| |
- src.structures.Residue
-
- Nucleic
-
- A
- C
- G
- T
- U
class A(Nucleic) |
|
Adenosine class
This class gives data about the Adenosine object, and inherits
off the base residue class. |
|
- Method resolution order:
- A
- Nucleic
- src.structures.Residue
Methods defined here:
- __init__(self, atoms, ref)
- Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
- setState(self)
- Set the state to distinguish RNA from DNA.
Methods inherited from Nucleic:
- addAtom(self, atom)
- Override the existing addAtom - include the link to the
reference object
- addDihedralAngle(self, value)
- Add the value to the list of chiangles
Parameters
value: The value to be added (float)
- createAtom(self, atomname, newcoords)
- Create an atom. Overrides the generic residue's createAtom().
Parameters
atomname: The name of the atom to add (string)
newcoords: The coordinates of the atom (list)
Methods inherited from src.structures.Residue:
- __str__(self)
- Basic string representation for debugging
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- get(self, name)
- Get a member of the Residue class
Parameters
name: The name of the member (string)
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chainID: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
missing: List of missing atoms of the residue
Returns
item: The value of the member
- getAtom(self, name)
- Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
- getAtoms(self)
- getCharge(self)
- Get the total charge of the residue. In order to get rid
of floating point rounding error, do the string
transformation.
Returns:
charge: The charge of the residue (float)
- hasAtom(self, name)
- numAtoms(self)
- Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
- removeAtom(self, atomname)
- Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
- renameAtom(self, oldname, newname)
- Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
- renameResidue(self, name)
- Rename a given residue
Parameters
name: The new name of the residue
- reorder(self)
- Reorder the atoms to start with N, CA, C, O if they exist
- rotateTetrahedral(self, atom1, atom2, angle)
- Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.
Parameters:
atom1: The first atom of the bond to rotate about (atom)
atom2: The second atom of the bond to rotate about (atom)
angle: The number of degrees to rotate (float)
- set(self, name, value)
- Set a member of the Residue class to a specific value
Parameters
name: The name of the object to set (string)
value: The object to append
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chain: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
isDirty: 1 if the residue is not missing atoms,
0 otherwise
Notes
resSeq points to the residue.setResSeq function
Returns
item: The value of the member
- setChainID(self, value)
- Set the chainID field to a certain value
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the residue
- setResSeq(self, value)
- Set the atom field resSeq to a certain value and
change the residue's information. The icode field is no longer
useful.
Parameters
value: The new value of resSeq (int)
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class C(Nucleic) |
|
Cytidine class
This class gives data about the Cytidine object, and inherits
off the base residue class. |
|
- Method resolution order:
- C
- Nucleic
- src.structures.Residue
Methods defined here:
- __init__(self, atoms, ref)
- Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
- setState(self)
- Set the state to distinguish RNA from DNA.
Methods inherited from Nucleic:
- addAtom(self, atom)
- Override the existing addAtom - include the link to the
reference object
- addDihedralAngle(self, value)
- Add the value to the list of chiangles
Parameters
value: The value to be added (float)
- createAtom(self, atomname, newcoords)
- Create an atom. Overrides the generic residue's createAtom().
Parameters
atomname: The name of the atom to add (string)
newcoords: The coordinates of the atom (list)
Methods inherited from src.structures.Residue:
- __str__(self)
- Basic string representation for debugging
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- get(self, name)
- Get a member of the Residue class
Parameters
name: The name of the member (string)
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chainID: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
missing: List of missing atoms of the residue
Returns
item: The value of the member
- getAtom(self, name)
- Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
- getAtoms(self)
- getCharge(self)
- Get the total charge of the residue. In order to get rid
of floating point rounding error, do the string
transformation.
Returns:
charge: The charge of the residue (float)
- hasAtom(self, name)
- numAtoms(self)
- Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
- removeAtom(self, atomname)
- Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
- renameAtom(self, oldname, newname)
- Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
- renameResidue(self, name)
- Rename a given residue
Parameters
name: The new name of the residue
- reorder(self)
- Reorder the atoms to start with N, CA, C, O if they exist
- rotateTetrahedral(self, atom1, atom2, angle)
- Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.
Parameters:
atom1: The first atom of the bond to rotate about (atom)
atom2: The second atom of the bond to rotate about (atom)
angle: The number of degrees to rotate (float)
- set(self, name, value)
- Set a member of the Residue class to a specific value
Parameters
name: The name of the object to set (string)
value: The object to append
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chain: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
isDirty: 1 if the residue is not missing atoms,
0 otherwise
Notes
resSeq points to the residue.setResSeq function
Returns
item: The value of the member
- setChainID(self, value)
- Set the chainID field to a certain value
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the residue
- setResSeq(self, value)
- Set the atom field resSeq to a certain value and
change the residue's information. The icode field is no longer
useful.
Parameters
value: The new value of resSeq (int)
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class G(Nucleic) |
|
Guanosine class
This class gives data about the Guanosine object, and inherits
off the base residue class. |
|
- Method resolution order:
- G
- Nucleic
- src.structures.Residue
Methods defined here:
- __init__(self, atoms, ref)
- Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
- setState(self)
- Set the state to distinguish RNA from DNA.
Methods inherited from Nucleic:
- addAtom(self, atom)
- Override the existing addAtom - include the link to the
reference object
- addDihedralAngle(self, value)
- Add the value to the list of chiangles
Parameters
value: The value to be added (float)
- createAtom(self, atomname, newcoords)
- Create an atom. Overrides the generic residue's createAtom().
Parameters
atomname: The name of the atom to add (string)
newcoords: The coordinates of the atom (list)
Methods inherited from src.structures.Residue:
- __str__(self)
- Basic string representation for debugging
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- get(self, name)
- Get a member of the Residue class
Parameters
name: The name of the member (string)
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chainID: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
missing: List of missing atoms of the residue
Returns
item: The value of the member
- getAtom(self, name)
- Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
- getAtoms(self)
- getCharge(self)
- Get the total charge of the residue. In order to get rid
of floating point rounding error, do the string
transformation.
Returns:
charge: The charge of the residue (float)
- hasAtom(self, name)
- numAtoms(self)
- Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
- removeAtom(self, atomname)
- Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
- renameAtom(self, oldname, newname)
- Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
- renameResidue(self, name)
- Rename a given residue
Parameters
name: The new name of the residue
- reorder(self)
- Reorder the atoms to start with N, CA, C, O if they exist
- rotateTetrahedral(self, atom1, atom2, angle)
- Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.
Parameters:
atom1: The first atom of the bond to rotate about (atom)
atom2: The second atom of the bond to rotate about (atom)
angle: The number of degrees to rotate (float)
- set(self, name, value)
- Set a member of the Residue class to a specific value
Parameters
name: The name of the object to set (string)
value: The object to append
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chain: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
isDirty: 1 if the residue is not missing atoms,
0 otherwise
Notes
resSeq points to the residue.setResSeq function
Returns
item: The value of the member
- setChainID(self, value)
- Set the chainID field to a certain value
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the residue
- setResSeq(self, value)
- Set the atom field resSeq to a certain value and
change the residue's information. The icode field is no longer
useful.
Parameters
value: The new value of resSeq (int)
|
class Nucleic(src.structures.Residue) |
|
Nucleic class
This class provides standard features of the nucleic acids listed
below
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
ref: The reference object for the amino acid. Used to
convert from the alternate naming scheme to the
main naming scheme. |
|
Methods defined here:
- __init__(self, atoms, ref)
- addAtom(self, atom)
- Override the existing addAtom - include the link to the
reference object
- addDihedralAngle(self, value)
- Add the value to the list of chiangles
Parameters
value: The value to be added (float)
- createAtom(self, atomname, newcoords)
- Create an atom. Overrides the generic residue's createAtom().
Parameters
atomname: The name of the atom to add (string)
newcoords: The coordinates of the atom (list)
- setState(self)
- Adds the termini for all inherited objects
Methods inherited from src.structures.Residue:
- __str__(self)
- Basic string representation for debugging
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- get(self, name)
- Get a member of the Residue class
Parameters
name: The name of the member (string)
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chainID: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
missing: List of missing atoms of the residue
Returns
item: The value of the member
- getAtom(self, name)
- Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
- getAtoms(self)
- getCharge(self)
- Get the total charge of the residue. In order to get rid
of floating point rounding error, do the string
transformation.
Returns:
charge: The charge of the residue (float)
- hasAtom(self, name)
- numAtoms(self)
- Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
- removeAtom(self, atomname)
- Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
- renameAtom(self, oldname, newname)
- Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
- renameResidue(self, name)
- Rename a given residue
Parameters
name: The new name of the residue
- reorder(self)
- Reorder the atoms to start with N, CA, C, O if they exist
- rotateTetrahedral(self, atom1, atom2, angle)
- Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.
Parameters:
atom1: The first atom of the bond to rotate about (atom)
atom2: The second atom of the bond to rotate about (atom)
angle: The number of degrees to rotate (float)
- set(self, name, value)
- Set a member of the Residue class to a specific value
Parameters
name: The name of the object to set (string)
value: The object to append
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chain: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
isDirty: 1 if the residue is not missing atoms,
0 otherwise
Notes
resSeq points to the residue.setResSeq function
Returns
item: The value of the member
- setChainID(self, value)
- Set the chainID field to a certain value
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the residue
- setResSeq(self, value)
- Set the atom field resSeq to a certain value and
change the residue's information. The icode field is no longer
useful.
Parameters
value: The new value of resSeq (int)
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class T(Nucleic) |
|
Thymine class
This class gives data about the Thymine object, and inherits
off the base residue class. |
|
- Method resolution order:
- T
- Nucleic
- src.structures.Residue
Methods defined here:
- __init__(self, atoms, ref)
- Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
- setState(self)
- Set the state to distinguish RNA from DNA. In this case it is
always DNA.
Methods inherited from Nucleic:
- addAtom(self, atom)
- Override the existing addAtom - include the link to the
reference object
- addDihedralAngle(self, value)
- Add the value to the list of chiangles
Parameters
value: The value to be added (float)
- createAtom(self, atomname, newcoords)
- Create an atom. Overrides the generic residue's createAtom().
Parameters
atomname: The name of the atom to add (string)
newcoords: The coordinates of the atom (list)
Methods inherited from src.structures.Residue:
- __str__(self)
- Basic string representation for debugging
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- get(self, name)
- Get a member of the Residue class
Parameters
name: The name of the member (string)
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chainID: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
missing: List of missing atoms of the residue
Returns
item: The value of the member
- getAtom(self, name)
- Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
- getAtoms(self)
- getCharge(self)
- Get the total charge of the residue. In order to get rid
of floating point rounding error, do the string
transformation.
Returns:
charge: The charge of the residue (float)
- hasAtom(self, name)
- numAtoms(self)
- Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
- removeAtom(self, atomname)
- Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
- renameAtom(self, oldname, newname)
- Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
- renameResidue(self, name)
- Rename a given residue
Parameters
name: The new name of the residue
- reorder(self)
- Reorder the atoms to start with N, CA, C, O if they exist
- rotateTetrahedral(self, atom1, atom2, angle)
- Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.
Parameters:
atom1: The first atom of the bond to rotate about (atom)
atom2: The second atom of the bond to rotate about (atom)
angle: The number of degrees to rotate (float)
- set(self, name, value)
- Set a member of the Residue class to a specific value
Parameters
name: The name of the object to set (string)
value: The object to append
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chain: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
isDirty: 1 if the residue is not missing atoms,
0 otherwise
Notes
resSeq points to the residue.setResSeq function
Returns
item: The value of the member
- setChainID(self, value)
- Set the chainID field to a certain value
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the residue
- setResSeq(self, value)
- Set the atom field resSeq to a certain value and
change the residue's information. The icode field is no longer
useful.
Parameters
value: The new value of resSeq (int)
|
class U(Nucleic) |
|
Uridine class
This class gives data about the Uridine object, and inherits
off the base residue class. |
|
- Method resolution order:
- U
- Nucleic
- src.structures.Residue
Methods defined here:
- __init__(self, atoms, ref)
- Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
- setState(self)
- Set the state to distinguish RNA from DNA. In this case it is
always RNA.
Methods inherited from Nucleic:
- addAtom(self, atom)
- Override the existing addAtom - include the link to the
reference object
- addDihedralAngle(self, value)
- Add the value to the list of chiangles
Parameters
value: The value to be added (float)
- createAtom(self, atomname, newcoords)
- Create an atom. Overrides the generic residue's createAtom().
Parameters
atomname: The name of the atom to add (string)
newcoords: The coordinates of the atom (list)
Methods inherited from src.structures.Residue:
- __str__(self)
- Basic string representation for debugging
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- get(self, name)
- Get a member of the Residue class
Parameters
name: The name of the member (string)
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chainID: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
missing: List of missing atoms of the residue
Returns
item: The value of the member
- getAtom(self, name)
- Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
- getAtoms(self)
- getCharge(self)
- Get the total charge of the residue. In order to get rid
of floating point rounding error, do the string
transformation.
Returns:
charge: The charge of the residue (float)
- hasAtom(self, name)
- numAtoms(self)
- Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
- removeAtom(self, atomname)
- Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
- renameAtom(self, oldname, newname)
- Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
- renameResidue(self, name)
- Rename a given residue
Parameters
name: The new name of the residue
- reorder(self)
- Reorder the atoms to start with N, CA, C, O if they exist
- rotateTetrahedral(self, atom1, atom2, angle)
- Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.
Parameters:
atom1: The first atom of the bond to rotate about (atom)
atom2: The second atom of the bond to rotate about (atom)
angle: The number of degrees to rotate (float)
- set(self, name, value)
- Set a member of the Residue class to a specific value
Parameters
name: The name of the object to set (string)
value: The object to append
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chain: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
isDirty: 1 if the residue is not missing atoms,
0 otherwise
Notes
resSeq points to the residue.setResSeq function
Returns
item: The value of the member
- setChainID(self, value)
- Set the chainID field to a certain value
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the residue
- setResSeq(self, value)
- Set the atom field resSeq to a certain value and
change the residue's information. The icode field is no longer
useful.
Parameters
value: The new value of resSeq (int)
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