Xponge.process

SPONGE 1.4 Xponge API documentation.

¶ Xponge.process

This module is used to process topology and conformations

¶ subpackages

¶ submodules

¶ functions

¶ impose_bond

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

return	None

¶ impose_angle

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

return	None

¶ impose_dihedral

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

return	None

¶ add_solvent_box

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

¶ h_mass_repartition

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.

return	None

¶ solvent_replace

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

return	None

¶ 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.

return	None

¶ get_peptide_from_sequence

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

¶ optimize

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

return	None

¶ classes

¶ Region

This abstract class is used to define a region

¶ side

This function is used to set the side of the region"

parameters	explanation
side	either "in" or "out"

return	None

¶ IntersectRegion

This class is used to get the interset region of some regions

parameters	explanation
*regions	the regions

¶ UnionRegion

This class is used to get the union region of some regions

parameters	explanation
*regions	the regions

¶ BlockRegion

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

¶ SphereRegion

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

¶ FrustumRegion

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

¶ PrismRegion

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

¶ Lattice

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

¶ create

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`