Re: [Rdkit-discuss] Best Practice: Git model for code submissions to the RDkit
Hi JP, Best is to use branches for committing changes. And once the changes are in a state to share, then you merge the branch with master and do a pull request. Also try to use short meaningful names for branches. Regards, Christos On Thu, Oct 24, 2013 at 1:06 PM, JP jeanpaul.ebe...@inhibox.com wrote: Hi RDkit-Devs, ** Disclaimer: Just used git as svn till now ** What are the best practices for submitting code changes to the RDKit codebase via git? Right now I do the following: 0. Fork the rdkit repository (upstream) 1. Make my changes on the master 2. Send a pull request to original RDKit repo I have local commits I do not want to send in the pull request (e.g. .gitignore file which ignores all build files). Also I have some erroneous commits in my forked repo which I would not like to send over). The solution probably lies in using branches - but what is the best practice to do this? Should all commits which I want to send be in the branch and the commits I want to keep private be on the master (or on another branch). How do you do it? Perhaps I am thinking too much in terms of SVN. Cheers JP [small note: By mistake, I sent this email from another address to the mailing list and I got the Waiting for moderator approval message ... just pointing this out perhaps there are other messages stuck in that queue] -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Christos Kannas Researcher Ph.D Student e-Health Laboratory http://www.medinfo.cs.ucy.ac.cy/ kannas.chris...@ucy.ac.cy kannas.chris...@cs.ucy.ac.cy chriskan...@gmail.com Mob: (+357) 99530608 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Beta of Q3 2013 release available
Hi Greg (et al.), Thanks for the beta! I have been going through some of the recently-added functionality, and had a couple of questions regarding the PDB reading / writing. 1. Do I remember correctly that there was a proposal (from Roger) to add some auto bond-type perception to the PDB parser for ligands (or is that just wishful thinking!)? 2. If not, I notice that there is an AssignBondOrdersFromTemplate() method - but the example in the doc-string only shows (I think) the case where the input PDB is just a single small molecule - so the matching is pretty easy! I think a more real-World case is when one wants to set the bond orders for multiple ligands (HETATM residues) based on substructure matches - which will then return an atom index selection that can be used as a start point. Is there any way to have the AssignBondOrdersFromTemplate() convenience function optionally accept a list of atom indexes to specify a substructure? 3. Is there some explanation for what the 'flavor' option does for reading/writing PDB? 4. Having read in a PDB file I see the correct atoms flagged as HETATM (from GetIsHeteroAtom()). But when call Chem.MolToPDBBlock() these atoms get written as ATOM records... Also, a Chem.MolToPDBFile() method would be nice for completeness / symmetry : ) 5. It seems to me that GetResidueNumber() and GetSerialNumber() may have got mixed-up at some point(?). At least, when I call GetSerialNumber() I see what appears to be the residue number; and when I call GetResidueNumber() I get 0! 6. I also seem to be seeing all of the bonds (for all residues) being written out in CONECT records - such that they all appear as single bonds in eg PyMOL - is this expected behaviour at the moment? Cheers 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 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 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.. __-- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
