Ecosyste.ms: Issues

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GitHub / mdtraj/mdtraj issues and pull requests

#1693 - how to skip "WARNING: two consecutive residues with same number (PRO, VAL)" when loading a gro file?

Issue - State: closed - Opened by lucl13 over 3 years ago - 1 comment
Labels: wontfix

#1691 - Support from reading from File like objects

Issue - State: closed - Opened by salotz-sitx over 3 years ago - 4 comments
Labels: wontfix

#1690 - Cannot load trajectory file from Desmond for two small molecules.

Issue - State: closed - Opened by kurokawaikki over 3 years ago - 3 comments
Labels: wontfix

#1689 - Molecules center of mass

Issue - State: closed - Opened by gabriela-correa over 3 years ago - 3 comments
Labels: wontfix

#1678 - Baker Hubbard return prevalence

Issue - State: closed - Opened by agheeraert over 3 years ago - 1 comment
Labels: wontfix

#1675 - Added handling of chimera-style indexing for PDB

Pull Request - State: closed - Opened by PolyachenkoYA over 3 years ago - 7 comments
Labels: wontfix

#1673 - Support for loading only specific fields on `File.read`

Issue - State: closed - Opened by salotz-sitx over 3 years ago - 1 comment
Labels: wontfix

#1672 - Support unitcell/box vectors as `Trajectory()` constructor argument

Issue - State: closed - Opened by salotz-sitx over 3 years ago - 1 comment
Labels: wontfix

#1671 - Add atom selection via `atom_indices` to SASA computation, tests added

Pull Request - State: closed - Opened by gph82 over 3 years ago - 1 comment
Labels: wontfix

#1670 - Added atom selection for SASA

Issue - State: closed - Opened by gph82 over 3 years ago - 5 comments
Labels: wontfix

#1669 - `XTCTrajectoryFile` missing `n_frames` attribute

Issue - State: closed - Opened by salotz-sitx over 3 years ago - 1 comment
Labels: wontfix

#1667 - Exporting an pdb file of a centroid from traj clustering

Issue - State: closed - Opened by tanoury1 over 3 years ago - 1 comment
Labels: wontfix

#1666 - getting a average of some PDB structure from trajectory

Issue - State: closed - Opened by AhmetGG over 3 years ago - 4 comments
Labels: wontfix

#1665 - don't allow non-sorted or non-unique indices in atom_slice

Pull Request - State: closed - Opened by sroet over 3 years ago - 5 comments
Labels: wontfix

#1664 - using atom_slice with nonsequential indices gives incorrect topology

Issue - State: closed - Opened by mizimmer90 over 3 years ago - 1 comment
Labels: bug, wontfix

#1662 - compute_displacement_t function

Issue - State: closed - Opened by VietNguyen120195 over 3 years ago - 2 comments
Labels: wontfix

#1660 - `AmberRestartFile` missing `num_frames` kwarg in `read_as_traj`

Issue - State: closed - Opened by salotz-sitx over 3 years ago - 2 comments
Labels: wontfix

#1658 - compute_neighbors compute_neighborlist and compute_contacts are giving me a strange result

Issue - State: closed - Opened by MauriceKarrenbrock over 3 years ago - 4 comments
Labels: wontfix

#1653 - Unknown format errors should not be `IOError`/`OSError`

Issue - State: closed - Opened by salotz-sitx over 3 years ago - 3 comments
Labels: wontfix

#1649 - Make all the _TOPOLOGY_EXTS file parsers accept top as an input

Issue - State: closed - Opened by MauriceKarrenbrock almost 4 years ago - 1 comment
Labels: wontfix

#1636 - Possible MDtraj reading issue for a 1 atom molecule mol2 files

Issue - State: closed - Opened by bc118 almost 4 years ago - 8 comments
Labels: bug, wontfix

#1611 - Incorrect PDB atom indices

Issue - State: closed - Opened by SimonBoothroyd about 4 years ago - 6 comments
Labels: wontfix

#1600 - Selecting atom indices within a particular distance

Issue - State: closed - Opened by mayankb3192 over 4 years ago - 6 comments
Labels: wontfix

#1594 - memory allocation when opening XTC trajectory on OSX Catalina

Issue - State: closed - Opened by tubiana over 4 years ago - 8 comments

#1590 - doc build for out-of-core (iterload) can't find data/frame0.h5

Issue - State: closed - Opened by drew-parsons over 4 years ago - 4 comments
Labels: bug, docs, wontfix

#1531 - mdconvert can not convert .DCD file (2.8 GB) to .pdb file

Issue - State: closed - Opened by hima111997 almost 5 years ago - 8 comments
Labels: wontfix

#1398 - residue.is_nucleic and 'nucleic' in atom selection DSL

Pull Request - State: open - Opened by dwhswenson over 6 years ago - 10 comments
Labels: wontfix

#1261 - convert amber trajectory to desmond compatible (cms with trj)

Issue - State: closed - Opened by amrhamedp almost 8 years ago - 8 comments

#1127 - Problem with Baker-Hubbard H-bond analysis

Issue - State: closed - Opened by karel10 over 8 years ago - 5 comments

#1016 - atom-names in MET residue

Issue - State: closed - Opened by gph82 about 9 years ago - 27 comments
Labels: wontfix