Pytraj Versions Save

v.2.0.5

• Compatible with https://github.com/Amber-MD/cpptraj/commit/bf25b27ce2009e5f657132429db2910b68734584
• FIX getting segmentation fault if loading a trajectory with force but not velocity (#1487)
• FIX cluster analysis: make sure to write datafiles (#1493)

Compatible with cpptraj's commit: https://github.com/Amber-MD/cpptraj/commit/4bc498d0a9caa437b549682144a346c0c5ef6c66

• ADD: writing traj with time #1456
• ADD: xtalsymm (#1477)
• ADD hausdorff + permute_dihedrals (#1483)
• FIX distance in native contacts #1468

Compatible with https://github.com/Amber-MD/cpptraj/releases/tag/18.00

This is the version released along with AmberTools 18.

Same as the version in AmberTools 17

What's new (vs v1.0.7)

• ADD: support xtc format
• ADD: support hieragglo and dbscan clustering
• ADD: pytraj.io.read_data and pytraj.io.write_data
• ADD: progress bar
• ADD: pytraj.density
• ADD: pytraj.gist
• ADD: pytraj.image
• ADD: pytraj.io.load_leap to use tleap
• ADD: pytraj.io.load_antechamber to load file formats that antachamber supports
• ADD: pytraj.datafiles.convert for data file convert (e.g dx to ccp4, ...)
• FIX: do not link to libsander
• ENH: setup.py

Note I (Hai) messed up with version, so v1.0.8.1 installed by conda is equal to 1.0.9 installed by pi.

from conda: conda install -c ambermd pytraj
from pip: pip install pytraj

(cpptraj git commit: 7d95f6149063e004622d1d16bdbd7066ae858235)

• add StrippedTrajectoryIterator #1262
• add load_url #1260
• add pickling TrajectoryIterator with tranformation

• add baseref for nastruct #1255
• add view for trajectory #1253, #1250
• add symmrmsd #1245
• add autoimage, superpose, ... to pytraj.TrajectoryIterator
• add freq to NH_order_paramters method
• add velocityautocorr #1228
• add rotdif #1225
• add writing force and velocity #1223
• fix alignment for two structures with different topology #1249