Re: [Rdkit-discuss] Extracting data of a standard structural formula
Hi Jason,
yes, indeed it helped!
Many many thanks!
Regards,
Peleg
On Sun, Aug 13, 2017 at 4:29 PM, Jason Biggs wrote:
> Peleg,
> I was doing something similar using the c++ function compute2DCoords,
> where you can give a coordinate map as the second argument. It looks like
> this is exposed in python, using the Compute2DCoords method (
> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-
> class.html#Compute2DCoords), so you could do something like this
>
> int generate2DCoordinatesPlacintHeavyAtomsFirst( RDKit::RWMol
> *thisMolecule,
> bool placeHeavyAtomsFirst,
> bool canonicalize,
> int randomseed)
> {
>
>
> int hydrogenFreeConformerIndex =
> RDDepict::compute2DCoords(*thisMolecule, 0,
> canonicalize);
>
> //now make a map of the coordinates which were optimized
> //sans hydrogens
>
> RDGeom::INT_POINT2D_MAP coordMap;
> if(placeHeavyAtomsFirst)
> {
> int numAtoms = thisMolecule->getNumAtoms();
> RDKit::Conformer hydrogenFreeConformer =
> thisMolecule->getConformer(hydrogenFreeConformerIndex);
> for (int i=0; i < numAtoms; i++)
> {
> RDGeom::Point3D pt =
> hydrogenFreeConformer.getAtomPos(i);
> RDGeom::Point2D pt2;
> pt2.x = pt.x;
> pt2.y = pt.y;
> coordMap[i] = pt2;
> }
> }
>
> RDKit::MolOps::addHs(*thisMolecule, false, false);
>
> int confID = RDDepict::compute2DCoords(
> *thisMolecule,
> placeHeavyAtomsFirst ? &coordMap : 0, true);
> const RDKit::Conformer &conf =
> thisMolecule->getConformer(confID);
> RDKit::WedgeMolBonds(*thisMolecule, &conf);
> return confID;
>
> }
>
>
> Now when I feed the result to my plotting program, I can give the option
> of showing hydrogens or not, getting these two diagrams
>
> Hope this helps,
>
> Jason
>
>
> On Sun, Aug 13, 2017 at 6:45 AM, Peleg Bar-Sapir wrote:
>
>> Greg,
>>
>> sorry for flooding you with replies, I think I understand where they
>> issue stems from: the added hydrogens.
>> Without the hydrogens the positions look fine (see C9_acid_out.png).
>> Is there a way to add hydrogens so it will form a more "classic"
>> representation? (e.g. C9_acid_expect.png)
>>
>> Best,
>> Peleg
>>
>> On Sun, Aug 13, 2017 at 1:36 PM, Peleg Bar-Sapir
>> wrote:
>>
>>> To further clarify what I mean: I created a nonanoic acid representation
>>> (via the smiles code "C(=O)O").
>>> "Pelarginic_acid.svg.png" is what I expect to get in terms of
>>> coordinates, while "test_out.png" are the coordinates I actually get.
>>>
>>> On Sun, Aug 13, 2017 at 1:30 PM, Peleg Bar-Sapir
>>> wrote:
>>>
Hi Greg,
Thank you for your reply!
I tested the method you suggested, but it seems like
rdMolDraw2D.PrepareMolForDrawing() has no affect.
e.g, I have a molecule m, to which I add hydrogens. I then compute the
2D coordinates of m, and use rdMolDraw2D.PrepareMolForDrawing() as you
suggested.
To test it, I compare the outputs of Chem.MolToMolBlock() on the
molecule and on the prepared drawing.
The results are the same, and it is defently not what you would expect
from a standard representation (i.e. the ketone oxygen is not vertically up
from its carbon, the chain is not oriented right, etc.).
See the following explicit example:
In[5]: m = Chem.MolFromSmiles('CCC(O)=O')
In[6]: m = Chem.AddHs(m)
In[7]: AllChem.Compute2DCoords(m)
In[8]: m_draw = Chem.Draw.rdMolDraw2D.PrepareMolForDrawing(m)
In[9]: print (Chem.MolToMolBlock(m))
RDKit 2D
11 10 0 0 0 0 0 0 0 0999 V2000
1.3490 -0.43400. C 0 0 0 0 0 0 0 0 0 0 0 0
0.34210.67780. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.12420.36170. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5836 -1.06620. O 0 0 0 0 0 0 0 0 0 0 0 0
-2.13111.47350. O 0 0 0 0 0 0 0 0 0 0 0 0
2.8153 -0.11800. H 0 0 0 0 0 0 0 0 0 0 0 0
1.9149 -1.82320. H 0 0 0 0 0 0 0 0 0 0 0 0
0.0792 -1.23260. H 0 0 0 0 0 0 0 0 0 0 0 0
1.61191.47630. H 0 0 0 0 0 0 0 0 0 0 0 0
-0.22382.06690. H 0 0 0 0 0 0 0 0 0 0 0 0
-3.0499 -1.38230. H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3
Re: [Rdkit-discuss] Extracting data of a standard structural formula
Peleg,
I was doing something similar using the c++ function compute2DCoords, where
you can give a coordinate map as the second argument. It looks like this
is exposed in python, using the Compute2DCoords method (
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-class.html#Compute2DCoords),
so you could do something like this
int generate2DCoordinatesPlacintHeavyAtomsFirst( RDKit::RWMol
*thisMolecule,
bool placeHeavyAtomsFirst,
bool canonicalize,
int randomseed)
{
int hydrogenFreeConformerIndex =
RDDepict::compute2DCoords(*thisMolecule, 0,
canonicalize);
//now make a map of the coordinates which were optimized
//sans hydrogens
RDGeom::INT_POINT2D_MAP coordMap;
if(placeHeavyAtomsFirst)
{
int numAtoms = thisMolecule->getNumAtoms();
RDKit::Conformer hydrogenFreeConformer =
thisMolecule->getConformer(hydrogenFreeConformerIndex);
for (int i=0; i < numAtoms; i++)
{
RDGeom::Point3D pt =
hydrogenFreeConformer.getAtomPos(i);
RDGeom::Point2D pt2;
pt2.x = pt.x;
pt2.y = pt.y;
coordMap[i] = pt2;
}
}
RDKit::MolOps::addHs(*thisMolecule, false, false);
int confID = RDDepict::compute2DCoords(
*thisMolecule,
placeHeavyAtomsFirst ? &coordMap : 0, true);
const RDKit::Conformer &conf =
thisMolecule->getConformer(confID);
RDKit::WedgeMolBonds(*thisMolecule, &conf);
return confID;
}
Now when I feed the result to my plotting program, I can give the option of
showing hydrogens or not, getting these two diagrams
Hope this helps,
Jason
On Sun, Aug 13, 2017 at 6:45 AM, Peleg Bar-Sapir wrote:
> Greg,
>
> sorry for flooding you with replies, I think I understand where they issue
> stems from: the added hydrogens.
> Without the hydrogens the positions look fine (see C9_acid_out.png).
> Is there a way to add hydrogens so it will form a more "classic"
> representation? (e.g. C9_acid_expect.png)
>
> Best,
> Peleg
>
> On Sun, Aug 13, 2017 at 1:36 PM, Peleg Bar-Sapir wrote:
>
>> To further clarify what I mean: I created a nonanoic acid representation
>> (via the smiles code "C(=O)O").
>> "Pelarginic_acid.svg.png" is what I expect to get in terms of
>> coordinates, while "test_out.png" are the coordinates I actually get.
>>
>> On Sun, Aug 13, 2017 at 1:30 PM, Peleg Bar-Sapir
>> wrote:
>>
>>> Hi Greg,
>>>
>>> Thank you for your reply!
>>> I tested the method you suggested, but it seems like
>>> rdMolDraw2D.PrepareMolForDrawing() has no affect.
>>> e.g, I have a molecule m, to which I add hydrogens. I then compute the
>>> 2D coordinates of m, and use rdMolDraw2D.PrepareMolForDrawing() as you
>>> suggested.
>>> To test it, I compare the outputs of Chem.MolToMolBlock() on the
>>> molecule and on the prepared drawing.
>>> The results are the same, and it is defently not what you would expect
>>> from a standard representation (i.e. the ketone oxygen is not vertically up
>>> from its carbon, the chain is not oriented right, etc.).
>>>
>>> See the following explicit example:
>>>
>>> In[5]: m = Chem.MolFromSmiles('CCC(O)=O')
>>>
>>> In[6]: m = Chem.AddHs(m)
>>>
>>> In[7]: AllChem.Compute2DCoords(m)
>>>
>>> In[8]: m_draw = Chem.Draw.rdMolDraw2D.PrepareMolForDrawing(m)
>>>
>>> In[9]: print (Chem.MolToMolBlock(m))
>>>
>>> RDKit 2D
>>>
>>> 11 10 0 0 0 0 0 0 0 0999 V2000
>>> 1.3490 -0.43400. C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 0.34210.67780. C 0 0 0 0 0 0 0 0 0 0 0 0
>>>-1.12420.36170. C 0 0 0 0 0 0 0 0 0 0 0 0
>>>-1.5836 -1.06620. O 0 0 0 0 0 0 0 0 0 0 0 0
>>>-2.13111.47350. O 0 0 0 0 0 0 0 0 0 0 0 0
>>> 2.8153 -0.11800. H 0 0 0 0 0 0 0 0 0 0 0 0
>>> 1.9149 -1.82320. H 0 0 0 0 0 0 0 0 0 0 0 0
>>> 0.0792 -1.23260. H 0 0 0 0 0 0 0 0 0 0 0 0
>>> 1.61191.47630. H 0 0 0 0 0 0 0 0 0 0 0 0
>>>-0.22382.06690. H 0 0 0 0 0 0 0 0 0 0 0 0
>>>-3.0499 -1.38230. H 0 0 0 0 0 0 0 0 0 0 0 0
>>> 1 2 1 0
>>> 2 3 1 0
>>> 3 4 1 0
>>> 3 5 2 0
>>> 1 6 1 0
>>> 1 7 1 0
>>> 1 8 1 0
>>> 2 9 1 0
>>> 2 10 1 0
>>> 4 11 1 0
>>> M END
>>>
>>> In[10]: print (Chem.MolToMolBlock(m_draw))
>>>
>>> RDKit 2D
>>>
>>> 11 10 0
Re: [Rdkit-discuss] Extracting data of a standard structural formula
To further clarify what I mean: I created a nonanoic acid representation
(via the smiles code "C(=O)O").
"Pelarginic_acid.svg.png" is what I expect to get in terms of coordinates,
while "test_out.png" are the coordinates I actually get.
On Sun, Aug 13, 2017 at 1:30 PM, Peleg Bar-Sapir wrote:
> Hi Greg,
>
> Thank you for your reply!
> I tested the method you suggested, but it seems like
> rdMolDraw2D.PrepareMolForDrawing()
> has no affect.
> e.g, I have a molecule m, to which I add hydrogens. I then compute the 2D
> coordinates of m, and use rdMolDraw2D.PrepareMolForDrawing() as you
> suggested.
> To test it, I compare the outputs of Chem.MolToMolBlock() on the molecule
> and on the prepared drawing.
> The results are the same, and it is defently not what you would expect
> from a standard representation (i.e. the ketone oxygen is not vertically up
> from its carbon, the chain is not oriented right, etc.).
>
> See the following explicit example:
>
> In[5]: m = Chem.MolFromSmiles('CCC(O)=O')
>
> In[6]: m = Chem.AddHs(m)
>
> In[7]: AllChem.Compute2DCoords(m)
>
> In[8]: m_draw = Chem.Draw.rdMolDraw2D.PrepareMolForDrawing(m)
>
> In[9]: print (Chem.MolToMolBlock(m))
>
> RDKit 2D
>
> 11 10 0 0 0 0 0 0 0 0999 V2000
> 1.3490 -0.43400. C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.34210.67780. C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.12420.36170. C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.5836 -1.06620. O 0 0 0 0 0 0 0 0 0 0 0 0
>-2.13111.47350. O 0 0 0 0 0 0 0 0 0 0 0 0
> 2.8153 -0.11800. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.9149 -1.82320. H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0792 -1.23260. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.61191.47630. H 0 0 0 0 0 0 0 0 0 0 0 0
>-0.22382.06690. H 0 0 0 0 0 0 0 0 0 0 0 0
>-3.0499 -1.38230. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> 3 5 2 0
> 1 6 1 0
> 1 7 1 0
> 1 8 1 0
> 2 9 1 0
> 2 10 1 0
> 4 11 1 0
> M END
>
> In[10]: print (Chem.MolToMolBlock(m_draw))
>
> RDKit 2D
>
> 11 10 0 0 0 0 0 0 0 0999 V2000
> 1.3490 -0.43400. C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.34210.67780. C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.12420.36170. C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.5836 -1.06620. O 0 0 0 0 0 0 0 0 0 0 0 0
>-2.13111.47350. O 0 0 0 0 0 0 0 0 0 0 0 0
> 2.8153 -0.11800. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.9149 -1.82320. H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0792 -1.23260. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.61191.47630. H 0 0 0 0 0 0 0 0 0 0 0 0
>-0.22382.06690. H 0 0 0 0 0 0 0 0 0 0 0 0
>-3.0499 -1.38230. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> 3 5 2 0
> 1 6 1 0
> 1 7 1 0
> 1 8 1 0
> 2 9 1 0
> 2 10 1 0
> 4 11 1 0
> M END
>
>
> Am I missing something?
>
> Best,
> Peleg
>
> On Sun, Aug 13, 2017 at 11:59 AM, Greg Landrum
> wrote:
>
>> Hi Peleg,
>>
>> On Sat, Aug 12, 2017 at 4:08 PM, Peleg Bar-Sapir
>> wrote:
>>
>>>
>>> I'm trying to get the 2D coordinates and info of all the atoms and
>>> bonds, including hydrogens (i.e. atom type, bond type, etc.) of a molecule
>>> in a standard structural formula. To clarify: I'm not referring to
>>> Chem.MolToMolBlock(), but the coordinates used by the Draw class (e.g. in
>>> MolToFile()) to create standard representations.
>>>
>>> Any advice on how to extract those? Maybe one can reach them via one of
>>> the Draw member functions/variables?
>>>
>>
>> The drawing code calls rdMolDraw2D.PrepareMolForDrawing() before
>> actually doing the drawing. This function, among other things, assigns
>> coordinates. Assuming that you're looking for the coordinates in the
>> molecule's coordinate space, you can get access to them by calling
>> PrepareMolForDrawing() and then either getting a mol block:
>>
>> In [7]: m = Chem.AddHs(Chem.MolFromSmiles('CC#C'))
>>
>> In [8]: nm = rdMolDraw2D.PrepareMolForDrawing(m)
>>
>> In [9]: print(Chem.MolToMolBlock(nm))
>>
>> RDKit 2D
>>
>> 7 6 0 0 0 0 0 0 0 0999 V2000
>>-0.6887 -0.07950. C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.8112 -0.06140. C 0 0 0 0 0 0 0 0 0 0 0 0
>> 2.3111 -0.04330. C 0 0 0 0 0 0 0 0 0 0 0 0
>>-1.4230 -1.38750. H 0 0 0 0 0 0 0 0 0 0 0 0
>>-2.10440.41650. H 0 0 0 0 0 0 0 0 0 0 0 0
>>-0.44611.40070. H 0 0 0 0 0 0 0 0 0 0 0 0
>> 1.5400 -0.2455
Re: [Rdkit-discuss] Extracting data of a standard structural formula
Hi Greg,
Thank you for your reply!
I tested the method you suggested, but it seems like
rdMolDraw2D.PrepareMolForDrawing() has no affect.
e.g, I have a molecule m, to which I add hydrogens. I then compute the 2D
coordinates of m, and use rdMolDraw2D.PrepareMolForDrawing() as you
suggested.
To test it, I compare the outputs of Chem.MolToMolBlock() on the molecule
and on the prepared drawing.
The results are the same, and it is defently not what you would expect from
a standard representation (i.e. the ketone oxygen is not vertically up from
its carbon, the chain is not oriented right, etc.).
See the following explicit example:
In[5]: m = Chem.MolFromSmiles('CCC(O)=O')
In[6]: m = Chem.AddHs(m)
In[7]: AllChem.Compute2DCoords(m)
In[8]: m_draw = Chem.Draw.rdMolDraw2D.PrepareMolForDrawing(m)
In[9]: print (Chem.MolToMolBlock(m))
RDKit 2D
11 10 0 0 0 0 0 0 0 0999 V2000
1.3490 -0.43400. C 0 0 0 0 0 0 0 0 0 0 0 0
0.34210.67780. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.12420.36170. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5836 -1.06620. O 0 0 0 0 0 0 0 0 0 0 0 0
-2.13111.47350. O 0 0 0 0 0 0 0 0 0 0 0 0
2.8153 -0.11800. H 0 0 0 0 0 0 0 0 0 0 0 0
1.9149 -1.82320. H 0 0 0 0 0 0 0 0 0 0 0 0
0.0792 -1.23260. H 0 0 0 0 0 0 0 0 0 0 0 0
1.61191.47630. H 0 0 0 0 0 0 0 0 0 0 0 0
-0.22382.06690. H 0 0 0 0 0 0 0 0 0 0 0 0
-3.0499 -1.38230. H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
3 5 2 0
1 6 1 0
1 7 1 0
1 8 1 0
2 9 1 0
2 10 1 0
4 11 1 0
M END
In[10]: print (Chem.MolToMolBlock(m_draw))
RDKit 2D
11 10 0 0 0 0 0 0 0 0999 V2000
1.3490 -0.43400. C 0 0 0 0 0 0 0 0 0 0 0 0
0.34210.67780. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.12420.36170. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5836 -1.06620. O 0 0 0 0 0 0 0 0 0 0 0 0
-2.13111.47350. O 0 0 0 0 0 0 0 0 0 0 0 0
2.8153 -0.11800. H 0 0 0 0 0 0 0 0 0 0 0 0
1.9149 -1.82320. H 0 0 0 0 0 0 0 0 0 0 0 0
0.0792 -1.23260. H 0 0 0 0 0 0 0 0 0 0 0 0
1.61191.47630. H 0 0 0 0 0 0 0 0 0 0 0 0
-0.22382.06690. H 0 0 0 0 0 0 0 0 0 0 0 0
-3.0499 -1.38230. H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
3 5 2 0
1 6 1 0
1 7 1 0
1 8 1 0
2 9 1 0
2 10 1 0
4 11 1 0
M END
Am I missing something?
Best,
Peleg
On Sun, Aug 13, 2017 at 11:59 AM, Greg Landrum
wrote:
> Hi Peleg,
>
> On Sat, Aug 12, 2017 at 4:08 PM, Peleg Bar-Sapir wrote:
>
>>
>> I'm trying to get the 2D coordinates and info of all the atoms and bonds,
>> including hydrogens (i.e. atom type, bond type, etc.) of a molecule in a
>> standard structural formula. To clarify: I'm not referring to
>> Chem.MolToMolBlock(), but the coordinates used by the Draw class (e.g. in
>> MolToFile()) to create standard representations.
>>
>> Any advice on how to extract those? Maybe one can reach them via one of
>> the Draw member functions/variables?
>>
>
> The drawing code calls rdMolDraw2D.PrepareMolForDrawing() before actually
> doing the drawing. This function, among other things, assigns coordinates.
> Assuming that you're looking for the coordinates in the molecule's
> coordinate space, you can get access to them by calling
> PrepareMolForDrawing() and then either getting a mol block:
>
> In [7]: m = Chem.AddHs(Chem.MolFromSmiles('CC#C'))
>
> In [8]: nm = rdMolDraw2D.PrepareMolForDrawing(m)
>
> In [9]: print(Chem.MolToMolBlock(nm))
>
> RDKit 2D
>
> 7 6 0 0 0 0 0 0 0 0999 V2000
>-0.6887 -0.07950. C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.8112 -0.06140. C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.3111 -0.04330. C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.4230 -1.38750. H 0 0 0 0 0 0 0 0 0 0 0 0
>-2.10440.41650. H 0 0 0 0 0 0 0 0 0 0 0 0
>-0.44611.40070. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5400 -0.24550. H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 3 0
> 1 4 1 0
> 1 5 1 0
> 1 6 1 0
> 3 7 1 0
> M END
>
>
> Or by using the molecule's conformer object:
>
> In [13]: conf = nm.GetConformer()
>
> In [14]: for aidx in range(conf.GetNumAtoms()):
> ...: pos = conf.GetAtomPosition(aidx)
> ...: print(pos.x, pos.y, pos.z)
> ...:
> -0.6887274130576998 -0.07950997820751476 0.0
> 0.8111632161215289 -0.0613964335423347 0.0
> 2.311053845300757 -0.043
Re: [Rdkit-discuss] Extracting data of a standard structural formula
Hi Peleg,
On Sat, Aug 12, 2017 at 4:08 PM, Peleg Bar-Sapir wrote:
>
> I'm trying to get the 2D coordinates and info of all the atoms and bonds,
> including hydrogens (i.e. atom type, bond type, etc.) of a molecule in a
> standard structural formula. To clarify: I'm not referring to
> Chem.MolToMolBlock(), but the coordinates used by the Draw class (e.g. in
> MolToFile()) to create standard representations.
>
> Any advice on how to extract those? Maybe one can reach them via one of
> the Draw member functions/variables?
>
The drawing code calls rdMolDraw2D.PrepareMolForDrawing() before actually
doing the drawing. This function, among other things, assigns coordinates.
Assuming that you're looking for the coordinates in the molecule's
coordinate space, you can get access to them by calling
PrepareMolForDrawing() and then either getting a mol block:
In [7]: m = Chem.AddHs(Chem.MolFromSmiles('CC#C'))
In [8]: nm = rdMolDraw2D.PrepareMolForDrawing(m)
In [9]: print(Chem.MolToMolBlock(nm))
RDKit 2D
7 6 0 0 0 0 0 0 0 0999 V2000
-0.6887 -0.07950. C 0 0 0 0 0 0 0 0 0 0 0 0
0.8112 -0.06140. C 0 0 0 0 0 0 0 0 0 0 0 0
2.3111 -0.04330. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4230 -1.38750. H 0 0 0 0 0 0 0 0 0 0 0 0
-2.10440.41650. H 0 0 0 0 0 0 0 0 0 0 0 0
-0.44611.40070. H 0 0 0 0 0 0 0 0 0 0 0 0
1.5400 -0.24550. H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 3 0
1 4 1 0
1 5 1 0
1 6 1 0
3 7 1 0
M END
Or by using the molecule's conformer object:
In [13]: conf = nm.GetConformer()
In [14]: for aidx in range(conf.GetNumAtoms()):
...: pos = conf.GetAtomPosition(aidx)
...: print(pos.x, pos.y, pos.z)
...:
-0.6887274130576998 -0.07950997820751476 0.0
0.8111632161215289 -0.0613964335423347 0.0
2.311053845300757 -0.0432827715446 0.0
-1.4229859378146839 -1.387510138307542 0.0
-2.104358766425875 0.416461665499047 0.0
-0.4461124978218231 1.4007393261007453 0.0
1.5399675536977953 -0.24550155266524612 0.0
I'm not sure what kind of additional info you are looking for, but maybe
this much helps?
-greg
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[Rdkit-discuss] Extracting data of a standard structural formula
Hello all, I'm trying to get the 2D coordinates and info of all the atoms and bonds, including hydrogens (i.e. atom type, bond type, etc.) of a molecule in a standard structural formula. To clarify: I'm not referring to Chem.MolToMolBlock(), but the coordinates used by the Draw class (e.g. in MolToFile()) to create standard representations. Any advice on how to extract those? Maybe one can reach them via one of the Draw member functions/variables? Best, Peleg -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
