutOfPlaneBendRad(), with the following modifications: * omit line 375: if(queryIsBondInRing(bondJK)) throw ValueErrorException(bond (j,k) must not belong to a ring); instead perhaps check if bond k,l belongs to a ring * change line 401: _toBeMovedIdxList(mol, jAtomId, kAtomId, alist); to _toBeMovedIdxList(mol, kAtomId, lAtomId, alist); (we want to rotate the tree rooted in atom l, not atom k) Best regards, Michal -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
