Activity for jdurrant
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jdurrant posted a comment on discussion General Discussion
Hi Wesley. Wanted to let you know that the latest version is posted here: https://git.durrantlab.pitt.edu/jdurrant/wisp All the best.
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Hi Douglas. Wanted to let you know that the latest version is posted here: https://git.durrantlab.pitt.edu/jdurrant/wisp All the best.
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Hi Patrick. Much thanks for your interest in AutoGrow, and please forgive my delay in getting back to you. We're currently putting together a new version of AutoGrow with some major improvements. My student Jake Spiegel has rewritten and modernized almost the entire codebase. We hope to submit the work for publication in a few months. I'm not sure why exactly the old version isn't processing your input molecules properly, but I'm confident the new version will be able to handle them if they are amenable...
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Hi Douglas. Sorry for the delay. You're right that NNScore could use an update. It's remarkable how quickly the PDBbind database expands! :) I do think it would take a bit more to create a new version of NNScore than applying my existing scripts, though. Here are just a few things that come to mind: 1) It would need to be Python3 compatible, since Python2 will soon reach end of life. All my scripts are written in Python2. 2) It would probably be best if it used a more modern neural-network library...
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Hi Dr. Houston. Much thanks for your interest in nnscore. I believe that error occurs when nnscore encounters two adjacent atoms with types that were not commonly found to be adjacent in the training data. Rather than trying to make a guess based on insufficient data, nnscore simply throws the error. In practice, though, the fact that these atoms are adjacent is probably a good indication that the pose is not correct. Hope this answer helps. All the best.
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Hi Wesley. Just wanted to let you know that I got your code. Much thanks for this contribution! I've gotten this version running on Python 3 as well. We're going to test it intnerally for a bit and then publish it for others to use. Can I include you in the CONTRIBUTORS.md file? All the best.
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Wesley, please forgive me for my delay in getting back to you! My sourceforge emails were going to my old UCSD email address, but I'm now at the University of Pittsburgh. Wonderful that you were able to patch the code to work with the latest version of networkx. Would you mind emailing your updated code to me at durrantj at pitt dot edu? All the best.
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Hi Andrew. Please forgive my ridiculous delay in getting back to you. I wanted to let you know that we have begun to work on Autogrow 4. We intend to make it more modular so that custom filters can be easily added. I expect we won't be ready to publish for some months, but I wanted to let you know we're working on it! All the best.
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Hi Francesco. Did you end up getting the run to work?
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Hi Francesco. If I'm not mistaken, autogrow can filter my molecular weight. That's one of Lipinski's rules.
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Autogrow does have settings to optionally eliminate compounds if they violate Lipinski's rules, and one of those rules is MW < 500. Could that be the problem?
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Hi Francesco. I completely understand the need to avoid posting the molecules publicly! It might help with debugging if I had a copy, though. But before we talk further about that, have you tried running autogrow several times? Evolutionary algorithms depend on a lot of random choices. Sometimes the algorithm gets stuck in an evolutionary dead end, but if you rerun it will take a different, more productive path. Could you try running it several times, and if that still doesn't work we could talk...
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No worries, Francesco! Happy you were able to resolve the question. All the best.
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Hi Francesco. What do your input molecules look like? Is it just one molecule, or is it multiple ones?
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Hi Francesco. These are all SciPy errors, so you'll want to get that running. Modifying the autogrow source code (by commenting out critical lines, for example) is likely to cause you problems in the future. It is true that python modules are directories, but it's often best just to install them globally so you can access them from anywhere. That way you don't have to look into the package contents themselves. SciPy installation on Debian is described here: https://www.scipy.org/install.html#ubuntu-debian...
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Hi Francesco. I think I might understand the problem. Please correct me if I'm wrong... Autogrow and Autodock (i.e., MGLTools) are entirely different programs that are similarly named. I am not involved in the Autodock project. For reasons I don't understand, their scripts like prepare_ligand4.py sometimes require the user to use the version of Python they distribute with MGLTools. I imagine they have not included SciPy in that distribution. My program (Autogrow) does require SciPy. So it should...
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It is true that you're using an older version of SciPy, though 0.14.0 does seem to have scipy.optimize: https://docs.scipy.org/doc/scipy-0.14.0/reference/optimize.html I'm using scipy 0.18.1 and had no trouble importing the package: Python 2.7.13 |Anaconda custom (x86_64)| (default, Dec 20 2016, 23:05:08) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin Type "help", "copyright", "credits" or "license" for more information. Anaconda is brought to you by Continuum Analytics. Please...
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Thanks for your interest in autogrow. This seems to be a problem with your SciPy installation rather than with autogrow itself. Can you tell me which version of SciPy you have installed? Within Python: import scipy print scipy.version If it's not a very recent version of the module, you might need to upgrade to the latest version. I also recommend using anaconda Python, which often provided access to more recent versions of modules: https://www.continuum.io/downloads Let me know if your SciPy version...
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Hi Suhad. It seems both Vina and NNScore are giving you the same answer. Also, glycerol...
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Hi Suhad. If you're getting a vina score of zero, there might be something else wrong...
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Hi Suhad. Happy to help. As with other docking programs, NNScore isn't well suited...
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I recently got an email from an AutoGrow user who couldn't generate any reactions....
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Hi Suhad. Sorry for my delay. 1) They are right in recognizing that NNScore isn't...
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Hi Jerry. Happy to hear you've got AutoGrow installed. Would you mind sending me...
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Hi Jerry. I'm happy you're interested in trying AutoGrow. AutoGrow uses Open Babel...
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Hi Suhad. I'm happy that the ODDT authors have included an nnscore-like scoring function...
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Hi Albert. Please forgive my delay in getting back to you. As currently implemented,...
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Very happy you were able to get this to work, Suhad. Thanks again for your interest...
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Hi Suhad. I can't be sure without seeing your files, but I wonder if your ligand...
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Hi Steve. You aren't by chance using an ancient version of scipy, are you? I think...
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Hi Steve. I'm happy you're planning on using AutoGrow in your research. AutoGrow...
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Hi Albert. Thanks for this question. I did some investigating and was able to figure...
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Hi Albert. AutoGrow uses a program called AutoClickChem to add fragments to your...
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Hi Albert. I'll look into adding some other open-source scoring functions (e.g.,...
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Hi Albert. I'll look into adding some other opensource scoring functions (e.g., RF-SCORE)...
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Hi Albert. If I'm not mistaken, it is possible to restart an AutoGrow job. If you...
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Hi Albert. Happy my answers helped. There are two publications: Durrant, J. D., et...
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Hi Albert. The long bond you're seeing is actually an azide group. If you show the...
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Hi Albert. Not sure, but it could be because you didn't put a space between the "openbabel_bin_directory"...
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Hi Albert. I'm happy you're using AutoGrow in your research. I think the problem...
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Hi Frits. I'm happy you're interested in AutoGrow. Allow me to answer your questions:...
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You can register for this forum using this link: https://sourceforge.net/user/re...
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Initial commit
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Hi Adam. Happy to hear that the Phenix output PDB does have the right columns. All...
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Corrected wrong version number in autogrow_3_1_...
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Minor updates. Now version 3.1.1.
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Hi Adam. Thanks for posting your question, and for giving me the idea of starting...
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Further minor updates.
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Minor updates/improvements, version number now ...
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Corrected an error in the way the bilayer chunk...
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Separated things into different files to improv...
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Adding coarse-grained models correctly.
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Added coarse-grained planar bilayer models to ....
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Update git repository to LipidWrapper 1.14
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