Hi Giulio,
Problem 1: check out vectorVector3. Initialized with a list of vector3,
e.g. my_vv = ob.vectorVector3([a, b])
Problem 3: What I meant is that the RMSD only takes into account the
aligned coordinates. If you want to include the RMSD of the other
coordinates, you need to work it out yourself.
Problem 2: Your pseduocode looks fine to me. Maybe use a set for atomlist
for a miniscule speedup. I hope all of your molecules are the same though,
and the atoms are in the same order, as otherwise it doesn't make sense as
the target and reference will involve things which don't correspond.
- Noel
On 3 June 2014 15:25, Giulio Pepe <gp...@cam.ac.uk> wrote:
> Dear Noel,
>
> just a few problems I am stuck with, using this procedure:
>
> - SetRef() and SetTarget() need a vector of vector3 objects as argument.
> While vector3 is an OpenBabel class, vector is not (I assume it is the C++
> vector?). How do I feed them a vector? Is a python list going to be fine?
>
> - The match to the SMARTS is to exclude from the alignment, so did I get
> it right if the one below is the procedure to do it, or is there a SMARTer
> (sorry, the pun was too tempting) way? Although this seems similar to the
> old (non-working) way.
>
> ob = pybel.ob
>
> smarts = pybel.Smarts("[OH]C=O")
>
> atomlist = []
> for i in smarts.findall(mol):
> for j in i:
> atomlist.append(j),
> for atom in mol:
> if atom.OBAtom.GetIdx() not in atomlist:
> reference.append(atom.vector)
>
> ob.OBAlign().SetTarget(reference)
> ...
>
> - Why ob.OBAlign().GetRMSD() should not work after using
> ob.OBAlign().Align() with this procedure? I am not sure why shall I apply
> the rotation matrix.
>
> Thanks a lot for your help!
> Best,
> Pepe
>
>
>
> On 30/05/14 19:46, Noel O'Boyle wrote:
>
> Try using SetRef() and SetTarget() instead with just the coordinates for
> the atoms you want to align (in the same order for both, as given by the
> match to the Smarts). Afterwards, if you want the RMSD for the whole
> molecule, you can manually calculate the whole molecule RMSD by translating
> one of the molecules to its centroid and applying the rotation matrix. (I
> can explain more if this is confusing.)
>
> - Noel
>
>
> On 24 May 2014 13:14, Giulio Pepe <gp...@cam.ac.uk> wrote:
>
>> Hi there,
>>
>> I am building a script in python that removes a certain moiety from two
>> molecules and calculates the RMSD between the remaining structure.
>>
>> I am doing this by asking for one or more SMARTS strings to find in the
>> molecules, labelling these atoms and deleting them using
>> OBMol.DeleteAtom(). Then, I align the molecules and find the RMSD using
>> the OBAlign() class.
>>
>> This works fine for some SMARTS string, but for others it gives a very
>> high and unrealistic RMSD value. I investigated the reason for this and
>> I found out that this is caused by a bad alignment of the two molecules.
>> I suspect that this is caused by a disordering of the atom labels caused
>> by removing certain SMARTS strings. I tested this by printing the
>> canonical labels.
>>
>> I tried to renumber the atoms using OBMol.RenumberAtoms(),
>> unsuccessfully. Symmetry should not be a problem in these molecules.
>>
>> Did anyone come across this, or have a better solution? I am attaching a
>> simplified version of my code below:
>>
>>
>> import pybel
>> ob = pybel.ob
>>
>> mol = [mola,molb]
>> smarts = [pybel.Smarts("[OH]C=O"),pybel.Smarts("C=C(C#N)C(=O)O")]
>>
>> for mols in mol:
>> mols.OBMol.StripSalts()
>> mols.removeh()
>>
>> if removemoiety:
>>
>> for ligands in smarts:
>>
>> i = 0
>> todelete = []
>> for mols in mol:
>> todelete.append([])
>> for atom in mols:
>> for l in ligands.findall(mol[i]):
>> if atom.OBAtom.GetIdx() in l:
>> todelete[i].append(atom.OBAtom)
>> i += 1
>>
>> j = 0
>> for mols in todelete:
>> for atom in mols:
>> mol[j].OBMol.DeleteAtom(atom)
>> j += 1
>>
>>
>> align = ob.OBAlign()
>> align.SetRefMol(mol[0].OBMol)
>> align.SetTargetMol(mol[1].OBMol)
>> align.Align()
>> print align.GetRMSD()
>>
>>
>> Thank you very much for your help!
>>
>> Best,
>> Pepe
>>
>>
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>
>
> --
> PhD Student
>
> Structure and Dynamics
> University of Cambridge
> Department of Physics
> Cavendish Laboratory
> J J Thomson Avenue
> CB3 0HE, UK
>
> Tel: +44 (0) 1223 337011 (Room 425)
> Fax: +44 (0) 1223 350266
> e-mail: gp...@cam.ac.uk
> web: www.giuliopepe.com
>
>
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