Rdkit mol object
I posted a memo about how to read maestro file format from RDKit. I would like to know the way to communicate rdkit from schrodinger python API. I read the API in lunch break and tested some methods. Fortunately it worked well. Example is below. Then sanitize mol and convert rdkit mol object to schrodinger mol object.
Now I could convert rdkit mol objects to schrodinger mol objects.
Next I tried conversion from schrodinger mol objects to rdkit mol objects. I could not show output because I wrote this blog post from my personal computer. But above code worked. And there are many methods are provided to schrodinger mol obj. Hmm it seems exciting for me. I check the API more deeply! You are commenting using your WordPress.
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At first read sample sdf from rdkit. SDMolSupplier "solubility.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Skip to content. Permalink Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.
Sign up. Branch: master. Find file Copy path. Cannot retrieve contributors at this time. Raw Blame History. The contents are covered by the terms of the BSD license which is included in the file license.
DeleteAll if not forcePDB and mol. Remedy that. Not going to worry about this too deeply since the files are in a temp dir anyway. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window.
All Rights Reserved. This file is part of the RDKit. The contents are covered by the terms of the BSD license. Python3 compatibility. GetConformer confId. GetAtomPosition idx. PyMol will interpret the path to be relative to where it was started. Not going to worry about this too deeply since. This was github GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.
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Draw RDKit mol/reaction object on HTML without static png image #RDKit #memo
My current solution works by using a slightly modified version of the method described hereand does a good job at solving my problem.
In this case, I have tried to neutralize both A and A' using this method modified to deal with rdkit mols only before comparing them. This works to solve part 1 of the problem, but wipes the atom molAtomMapNumber properties from the atoms that the neutralization function interacts with, making completing the mapping impossible. I haven't yet been able to figure out how to preserve atom numbers through the neutralization function I use - any idea about how to do this would be greatly appreciated.
Additionally, if anyone has ideas for how to better solve this problem, I would love to hear them! Am I correct in assuming that the atom mapping information you want to keep is located in the input molecules? The atom map information is stored as atom properties.
These are not copied along by the neutralization strategy from the RDKit Cookbook post.An Introduction to Molecular Dynamics
In order to make this work you would need to use an approach that preserves that information. I'm afraid that I can't come up with a quick answer to this one. An easier solution may be possible if you can provide a bit more information about what your input looks like and what you would like to have for output.
Yes that is correct: the input molecule A contains the mapping information in its atom's molAtomMapNumber property. One thing that would help is if somehow the mapping information could be carried through the substructure replacement done by the neutralization function. An ideal solution would look like this:.
In this case, the replace substruct process may look like this:. I think my issue is in step two. Skip to content. Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Sign up.
New issue. Jump to bottom. Labels question. Copy link Quote reply. I am currently trying to find a way to solve the following two part problem: Given a compound A represented as an rdkit mol object, find a compound A' in a list of compounds also represented as rdkit mols that has the same structure as A.You seem to have CSS turned off. Please don't fill out this field. Please provide the ad click URL, if possible:. Help Create Join Login. Operations Management.
IT Management. Project Management. Services Business VoIP. Resources Blog Articles Deals. Menu Help Create Join Login. Re: [Rdkit-discuss] How to sort a list of mol objects Re: [Rdkit-discuss] How to sort a list of mol objects. Re: [Rdkit-discuss] How to sort a list of mol objects. Oh no! Some styles failed to load. Sign Up No, Thank you. Thanks for helping keep SourceForge clean. X You seem to have CSS turned off.
Briefly describe the problem required :.
convert rdkit mol object to schrodinger’s mol object #RDKit #Chemoinformatics
Upload screenshot of ad required :. Hi Paolo, Your previous reply already helped me. If I need to sort multiple properties, with different directions, What would the code be? Would it be easier to put mols into a pandas dataframe? If so, how to do it? Could you help?
Hi Zhenting, you mean sort by a property value? Thanks, that is exactly What I want. One useful tip he gives is that in Python, you always get a stable sort. That means if you sort on one key and then on a second, items that have the same 2nd key will be left in the order they were in after the first sort. This makes sorting on multiple criteria a matter of doing individual sorts in succession. Hi, I've tested the code below, and found out that put mol objects into pandas is just straightforward.The chirality of an Atom is determined by two things:.
For tetrahedral coordination, the chiralTag tells you what direction you have to rotate to get from bond 2 to bond 3 while looking down bond 1.
NOTE: if an atom has an implicit H, the bond to that H is considered to be at the end of the list of other bonds. Definition at line 69 of file Atom.
Definition at line 76 of file Atom. Definition at line 91 of file Atom. Definition at line 79 of file Atom. Definition at line of file Atom. Referenced by RDKit::describeQuery. Notes: The general rule is that if a property on this atom has a non-default value, the property on the other atom must have the same value. The exception to this is H counts, which are ignored. These turns out to be impossible to handle generally, so rather than having odd and hard-to-explain exceptions, we ignore them entirely.
Referenced by setOwningMol. Definition at line 70 of file Atom. Definition at line 71 of file Atom. Definition at line 72 of file Atom. The class for representing atoms. Properties can be marked as calculatedin which case they will be cleared when the clearComputedProps method is called. Because they have no impact upon chemistry, all property operations are constthis allows extra flexibility for clients who need to store extra data on Atom objects.
Atom objects are lazy about computing their explicit and implicit valence values. These will not be computed until their values are requested. Chirality: The chirality of an Atom is determined by two things: its chiralTag the input order of its bonds see note below for handling of implicit Hs For tetrahedral coordination, the chiralTag tells you what direction you have to rotate to get from bond 2 to bond 3 while looking down bond 1.
Gets the atom map Number of the atom, if no atom map exists, 0 is returned. Parameters probe a list of bond indices. This must be the same length as our number of incoming bonds our degree. Returns the number of swaps required to convert the ordering of the probe list to match the order of our incoming bonds: e.
Notes: requires an owning molecule. Set the atom map Number of the atom. References setOwningMol. RDKit Open-source cheminformatics and machine learning. Atom unsigned int num.You seem to have CSS turned off. Please don't fill out this field. Please provide the ad click URL, if possible:. Help Create Join Login.
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Operations Management. IT Management. Project Management. Services Business VoIP. Resources Blog Articles Deals. Menu Help Create Join Login. Re: [Rdkit-discuss] serialization of EditableMol objects? Oh no! Some styles failed to load.
Sign Up No, Thank you. Thanks for helping keep SourceForge clean. X You seem to have CSS turned off. Briefly describe the problem required :. Upload screenshot of ad required :. I noticed that the calls to Chem. GetMol to get back the new molecule, and to em. Mol rwmol EditableMols will eventually be deprecated and shouldn't be used any more in new code.
Would rdkit-devel be better for this sort of question? Best, -greg. As part of an iterative computation on a molecule, I have to repeatedly remove different combinations of bonds from it. EditableMol to create the em, to em. RemoveBonds to remove the bonds were taking the most time in my code that loops over different combinations of bonds.
To speed things up, I though about storing copies of intermediate ems in a dictionary, but unfortunately no methods for pickling EditableMol objects seems to be available. For example, this code Also, I'm new to the rdkit community and hope I'm sending my message to the right place.The RDKit Book. Beginning with the If you need to continue using Python 2, please stick with a release from the This document is intended to provide an overview of how one can use the RDKit functionality from Python.
If you find mistakes, or have suggestions for improvements, please either fix them yourselves in the source document the. Contributing to the documentation is a great service both to the RDKit community and to your future self. The majority of the basic molecular functionality is found in module rdkit. Chem :. All of these functions return a rdkit. Mol object on success:. In each case the value None is returned:. Groups of molecules are read using a Supplier for example, an rdkit.
SDMolSupplier or a rdkit. SmilesMolSupplier :. An alternate type of Supplier, the rdkit. ForwardSDMolSupplier can be used to read from file-like objects:. Single molecules can be converted to text using several functions present in the rdkit. Chem module. Note that the SMILES provided is canonical, so the output should be the same no matter how a particular molecule is input:. Note: as of this writing Augthe smiles provided when one requests kekuleSmiles are not canonical.
Generating a mol block for a molecule that does not have coordinates will, by default, automatically cause coordinates to be generated.
These are not, however, stored with the molecule. Coordinates can be generated and stored with the molecule using functionality in the rdkit. AllChem module see the Chem vs AllChem section for more information.
Or you can add 3D coordinates by embedding the molecule this uses the ETKDG method, which is described in more detail below :. Multiple molecules can be written to a file using an rdkit.
SDWriter object:. Other available Writers include the rdkit. SmilesWriter and the rdkit. GetAtomWithIdxuse the rdkit.
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RingInfo class:. Normally molecules are stored in the RDKit with the hydrogen atoms implicit e. When it is useful to have the hydrogens explicitly present, for example when generating or optimizing the 3D geometry, the :py:func:rdkit.