Ecosyste.ms: Issues

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GitHub / mdtraj/mdtraj issues and pull requests

#1811 - Add ruff check to CI

Pull Request - State: open - Opened by speleo3 over 1 year ago - 4 comments

#1810 - Build docs

Issue - State: open - Opened by mattwthompson over 1 year ago - 2 comments

#1809 - Build docs in CI

Issue - State: open - Opened by mattwthompson over 1 year ago - 7 comments

#1808 - ValueError: invalid literal for int() with base 16:

Issue - State: open - Opened by inefable12 over 1 year ago - 1 comment

#1807 - Use raw strings to fix invalid escape sequences

Pull Request - State: open - Opened by speleo3 over 1 year ago - 2 comments

#1806 - DeprecationWarning: invalid escape sequence '\g'

Issue - State: open - Opened by speleo3 over 1 year ago - 2 comments

#1804 - Add v1.9.9 release notes

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

#1803 - Feature suggestion: guess bonds

Issue - State: closed - Opened by fwaibl over 1 year ago - 4 comments

#1802 - mdtraj pip install error

Issue - State: closed - Opened by Harshitasahni over 1 year ago - 2 comments

#1801 - Constrain `cython=0.29`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 6 comments

#1800 - Cython 3 breaks cythonization of _geometry.pyx

Issue - State: closed - Opened by jeremyleung521 over 1 year ago - 7 comments

#1799 - Error in Building wheel for mdtraj.

Issue - State: open - Opened by RubelMozumder over 1 year ago - 2 comments

#1797 - RMSD calculation

Issue - State: open - Opened by TalentSim over 1 year ago - 6 comments

#1796 - image_molecules does not work in mdtraj 1.9.7 with Python 3.10

Issue - State: open - Opened by nmroussey over 1 year ago - 2 comments

#1795 - Maintainer announcement update (to README, etc.)

Pull Request - State: closed - Opened by sukritsingh over 1 year ago - 6 comments

#1794 - Set up `cibuildwheel` to distribute wheels

Issue - State: open - Opened by mattwthompson over 1 year ago - 2 comments

#1791 - Add v1.9.8 release notes

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

#1790 - Pin `gsd=2`

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

#1789 - API changes for GSD 3.0

Issue - State: closed - Opened by mattwthompson over 1 year ago - 3 comments

#1788 - Failing TNG test on macOS

Issue - State: open - Opened by mattwthompson over 1 year ago - 2 comments

#1787 - Remove Python 2 compatibility

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

#1786 - Get CI working on Windows

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

#1785 - Remove stale bot

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 6 comments

#1784 - Wrong number of residues is detected by mdtraj

Issue - State: open - Opened by mahdikalhori over 1 year ago - 2 comments

#1781 - Issue #1780

Pull Request - State: closed - Opened by CharlieLaughton over 1 year ago - 2 comments

#1780 - Trajectory hashing fails if unitcell data is missing

Issue - State: closed - Opened by CharlieLaughton over 1 year ago - 2 comments

#1779 - Speeding up install in google colab (binary wheels?)

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

#1778 - Delete notes in issue-template

Pull Request - State: closed - Opened by bojunliu0818 almost 2 years ago

#1777 - fix bugs by nix-2.15

Pull Request - State: closed - Opened by bojunliu0818 almost 2 years ago - 2 comments

#1776 - Update issue-template

Pull Request - State: closed - Opened by bojunliu0818 almost 2 years ago - 2 comments

#1775 - Error with TNG imports

Issue - State: open - Opened by mastersubhadeep almost 2 years ago - 1 comment

#1774 - name CA not possible to select for atom_slicing

Issue - State: open - Opened by cloudella48 almost 2 years ago - 1 comment

#1773 - Loop potentialEnergy values on HDF5 files

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

#1771 - Update dcdplugin.c

Pull Request - State: open - Opened by reedharrison almost 2 years ago - 3 comments

#1770 - Iterload fails for large DCD files on Windows

Issue - State: closed - Opened by reedharrison almost 2 years ago - 3 comments

#1769 - image_molecules overwrites original coordinates even with inplace=False

Issue - State: open - Opened by CharlieLaughton almost 2 years ago - 1 comment

#1768 - pip install mdtraj failing on Ventura

Issue - State: closed - Opened by rbharath almost 2 years ago - 4 comments

#1767 - Wrong element assignment for Cl when loading Gro file

Issue - State: open - Opened by TaizoAyase almost 2 years ago - 3 comments

#1766 - Warn if atom_indices are not monotonically increasing

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

#1765 - success to install on M1 Ventura 13.2

Issue - State: closed - Opened by aspitaleri about 2 years ago - 1 comment

#1764 - compute_dssp near ACE, NME capped residue

Issue - State: open - Opened by smlee99 about 2 years ago - 1 comment

#1763 - save is not outputting any files

Issue - State: open - Opened by icaspell about 2 years ago - 1 comment

#1762 - mdtraj problem running

Issue - State: open - Opened by chesser247 about 2 years ago - 3 comments

#1761 - The 1.9.7 tarball contains code that does not build on Python 3.11

Issue - State: closed - Opened by tbabej about 2 years ago - 3 comments

#1759 - fix bug: resSeq changed when doing trajectory.atom_slice if resSeq==0

Pull Request - State: open - Opened by huhlim over 2 years ago

#1758 - Test on Python 3.11, switch CI to use `micromamba`

Pull Request - State: closed - Opened by mattwthompson over 2 years ago - 9 comments

#1757 - MDtraj python library for Python 3.9.13

Issue - State: closed - Opened by abdusemiabduweli over 2 years ago - 1 comment

#1756 - Unable to install mdtraj

Issue - State: closed - Opened by yangyangdotcom over 2 years ago - 1 comment

#1755 - Calculating distances between two atoms

Issue - State: open - Opened by jpspadeto2 over 2 years ago

#1754 - Will mdtraj run on Python 3.11?

Issue - State: closed - Opened by cclauss over 2 years ago - 16 comments

#1753 - atom_slice: provides a warning when input indices are not sorted or not unique

Issue - State: open - Opened by yaoyic over 2 years ago - 3 comments

#1752 - Add Python 3.11 release candidate 2 to testing

Pull Request - State: closed - Opened by cclauss over 2 years ago - 3 comments
Labels: wontfix

#1751 - Use oldest-supported-numpy instead of numpy version pinning for build system

Pull Request - State: closed - Opened by chajath over 2 years ago - 11 comments

#1750 - Support for appending mode for hdf5 writer?

Issue - State: open - Opened by ziyuanzhao2000 over 2 years ago

#1749 - ValueError: Mixing trajectories with and without unit cell

Issue - State: open - Opened by averysader over 2 years ago - 3 comments

#1748 - mdconvert fails when dcd contains only one frame

Issue - State: open - Opened by ehb54 over 2 years ago - 1 comment

#1746 - How to load topology from lammps data file

Issue - State: open - Opened by Roy-Kid over 2 years ago - 3 comments

#1744 - md.compute_distances error

Issue - State: open - Opened by fmusiani over 2 years ago - 3 comments

#1743 - Add selection of chains by name instead of index

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

#1742 - [Question] How to extract atom positions from compute_contacts

Issue - State: open - Opened by DanielWicz over 2 years ago - 1 comment

#1741 - BLD: Add a github actions workflow for building wheels and source distributions

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment

#1740 - [core.Topology.from_dataframe] BUGFIX: force new residue when creating new chain

Pull Request - State: closed - Opened by gph82 almost 3 years ago - 2 comments

#1739 - CONECT records in PDB files written by mdtraj always use atom index

Issue - State: open - Opened by proteins247 almost 3 years ago - 2 comments
Labels: wontfix

#1738 - Add note about project maintinance status to readme

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

#1737 - Topology.select() syntax

Issue - State: closed - Opened by mghattas100 almost 3 years ago - 2 comments

#1736 - MDTraj 1.9.7 on M1 chip fails with image_molecules()

Issue - State: closed - Opened by alexholehouse almost 3 years ago - 7 comments
Labels: wontfix

#1735 - unable to install

Issue - State: closed - Opened by debanjansen48 almost 3 years ago - 2 comments

#1734 - Loading Trajectory

Issue - State: closed - Opened by williambrown3 almost 3 years ago

#1733 - Extracting rotations from superpose

Issue - State: open - Opened by mrjoness almost 3 years ago - 2 comments
Labels: wishlist, api

#1732 - Lipid thickness

Issue - State: open - Opened by Amireng72 almost 3 years ago - 2 comments

#1731 - Cannot read OpenMM-generated PDB trajectory files

Issue - State: closed - Opened by bbye98 almost 3 years ago - 3 comments

#1730 - ValueError: unitcell angle < 0

Issue - State: open - Opened by d-beltran almost 3 years ago - 9 comments

#1729 - How should I add SPARTA+ available on my mac path for NMR chemical shift analysis?

Issue - State: open - Opened by TianmingQu almost 3 years ago - 1 comment
Labels: wontfix

#1728 - Adds lower-level `compute_distances_core` function

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

#1727 - Implement generic C code paths for non-accelerated architectures.

Pull Request - State: closed - Opened by tonigi almost 3 years ago - 13 comments

#1726 - RMSD between frames before and after translation/rotation is not 0

Issue - State: closed - Opened by wehs7661 almost 3 years ago - 1 comment

#1725 - Fix typo in docs

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

#1724 - Perform analysis on a subset of particles

Issue - State: closed - Opened by gyorgy-hantal almost 3 years ago - 7 comments
Labels: wontfix

#1723 - Some tests failed on Ubuntu 20.04.3 LTS.

Issue - State: closed - Opened by hongyi-zhao almost 3 years ago - 2 comments

#1722 - Support for "hybrid-36" PDB format?

Issue - State: closed - Opened by fpickard about 3 years ago - 3 comments
Labels: wontfix

#1721 - Sprinkle in some math

Pull Request - State: closed - Opened by ctk3b about 3 years ago

#1720 - Support for affinity propagation clustering?

Issue - State: closed - Opened by tanoury1 about 3 years ago - 2 comments
Labels: wontfix

#1719 - Update nix flake

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

#1718 - Implement reading and writing PDBx/mmCIF files

Pull Request - State: closed - Opened by peastman about 3 years ago - 13 comments

#1717 - load() removes first element from a list of filenames

Issue - State: closed - Opened by CharlieLaughton about 3 years ago - 3 comments
Labels: wontfix

#1716 - Custom loaders that already contain topologies fail _parse_topology() check

Issue - State: closed - Opened by nffaruk about 3 years ago - 4 comments
Labels: wontfix

#1712 - Reading Charges property PDB files

Issue - State: closed - Opened by JPBergsma about 3 years ago - 2 comments
Labels: wontfix

#1710 - load_mol2 cannot handle files with comments before first @<TRIPOS>

Issue - State: closed - Opened by roseane-reis about 3 years ago - 2 comments
Labels: wontfix

#1708 - Load_dcd has same issue as fixed load xtc

Issue - State: closed - Opened by orthonalmatrix about 3 years ago - 1 comment
Labels: wontfix

#1705 - XTCReporter Trajectories from killed runs can't be loaded?

Issue - State: closed - Opened by apayne97 about 3 years ago - 2 comments

#1702 - Baker-Hubbard docs not working

Issue - State: closed - Opened by p1224recursion about 3 years ago - 3 comments
Labels: wontfix

#1701 - Upload wheels as part of release process

Issue - State: closed - Opened by Seanny123 over 3 years ago - 8 comments
Labels: wontfix

#1696 - port openmm.unit

Pull Request - State: closed - Opened by sroet over 3 years ago - 1 comment