Re: [Rdkit-discuss] Aligning in 3D
Hi Kirk, Paolo has already pointed out the tools to use if you want to have control over the process. There's also a convenience function available, AllChem.ConstrainedEmbed(), that makes the process a bit easier: http://www.rdkit.org/docs/api/rdkit.Chem.AllChem-module.html#ConstrainedEmbed Best, -greg On Fri, Apr 22, 2016 at 10:14 PM, Robert DeLisle wrote: > In working with RDKit I've been able to align 2D structures based upon a > common core of MCS using > > AllChem.GenerateDepictionMatching2DStructure(m,p) > > The next step for me is to generate 3D structures and align them based > upon that same common core. Obviously this leads to multiple steps, not > the least of which is generating conformations that are consistent across > the common core for the various molecules. I seem to recall the ability to > generate a conformation and minimize it (either UFF or MMFF) and apply > constraints based upon an input substructure, but I cannot find the details. > > Any tips to accomplish this one? > > -Kirk > > > > > -- > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Aligning in 3D
Dear Kirk,
in $RDBASE/Code/ForceField/Wrap/testConstraints.py you'll find examples
how to set constraints on internal coordinates
with {MM,U}FFAddDistanceConstraint(), {MM,U}FFAddAngleConstraint(),
{MM,U}FFAddTorsionConstraint. You may also set harmonic positional
constraints on Cartesian coordinates with
{MM,U}FFAddPositionConstraint() and fix atoms by setting their gradient
to 0 during minimization with AddFixedPoint().
The relevant Python API documentation is here:
http://www.rdkit.org/docs/api/rdkit.ForceField.rdForceField.ForceField-class.html
Cheers,
p.
On 04/22/2016 09:14 PM, Robert DeLisle wrote:
In working with RDKit I've been able to align 2D structures based upon
a common core of MCS using
AllChem.GenerateDepictionMatching2DStructure(m,p)
The next step for me is to generate 3D structures and align them based
upon that same common core. Obviously this leads to multiple steps,
not the least of which is generating conformations that are consistent
across the common core for the various molecules. I seem to recall
the ability to generate a conformation and minimize it (either UFF or
MMFF) and apply constraints based upon an input substructure, but I
cannot find the details.
Any tips to accomplish this one?
-Kirk
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PyMOL from RDKit? (Resurrection)
Dear Robert,
I have just built the latest PyMOL 1.8.2.0 on CentOS 7, I started it:
pymol -R
and then I ran the following Python script:
#!/usr/bin/env python
import os
import rdkit
from rdkit import Chem
from rdkit.Chem import PyMol
from rdkit.Chem import AllChem
s = PyMol.MolViewer()
mol = Chem.MolFromSmiles \
('CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2c21')
mol = AllChem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.MMFFOptimizeMolecule(mol)
s.ShowMol(mol, name = 'bilastine', showOnly = False)
s.Zoom('bilastine')
s.SetDisplayStyle('bilastine', 'sticks')
I obtained the expected display:
Cheers,
p.
On 04/22/2016 09:09 PM, Robert DeLisle wrote:
Back again!
I apologize for resurrecting an old topic, but I'm once again trying
to work with PyMOL through RDKit. I've been following the approach in
this thread
(http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00325.html)
but it seems not to work any longer. I'm using PyMOL 1.8 on Fedora
and I see that the xml-rpc file is current, so that's no longer a
problem. When I step through the process and hit this step:
s.ShowMol(m,name='ligand',showOnly=False)
nothing happens in the PyMOL viewer. It just remains blank.
Any updates on operating with PyMOL?
-Kirk
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Aligning in 3D
In working with RDKit I've been able to align 2D structures based upon a common core of MCS using AllChem.GenerateDepictionMatching2DStructure(m,p) The next step for me is to generate 3D structures and align them based upon that same common core. Obviously this leads to multiple steps, not the least of which is generating conformations that are consistent across the common core for the various molecules. I seem to recall the ability to generate a conformation and minimize it (either UFF or MMFF) and apply constraints based upon an input substructure, but I cannot find the details. Any tips to accomplish this one? -Kirk -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] PyMOL from RDKit? (Resurrection)
Back again! I apologize for resurrecting an old topic, but I'm once again trying to work with PyMOL through RDKit. I've been following the approach in this thread ( http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00325.html) but it seems not to work any longer. I'm using PyMOL 1.8 on Fedora and I see that the xml-rpc file is current, so that's no longer a problem. When I step through the process and hit this step: s.ShowMol(m,name='ligand',showOnly=False) nothing happens in the PyMOL viewer. It just remains blank. Any updates on operating with PyMOL? -Kirk -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] conformation search and constraints
Dear Rafal,
On 22/04/2016 17:15, Rafal Roszak wrote:
> Hello,
>
> I want to find:
> A) "global minimum" [*] for given compound(s) and
> B) (for the same compound) minimum with constraint(s) (e.g. frozen
> angle)
>
> For problem A) I tried folowing code:
>
> self.MOLEC=Chem.MolFromSmiles(SMILES)
> self.MOLEC=Chem.AddHs(self.MOLEC)
> allconf=Chem.rdDistGeom.EmbedMultipleConfs(self.MOLEC,
> numConfs=HowMany, enforceChirality=True, pruneRmsThresh=limitRMS) for
> confId in range(len(allconf)): AllChem.UFFOptimizeMolecule(self.MOLEC,
> maxIters=12540, confId=confId) self.ff =
> AllChem.UFFGetMoleculeForceField(self.MOLEC) energy_value = str
> (self.ff.CalcEnergy()) print (energy_value)
>
Here you do generate and optimize many conformations, but then you
retrieve the force-field with UFFGetMoleculeForceField() always for
conformation -1 (the default), hence you get the same energy.
I slightly modified your script (see below) to actually generate a few
dozens of diverse conformations:
#!/usr/bin/env python
import sys
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
SMILES = 'CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2c21'
HowMany = 100
limitRMS = 2.0
mol = Chem.MolFromSmiles(SMILES)
mol = AllChem.AddHs(mol)
allconf = AllChem.EmbedMultipleConfs(mol,
numConfs = HowMany, enforceChirality=True, pruneRmsThresh = limitRMS)
w = Chem.SDWriter(sys.stdout)
for confId in allconf:
ff = AllChem.UFFGetMoleculeForceField(mol, confId = confId)
ff.Minimize()
energy_value = ff.CalcEnergy()
mol.SetProp('ENERGY', '{0:.2f}'.format(energy_value))
w.write(mol, confId = confId)
w.close()
> No matter what values are used for the numConfs or pruneRmsThresh after
> optimization I end up in conformer(s) with the same energy. The energy
> value vary from one run to another. In other words EmbedMultipleConfs()
> generate random structure (that make sense to me) but all conformation
> are very similar - after optimization all fall into one structure. Is
> it bug or feature? :) How effectively generate set of _different_
> conformation? I found two solution: a) execute presented above code
> multiple times b) set dihedral angle to unnatural value (using
> Chem.rdMolTransforms.SetDihedralDeg() function) for selected dihedral
> angle and then minimize structure Both works but seems to me that both
> are not optimal.
>
>
> For problem B:
>
> I want to minimize structure with frozen dihedral angle. I set the
> angle value using Chem.rdMolTransforms.SetDihedralDeg I could not find
> any possibility to freeze angle so I used
> rdForceField.ForceField.MMFFAddTorsionConstraint function. with very
> high forceConstant (relative=True minDihedralDeg=-5, maxDihedralDeg=5,
> forceConstant=999.9). The code is as follow:
>
>
> conformers=Chem.rdDistGeom.EmbedMultipleConfs(self.MOLEC,numConfs=confNum,
> enforceChirality=enforceChirality,numThreads=numThreads,
> pruneRmsThresh=RMSThreshold)
> for confId in range(len(conformers)):
> ff = AllChem.UFFGetMoleculeForceField(self.MOLEC, confId=confId)
> rdForceField.ForceField.MMFFAddTorsionConstraint( ff, idx0, idx1,
> idx2, idx3, True, minDihedralDeg=-5, maxDihedralDeg=5,
> forceConstant=999.9)
> Chem.rdMolTransforms.SetDihedralDeg(self.MOLEC.GetConformer(confId),
> idx0, idx1, idx2, idx3, 0.0 )
> AllChem.UFFOptimizeMolecule(self.MOLEC, maxIters=12540, confId=confId)
>
> but it does not work - i end up in structure with dihedral value far from
> this which was set. How can I force optimization with defined value (or some
> range of values)? In other words what I am doing wrong?
The problem here is that you are setting the constraint in MMFF and then
use UFF for minimization; furthermore MMFFAddTorsionConstraint() and
UFFAddTorsionConstraint() are member functions of the respective
force-fields. Please find below a sample script which should do what you
describe; here I read the value of the dihedral before and after
minimization, to verify that it is actually frozen.
#!/usr/bin/env python
import sys
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
SMILES = 'CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2c21'
HowMany = 100
limitRMS = 2.0
mol = Chem.MolFromSmiles(SMILES)
mol = AllChem.AddHs(mol)
tors = mol.GetSubstructMatch(Chem.MolFromSmarts('cCC[NH+]'))
allconf = AllChem.EmbedMultipleConfs(mol,
numConfs = HowMany, enforceChirality=True, pruneRmsThresh = limitRMS)
w = Chem.SDWriter(sys.stdout)
for confId in allconf:
ff = AllChem.UFFGetMoleculeForceField(mol, confId = confId)
before = AllChem.GetDihedralDeg(mol.GetConformer(confId),
tors[0], tors[1], tors[2], tors[3])
ff.UFFAddTorsionConstraint(tors[0], tors[1], tors[2], tors[3],
True, -5, 5, )
ff.Minimize()
energy_value = ff.CalcEnergy()
after = AllChem.GetDihedralDeg(mol.GetConformer(confId),
tors[0], tors[1], tors[2], tors[3])
mol.SetProp('DIHEDRAL', '{0:.2f},{1:.2f}'.format \
[Rdkit-discuss] conformation search and constraints
Hello, I want to find: A) "global minimum" [*] for given compound(s) and B) (for the same compound) minimum with constraint(s) (e.g. frozen angle) For problem A) I tried folowing code: self.MOLEC=Chem.MolFromSmiles(SMILES) self.MOLEC=Chem.AddHs(self.MOLEC) allconf=Chem.rdDistGeom.EmbedMultipleConfs(self.MOLEC, numConfs=HowMany, enforceChirality=True, pruneRmsThresh=limitRMS) for confId in range(len(allconf)): AllChem.UFFOptimizeMolecule(self.MOLEC, maxIters=12540, confId=confId) self.ff = AllChem.UFFGetMoleculeForceField(self.MOLEC) energy_value = str (self.ff.CalcEnergy()) print (energy_value) No matter what values are used for the numConfs or pruneRmsThresh after optimization I end up in conformer(s) with the same energy. The energy value vary from one run to another. In other words EmbedMultipleConfs() generate random structure (that make sense to me) but all conformation are very similar - after optimization all fall into one structure. Is it bug or feature? :) How effectively generate set of _different_ conformation? I found two solution: a) execute presented above code multiple times b) set dihedral angle to unnatural value (using Chem.rdMolTransforms.SetDihedralDeg() function) for selected dihedral angle and then minimize structure Both works but seems to me that both are not optimal. For problem B: I want to minimize structure with frozen dihedral angle. I set the angle value using Chem.rdMolTransforms.SetDihedralDeg I could not find any possibility to freeze angle so I used rdForceField.ForceField.MMFFAddTorsionConstraint function. with very high forceConstant (relative=True minDihedralDeg=-5, maxDihedralDeg=5, forceConstant=999.9). The code is as follow: conformers=Chem.rdDistGeom.EmbedMultipleConfs(self.MOLEC,numConfs=confNum, enforceChirality=enforceChirality,numThreads=numThreads, pruneRmsThresh=RMSThreshold) for confId in range(len(conformers)): ff = AllChem.UFFGetMoleculeForceField(self.MOLEC, confId=confId) rdForceField.ForceField.MMFFAddTorsionConstraint( ff, idx0, idx1, idx2, idx3, True, minDihedralDeg=-5, maxDihedralDeg=5, forceConstant=999.9) Chem.rdMolTransforms.SetDihedralDeg(self.MOLEC.GetConformer(confId), idx0, idx1, idx2, idx3, 0.0 ) AllChem.UFFOptimizeMolecule(self.MOLEC, maxIters=12540, confId=confId) but it does not work - i end up in structure with dihedral value far from this which was set. How can I force optimization with defined value (or some range of values)? In other words what I am doing wrong? Regards, Rafal [*] Yes I aware that it is very complex task to find a true global minima but I only want to find reasonably good/stable conformer, that why I wrote "global minimum" -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants
Now I think I know and I very much look forward to a more detailed
documentation.
many thanks,
-Monica
At 2016-04-22 17:48:39, "Greg Landrum" wrote:
There isn't great documentation for this, but the way the current code works is
reasonably simple.
If your reaction has two products (i.e. two molecules separated by a dot), you
will get two products (i.e. two separate molecules) when you call
RunReactants(); that's what you asked for.
Here's a very simple illustration of that with some silly isotope labels to
make it easier to see what's happening:
In [33]: rxn = AllChem.ReactionFromSmarts("[CH:1][O:2]>>[C:1].[O:2]")
In [34]: ps =
rxn.RunReactants((Chem.MolFromSmiles('[13CH2]1[12CH2][14CH2]O[15CH]1N'),))
In [35]: len(ps)
Out[35]: 1
In [36]: len(ps[0])
Out[36]: 2
In [37]: Chem.MolToSmiles(ps[0][0],True)
Out[37]: '[14CH2][12CH2][13CH2][15CH2]N'
In [39]: Chem.MolToSmiles(ps[0][1],True)
Out[39]: '[13CH2][12CH2][14CH2]O'
If you draw the molecule and the products, I think you'll see what's going on.
If you are just interested in breaking a bond, you need to use "component level
grouping", like this:
In [40]: rxn = AllChem.ReactionFromSmarts("[CH:1][O:2]>>([C:1].[O:2])")
In [41]: ps =
rxn.RunReactants((Chem.MolFromSmiles('[13CH2]1[12CH2][14CH2]O[15CH]1N'),))
In [42]: len(ps)
Out[42]: 1
In [43]: len(ps[0])
Out[43]: 1
In [44]: Chem.MolToSmiles(ps[0][0],True)
Out[44]: 'N[15CH2][13CH2][12CH2][14CH2]O'
That formulation says, in effect, "[C:1] and [O:2] should be in the same
product molecule, but there should be no bond between them".
I should probably do a blog post on this and then incorporate it into the
documentation.
I hope this helps clear things up,
-greg
On Fri, Apr 22, 2016 at 11:31 AM, 吴玲 wrote:
Hi Grégori,
Maybe I don't have a clear understanding of this function, I know the dot
represent disconncction of two fragments ,and I suppose changes just occurs
in mapped molecular fragment, the remaining part of reactant is invariable, in
other words, if mapped molecular fragment breaks based on input pattern, the
rest of the reactant is maintained.
So I still expect one site breaks, both ends would be connected by in-between
atons .Maybe I shoud deep study the documentation of rdkit and SMARTS
definition.
Thank for your helps!
Monica
At 2016-04-22 16:32:39, greg...@gerebtzoff.com wrote:
>Hi Monica,
>
>As Greg stated, why do you expect your product not to be fragmented?
>I suggest you to have a careful look at the SMARTS definition (for
>instance from Daylight:
>http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html)
>In SMARTS patterns, the dot indicates disconnected fragments. Thus you
>obtain in your product... disconnected fragments.
>
>Best,
>
>Grégori
>
>
>Le 2016-04-22 10:13, 吴玲 a écrit :
>> Greg,
>>
>> After changing the pattern into
>> "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11]
>> , I get the same result .A ring structure just like you said is broken
>> into pieces.
>> pattern:[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11]
>>
>> output:[O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=[O-].[NH4+].CCC=O
>>
>> The input reactant ([O-]C(=O)C1=CNC(=O)CC1) if mapped with
>> pattern'reactants ,it should be "
>> [O-:8][C:7](=[O:9])[C:6]1=[C:5][N:4][C:2](=[O:3])[C:1][C:*]1,
>>
>> what I mean is that the input reactant with a ring that CARBON6
>> connect with CARBON1 by CARBON* ,why the CARBON6 AND CARBON1 IN THE
>> product is not connected by the CARBON* ?
>>
>> Thanks a lot,
>>
>> -Monica
>>
>> At 2016-04-20 12:43:36, "Greg Landrum" wrote:
>>
>>> Monica,
>>>
>>> Why do you think you should get a single chain from the ring
>>> structure?
>>> If you look at the atom mapping in your input reaction:
>>>
>>>
>> [C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11]
>>>
>>> You've told it to put:
>>> - carbons 1 and 2 from the reactant into product 1
>>> - carbon 8 into product 2, carbon 7 into product 2 but converted
>>> into an oxygen first.
>>> - carbon 5 and 6 into product 4. In other words: you requested that
>>> the input molecule be broken into pieces.
>>>
>>> The atom mapping tells you which atoms in the reactants correspond
>>> to which atoms in the products.
>>>
>>> I would suggest that you look carefully at your reaction
>>> definitions, in particular the atom mapping numbers, in Marvin and
>>> make sure that you think that what you're asking for makes sense.
>>>
>>> -greg
>>>
>>> On Wed, Apr 20, 2016 at 6:04 AM, 吴玲
>>> wrote:
>>>
Hi Greg,
Thanks a lot for previous help! There is another question in
RunReactants I want to ask for some help.
when I input the pattern as
>>>
>> “[C:1][
Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants
There isn't great documentation for this, but the way the current code
works is reasonably simple.
If your reaction has two products (i.e. two molecules separated by a dot),
you will get two products (i.e. two separate molecules) when you call
RunReactants(); that's what you asked for.
Here's a very simple illustration of that with some silly isotope labels to
make it easier to see what's happening:
In [33]: rxn = AllChem.ReactionFromSmarts("[CH:1][O:2]>>[C:1].[O:2]")
In [34]: ps =
rxn.RunReactants((Chem.MolFromSmiles('[13CH2]1[12CH2][14CH2]O[15CH]1N'),))
In [35]: len(ps)
Out[35]: 1
In [36]: len(ps[0])
Out[36]: 2
In [37]: Chem.MolToSmiles(ps[0][0],True)
Out[37]: '[14CH2][12CH2][13CH2][15CH2]N'
In [39]: Chem.MolToSmiles(ps[0][1],True)
Out[39]: '[13CH2][12CH2][14CH2]O'
If you draw the molecule and the products, I think you'll see what's going
on.
If you are just interested in breaking a bond, you need to use "component
level grouping", like this:
In [40]: rxn = AllChem.ReactionFromSmarts("[CH:1][O:2]>>([C:1].[O:2])")
In [41]: ps =
rxn.RunReactants((Chem.MolFromSmiles('[13CH2]1[12CH2][14CH2]O[15CH]1N'),))
In [42]: len(ps)
Out[42]: 1
In [43]: len(ps[0])
Out[43]: 1
In [44]: Chem.MolToSmiles(ps[0][0],True)
Out[44]: 'N[15CH2][13CH2][12CH2][14CH2]O'
That formulation says, in effect, "[C:1] and [O:2] should be in the same
product molecule, but there should be no bond between them".
I should probably do a blog post on this and then incorporate it into the
documentation.
I hope this helps clear things up,
-greg
On Fri, Apr 22, 2016 at 11:31 AM, 吴玲 wrote:
> Hi Grégori,
>
> Maybe I don't have a clear understanding of this function, I know the dot
> represent disconncction of two fragments ,and I suppose changes just
> occurs in mapped molecular fragment, the remaining part of reactant is
> invariable, in other words, if mapped molecular fragment breaks based on
> input pattern, the rest of the reactant is maintained.
> So I still expect one site breaks, both ends would be connected by
> in-between atons .Maybe I shoud deep study the documentation of rdkit and
> SMARTS definition.
> Thank for your helps!
>
> Monica
>
>
>
>
>
> At 2016-04-22 16:32:39, greg...@gerebtzoff.com wrote:
> >Hi Monica,
> >
> >As Greg stated, why do you expect your product not to be fragmented?
> >I suggest you to have a careful look at the SMARTS definition (for
> >instance from Daylight:
> >http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html)
> >In SMARTS patterns, the dot indicates disconnected fragments. Thus you
> >obtain in your product... disconnected fragments.
> >
> >Best,
> >
> >Grégori
> >
> >
> >Le 2016-04-22 10:13, 吴玲 a écrit :
> >> Greg,
> >>
> >> After changing the pattern into
> >> "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11]
> >> , I get the same result .A ring structure just like you said is broken
> >> into pieces.
> >> pattern:[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11]
> >>
> >> output:[O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=[O-].[NH4+].CCC=O
> >>
> >> The input reactant ([O-]C(=O)C1=CNC(=O)CC1) if mapped with
> >> pattern'reactants ,it should be "
> >> [O-:8][C:7](=[O:9])[C:6]1=[C:5][N:4][C:2](=[O:3])[C:1][C:*]1,
> >>
> >> what I mean is that the input reactant with a ring that CARBON6
> >> connect with CARBON1 by CARBON* ,why the CARBON6 AND CARBON1 IN THE
> >> product is not connected by the CARBON* ?
> >>
> >> Thanks a lot,
> >>
> >> -Monica
> >>
> >> At 2016-04-20 12:43:36, "Greg Landrum" wrote:
> >>
> >>> Monica,
> >>>
> >>> Why do you think you should get a single chain from the ring
> >>> structure?
> >>> If you look at the atom mapping in your input reaction:
> >>>
> >>>
> >> [C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11]
> >>>
> >>> You've told it to put:
> >>> - carbons 1 and 2 from the reactant into product 1
> >>> - carbon 8 into product 2, carbon 7 into product 2 but converted
> >>> into an oxygen first.
> >>> - carbon 5 and 6 into product 4. In other words: you requested that
> >>> the input molecule be broken into pieces.
> >>>
> >>> The atom mapping tells you which atoms in the reactants correspond
> >>> to which atoms in the products.
> >>>
> >>> I would suggest that you look carefully at your reaction
> >>> definitions, in particular the atom mapping numbers, in Marvin and
> >>> make sure that you think that what you're asking for makes sense.
> >>>
> >>> -greg
> >>>
> >>> On Wed, Apr 20, 2016 at 6:04 AM, 吴玲
> >>> wrote:
> >>>
> Hi Greg,
>
> Thanks a lot for previous help! There is another question in
> RunReactants I want to ask for some help.
>
> when I input the pattern as
>
> >>>
> >> “[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][
Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants
Hi Grégori, Maybe I don't have a clear understanding of this function, I know the dot represent disconncction of two fragments ,and I suppose changes just occurs in mapped molecular fragment, the remaining part of reactant is invariable, in other words, if mapped molecular fragment breaks based on input pattern, the rest of the reactant is maintained. So I still expect one site breaks, both ends would be connected by in-between atons .Maybe I shoud deep study the documentation of rdkit and SMARTS definition. Thank for your helps! Monica At 2016-04-22 16:32:39, greg...@gerebtzoff.com wrote: >Hi Monica, > >As Greg stated, why do you expect your product not to be fragmented? >I suggest you to have a careful look at the SMARTS definition (for >instance from Daylight: >http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) >In SMARTS patterns, the dot indicates disconnected fragments. Thus you >obtain in your product... disconnected fragments. > >Best, > >Grégori > > >Le 2016-04-22 10:13, 吴玲 a écrit : >> Greg, >> >> After changing the pattern into >> "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] >> , I get the same result .A ring structure just like you said is broken >> into pieces. >> pattern:[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] >> >> output:[O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=[O-].[NH4+].CCC=O >> >> The input reactant ([O-]C(=O)C1=CNC(=O)CC1) if mapped with >> pattern'reactants ,it should be " >> [O-:8][C:7](=[O:9])[C:6]1=[C:5][N:4][C:2](=[O:3])[C:1][C:*]1, >> >> what I mean is that the input reactant with a ring that CARBON6 >> connect with CARBON1 by CARBON* ,why the CARBON6 AND CARBON1 IN THE >> product is not connected by the CARBON* ? >> >> Thanks a lot, >> >> -Monica >> >> At 2016-04-20 12:43:36, "Greg Landrum" wrote: >> >>> Monica, >>> >>> Why do you think you should get a single chain from the ring >>> structure? >>> If you look at the atom mapping in your input reaction: >>> >>> >> [C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11] >>> >>> You've told it to put: >>> - carbons 1 and 2 from the reactant into product 1 >>> - carbon 8 into product 2, carbon 7 into product 2 but converted >>> into an oxygen first. >>> - carbon 5 and 6 into product 4. In other words: you requested that >>> the input molecule be broken into pieces. >>> >>> The atom mapping tells you which atoms in the reactants correspond >>> to which atoms in the products. >>> >>> I would suggest that you look carefully at your reaction >>> definitions, in particular the atom mapping numbers, in Marvin and >>> make sure that you think that what you're asking for makes sense. >>> >>> -greg >>> >>> On Wed, Apr 20, 2016 at 6:04 AM, 吴玲 >>> wrote: >>> Hi Greg, Thanks a lot for previous help! There is another question in RunReactants I want to ask for some help. when I input the pattern as >>> >> “[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11]” and give the reactants rs1 = >>> >> ["[O-]C(=O)C1=CNC(=O)CC1","CC(=O)NC=C(CC([O-])=O)C([O-])=O","CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O"] ,rs2 = ['O'] , rs3 = ['O'], when I check the output product, I find that the first reactants with a ring structure divided into four sections instead of three parts containing a NH4+,a CO2,and a long chain composed by the remained two fragments.In other words , I think that the product should be like this: what's the matter with this pattern? why this reaction predicted is wrong and the other is correct?(output result attached below). pattern: 1 [O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=O.[NH4+].CCC=O 2 >>> >> CC(=O)NC=C(CC([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=(=O)[O-] 3 >>> >> CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=CCC(CO)C(=O)[O-] best wishes, monica >>> >> -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z [1] ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss [2] >
Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants
Hi Monica, As Greg stated, why do you expect your product not to be fragmented? I suggest you to have a careful look at the SMARTS definition (for instance from Daylight: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) In SMARTS patterns, the dot indicates disconnected fragments. Thus you obtain in your product... disconnected fragments. Best, Grégori Le 2016-04-22 10:13, 吴玲 a écrit : > Greg, > > After changing the pattern into > "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] > , I get the same result .A ring structure just like you said is broken > into pieces. > pattern:[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] > > output:[O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=[O-].[NH4+].CCC=O > > The input reactant ([O-]C(=O)C1=CNC(=O)CC1) if mapped with > pattern'reactants ,it should be " > [O-:8][C:7](=[O:9])[C:6]1=[C:5][N:4][C:2](=[O:3])[C:1][C:*]1, > > what I mean is that the input reactant with a ring that CARBON6 > connect with CARBON1 by CARBON* ,why the CARBON6 AND CARBON1 IN THE > product is not connected by the CARBON* ? > > Thanks a lot, > > -Monica > > At 2016-04-20 12:43:36, "Greg Landrum" wrote: > >> Monica, >> >> Why do you think you should get a single chain from the ring >> structure? >> If you look at the atom mapping in your input reaction: >> >> > [C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11] >> >> You've told it to put: >> - carbons 1 and 2 from the reactant into product 1 >> - carbon 8 into product 2, carbon 7 into product 2 but converted >> into an oxygen first. >> - carbon 5 and 6 into product 4. In other words: you requested that >> the input molecule be broken into pieces. >> >> The atom mapping tells you which atoms in the reactants correspond >> to which atoms in the products. >> >> I would suggest that you look carefully at your reaction >> definitions, in particular the atom mapping numbers, in Marvin and >> make sure that you think that what you're asking for makes sense. >> >> -greg >> >> On Wed, Apr 20, 2016 at 6:04 AM, 吴玲 >> wrote: >> >>> Hi Greg, >>> >>> Thanks a lot for previous help! There is another question in >>> RunReactants I want to ask for some help. >>> >>> when I input the pattern as >>> >> > “[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11]” >>> and give the reactants rs1 = >>> >> > ["[O-]C(=O)C1=CNC(=O)CC1","CC(=O)NC=C(CC([O-])=O)C([O-])=O","CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O"] >>> ,rs2 = ['O'] , rs3 = ['O'], >>> when I check the output product, I find that the first reactants >>> with a ring structure divided into four sections instead of three >>> parts containing a NH4+,a CO2,and a long chain composed by the >>> remained two fragments.In other words , I think that the product >>> should be like this: >>> >>> what's the matter with this pattern? why this reaction predicted >>> is wrong and the other is correct?(output result attached below). >>> >>> pattern: >>> >>> 1 [O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=O.[NH4+].CCC=O >>> >>> 2 >>> >> > CC(=O)NC=C(CC([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=(=O)[O-] >>> >>> 3 >>> >> > CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=CCC(CO)C(=O)[O-] >>> >>> best wishes, >>> >>> monica >>> >>> >> > -- >>> Find and fix application performance issues faster with >>> Applications Manager >>> Applications Manager provides deep performance insights into >>> multiple tiers of >>> your business applications. It resolves application problems >>> quickly and >>> reduces your MTTR. Get your free trial! >>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z [1] >>> ___ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss [2] > > > > Links: > -- > [1] https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > [2] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly > and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/list
[Rdkit-discuss] ReactionFromSmarts and RunReactants
Greg, After changing the pattern into "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] , I get the same result .A ring structure just like you said is broken into pieces. pattern:[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] output:[O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=[O-].[NH4+].CCC=O The input reactant ([O-]C(=O)C1=CNC(=O)CC1) if mapped with pattern'reactants ,it should be " [O-:8][C:7](=[O:9])[C:6]1=[C:5][N:4][C:2](=[O:3])[C:1][C:*]1, what I mean is that the input reactant with a ring that carbon6 connect with carbon1 by carbon* ,why the carbon6 and carbon1 in the product is not connected by the carbon* ? Thanks a lot, -Monica At 2016-04-20 12:43:36, "Greg Landrum" wrote: Monica, Why do you think you should get a single chain from the ring structure? If you look at the atom mapping in your input reaction: [C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11] You've told it to put: - carbons 1 and 2 from the reactant into product 1 - carbon 8 into product 2, carbon 7 into product 2 but converted into an oxygen first. - carbon 5 and 6 into product 4. In other words: you requested that the input molecule be broken into pieces. The atom mapping tells you which atoms in the reactants correspond to which atoms in the products. I would suggest that you look carefully at your reaction definitions, in particular the atom mapping numbers, in Marvin and make sure that you think that what you're asking for makes sense. -greg On Wed, Apr 20, 2016 at 6:04 AM, 吴玲 wrote: Hi Greg, Thanks a lot for previous help! There is another question in RunReactants I want to ask for some help. when I input the pattern as “[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11]” and give the reactants rs1 = ["[O-]C(=O)C1=CNC(=O)CC1","CC(=O)NC=C(CC([O-])=O)C([O-])=O","CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O"] ,rs2 = ['O'] , rs3 = ['O'], when I check the output product, I find that the first reactants with a ring structure divided into four sections instead of three parts containing a NH4+,a CO2,and a long chain composed by the remained two fragments.In other words , I think that the product should be like this: what's the matter with this pattern? why this reaction predicted is wrong and the other is correct?(output result attached below). pattern: 1 [O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=O.[NH4+].CCC=O 2 CC(=O)NC=C(CC([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=(=O)[O-] 3 CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=CCC(CO)C(=O)[O-] best wishes, monica -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
