Ecosyste.ms: Issues

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GitHub / Discngine/fpocket issues and pull requests

#112 - Wrong fpocket menu when testing the command

Issue - State: open - Opened by FerrarV 9 months ago

#111 - Can I use fpocket to generate cavity spheres?

Issue - State: open - Opened by DipeshSomvanshi 11 months ago
Labels: question

#110 - Reformat Info Text Output into Json Format

Issue - State: open - Opened by Spill-Tea 11 months ago

#109 - change umlauts to normal O's

Pull Request - State: closed - Opened by ElizaKartchner about 1 year ago - 1 comment

#107 - Chain names longer than two characters

Issue - State: open - Opened by nurulnad about 1 year ago - 4 comments

#106 - Provide Windows build

Issue - State: open - Opened by colingcresset about 1 year ago

#105 - Segmentation fault error with -P flag

Issue - State: open - Opened by tugceoruc about 1 year ago - 2 comments

#104 - Specify output directory with fpocket.

Issue - State: open - Opened by egurapha about 1 year ago
Labels: question

#103 - MDpocket protein-protein complex error #question

Issue - State: open - Opened by H-EKE over 1 year ago

#102 - dpocket on apo-structures

Issue - State: open - Opened by fgentile89 over 1 year ago
Labels: question

#101 - dpocket-pocket volume reduces in the presence of HETATMs

Issue - State: closed - Opened by Peter-obi over 1 year ago
Labels: question

#100 - Problem compiling fpocket 4.1

Issue - State: open - Opened by xavgit over 1 year ago - 4 comments

#99 - Running fpocket on Compute Canada

Issue - State: open - Opened by RC-2000 over 1 year ago - 1 comment
Labels: question

#98 - Unable to run fpocket due to missing stdlibc++ libraries

Issue - State: open - Opened by RC-2000 over 1 year ago

#97 - Adding support for definition of explicit pockets

Pull Request - State: closed - Opened by pschmidtke over 1 year ago

#96 - *

Issue - State: closed - Opened by danplischke over 1 year ago - 1 comment

#95 - mdpocket libnetcdf.so.15 error

Issue - State: open - Opened by anicoli over 1 year ago

#94 - MDpocket output not complete

Issue - State: open - Opened by debarati31 over 1 year ago - 1 comment
Labels: question

#93 - mdpocket on aligned AMBER trajectory in pdb format

Issue - State: open - Opened by debarati31 over 1 year ago

#92 - <mdpocket> analysing snapshot 46! No Pockets Found while refining

Issue - State: open - Opened by H-EKE over 1 year ago - 4 comments
Labels: question

#91 - pdbxplugin) ERROR: could not reallocate bonds array.

Issue - State: open - Opened by amin-sagar over 1 year ago

#90 - dpocket tying dpout_fpocketnp.txt pocket predictions to pocket locations in 3D space

Issue - State: closed - Opened by czabriskie over 1 year ago - 1 comment
Labels: question

#89 - Reinstating POL atom types

Pull Request - State: open - Opened by jepdavidson over 1 year ago - 1 comment

#88 - [Snyk] Security upgrade ubuntu from latest to kinetic-20220830

Pull Request - State: closed - Opened by PeyratG over 1 year ago - 1 comment

#87 - [Snyk] Security upgrade ubuntu from latest to 22.04

Pull Request - State: closed - Opened by PeyratG over 1 year ago - 1 comment

#86 - Fix header typo for easier parsing

Pull Request - State: closed - Opened by jordansafer over 1 year ago - 1 comment

#85 - data files

Pull Request - State: closed - Opened by pschmidtke over 1 year ago

#84 - Druggability score from MDpocket

Issue - State: open - Opened by aishwaryshivgan almost 2 years ago - 2 comments
Labels: question

#83 - About using mdpocket

Issue - State: open - Opened by TianmingQu about 2 years ago
Labels: question

#82 - Using in Google Colab

Issue - State: closed - Opened by drorhunvural about 2 years ago
Labels: question

#81 - Why is fpocket not rotationally invariant?

Issue - State: closed - Opened by Finnem about 2 years ago - 2 comments
Labels: question

#80 - Remove memory leak

Pull Request - State: open - Opened by AlbertoSibylla over 2 years ago - 1 comment

#79 - MDpocket doubt

Issue - State: closed - Opened by pschmidtke over 2 years ago - 3 comments
Labels: question

#78 - Cysteines number does not match the actual input

Issue - State: open - Opened by areyesromero over 2 years ago - 2 comments

#77 - Membrane protein

Issue - State: open - Opened by d-beltran over 2 years ago - 2 comments
Labels: enhancement, question

#76 - Writing pdb output with -w b is broken

Issue - State: open - Opened by pschmidtke over 2 years ago

#75 - Hardcoded /tmp fails on systems without it

Issue - State: closed - Opened by jsoerensen over 2 years ago - 7 comments

#74 - MDpocket pocket characterization segmentation fault

Issue - State: open - Opened by obaedaakkad over 2 years ago - 3 comments
Labels: bug

#73 - Explicit ligand definition only works for pdb, but not cif

Issue - State: open - Opened by pschmidtke over 2 years ago
Labels: bug

#71 - License for fpocket2

Issue - State: closed - Opened by durrantlab almost 3 years ago - 1 comment
Labels: question

#70 - change docker image from CentOS to Ubuntu

Pull Request - State: closed - Opened by hhaootian almost 3 years ago - 2 comments

#69 - Problems compiling with M1 chip Mac

Issue - State: closed - Opened by SianXiaoCHN almost 3 years ago - 6 comments
Labels: question, compilation

#68 - Docker image fail to run

Issue - State: closed - Opened by hhaootian almost 3 years ago - 3 comments
Labels: question

#66 - Asa speedup

Pull Request - State: closed - Opened by qyuan7 about 3 years ago

#65 - Know the location of each pocket

Issue - State: open - Opened by PabloIriso about 3 years ago - 2 comments
Labels: question

#64 - Segmentation fault running MDpocket

Issue - State: open - Opened by KleinesMesser about 3 years ago - 4 comments
Labels: bug

#63 - Correct typo in mdpout.c

Pull Request - State: closed - Opened by qyuan7 about 3 years ago

#62 - Why are the default parameters different from those published in the paper?

Issue - State: closed - Opened by qyuan7 about 3 years ago - 1 comment
Labels: question

#61 - what's behind "exceeding memory size for each grid element"?

Issue - State: open - Opened by leonardblaschek about 3 years ago - 3 comments
Labels: question

#60 - Which is the pocket volumes unit of measurement?

Issue - State: closed - Opened by d-beltran over 3 years ago - 2 comments
Labels: question

#59 - Documentation stuff missing

Pull Request - State: closed - Opened by pschmidtke over 3 years ago

#58 - issues to compile the code with macOS Big Sur 11.1

Issue - State: closed - Opened by rrako14 over 3 years ago - 2 comments
Labels: question

#57 - Generate pdb of only the ligand in the orignal pdb

Issue - State: closed - Opened by Chokerino over 3 years ago - 2 comments
Labels: question

#56 - Analyze or find specific pocket by xyz coordinates

Issue - State: closed - Opened by davidRFB over 3 years ago - 4 comments
Labels: question

#55 - Update GETTINGSTARTED.md

Pull Request - State: closed - Opened by hhaootian almost 4 years ago

#54 - Pytests fail after installation from source

Issue - State: closed - Opened by MSchauperl almost 4 years ago - 1 comment
Labels: question

#53 - Mmcif

Pull Request - State: closed - Opened by ShorkarMael almost 4 years ago

#52 - Running f-pocket on multiple protein structures

Issue - State: closed - Opened by islem1994 almost 4 years ago - 2 comments
Labels: bug, question

#51 - Explicit pocket and keep chains

Pull Request - State: closed - Opened by ShorkarMael about 4 years ago - 2 comments

#49 - docker file and documentation update

Pull Request - State: closed - Opened by pschmidtke about 4 years ago

#47 - Enable automated build & test on azure pipelines

Issue - State: closed - Opened by pschmidtke about 4 years ago

#46 - Test to delete

Pull Request - State: closed - Opened by ShorkarMael about 4 years ago - 5 comments

#45 - Testing

Pull Request - State: closed - Opened by pschmidtke about 4 years ago

#44 - Generate non regression testing framework

Issue - State: closed - Opened by pschmidtke about 4 years ago
Labels: testing

#43 - adding conda install instructions

Pull Request - State: closed - Opened by pschmidtke about 4 years ago

#42 - Documentation

Pull Request - State: closed - Opened by pschmidtke about 4 years ago

#41 - Integrate mmcif parser

Issue - State: closed - Opened by pschmidtke about 4 years ago
Labels: enhancement

#40 - Enable functional fpocket test

Issue - State: open - Opened by pschmidtke about 4 years ago

#39 - Port documentation to md on github

Issue - State: closed - Opened by pschmidtke about 4 years ago - 2 comments
Labels: documentation

#38 - Enable docker support for fpocket & mdpocket

Issue - State: closed - Opened by pschmidtke about 4 years ago

#37 - Enable use of external file to define a protected HETATM list

Issue - State: open - Opened by pschmidtke about 4 years ago
Labels: enhancement

#36 - Allow override of predefined HETATM's in fpocket

Issue - State: open - Opened by pschmidtke about 4 years ago
Labels: enhancement

#35 - Enable explicit pocket detection considering an entire chain as a ligand

Issue - State: closed - Opened by pschmidtke about 4 years ago
Labels: enhancement

#34 - test

Pull Request - State: closed - Opened by ShorkarMael about 4 years ago

#33 - fpocket generates huge pockets for 3qmn

Issue - State: open - Opened by pschmidtke about 4 years ago

#32 - topology file

Issue - State: closed - Opened by pschmidtke about 4 years ago

#31 - Additional OS-X install instructions

Issue - State: closed - Opened by PatWalters about 4 years ago - 1 comment

#30 - Error analyzing Gromacs xtc file with mdpocket

Issue - State: open - Opened by mverissi about 4 years ago - 1 comment
Labels: bug

#29 - fix mdpocket to allow for reading in list of pdb files

Pull Request - State: closed - Opened by drewnutt about 4 years ago - 1 comment

#28 - Create LICENSE

Pull Request - State: closed - Opened by pschmidtke over 4 years ago

#27 - Erroneously accusing missing file

Issue - State: open - Opened by pslacerda over 4 years ago - 1 comment
Labels: bug

#26 - Segmentation fault on large dataset

Issue - State: open - Opened by pslacerda over 4 years ago - 4 comments

#25 - qhull input error

Issue - State: open - Opened by pslacerda over 4 years ago - 2 comments

#24 - mdpocket with --pdb_list flag just returns the help page

Issue - State: closed - Opened by joanGmcd over 4 years ago - 7 comments
Labels: bug

#23 - Containerized deployment option

Issue - State: open - Opened by CharlieLaughton over 4 years ago - 1 comment

#22 - Can I write a PKGBUILD and upload your script in AUR

Issue - State: closed - Opened by artefaritaKuniklo over 4 years ago - 1 comment

#21 - License

Issue - State: closed - Opened by simonbray almost 5 years ago - 2 comments

#20 - Conda package

Issue - State: closed - Opened by simonbray almost 5 years ago - 3 comments

#19 - Output score interpretation (fpocket)

Issue - State: open - Opened by V-JJ almost 5 years ago

#18 - fpocket installation error in MacOS Mojave

Issue - State: closed - Opened by rajiv03 over 5 years ago - 4 comments

#17 - drug_score value is zero in dpocket output results

Issue - State: open - Opened by SuMinyi over 5 years ago - 5 comments

#16 - Is it possible to use fpocket to compare two binding sites?

Issue - State: closed - Opened by diallobakary4 over 5 years ago - 1 comment

#15 - No output from mdpocket on ubuntu 16.04

Issue - State: closed - Opened by compchemeric almost 6 years ago - 2 comments

#14 - Examples / tests / manual entry for mdpocket

Issue - State: open - Opened by gmseabra almost 6 years ago

#13 - Pocket detection fails on batch of structures

Issue - State: closed - Opened by pschmidtke almost 6 years ago - 1 comment