Xponge.analysis.md_analysis
SPONGE 1.4 的 Xponge API 文档。¶ Xponge.analysis.md_analysis
This module gives functions and classes to use MDAnalysis to analyze the trajectories
¶ subpackages
¶ submodules
¶ functions
¶ open_trajectory
Open the trajectory file
| return | trajectory file and box file |
|---|
¶ classes
¶ SpongeNoneReader
This class is used to give a universe with no coordinate
¶ close
fake close function for api
¶ SpongeInputReader
This class is used to read the SPONGE input to mdanalysis
¶ parse
This function reads the file and returns the structure
| parameters | explanation |
|---|---|
| kwargs | keyword arguments |
| return | MDAnalysis Topology object |
|---|
¶ XpongeResidueReader
This class is used to read the Xponge Residue or ResidueType to mdanalysis
¶ parse
This function reads the file and returns the structure
| parameters | explanation |
|---|---|
| kwargs | keyword arguments |
| return | MDAnalysis Topology object |
|---|
¶ XpongeMoleculeReader
This class is used to read the Xponge Molecule to mdanalysis
¶ parse
This function reads the file and returns the structure
| parameters | explanation |
|---|---|
| kwargs | keyword arguments |
| return | MDAnalysis Topology object |
|---|
¶ SpongeTrajectoryReader
This class is the interface to MDAnalysis.
| parameters | explanation |
|---|---|
| dat_file_name | the name of the SPONGE dat trajectory file |
| box | the name of the box file or a list of 6 int or float representing the 3 box lengths and 3 box angles. |
| n_atoms | the number of atoms |
¶ n_frames
The total number of frames in the trajectory file
¶ n_atoms
The total number of atoms in the trajectory file
¶ with_arguments
This function binds the arguments to the reader to initialize
| parameters | explanation |
|---|---|
| kwargs | the arguments |
| return | a subclass of SpongeTrajectoryReader |
|---|
¶ SpongeTrajectoryReaderWithArguments
¶ SpongeTrajectoryWriter
This class is used to write the SPONGE trajectory (xxx.dat and xxx.box)
| parameters | explanation |
|---|---|
| filename | the filename of the output files |
| write_box | whether to write the box file New From 1.2.7.0 |
¶ open
This function opens the trajectory files
| return | None |
|---|
¶ close
This function closes the trajectory files
| return | None |
|---|
¶ write
This function writes the coordinates of the Universe to the output files
| parameters | explanation |
|---|---|
| u | an MDAnalysis.Universe instance |
| return | None |
|---|
¶ SpongeCoordinateReader
This class is the interface to MDAnalysis.
| parameters | explanation |
|---|---|
| file_name | the name of the SPONGE coordinate trajectory file |
¶ n_frames
The total number of frames in the trajectory file
¶ n_atoms
The total number of atoms in the trajectory file
¶ close
Close all the opened file
| return | None |
|---|
¶ open_file
Open the coordinate file
| return | trajectory file and box file |
|---|
¶ SpongeCoordinateWriter
This class is used to write the SPONGE coordinate file
| parameters | explanation |
|---|---|
| file_name | the name of the output file |
| n_atoms | the total number of atoms this Timestep describes |
¶ open
This function opens the coordinate file
| return | None |
|---|
¶ close
This function closes the coordinate file
| return | None |
|---|
¶ write
This function writes the coordinates of the Universe to the output files
| parameters | explanation |
|---|---|
| u | an MDAnalysis.Universe instance |
| return | None |
|---|
¶ SPONGEH5MDReader
This class is the interface to MDAnalysis.
| parameters | explanation |
|---|---|
| dat_file_name | the name of the SPONGE h5md trajectory file |
| n_atoms | the number of atoms |
¶ n_frames
The total number of frames in the trajectory file
¶ n_atoms
The total number of atoms in the trajectory file
¶ close
Close all the opened file
| return | None |
|---|