| f1302d5 | patrickfuchs | 27 May 2019, 13:46:15 UTC | Remove old files | 27 May 2019, 13:46:15 UTC |
| 98a31e6 | patrickfuchs | 27 May 2019, 13:44:09 UTC | Clean up some old files | 27 May 2019, 13:44:09 UTC |
| 5ed7e2b | patrickfuchs | 19 May 2019, 13:38:50 UTC | Remove old function pandas and add docstring to main function | 19 May 2019, 13:38:50 UTC |
| 7f59246 | patrickfuchs | 19 May 2019, 13:33:00 UTC | Clean up code + add comments | 19 May 2019, 13:33:00 UTC |
| 5421c90 | patrickfuchs | 18 May 2019, 16:17:41 UTC | Add CH3 reconstruction + cleaning up | 18 May 2019, 16:17:41 UTC |
| 3d3d84d | patrickfuchs | 18 May 2019, 14:06:03 UTC | Add CH double bond reconstruction | 18 May 2019, 14:06:03 UTC |
| a483781 | patrickfuchs | 15 May 2019, 10:12:30 UTC | Switch to MDAnalysis & add single CH reconstruction | 15 May 2019, 10:12:30 UTC |
| fc63955 | patrickfuchs | 13 May 2019, 20:48:32 UTC | Update README | 13 May 2019, 20:48:32 UTC |
| 4e80018 | patrickfuchs | 12 May 2019, 17:27:55 UTC | Retrieve helpers using row index | 12 May 2019, 17:27:55 UTC |
| bd086da | patrickfuchs | 12 May 2019, 17:07:18 UTC | Add index (atom name) to pandas dataframe rows | 12 May 2019, 17:07:18 UTC |
| 564cc7c | patrickfuchs | 12 May 2019, 16:54:05 UTC | Switch to Unix newline | 12 May 2019, 17:01:18 UTC |
| d799a36 | patrickfuchs | 12 May 2019, 16:31:33 UTC | Remove (now) useless functions reconstruct_hydrogens() and reconstruct_hydrogens2() | 12 May 2019, 16:31:33 UTC |
| 7c69f90 | patrickfuchs | 12 May 2019, 16:29:59 UTC | Reconstruct H residue by residue (function reconstruct_hydrogens3) | 12 May 2019, 16:29:59 UTC |
| ddbe7b3 | patrickfuchs | 12 May 2019, 15:53:01 UTC | Make a list of pandas dataframe residues (function pdb2list_pandasdf_residues) | 12 May 2019, 15:53:01 UTC |
| 882e47b | patrickfuchs | 11 May 2019, 15:12:43 UTC | Avoid append with pandas dataframes (function reconstruct_hydrogens2) | 11 May 2019, 15:12:43 UTC |
| b43048b | patrickfuchs | 10 May 2019, 22:28:33 UTC | Move reconstruct_hydrogens to a function | 10 May 2019, 22:28:33 UTC |
| a685ee0 | patrickfuchs | 10 May 2019, 21:35:21 UTC | Change a few comments | 10 May 2019, 21:35:21 UTC |
| 60802f3 | patrickfuchs | 28 April 2019, 18:54:35 UTC | Clean up a few minor things | 28 April 2019, 18:54:35 UTC |
| 6012afa | patrickfuchs | 28 April 2019, 18:52:07 UTC | Add 1POPC.pdb | 28 April 2019, 18:52:07 UTC |
| 352327e | patrickfuchs | 28 April 2019, 18:35:45 UTC | Clean up the merge on add_hydrogens.py | 28 April 2019, 18:35:45 UTC |
| 9a11e20 | patrickfuchs | 28 April 2019, 17:59:06 UTC | Reconstruct H on many POPC with pandas df | 28 April 2019, 17:59:06 UTC |
| 4264fd1 | ABacle | 28 April 2019, 00:05:05 UTC | Add of the cases 4-5-6 (CH3) and tests on the terminal C. Result in the CH3_GOGO.pdb | 28 April 2019, 00:05:05 UTC |
| 309e2f4 | ABacle | 27 April 2019, 23:24:37 UTC | CH double bond corrected. Worked on C24 and C25 carbon. Result in CH_db_GOGO.pdb file | 27 April 2019, 23:24:37 UTC |
| 01bc4ec | patrickfuchs | 27 April 2019, 19:28:40 UTC | Reconstruct all H from one POPC | 27 April 2019, 19:28:40 UTC |
| 2bd837c | patrickfuchs | 27 April 2019, 18:05:29 UTC | Fix dataframe conversion to a 2D-array Fixes #1 | 27 April 2019, 18:05:29 UTC |
| c44508a | patrickfuchs | 27 April 2019, 17:52:14 UTC | Fix read_pdb() docstring | 27 April 2019, 17:52:14 UTC |
| a816043 | patrickfuchs | 27 April 2019, 17:35:11 UTC | Clean up Amelie's dev tries | 27 April 2019, 17:35:11 UTC |
| 6fd603a | ABacle | 27 April 2019, 01:22:02 UTC | Test for CH double bond but not effective yet. A bug to correct | 27 April 2019, 01:22:02 UTC |
| 22bc5ed | ABacle | 26 April 2019, 22:27:50 UTC | First test and success of reconstructing H of the C-H case | 26 April 2019, 22:27:50 UTC |
| 49dbd39 | patrickfuchs | 26 April 2019, 20:29:45 UTC | Quick and dirty try with pandas dataframe | 26 April 2019, 20:29:45 UTC |
| 91ebf32 | patrickfuchs | 26 April 2019, 20:29:08 UTC | Add POPC files | 26 April 2019, 20:29:08 UTC |
| 2d6a8a0 | patrickfuchs | 26 April 2019, 16:38:46 UTC | Rename gro file | 26 April 2019, 16:38:46 UTC |
| f043ffa | patrickfuchs | 26 April 2019, 16:34:04 UTC | Make docstrings PEP257 compliant | 26 April 2019, 16:34:04 UTC |
| 30391cb | ABacle | 26 April 2019, 10:47:38 UTC | Functions for rotation and hydrogen reconstruction. Test of those functions on simple cases. carbon_test.gro is the file generated by gromacs, carbon_H.pdb are the carbon and hydrogens reconstruct with this tool. | 26 April 2019, 10:47:38 UTC |
| 66323f4 | ABacle | 25 April 2019, 16:33:27 UTC | Correction distance C-H | 25 April 2019, 16:33:27 UTC |
| 7b0f536 | ABacle | 25 April 2019, 12:34:51 UTC | Remove screenshots | 25 April 2019, 12:34:51 UTC |
| 056ee57 | ABacle | 01 April 2019, 13:57:43 UTC | Corrected python file and updated nmm files | 01 April 2019, 13:57:43 UTC |
| 17afcef | Abacle | 25 March 2019, 14:14:17 UTC | Tests avec VMD Tests with VMD to try to understand how the tool works, what are the different vectors computed and what are the results returned. | 25 March 2019, 14:14:17 UTC |
| 2b1b32f | Abacle | 07 March 2019, 10:35:26 UTC | Add files via upload First version of the tool. Adaptation of the Fortran program (subroutine_add_hydrogen.f) in Python (subroutine_add_hydrogen.py). The three functions in Python has been tested on simple examples and returned correct answers. I tried to translate the case 3 (CH2) of the Fortran switch in Python using the previous functions. I've done several tests with the C5 carbon of the first lipid in the start_protonateded.gro structure (generated with Gromacs tool and ffgmx2.hdb parameter file). So far, wasn't able to get correct 3D coordinates for the hydrogens. But, when I checked the structure of the lipid, there is not an angle of 109.5° between the hydrogens and N4/C5/C6 atoms. I assume that in the Fortran code, v1 is the central atom meaning C5 here. v2 and v3 are named helpers meaning N4 (-> v2) and C6 (->v3) in my example. Also, I have no effective way to test if the vectors that I used are correctly computed (using VMD for example) and doing so I'm not sure that the procedure that I've coded is correct too. | 07 March 2019, 10:35:26 UTC |
| ae8ea07 | patrickfuchs | 06 March 2019, 16:54:03 UTC | Update README | 06 March 2019, 16:54:03 UTC |
| 1de6298 | patrickfuchs | 06 March 2019, 16:52:57 UTC | Initial commit | 06 March 2019, 16:52:57 UTC |
