This module is used to load and read
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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |