haddocking/pdb-tools issues and pull requests

#169 - Any rotation / translation commands? [feature request] [question]

Issue - State: open - Opened by UnixJunkie 23 days ago - 2 comments
Labels: Tool Request

#168 - CIF to PDB: issue in pdb_fromcif for predicted structures

Issue - State: open - Opened by venzera 3 months ago
Labels: bug

#167 - chain renaming when converting cif to pdb

Issue - State: open - Opened by zzhangzzhang 3 months ago
Labels: Tool Request

#166 - Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#165 - How to add insertion codes on PDB

Issue - State: open - Opened by Sofia-FR 9 months ago - 1 comment
Labels: Tool Request

#164 - Added pdb_selb to filter by B-factor values

Pull Request - State: open - Opened by ahmedselim2017 10 months ago - 2 comments

#163 - pdb_selb

Issue - State: open - Opened by amjjbonvin 11 months ago
Labels: Tool Request

#162 - Update build_and_test.yml to remove Py2 images.

Pull Request - State: closed - Opened by JoaoRodrigues about 1 year ago - 3 comments

#161 - Adds missing `ENDMDL` on `HETATM` in `pdb_tidy`

Pull Request - State: closed - Opened by joaomcteixeira about 1 year ago - 1 comment
Labels: bug

#160 - pdb_tidy discards ENDMDL statements for HETATM ensembles

Issue - State: closed - Opened by amjjbonvin about 1 year ago
Labels: bug

#159 - pdb_merge should discard MODEL/ENDMDL statements

Issue - State: open - Opened by amjjbonvin over 1 year ago
Labels: enhancement

#158 - fix bug pdb_selaltloc.py

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

#157 - Remove support to py3.6

Pull Request - State: closed - Opened by joaomcteixeira almost 2 years ago

#156 - [FEATURE] improved/corrected `pdb_selaltloc` tool

Pull Request - State: open - Opened by joaomcteixeira almost 2 years ago - 2 comments
Labels: bug, enhancement

#155 - `pdb_tidy` removes the `TER` record between chains and removes last `ENDMDL` in a multi-model PDB

Issue - State: open - Opened by rvhonorato almost 2 years ago - 8 comments
Labels: bug

#154 - first draft of solution to selaltloc bug

Pull Request - State: closed - Opened by mgiulini about 2 years ago - 7 comments

#153 - pdb_selaltloc removes residues with (only) alternate locations

Issue - State: open - Opened by mgiulini about 2 years ago - 22 comments
Labels: bug

#152 - Question on `pdb_keepcoord`

Issue - State: closed - Opened by joaomcteixeira about 2 years ago - 4 comments

#151 - Inverts `-strict` behaviour in `pdb_tidy`

Pull Request - State: open - Opened by joaomcteixeira over 2 years ago
Labels: enhancement

#150 - Improve `pdb_merge` to include `TER`s and `END` lines

Pull Request - State: open - Opened by joaomcteixeira over 2 years ago - 13 comments
Labels: bug, enhancement

#149 - pdb_merge not adding END statement

Issue - State: closed - Opened by amjjbonvin over 2 years ago - 1 comment
Labels: bug, enhancement

#148 - pdb_fixinsert can't handle the PDB, which has missing residue in insertion code region

Issue - State: open - Opened by hw-protein over 2 years ago - 3 comments
Labels: enhancement, users

#147 - Improve `pdb_mkensemble` to work as lib

Issue - State: open - Opened by joaomcteixeira over 2 years ago
Labels: enhancement

#146 - pdb_mkensemble includes the PDB filename when using a redirect

Issue - State: closed - Opened by amjjbonvin over 2 years ago - 6 comments
Labels: bug

#145 - Use HEADER info if available to name FASTA records.

Pull Request - State: closed - Opened by JoaoRodrigues over 2 years ago
Labels: enhancement

#144 - Implement pdb_selmodel for model selection in ensemble PDB files.

Pull Request - State: closed - Opened by JoaoRodrigues over 2 years ago

#143 - Refactor CI

Pull Request - State: closed - Opened by JoaoRodrigues over 2 years ago - 7 comments

#142 - Update and rename ci.yml to build_and_test.yml

Pull Request - State: closed - Opened by JoaoRodrigues over 2 years ago - 1 comment

#141 - Add build and coverage to every OS. Drop codecov.

Pull Request - State: closed - Opened by JoaoRodrigues over 2 years ago

#140 - Correct `pdb_tidy` when used with lists in lib

Pull Request - State: closed - Opened by joaomcteixeira over 2 years ago - 1 comment
Labels: bug

#139 - Re-add Py2.7 to CI. Explicit codecov configs

Pull Request - State: closed - Opened by JoaoRodrigues over 2 years ago - 1 comment

#138 - Corrects `selaltloc` for python 2.7 using OrderedDict

Pull Request - State: closed - Opened by joaomcteixeira over 2 years ago - 1 comment
Labels: bug

#137 - Adds missing file in `pdb_selaltloc` tests

Pull Request - State: closed - Opened by joaomcteixeira over 2 years ago

#136 - Correct behaviour and improves `selaltloc`

Pull Request - State: closed - Opened by joaomcteixeira over 2 years ago
Labels: bug, enhancement

#135 - `pdb_wc` should report the list of chain IDs of the PDB

Issue - State: open - Opened by joaomcteixeira over 2 years ago
Labels: enhancement

#134 - Help with badly formatted PDB file

Issue - State: closed - Opened by LilySnow over 2 years ago - 3 comments
Labels: help wanted, users

#133 - Development suggestion: Behaviour of pdb_reres and pdb_shiftres

Issue - State: closed - Opened by KasperBuskPedersen almost 3 years ago - 3 comments
Labels: help wanted, users

#132 - Increase footer size in the web page

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

#131 - Corrects behavior with `ANISOU` lines in `pdb_selaltloc`

Pull Request - State: closed - Opened by joaomcteixeira almost 3 years ago - 3 comments
Labels: bug, enhancement

#130 - `pdb_selaltloc` is breaking with ANISOU lines for `7K2U.pdb`

Issue - State: closed - Opened by joaomcteixeira almost 3 years ago
Labels: bug

#129 - add MANIFEST file to better control which files are packaged to PyPI

Pull Request - State: closed - Opened by joaomcteixeira almost 3 years ago - 1 comment

#128 - Bug in the `pdb-tools` website

Issue - State: closed - Opened by joaomcteixeira almost 3 years ago - 3 comments
Labels: bug

#127 - improve `pdb_wc` when using as library.

Issue - State: open - Opened by joaomcteixeira almost 3 years ago
Labels: enhancement

#126 - `ValueError: invalid literal for int() with base 10: '?'` when handling `HETATM`

Issue - State: closed - Opened by multimeric almost 3 years ago - 7 comments
Labels: bug, help wanted, users

#125 - Possible bug in Molprobity

Issue - State: closed - Opened by Mr-MOPAC almost 3 years ago - 4 comments
Labels: question, users

#124 - `pdb_fetch` could return `.cif` if the `.pdb` is not available

Issue - State: closed - Opened by rvhonorato about 3 years ago - 3 comments
Labels: enhancement

#123 - Better naming of pdb_tofasta entries

Issue - State: closed - Opened by sbliven about 3 years ago - 2 comments
Labels: enhancement, users

#122 - Implement `pdb_selmodel`

Issue - State: closed - Opened by rvhonorato about 3 years ago - 1 comment
Labels: Tool Request

#121 - Consider HEXADECIMAL for `pdb_fromcif`

Issue - State: open - Opened by joaomcteixeira about 3 years ago - 1 comment
Labels: enhancement

#120 - `pdb_rplresname` should accept several substitutions maps

Issue - State: open - Opened by joaomcteixeira about 3 years ago - 1 comment
Labels: enhancement

#119 - Correct `MODEL`, `END` and `ENDMDL` in `pdb_tidy`

Pull Request - State: closed - Opened by joaomcteixeira about 3 years ago - 1 comment
Labels: enhancement

#118 - `pdb_tidy` does not correct `MODEL` records

Issue - State: closed - Opened by rvhonorato about 3 years ago - 1 comment
Labels: enhancement

#117 - Improved `pdb_selaltloc`

Pull Request - State: closed - Opened by joaomcteixeira about 3 years ago
Labels: bug, enhancement

#116 - Behaviour of `pdb_selres`

Issue - State: closed - Opened by TianyiShi2001 about 3 years ago - 3 comments
Labels: bug, users

#115 - Behaviour in `selaltloc`

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

#114 - Tool to convert between atom names conventions

Pull Request - State: closed - Opened by joaomcteixeira over 3 years ago - 4 comments
Labels: Tool Request

#113 - `pdb_renameatom` - Renames atoms.

Pull Request - State: closed - Opened by joaomcteixeira over 3 years ago - 4 comments
Labels: Tool Request

#112 - Adding pdb_addter

Pull Request - State: open - Opened by andrewsb8 over 3 years ago - 15 comments
Labels: Tool Request

#111 - Issue with doctools.py

Issue - State: closed - Opened by andrewsb8 over 3 years ago - 6 comments
Labels: bug, users

#110 - `pdb_fixinsert` and its impact on numbering

Issue - State: closed - Opened by aanastasiou over 3 years ago - 3 comments
Labels: users

#109 - Adjust fhandle names to files and iterables.

Pull Request - State: closed - Opened by joaomcteixeira over 3 years ago - 1 comment
Labels: bug

#108 - Add GitHub actions for testing

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

#107 - Facilitates use of pdb-tools as a library

Pull Request - State: closed - Opened by joaomcteixeira over 3 years ago - 4 comments
Labels: enhancement

#106 - Using pdb-tools as a lib (also)

Issue - State: closed - Opened by joaomcteixeira over 3 years ago
Labels: enhancement

#105 - New tools for protein, nucleic, carbo, ligands

Issue - State: closed - Opened by joaomcteixeira over 3 years ago - 6 comments
Labels: Tool Request

#104 - molprobity.py gives a TypeError

Issue - State: closed - Opened by jbibbe4 over 3 years ago - 2 comments
Labels: bug

#103 - Adding option for subcommands

Pull Request - State: closed - Opened by joaomcteixeira almost 4 years ago - 1 comment
Labels: enhancement, v3

#102 - sub commands?

Issue - State: closed - Opened by jyesselm almost 4 years ago - 18 comments
Labels: enhancement, v3

#101 - Add option to pdb_tidy to only add TER between different chains

Issue - State: closed - Opened by amjjbonvin almost 4 years ago - 3 comments
Labels: enhancement, v3

#100 - Migrate to GitHub Actions

Issue - State: closed - Opened by joaomcteixeira almost 4 years ago - 1 comment
Labels: enhancement

#99 - Ignore residues with non-matching altlocs when only one is present.

Pull Request - State: closed - Opened by JoaoRodrigues almost 4 years ago - 2 comments
Labels: enhancement

#98 - Updated citation in the web page.

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

#97 - Update documentation tooling and added cookbook

Pull Request - State: closed - Opened by JoaoRodrigues almost 4 years ago - 1 comment
Labels: enhancement

#96 - Ignore residues with non-matching altlocs when only one is present.

Pull Request - State: closed - Opened by JoaoRodrigues about 4 years ago - 6 comments

#95 - Adds for loop example to docs

Pull Request - State: closed - Opened by joaomcteixeira about 4 years ago - 5 comments
Labels: enhancement

#94 - Coot can't open the output file of pdb_merge

Issue - State: closed - Opened by 1ut about 4 years ago - 2 comments
Labels: help wanted

#93 - pip install does not install LICENSE file

Issue - State: closed - Opened by Gerardwx about 4 years ago - 7 comments

#92 - renamed pdb_delinsertion

Pull Request - State: closed - Opened by joaomcteixeira about 4 years ago - 12 comments
Labels: enhancement

#91 - pdb_delinsertion - naming is confusing

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

#90 - pdb_selatlloc fails on single locs

Issue - State: closed - Opened by joaomcteixeira about 4 years ago - 1 comment
Labels: bug, enhancement

#89 - treatment of MASTER lines

Pull Request - State: closed - Opened by joaomcteixeira about 4 years ago - 2 comments
Labels: enhancement

#88 - Chain selection should be case-sensitive

Issue - State: closed - Opened by JoaoRodrigues about 4 years ago - 1 comment
Labels: bug

#86 - Fix pdb_selres on piped input files

Pull Request - State: closed - Opened by JoaoRodrigues over 4 years ago - 7 comments
Labels: bug

#85 - Fix count of HETATM to include all HETATM atoms, not residues.

Pull Request - State: closed - Opened by JoaoRodrigues over 4 years ago - 1 comment

#84 - Updated citation from biorxiv to F1000R

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

#83 - Change import in test to support Py2

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

#82 - Improve documentation updates

Issue - State: closed - Opened by JoaoRodrigues over 4 years ago - 1 comment
Labels: enhancement

#81 - Adds tool pdb_chainbows to sequentially assign chain identifiers

Pull Request - State: closed - Opened by JoaoRodrigues over 4 years ago - 4 comments
Labels: enhancement, Tool Request

#80 - Added -strict option to pdb_tidy to avoid adding intra-chain TERs

Pull Request - State: closed - Opened by JoaoRodrigues over 4 years ago - 3 comments
Labels: enhancement

#79 - pdb_reatom misaligning with TER lines

Issue - State: closed - Opened by edarl over 4 years ago - 3 comments
Labels: bug

#78 - [SKIP] updates CONTRIBUTING

Pull Request - State: closed - Opened by joaomcteixeira over 4 years ago - 14 comments

#77 - [SKIP] add pdb_uniqname to docs index

Pull Request - State: closed - Opened by joaomcteixeira over 4 years ago - 2 comments

#76 - Deleted unreachable/duplicated return statements

Pull Request - State: closed - Opened by JoaoRodrigues over 4 years ago - 1 comment
Labels: bug

#75 - [FEATURE] Added new tool to assign unique names to HETATM atoms + tests

Pull Request - State: closed - Opened by JoaoRodrigues over 4 years ago - 6 comments
Labels: enhancement

#74 - Ignores CONECT lines in pdb_tidy

Pull Request - State: closed - Opened by joaomcteixeira over 4 years ago - 2 comments
Labels: enhancement

#73 - input PDB file

Issue - State: closed - Opened by fedeserral over 4 years ago - 2 comments
Labels: question

#72 - Handling CONECT entries

Issue - State: closed - Opened by joaomcteixeira over 4 years ago - 4 comments
Labels: enhancement, Tool Request

#71 - Adds numbers to equal atom names in HETATM entries

Issue - State: closed - Opened by joaomcteixeira over 4 years ago - 6 comments
Labels: Tool Request

#70 - Add chain IDs on missing chains with TER

Issue - State: closed - Opened by joaomcteixeira over 4 years ago - 9 comments
Labels: enhancement, Tool Request

#69 - pdb_reres was ignoring MODEL lines

Pull Request - State: closed - Opened by joaomcteixeira over 4 years ago - 4 comments
Labels: bug

GitHub / haddocking/pdb-tools issues and pull requests