This module is used to process topology and conformations
This function is used to impose the distance in molecule between atom1 and atom2 to length
| parameters |
explanation |
| molecule |
a Molecule instance |
| atom1 |
the base atom, which will not change its coordinate |
| atom2 |
the atom to change its coordinate to fit the length |
| length |
distance in the unit of angstrom |
This function is used to impose the angle in molecule between atom1, atom2 and atom3 to angle.
| parameters |
explanation |
| molecule |
a Molecule instance |
| atom1 |
the base atom, which will not change its coordinate |
| atom2 |
the base atom, which will not change its coordinate |
| atom3 |
the atom to change its coordinate to fit the angle |
| angle |
angle in the unit of rad |
This function is used to impose the dihedral in molecule between atom1, atom2, atom3 and atom4 to dihedral.
| parameters |
explanation |
| molecule |
a Molecule instance |
| atom1 |
the base atom, which will not change its coordinate |
| atom2 |
the base atom, which will not change its coordinate |
| atom3 |
the atom to change its coordinate to fit the angle |
| atom4 |
the atom to change its coordinate to fit the angle |
| dihedral |
dihedral angle in the unit of rad |
| keep_atom3 |
whether the other atoms linked to atom3 will be rotated |
This function adds a box full of solvents to a molecule.
| parameters |
explanation |
| molecule |
the molecule to add the box, either a Molecule or a ResidueType |
| solvent |
the solvent molecule, either a Molecule or a ResidueType |
| distance |
the distance between the molecule and the box in the unit of Angstrom. This can be an int or a float, and it can be also a list of them with the length 3 or 6, which represents the 3 or 6 directions respectively. |
| tolerance |
the distance between two molecules. 2.5 for default. |
| n_solvent |
the number of solvent molecules. |
| return |
the Molecule instance |
This function repartition the mass of light atoms to the connected heavy atoms. This can help the simulation run with a time step of 4 fs.
| parameters |
explanation |
| molecules |
a Molecule |
| repartition_mass |
if the mass of the atom is not greater than this value, it will be seen as a light atom. 1.1 for default and in the unit of Dalton. |
| repartition_rate |
The mass of the light atom will multiplied by this value. |
| exclude_residue_name |
the residue name which will not do the repartition. "WAT" for default. |
This function replaces the solvent to some other molecules randomly.
| parameters |
explanation |
| molecule |
a Molecule instance |
| select |
a function to decide which residues should be replaced, or a Residue, a ResidueType or a Molecule with only one Residue, which the residues to be replaced have the same name |
| toreplace |
a dict, which stores the mapping of molecules to replace and the number of molecules. Every molecule should be a ResidueType, a Residue or a Molecule with only one Residue. |
| sort |
whether to sort the residues after replacing |
¶ main_axis_rotate
This function rotates the main axis of the molecule to the desired direction
| parameters |
explanation |
| molecule |
a Molecule instance |
| direction_long |
a list of three int or float to represent the direction vector. The long main axis will rotate to this direction. |
| direction_middle |
a list of three int or float to represent the direction vector. The middle main axis will rotate to this direction. |
| direction_short |
a list of three int or float to represent the direction vector. The short main axis will rotate to this direction. |
This function is used to get a peptide from the sequence
| parameters |
explanation |
| sequence |
a string, the serial |
| charged_terminal |
whether to change the terminal residues to the corresponding charged residue |
| return |
a Molecule instance, the peptide |
This function is used to optimize the structure of the Molecule instance
| parameters |
explanation |
| mol |
the molecule to optimize |
| step |
the limited step for each epoch for minimization, 2000 for default |
| only_bad_coordinate |
whether to optimize all the atoms or the atoms whose coordinates are bad |
| dt |
the start dt for minimization |
| pbc |
whether to use the periodic box condition |
| extra_commands |
a dict, with the extra commands to pass to the MD engine |
This abstract class is used to define a region
This function is used to set the side of the region"
| parameters |
explanation |
| side |
either "in" or "out" |
This class is used to get the interset region of some regions
| parameters |
explanation |
| *regions |
the regions |
This class is used to get the union region of some regions
| parameters |
explanation |
| *regions |
the regions |
This class is used to define a block region
| parameters |
explanation |
| x_low |
the lowest x coordinate of the block region |
| y_low |
the lowest y coordinate of the block region |
| z_low |
the lowest z coordinate of the block region |
| x_high |
the highest x coordinate of the block region |
| y_high |
the highest y coordinate of the block region |
| z_high |
the highest z coordinate of the block region |
| side |
either "in" or "out" |
| boundary |
whether the boudary is seen as in the region |
This class is used to define a sphere region
| parameters |
explanation |
| x |
the x coordinate of the sphere origin |
| y |
the y coordinate of the sphere origin |
| z |
the z coordinate of the sphere origin |
| r |
the radius of the sphere |
| side |
either "in" or "out" |
| boundary |
whether the boudary is seen as in the region |
This class is used to define a frustum region
| parameters |
explanation |
| x1 |
the x coordinate of the first circle origin |
| y1 |
the y coordinate of the first circle origin |
| z1 |
the z coordinate of the first circle origin |
| r1 |
the radius of the first circle origin |
| x2 |
the x coordinate of the second circle origin |
| y2 |
the y coordinate of the second circle origin |
| z2 |
the z coordinate of the second circle origin |
| r2 |
the radius of the second circle origin |
| side |
either "in" or "out" |
| boundary |
whether the boudary is seen as in the region |
This class is used to define a prism (parallelepiped) region
| parameters |
explanation |
| x0 |
the x coordinate of the origin |
| y0 |
the y coordinate of the origin |
| z0 |
the z coordinate of the origin |
| x1 |
the x coordinate of the first basis vector |
| y1 |
the y coordinate of the first basis vector |
| z1 |
the z coordinate of the first basis vector |
| x2 |
the x coordinate of the second basis vector |
| y2 |
the y coordinate of the second basis vector |
| zz |
the z coordinate of the second basis vector |
| x3 |
the x coordinate of the third basis vector |
| y3 |
the y coordinate of the third basis vector |
| z3 |
the z coordinate of the third basis vector |
| side |
either "in" or "out" |
| boundary |
whether the boudary is seen as in the region |
This class is used to help with the process of the lattice
| parameters |
explanation |
| style |
the style of the lattice. "custom", "template:NAME" or the key values in Lattice.styles |
| basis_molecule |
the unit to repeat, a Residue, a ResidueType or a Molecule |
| scale |
the scale of the lattice |
| origin |
a list with 3 numbers, the origin of the lattice. [0,0,0] for default. |
| cell_length |
the length of the unit cell. [1,1,1] for default. |
| cell_angle |
the angle of the unit cell. [90,90,90] for default. |
| basis_position |
a list of lists, every sublist has 3 numbers for coordinates. |
| spacing |
a list with 3 numbers, the spacing distance in three cell basis vectors. |
| periodic_bonds |
a set of atom pair names. This can be from ResidueType.remove_periodic_connectivity |
| periodic_cutoff |
a float. 3 for default. The cutoff of the bond to be recognized as periodic or not |
This function is used to create basis molecules to the region in the box
| parameters |
explanation |
| box |
the box of the system |
| region |
the region to create the basis_molecule |
| mol |
if mol the Molecule instance is provided, basis molecules will be added to mol |
| return |
a new Molecule instance, or the Molecule instance mol |