Xponge.helper

SPONGE 1.4 Xponge API documentation.

¶ Xponge.helper

This module is used to provide help functions and classes

¶ subpackages

¶ submodules

¶ Xponge.helper.cv

¶ Xponge.helper.file

¶ Xponge.helper.gromacs

¶ Xponge.helper.math

¶ Xponge.helper.namespace

¶ Xponge.helper.rdkit

¶ functions

¶ xprint

This function is used to print some contents according to the verbose level in GlobalSetting

parameters	explanation
to_print	the contents to print
verbose	only print when the verbose level is not less than this value

return	None

¶ debug

This function sets the mode to debug or not

parameters	explanation
mode	the value to set the debug mode

¶ set_unit_transfer_function

This function is used to return a function to add a static method _unit_transfer for a class.

parameters	explanation
sometype	the class

return	the decorator

¶ add_unit_transfer_function

This function is used to return a function to add a static method _unit_transfer for a class.

parameters	explanation
sometype	the class

return	the decorator

¶ verbose

the gloabl verbose level

¶ add_pdb_residue_name_mapping

This function is used to add the residue name mapping to the property PDBResidueNameMap

parameters	explanation
place	head or tail
pdb_name	the residue name in pdb
real_name	the residue name in Python

return	None

¶ set_invisible_bonded_forces

This function is used to disables the types of bonded forces when building.

parameters	explanation
types	the types to set

return	None

¶ set_visible_bonded_forces

This function is used to disables the types of bonded forces except named here when building.

parameters	explanation
types	the types to set

return	None

¶ classes

¶ Xdict

This class is used to be a dict which can give not_found_message

parameters	explanation
not_found_method	the method (function) which will accept the key and return the value when the key is not found. New From 1.2.6.7
not_found_message	the string to print when the key is not found

¶ ReasonedBool

This class is a boolean value with a reason

parameters	explanation
value	True or False
reason	the reason why the boolean value is given

¶ Type

This class is the abstract class of the types (atom types, bonded force types and so on).

parameters	explanation
name	the name of the type
kwargs	parameters of the type

¶ add_property

This function is used to add a property to the class

parameters	explanation
parm_fmt	a dict mapping the name and the format of the property
parm_default	a dict mapping the name and the default value of the property

return	None

¶ set_property_unit

This function is used to set the unit of the property of the class

parameters	explanation
prop	the name of the property
unit_type	the type of the unit
base_unit	the basic unit used in Python

return	None

¶ new_from_string

This function is used to update the types of the class

parameters	explanation
string	the string to update
skip_lines	skip the first `skip_lines` line(s)

return	None

¶ new_from_file

This function is used to update the types of the class

parameters	explanation
filename	the name of the file
skip_lines	skip the first `skip_lines` line(s)

return	None

¶ new_from_dict

This function is used to update the types of the class

parameters	explanation
dic	the dict of the parameters

return	None

¶ get_class_name

This function gives the ._name of the class

return	the name of the class

¶ clear_type

This function clears the instance(s) of the class

parameters	explanation
name	the instance name to clear. If None, all instances will be cleared

return	None

¶ set_type

This function sets the instance into the class

parameters	explanation
name	the instance name
toset	the instance to set

return	None

¶ get_type

This function gets the instance of the class

parameters	explanation
name	the instance name

return	the instance to set

¶ get_all_types

This function gets the all instances of the class

return	a dict mapping the name and the instance

¶ update

This function is used to update the properties of the instance

parameters	explanation
kwargs	parameters to update

return	None

¶ AbstractMolecule

This abstract class is used to judge whether a class can be treated as a molecule

¶ AtomType

This class is a subclass of Type, for atom types

parameters	explanation
name	the name of the type
kwargs	parameters of the type

¶ ResidueType

This class is a subclass of Type, for residue types

parameters	explanation
name	the name of the type
kwargs	parameters of the type

¶ head

the name of the first atom in the head

¶ tail

the name of the first atom in the tail

¶ head_next

the name of the second atom in the head

¶ tail_next

the name of the second atom in the tail

¶ head_length

the length of the bond connected to the last residue

¶ tail_length

the length of the bond connected to the next residue

¶ head_link_conditions

the link conditions to the last residue

¶ tail_link_conditions

the link conditions to the next residue

¶ name2atom

This function convert an atom name to an Atom instance

parameters	explanation
name	the name

return	the Atom instance

¶ atom2index

This function convert an Atom instance to its index

parameters	explanation
atom	the Atom instance

return	the index

¶ atom2name

This function convert an Atom instance to its name

parameters	explanation
atom	the Atom instance

return	the name

¶ name2index

This function convert an atom name to its index

parameters	explanation
name	the name

return	the index

¶ add_atom

This function is used to add an atom to the residue type.

parameters	explanation
name	the name of the atom
atom_type	the type of the atom
x	the coordinate x
y	the coordinate y
z	the coordinate z

return	None

¶ omit_atoms

This function omits some atoms from the ResidueType

parameters	explanation
atoms	the atom(s) to omit
charge	the total charge of the residue type after the omission. None to use the charge sum of the unomitted atoms

return	None

¶ add_connectivity

This function is used to add the connectivity between two atoms to the residue type.

parameters	explanation
atom0	the atom name or the Atom instance
atom1	the atom name or the Atom instance

return	None

¶ remove_connectivity

This function is used to remove the connectivity between two atoms from the residue type.

parameters	explanation
atom0	the atom name or the Atom instance
atom1	the atom name or the Atom instance

return	None

¶ remove_periodic_connectivity

This function is used to remove the connectivity between atoms larger than the given cutoff

parameters	explanation
cutoff	the cutoff distance to recognize the connectivity as periodic or unperiodic

return	a list of the removed connected atom pair names

¶ add_bonded_force

This function is used to add the bonded force to the residue type.

parameters	explanation
bonded_force_entity	the bonded force instance
typename	the bonded force type name. If None, get_class_name will be used to get the name

return	None

¶ deepcopy

This function is used to deep copy the instance

parameters	explanation
name	the new ResidueType name
forcopy	the key to help you find who it is from

return	the new instance

¶ Entity

This class is the abstract class of the entities (atoms, bonded forces, residues and so on).

parameters	explanation
entity_type	the type of the entity
name	the name of the entity

¶ get_class_name

This function gives the name of the class

return	the name of the class

¶ update

This function is used to update the properties of the instance

parameters	explanation
kwargs	the properties to update

return	None

¶ Atom

This class is a subclass of Entity, for atoms

parameters	explanation
entity_type	a string or a AtomType instance, the type of the entity
name	the name of the entity

¶ extra_excluded_atoms

the extra excluded atoms of this atom

return	a set of atoms

¶ deepcopy

This function is used to deep copy the instance

parameters	explanation
forcopy	the key to help you find who it is from

return	the new instance

¶ link_atom

This function is used to link atoms for building

parameters	explanation
link_type	the type to link
atom	the atom to link

return	None

¶ extra_exclude_atom

This function is used to extra exclude one atom

parameters	explanation
atom	an Atom instance

return	None

¶ extra_exclude_atoms

This function is used to extra exclude a list of atoms

parameters	explanation
atom_list	the atom list

return	None

¶ Residue

This class is a subclass of Entity, for residues

parameters	explanation
entity_type	a string or a ResidueType instance, the type of the entity
name	the name of the entity
directly_copy	if True, directly copy the Residue instance from the ResidueType instance

¶ set_type

This function is used to change the type of the residue to a new type

parameters	explanation
new_type	the instance or the name of the new residue type
add_missing_atoms	whether to add missing atoms after deleting the terminal atoms

return	None

¶ unterminal

This function is used to turn the terminal residue to be unterminal

parameters	explanation
add_missing_atoms	whether to add missing atoms after deleting the terminal atoms

return	1 for success, 0 for failure

¶ name2atom

This function convert an atom name to an Atom instance

parameters	explanation
name	the name

return	the Atom instance

¶ atom2index

This function convert an Atom instance to its index

parameters	explanation
atom	the Atom instance

return	the index

¶ name2index

This function convert an atom name to its index

parameters	explanation
name	the name

return	the index

¶ add_atom

This function is used to add an atom to the residue

parameters	explanation
name	the name of the atom. If an Atom instance is given, only the name and type are used.
atom_type	the type of the atom. If None, it will copy from the ResidueType.
x	the coordinate x. If None, it will copy from the ResidueType.
y	the coordinate y. If None, it will copy from the ResidueType.
z	the coordinate z. If None, it will copy from the ResidueType.

return	None

¶ add_connectivity

This function is used to add the connectivity between two atoms to the residue entity.

parameters	explanation
atom0	the atom name or the Atom instance
atom1	the atom name or the Atom instance

return	None

¶ add_bonded_force

This function is used to add the bonded force to the residue entity.

parameters	explanation
bonded_force_entity	the bonded force instance

return	None

¶ add_missing_atoms

This function is used to add the missing atoms from the ResidueType to the residue entity.

return	None

¶ deepcopy

This function is used to deep copy the instance

parameters	explanation
forcopy	the key to help you find who it is from

return	the new instance

¶ ResidueLink

This class is a class for the link between residues

parameters	explanation
atom1	the first atom to link
atom2	the second atom to link

¶ get_hash

This function is used to get the hash value of the ResidueLink

parameters	explanation
one	one Atom or Residue of the link
other	the other Atom or Residue of the link

return	the hash value

¶ add_bonded_force

This function is used to add the bonded force to the residue link

parameters	explanation
bonded_force_entity	the bonded force instance

return	None

¶ deepcopy

This function is used to deep copy the instance

parameters	explanation
forcopy	the key to help you find who it is from

return	the new instance

¶ Molecule

This class is a class for molecules

parameters	explanation
name	a string, the name of the Molecule or a ResidueType instance

¶ cast

This function casts a Residue, a ResidueType or a Molecule to a Molecule

parameters	explanation
other	a Residue, a ResidueType or a Molecule instance
deepcopy	whether to deepcopy the other instance

return	a Molecule instance

¶ set_save_sponge_input

This function is used to set the function when Save_SPONGE_Input.

parameters	explanation
keyname	the file prefix to save

return	the decorator

¶ del_save_sponge_input

This function is used to delete the function when Save_SPONGE_Input.

parameters	explanation
keyname	the file prefix to save

return	None

¶ set_mindsponge_todo

This function is used to set the function when Save_SPONGE_Input.

parameters	explanation
keyname	the file prefix to save

return	the decorator

¶ del_mindsponge_todo

This function is used to delete the function when Save_SPONGE_Input.

parameters	explanation
keyname	the file prefix to save

return	None

¶ find_spacious_direction

This function is used to find the most spacious (lowest atom density) direction of the givin point around the atom positions

parameters	explanation
point	a list of 3 numbers, the point to find the most spacious direction
atom_positions	the atom positions around the point. If None, this will use the positions of the atoms in this Molecule

return	a numpy array with the shape (3,), the most spacious direction

¶ add_residue

This function is used to add a residue to the molecule

parameters	explanation
residue	the residue to add, either a Residue instance or a ResidueType instance

return	None

¶ add_bonded_force

This function is used to add the bonded force to the residue type.

parameters	explanation
bonded_force_entity	the bonded force instance

return	None

¶ add_residue_link

This function is used to add the connectivity between two atoms of two residues in the molecule.

parameters	explanation
atom1	the first atom
atom2	the second atom

return	None

¶ get_residue_link

This function is used to get the ResidueLink between two residues

parameters	explanation
one	one Atom or Residue of the ResidueLink
other	the other Atom or Residue of the ResidueLink

return	the ResidueLink or None if not found

¶ del_residue_link

This function is used to delete the ResidueLink between two residues

parameters	explanation
one	one Atom or Residue of the ResidueLink
other	the other Atom or Residue of the ResidueLink
key	"atom" or "residue", to specify the key

return	None

¶ add_missing_atoms

This function is used to add the missing atoms from the ResidueType instances to the molecule.

return	None

¶ set_missing_residues_info

This function is used to set the information about the missing residues

parameters	explanation
start	the residue or the residue index where the missing residues start. `None` for no starting residue.
end	the residue or the residue index where the missing residues end. `None` for no ending residue.
missing_residues	the missing residues. The parameter can be a string separated by space, or a list of residue names, or a list of ResidueType or None. If None, the information will be deleted between start and end

return	True for success, False for failure to set

¶ clear_missing_residues_info

This function is used to clear the information about the missing residues

return	None

¶ add_missing_residues

This function is used to add the missing residues according to the information of the missing residues.

parameters	explanation
add_head	whether to add the missing residues at the head of the chain
add_tail	whether to add the missing residues at the tail of the chain

return	None

¶ deepcopy

This function is used to deep copy the instance

return	the new instance

¶ get_atoms

This function is used to get the atoms in the molecule.

return	a list of atoms

¶ get_atom_coordinates

This function is used to get the atom coordinates

return	a numpy array, the coordinates of atoms

¶ divide_into_two_parts

This function is used to divide the molecule into two parts

parameters	explanation
atom1	the first atom
atom2	the second atom

return	two numpy arrays, the index of the two parts

¶ restrain_position

This function is used to generate the atoms for restraints

parameters	explanation
select	a string of MDAnalysis selection
filename	the name of the output atom index file

return	None

¶ constrain_position

This function is used to generate the mass in file for constraints

parameters	explanation
select	a string of MDAnalysis selection
filename	the name of the output atom index file

return	None

¶ BondedForceEntity

This class is a subclass of Entity, for bonded forces

¶ deepcopy

This function is used to deep copy the instance

return	None

¶ BondedForceType

This class is a subclass of Type, for bonded force types

¶ same_force

This function receives a list of atoms and output all the same force permutations for the list

parameters	explanation
atom_list

return	None

¶ PairwiseForceType

This class is a subclass of Type, for pairwise force types