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- src.pdb.ATOM
-
- Atom
- Chain
- Residue
class Atom(src.pdb.ATOM) |
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Class Atom
The Atom class inherits off the ATOM object in pdb.py. It is used
for adding fields not found in the pdb that may be useful for analysis.
Also simplifies code by combining ATOM and HETATM objects into a
single class.
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Methods defined here:
- __init__(self, atom, type, residue)
- Initialize the new Atom object by using the old object.
Parameters
atom: The original ATOM object (ATOM)
type: Either ATOM or HETATM (string)
residue: A pointer back to the parent residue object (Residue)
- __str__(self)
- Returns a string of the new atom type. Uses the ATOM string
output but changes the first field to either by ATOM or
HETATM as necessary.
Returns
str: String with ATOM/HETATM field set appropriately
- addBond(self, bondedatom)
- Add a bond to the list of bonds
Parameters:
bondedatom: The atom to bond to (Atom)
- get(self, name)
- Get a member of the Atom class
Parameters
name: The name of the member (string)
Possible Values
type: The type of Atom (either ATOM or HETATM)
serial: Atom serial number
name: Atom name
altLoc: Alternate location
resName: Residue name
chainID: Chain identifier
resSeq: Residue sequence number
iCode: Code for insertion of residues
x: Orthogonal coordinates for X in Angstroms.
y: Orthogonal coordinates for Y in Angstroms.
z: Orthogonal coordinates for Z in Angstroms.
occupancy: Occupancy
tempFactor: Temperature Factor
segID: Segment identifier
element: Element symbol
charge: Charge on the atom
bonds: The bonds associated with the atom
interbonds: The intrabonds associated with the atom
extrabonds: The extrabonds assocaited with the atom
residue: The parent residue of the atom
radius: The radius of the atom
ffcharge: The forcefield charge on the atom
hdonor: Whether the atom is a hydrogen donor
hacceptor: Whether the atom is a hydrogen acceptor
Returns
item: The value of the member
- getCoords(self)
- Return the x,y,z coordinates of the atom in list form
Returns
List of the coordinates (list)
- hasReference(self)
- Determine if the atom object has a reference object or not.
All known atoms should have reference objects.
Returns
1 if atom has a reference object, 0 otherwise.
- isBackbone(self)
- Return true if atom name is in backbone, otherwise false
Returns
state: 1 if true, 0 if false
- isHydrogen(self)
- Is this atom a Hydrogen atom?
Returns
value: 1 if Atom is a Hydrogen, 0 otherwise
- set(self, name, value)
- Set a member of the Atom class
Parameters
name: The name of the member (string)
value: The value to set the member to
Possible Values
type: The type of Atom (either ATOM or HETATM)
serial: Atom serial number
name: Atom name
altLoc: Alternate location
resName: Residue name
chainID: Chain identifier
resSeq: Residue sequence number
iCode: Code for insertion of residues
x: Orthogonal coordinates for X in Angstroms.
y: Orthogonal coordinates for Y in Angstroms.
z: Orthogonal coordinates for Z in Angstroms.
occupancy: Occupancy
tempFactor: Temperature Factor
segID: Segment identifier
element: Element symbol
charge: Charge on the atom
residue: The parent residue of the atom
radius: The radius of the atom
ffcharge: The forcefield charge on the atom
hdonor: Whether the atom is a hydrogen donor
hacceptor: Whether the atom is a hydrogen acceptor
Returns
item: The value of the member
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class Chain |
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Chain class
The chain class contains information about each chain within a given
Protein object.
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Methods defined here:
- __init__(self, chainID)
- Initialize the class
Parameters
chainID: The chainID for this chain as denoted in
the PDB file (string)
- addResidue(self, residue)
- Add a residue to the chain
Parameters
residue: The residue to be added (Residue)
- get(self, name)
- Get a member of the Chain class
Parameters
name: The name of the member
Possible Values
ID: The ID of the chain
Residues: The list of residues within the Chain
Returns
item: The value of the member
- getAtoms(self)
- Return a list of Atom objects contained in this chain
Returns
atomlist: List of Atom objects (list)
- getResidues(self)
- Return a list of Residue objects in this chain
- numAtoms(self)
- Get the number of atoms for the chain
Returns
count: Number of atoms in the chain (int)
- numResidues(self)
- Get the number of residues for the chain
Returns
count: Number of residues in the chain (int)
- renumberResidues(self)
- Renumber Atoms based on actual Residue number and not PDB resSeq
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class Residue |
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Residue class
The residue class contains a list of Atom objects associated with that
residue and other helper functions.
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Methods defined here:
- __init__(self, atoms)
- Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
- __str__(self)
- Basic string representation for debugging
- addAtom(self, atom)
- Add the atom object to the residue.
Parameters
atom: The object to be added (ATOM)
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- createAtom(self, name, newcoords, type)
- Add a new atom object to the residue. Uses an atom
currently in the residue to seed the new atom
object, then replaces the coordinates and name accordingly.
Parameters
name: The name of the new atom (string)
newcoords: The x,y,z coordinates of the new atom (list)
type: The type of atom, ATOM or HETATM
- 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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