¶ Xponge.load
This module is used to load and read
¶ subpackages
¶ submodules
¶ functions
¶ load_mol2
This function is used to load a mol2 file
| parameters |
explanation |
| file |
the name of the input file or an instance of io.IOBase |
| ignore_atom_type |
ignore the atom types in the mol2 file |
| as_template |
only read the mol2 file as some residue types and no molecule will created |
| return |
a Molecule instance if as_template is False |
¶ load_coordinate
This function is used to read the SPONGE coordinate in file
| parameters |
explanation |
| filename |
the coordinate file to load |
| mol |
the molecule or residue to load the coordinate into |
| return |
two numpy arrays, representing the coordinates and the box information respectively |
¶ load_frcmod
This function is used to load a frcmod file
| parameters |
explanation |
| filename |
the name of the file to load |
| nbtype |
the non-bonded interaction recording type in the frcmod file. |
| return |
a list of strings, including atoms, bonds, angles, propers, impropers, ljs, cmap information respectively |
¶ load_parmdat
This function is used to load a parmdat file
| parameters |
explanation |
| filename |
the name of the file to load |
| return |
a list of strings, including atoms, bonds, angles, propers, impropers, ljs, nb14s information respectively |
¶ load_rst7
This function is used to load a rst7 file
| parameters |
explanation |
| filename |
the name of the file to load |
| mol |
the molecule to load the coordinates |
| return |
a tuple including coordinates and box information |
¶ load_molitp
This function is used to load a molitp file
| parameters |
explanation |
| filename |
the name of the file to load |
| water_replace |
whether to change water to SPONGE. True as default. |
| head_prefix |
a string, the prefix will be added to the name of the first residue of each molecule |
| tail_prefix |
a string, the prefix will be added to the name of the last residue of each molecule |
| macros |
the macros used to read the Gromacs topology file |
| return |
1. an Xponge.Molecule representing the systema. None if not define |
¶ load_gro
This function is used to read the GROMACS coordinate file
| parameters |
explanation |
| filename |
the coordinate file to load |
| mol |
the molecule or residue to load the coordinate into |
| return |
two numpy arrays, representing the coordinates and the box information respectively |
¶ classes
¶ GromacsTopologyIterator
This class is used to read a GROMACS topology file
| parameters |
explanation |
| filename |
the name of the file to read |
| macros |
the macros used to read the Gromacs topology file |
