project-gemmi/gemmi

Issues

• Segfault when using the result of Chain.subchains()

  #317 opened 23 days ago by jackdent
  4

• ItemPair conversion to ItemLoop

  #346 opened a month ago by cycle20
  1

• FloatGrid resample_to missing?

  #343 opened a month ago by Dialpuri
  1

• Issue with find_nearest_pbc_position in Gemmi Neighbor Search

  #340 opened 2 months ago by MichalGucwa
  2

• calculating 1/d^2 is returning an array containing the same number.

  #339 opened 3 months ago by scatter3d
  4

• pdbx_PDB_model_num type & content

  #332 opened 2 months ago by rimmartin
  2

• "gemmi convert" - HETNAM record

  #331 opened 4 months ago by CV-GPhL
  8

• Interpolating many points in Python

  #323 opened 3 months ago by jrobsontull
  2

• Add support for BinaryCIF

  #335 opened 4 months ago by jasondbiggs
  1

• Crash when reading an mmjson file created by gemmi

  #336 opened 4 months ago by jasondbiggs
  1

• python bindings: convert from pybind11 to nanobind, add type stubs

  #293 opened 4 months ago by wojdyr
  1

• I still suggest gemmi can generate crystal slab or surface. Thanks!

  #334 opened 4 months ago by zhangfq-chemistry
  1

• Feature request: Gemmi alternative to 'NOISE' option of PDBSET

  #326 opened 4 months ago by drlemmus
  3

• Segmentation Fault, Core Dumped

  #330 opened 4 months ago by m-crown
  9

• `gemmi.read_structure` fails to load some cif files from PDB-Dev

  #329 opened 4 months ago by NatureGeorge
  1

• compile error under ubuntu 24

  #328 opened 4 months ago by zhangfq-chemistry
  1

• got zero models from mmcif written from pymol selection, expected one model

  #327 opened 5 months ago by diogomart
  2

• Gemmi setup MapReorderOnly never sets AxisOrder for a grid

  #322 opened 6 months ago by gabriellareggiano
  1

• -f <file> seems not to work as I expect

  #321 opened 6 months ago by KayDiederichs
  2

• Shared library is unversioned

  #320 opened 7 months ago by badshah400
  4

• Float comparison fails `static_assert(weights[static_cast<int>(El::D)] == 2.0141, "Hmm")` on some architectures

  #316 opened 7 months ago by merkys
  7

• Creating a structure from list of residues and their coordinates

  #315 opened 7 months ago by marinegor
  2

• [Bug Report] read_pdb mishandle the columns of extreme wild pdb files

  #313 opened 8 months ago by minhuanli
  5

• [Question] bulk reading mmcif coordinates into a numpy array

  #314 opened 8 months ago by marinegor
  2

• Gemmi read_ccp4_map fails to correctly set the correct spacing from a .MAP file

  #312 opened 8 months ago by jrobsontull
  2

• Advice to deal with AF3's broken CIF files

  #311 opened 8 months ago by milot-mirdita
  1

• Bug in `get_all_unit_cell_sites()`

  #308 opened 8 months ago by fxcoudert
  5

• Adding additional properties to the Structure object present in the cif atom_site table

  #304 opened 8 months ago by danny305
  1

• pdb/cif entity subchain comparisons

  #309 opened 8 months ago by rimmartin
  1

• crash with set_extent

  #307 opened 8 months ago by JoshRackers
  4

• [FEATURE REQUEST] Add Python typing for `Vec3.__iter__`

  #306 opened 9 months ago by rjdirisio
  2

• sequence aligning with align_sequence_to_polymer

  #302 opened 9 months ago by rimmartin
  10

• TER's effecting aligning

  #303 opened 10 months ago by rimmartin
  4

• Apparent sudden extra dependency for gemmi (zlib)

  #301 opened 10 months ago by helenginn
  5

• crash with very large mmCIF files (and large number of datablock) in gemmi grep

  #298 opened 10 months ago by CV-GPhL
  11

• Missing _struct_ref_seq in cif generated from PDB without optional TER.

  #299 opened 10 months ago by xvlaurent
  2

• Segfault when importing `gemmi.cif`

  #297 opened 10 months ago by j-c-c
  2

• Uses of graph isomorphism and pynauty?

  #296 opened a year ago by j2kun
  2

• auto completion for gemmi grep

  #295 opened a year ago by frmupe
  1

• CID parser syntax error when negative sequence number is present

  #294 opened a year ago by scotthoh
  0

• 1 test fails

  #291 opened a year ago by yurivict
  1

• Vulnerability in `tinydir_file_open()`: buffer overflow

  #292 opened a year ago by merkys
  2

• Issue creating gemmi selections

  #289 opened a year ago by FilomenoSanchez
  4

• Issues with `gemmi::remove_ligands_and_waters`

  #290 opened a year ago by FilomenoSanchez
  4

• Gemmi fails to set the true grid spacing if origin is not (0, 0 ,0) for a CCP4 map

  #288 opened a year ago by jrobsontull
  4

• Publishing PDB REMARK X's

  #287 opened a year ago by rimmartin
  4

• False positive validation of a cif file with a missing category

  #285 opened a year ago by PeyratG
  4

• OBSLTE from pdb and cif input

  #284 opened a year ago by rimmartin
  6

• C++ types in python docstrings

  #280 opened a year ago by sizmailov
  2

• Enhancement: Extend Python API to Support --nfree Argument Functionality

  #278 opened a year ago by vivek8031
  1