pytraj - v.2.0.5

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)

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Published by hainm almost 6 years ago

pytraj - v.2.0.4

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

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Published by hainm almost 7 years ago

pytraj - v2.0.3

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

This is the version released along with AmberTools 18.

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Published by hainm almost 8 years ago

pytraj - v2.0.0

Same as the version in AmberTools 17

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Published by hainm almost 9 years ago

pytraj - v1.0.9

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.

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

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Published by hainm over 9 years ago

pytraj - v1.0.8.1

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Published by hainm over 9 years ago

pytraj - v1.0.8

(cpptraj git commit: 7d95f6149063e004622d1d16bdbd7066ae858235)

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Published by hainm over 9 years ago

pytraj - v1.0.7

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

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Published by hainm over 9 years ago

pytraj - v1.0.6

• 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

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Published by hainm over 9 years ago

pytraj - v1.0.0.dev1

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Published by hainm about 10 years ago

pytraj - v1.0.0.rc0

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Published by hainm about 10 years ago

pytraj - v0.1.2.dev4

What's new?

• add pretty print for DataSetList when having pandas
• enhance speed for frameiter and chunkiter
• add 'merge_traj'
• add apply method to change traj's internal data
• add basic math for Trajectory
• add XYZ class as a simple wrapper for numpy ndarray traj.xyz is no longer ndarray, just a read-only wrapper
• add TrajectoryMDAnalysisIterator
• add read_data for DataFile and DataSetList
• add frame swap for Trajectory
• add atom coords assignment traj['@CA'] = xyz
• add stack for DataSetList to join 2 datasets
• rename set_frame_m to set_frame_mass
• update to_amber_mask to convert integer array-like to string mask
• add autoimage and rmsfitto for chunkiter and frame_iter
• tune speed for chunkiter and frameiter for TrajectoryIterator
• add plot method for DataSet
• add write_to_cpptraj_format
• add array for Frame
• introduce array interface to numpy for cpptraj's DataSet
• add median, std, ... for DataSetList
• update runallandfindfails.py for capturing segmetation fault
• add Trajectory joining (traj += traj)
• optimize slicing for TrajectoryIterator
• optimize strip_atoms (1000 times speed up)
• add copy method for DataSet
• add fancy indexing for DataSetList
• add _fast_slice for Trajectory (1000 times faster)
• add regular expression for groupby
• add to_pickle, to_json, read_pickle, read_json
• add _guess_filetype
• change fit_to to rmsfit_to
• enhance smart frameiter_master
• create alias rmsd for calc_rmsd in common_actions module
• update loading hd5f file without going through mdtraj
• correctly handle box in api.Trajectory
• add TrajectoryREMDIterator class to handal REMD
• change io.load_remd_iterator to io.iterload_remd
• add io._iterload_from_filelist and io._load_from_filelist
• add count for DataSet_integer
• API CHANGE (05-06-2015):
  • change FrameArray to Trajectory
  • change TrajReadOnly to TrajectoryIterator (issue #262) (https://github.com/pytraj/pytraj/issues/262)
  • io.load will return Trajectory instead of TrajectoryIterator
  • io.iterload will return TrajectoryIterator
• add "legend" as property of DataSet
• remove "get_box" from Frame. use "box"
• support autoimage when loading mdtraj object
• bugfix for io.loadpdb_rcsb
• add 'calc_rdf'
• trick to add reference to Action
  • Example: calc_abcxyz([[ref,], traj], command), where ref is a Frame object, abcxyz is a specific action.
• add option to load coords from ParmEd object
• add align_principal_axis
• fix iteration in api.Trajectory: 2 orders of magniture faster
• add "asndmatrix" for Matrix3x3

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Published by hainm over 10 years ago

pytraj - v0.1.2.dev3

What's new?

• add set_nobox for FrameArray
• add dtype in calculate method to return list, pyarray, dataset or ndarray
• support ParmEd with bonds, dih, angles loading
• add support loading more infor (bonds, box, angles, dihedrals) from MDAnalysis and mdtraj
• add bonds, angles and dihedrals iterators for Topology
• support MPI (with mpi4py)
• add calc_rmsd
• rename "dorotation" to "rotate", "dotranslation" to "translate" "do_autoimage" to "autoimage"
• add "box" to Topology
• reorganize folders (04-25-2015)
  • moved Atom, Molecule, Residue, Box to pytraj.core
  • moved Trajin_Single to pytraj.trajs
  • moved Matrix_3x3, Vec3, Grid ... to pytraj.math
  • moved all unused files away from main folder
  • dont support Energy routine in cpptraj, use pysander instead
  • move all optional package importing to pytraj.externals.
  • enhance groupby method: dslist.groupby("omega", mode='aspect')
  • added pytraj.api.Trajectory as a new Trajectory object with xyz is a numpy array
• add universal gettop method gettop(traj, top)
• add DataSet_Mesh
• better setup.py: automatically install libcpptraj
• change API of FrameArray and TrajReadOnly traj['CA'] return a stripped-atoms traj (not a xyz coords)
• add calc_temperature

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Published by hainm almost 11 years ago

pytraj - v0.1.2.dev2

what's new

• add "groupby" method for DataSetList
• directly access "calc..." methods from FrameArray and TrajReadOnly (traj.calcCOM, ...)
• "tolist" in Traj should return 3D list (nframe, natoms, 3)
• "tolist" of Frame should return 2D list (n_atoms, 3)
• add "tolist" for DataSet_Vector
• add "keys()" to DataSetList class. Now we can use this as a list and a dict
• support Grid calculation (calc_volmap, ...)
• enhance speed of AtomMask selection (about 5 times faster)
• add set_error_silent to turn-off (and on) cpptraj' warning
• add attribute indices for AtomMask object (shorter than selected_indices method's name
• support loading MDAnalysis objects (Universe)
• add method load_pseudo_parm to load ParmEd and mdtraj Topology objects
• fully compat with cpptraj, user can get CpptrajState from trajin.in file (pytraj.io.load_cpptraj_file)
• add to_ndarray for DataSet, Frame, Vec3,... objects
• introduce memoryview for DataSet
• fix memory for calculate method
• add simple wrapper to pysander to be used with pandas' DataFrame
• add calc_multidihedral for quickly scanning dihedral
• improve code for AtomMask: add_selected_indices could accept memview
• add _frame_iter_master to iterate anything that results Frame objects
• add frameiter with atom indices (before: only support atom mask): traj(mask=indexarray)

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Published by hainm almost 11 years ago

pytraj - v0.1.2.dev0.1

What's new

• Can combine with pysander to get energy
• Update DataSet class inheritance (following cpptraj changes)
• Support Analysis classes in cpptraj (including clustering)
• Introduce dataframe to interact with pandas (to_dataframe)
• Support OPENMP
• Have option to make faster building (less than 2 minutes) by using multiprocess
• load method of FrameArray is much more robust (it can load raw numpy, list, tuple of numbers, any iterable objects that resulting Frame ... and much more)
• Support loading mdtraj objects (Trajectory and Topology). Support loading array with ndim=1, 2, 3
• Support more than 100 kinds of calculations and analyses in cpptraj
• Many bugfixs to avoid segmentation fault

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Published by hainm almost 11 years ago

pytraj - v0.1.2.dev0

[check v0.1.2.dev0.1]

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Published by hainm almost 11 years ago

pytraj - v0.1.0.1

What's new?

• Features
  • Turn on profiling
  • Add fit_to method for structure alignment
• Bug fix
  • Turn off AMBERHOME requirement

Install

wget https://github.com/pytraj/pytraj/archive/v0.1.0.1.tar.gz tar -xf v0.1.0.1.tar.gz cd pytraj* python ./setup.py install

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Published by hainm almost 11 years ago

pytraj - 0.1.beta.20

wget https://github.com/pytraj/pytraj/archive/0.1.beta.20.tar.gz tar -xf 0.1.beta.20.tar.gz cd pytraj* python setup.py install

What's new? - faster iterator for loading trajectory - simpler setup process (not yet supported pip or conda install) - bug fixes

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Published by hainm about 11 years ago

pytraj - 0.1.beta.10

wget https://github.com/pytraj/pytraj/archive/0.1.beta.10.tar.gz tar -xf 0.1.beta.10.tar.gz cd pytraj* python setup.py install

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Published by hainm about 11 years ago

pytraj - 0.1.beta.9

wget https://github.com/pytraj/pytraj/archive/0.1.beta.9.tar.gz tar -xf 0.1.beta.9.tar.gz cd pytraj* python setup.py install

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Published by hainm about 11 years ago

pytraj - 0.1.beta.8

add more examples for frame_iter and other small stuff

wget https://github.com/pytraj/pytraj/archive/0.1.beta.8.tar.gz tar -xf 0.1.beta.8.tar.gz cd pytraj* python setup.py install

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Published by hainm about 11 years ago

pytraj - 0.1.beta.7

smarter build

wget https://github.com/pytraj/pytraj/archive/0.1.beta.7.tar.gz tar -xf 0.1.beta.7.tar.gz cd pytraj* python setup.py install

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Published by hainm about 11 years ago