[Rdkit-discuss] Interacting with molecules in PyMOL
Dear All, I am trying to work out the best way to accomplish some tasks involving RDKit, using PyMOL as an interface, and would appreciate some help. I would like to be able to start from a PDB file of a ligand-bound crystal structure loaded in PyMOL and be able to 'virtually' build some analogues - initially just simple substitutions - and visually inspect the results. (1) So my first question is - having started PyMOL with the -R option, is there an easy or recommended way of transferring molecules from PyMOL to RDKit? I can accomplish this by writing molfiles to a temporary file, but wondered if I am creating work, if eg RDKit could automatically create Mol objects from non-biopolymer atoms in PyMol(?). ie it would be nice if: from rdkit import Chem from rdkit.Chem import PyMol v = PyMol.MolViewer() # Invented function to create an RDKit mol object mol = v.GetAtomsAsMol(selection) (2) Once the ligand is converted to an RDKit mol object (by whatever means) I want to enumrate some libraries of virtual products - eg choosing an atom in PyMol as the attachment point, then running a set of reactions to get products with a set of substituents added. In principle I think this is quite straightforward; however, what I am struggling with is a mechanism to 'freeze' the 3D coordintes of the original ligand atoms, but still be able to use RDKit to generate sensible 3D positions for the newly added atoms so that the products can be passed back to PyMOL and minimised in situ (if required) using 'mengine.exe'. Am I looking at this the wrong way, and should I actually try aligning the virtual products back on the starting ligand conformation? (3) Apologies that this last point is maybe a bit off-topic, but I wondered if anyone has an opinion as to whether MMTK is the way to go for 'simple' minimisations of modified ligands bound to proteins? (I don't have any real experience with MMTK... Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __-- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Interacting with molecules in PyMOL
Dear Greg, Thanks for your very rapid response - 'AllChem.ConstrainedEmbed' was just what I was looking for! Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Interacting with molecules in PyMOL
I just wanted to quickly update the List on how I've got on with this,
in case it is of use / interest to others. I followed Greg's advice and
did the following:
1. Exported molfile from PyMOL
2. Read into RDKit
3. Read in an SDF of already-constructed molecules based on the core
(could have built the products in RDKit, but the SDF was already
available!)
4. Iterated over the objects in the supplier to do the
AllChem.ConstrainedEmbed as discussed, then load the results into PyMOL
NOTE - Because the molecules weren't built in RDKit, I couldn't rely on
the atom numbering when read into PyMOL (maybe this can't be relied on
anyway?). So I ran mol.GetSubstructMatch(core) for each molecule to get
the aligned product atom IDs that matched the core. I then flagged
these in PyMOL with flag 3 [Fixed Atoms (no movement allowed)] (flag 2 -
harmonically constrained may be better..?) so that I could subsequently
run the mengine 'clean' command in PyMOL to tidy-up the UFF output
without allowing the template to move:
from rdkit import Chem
core = Chem.MolFromMolFile(mol_filepath)
supplier = Chem.SDMolSupplier(sdf_filepath)
for n,mol in enumerate(supplier):
mol = Chem.AddHs(mol)
newMol = AllChem.ConstrainedEmbed(mol, core, True)
name = mol+str(n)
fix = ','.join([str(n) for n in mol.GetSubstructMatch(core)])
v.ShowMol(newMol, name=name, showOnly=False)
selection = '('+name+' and (id '+fix+'))'
v.server.do('flag 3, '+selection+', set')
Kind regards
James
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for the named addressee(s) only and access to it by anyone else is
unauthorised. If you are not an addressee, any disclosure or copying of the
contents of this email or any action taken (or not taken) in reliance on it is
unauthorised and may be unlawful. If you have received this email in error,
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accuracy or completeness of this message or any attachment(s). Please check
this email for virus infection for which the Company accepts no responsibility.
If verification of this email is sought then please request a hard copy. Unless
otherwise stated, any views or opinions presented are solely those of the
author and do not represent those of the Company.
The Vernalis Group of Companies
Oakdene Court
613 Reading Road
Winnersh, Berkshire
RG41 5UA.
Tel: +44 118 977 3133
To access trading company registration and address details, please go to the
Vernalis website at www.vernalis.com and click on the Company address and
registration details link at the bottom of the page..
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Re: [Rdkit-discuss] Interacting with molecules in PyMOL
Dear James,
Thanks for sending along the information about how you did the pymol
steps; I'm sure it will be useful to others. Tighter RDKit-PyMol
integration is definitely a good thing.
Best Regards,
-greg
On Fri, Jul 2, 2010 at 8:09 PM, James Davidson j.david...@vernalis.com wrote:
I just wanted to quickly update the List on how I've got on with this, in
case it is of use / interest to others. I followed Greg's advice and did
the following:
1. Exported molfile from PyMOL
2. Read into RDKit
3. Read in an SDF of already-constructed molecules based on the core (could
have built the products in RDKit, but the SDF was already available!)
4. Iterated over the objects in the supplier to do the
AllChem.ConstrainedEmbed as discussed, then load the results into PyMOL
NOTE - Because the molecules weren't built in RDKit, I couldn't rely on the
atom numbering when read into PyMOL (maybe this can't be relied on
anyway?). So I ran mol.GetSubstructMatch(core) for each molecule to get the
aligned product atom IDs that matched the core. I then flagged these in
PyMOL with flag 3 [Fixed Atoms (no movement allowed)] (flag 2 - harmonically
constrained may be better..?) so that I could subsequently run the mengine
'clean' command in PyMOL to tidy-up the UFF output without allowing the
template to move:
from rdkit import Chem
core = Chem.MolFromMolFile(mol_filepath)
supplier = Chem.SDMolSupplier(sdf_filepath)
for n,mol in enumerate(supplier):
mol = Chem.AddHs(mol)
newMol = AllChem.ConstrainedEmbed(mol, core, True)
name = mol+str(n)
fix = ','.join([str(n) for n in mol.GetSubstructMatch(core)])
v.ShowMol(newMol, name=name, showOnly=False)
selection = '('+name+' and (id '+fix+'))'
v.server.do('flag 3, '+selection+', set')
Kind regards
James
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