SPONGEMM

Xponge.assign

SPONGE 1.4 Xponge API documentation.

Xponge.assign

This package is used to assign the properties for atoms, residues and molecules

subpackages

Xponge.assign.tpacm4

submodules

Xponge.assign.bond_order

Xponge.assign.gasteiger

Xponge.assign.phmodel

Xponge.assign.resp

functions

get_assignment_from_smiles

This function gets an Assign instance from smiles

parameters explanation
smiles the smiles to get
return the Assign instance

get_assignment_from_pdb

This function gets an Assign instance from a pdb file

parameters explanation
file the name of the input file or an instance of io.IOBase
only_residue only get the residue with the name same as only_residue
bond_tolerance the parameter to determine the atomic connections. The larger tolerance, the easier to set a bond between two atoms
total_charge the total charge of the molecule used when aligning bond orders. If None is given, the total charge will not be checked
return the Assign instance

get_assignment_from_residuetype

This function gets an Assign instance from a ResidueType instance

parameters explanation
restype the ResidueType instance
return the Assign instance

get_assignment_from_xyz

This function gets an Assign instance from a xyz file

parameters explanation
file the name of the input file or an instance of io.IOBase
bond_tolerance the parameter to determine the atomic connections. The larger tolerance, the easier to set a bond between two atoms
total_charge the total charge of the molecule used when aligning bond orders. If None is given, the total charge will not be checked
return the Assign instance

get_assignment_from_mol2

This function gets an Assign instance from a mol2 file

parameters explanation
file the name of the input file or an instance of io.IOBase
total_charge the total charge of the molecule used when aligning bond orders. If "sum" is given, the sum of the partial charges will be used; If None is given, the total charge will not be checked
return the Assign instance

get_assignment_from_cif

This function gets an Assign instance and a preprocessed lattice information from a cif file

parameters explanation
file the name of the input file or an instance of io.IOBase
total_charge the total charge of the molecule used when aligning bond orders. 0 for default.
orthogonal_threshold cell angle with the difference less than this parameter will be considered to be orthogonal (in degree, and 5 for default)
return the Assign instance and a dict which stores the preprocessed lattice information

classes

AssignRule

This class is to be the rule to determine the atom type for one atom

parameters explanation
name the name of the rule

add_rule

This function is used as a decorator to add the atom type - judge function

parameters explanation
atomtype a string or an AtomType instance
priority if more than one judge function returns True, the atom type with higher priority will be chosen. If the priority levels of the functions are the same, the atom type which is added first will be chosen.
return a function, which wraps a judge function (receiving the Assign instance and the atom index and giving True or False as a result)

add_rings_basic_marker

parameters explanation
assign
rings
return None

check_rings_type

parameters explanation
assign
rings
return None

get_rings

parameters explanation
assign
return None

get_3_neighbors

return None

check_pure_aromatic

parameters explanation
assign
return None

check_pure_aliphatic_and_planar

parameters explanation
assign
return None

check_out_plane_double_bond

parameters explanation
assign
return None

check_aromatic

parameters explanation
assign
return None

Assign

This class is used to assign properties for atoms, which is called an "assignment"

parameters explanation
name the name of the molecule

add_index_to_name

This function renames the atoms by adding the index to the element name

return None

atom_judge

This function helps judge whether the atom belongs to the mask. For example, "O2" means an oxygen atom connected to two other atoms, "N4" means a nitrogen atom connected to four other atoms.

parameters explanation
atom the index of the atom
string a string mask of a list of string masks.
return None

add_atom

This function adds an atom to the Assign

parameters explanation
element the chemical symbol for the element. "O" - oxygen, "H" - hydrogen for example.
x the x coordinate
y the y coordinate
z the z coordinate
name the name of the atom
charge the charge of the atom
return None

add_atom_marker

This function adds a marker to an atom

parameters explanation
atom the atom index
marker the marker
return None

add_bond

This function adds a bond to two atoms

parameters explanation
atom1 the index of the first atom
atom2 the index of the the second atom
order the bond order
return None

add_bond_marker

This function adds a marker to a bond

parameters explanation
atom1 the index of the first atom
atom2 the index of the the second atom
marker the marker
only1 only add the marker to the atom1 - atom2 bond instead of the atom2 - atom1 bond
return None

delete_atom

This function deletes the atom

parameters explanation
atom the index of the atom to delete
return None

delete_bond

This function deletes the bond between two atoms

parameters explanation
atom1 the index of the first atom
atom2 the index of the the second atom
return None

determine_equal_atoms

This function dertermines the chemical equalvalent atoms

return a list of equalvalent atom index lists

determine_ring_and_bond_type

This function determine the ring and the bond type

return None

determine_atom_type

This function determines the atom type.

parameters explanation
rule a string or an AssignRule instance
return if the attribute "pure_string" of the rule is False, the atom types will be saved inplace and return

determine_connectivity

This function determines the connectivity based on atomic distances

parameters explanation
simple_cutoff the distance cutoff to determine whether the two atoms are connected. If None (default),
tolerance the tolerance factor for the default method
return None

check_connectivity

This function checks whether all atoms are connected in one graph

return True or False

to_residuetype

This function converts the Assign instance to the ResidueType instance

parameters explanation
name the name of the ResidueType instance
charge the charge of atoms. If set to None, internal charge will be used
return the ResidueType instance

calculate_charge

This function calculates the partial charge for every atom.

parameters explanation
method the method to calculate the charge
parameters the parameters to calculate the charge
return None

kekulize

This function kekulizes the structure.

return None

uff_optimize

This function uses rdkit and uff to optimize the structure

save_as_pdb

This function saves the instance as a pdb file

parameters explanation
filename the name of the output file
return None

save_as_mol2

This function saves the instance as a mol2 file

parameters explanation
filename the name of the output file
atomtype the rule of atom types.
return None

set_ph

This function sets the pH value, and adds or deletes the related hydrogens.

parameters explanation
ph the pH value
return the sum of final formal charge