Python: module src.na

src.na (28 February 2006) | index /Users/baker/coding/manifold/pdb2pqr/trunk/pdb2pqr/src/na.py

`Nucleic Acid Structures for PDB2PQR
This module contains the base nucleic acid structures for
pdb2pqr.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Nathan A. Baker (baker@biochem.wustl.edu)
Todd Dolinsky (todd@ccb.wustl.edu)
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Jens Nielsen (Jens.Nielsen@ucd.ie)
University College Dublin
Additional contributing authors listed in documentation and supporting
package licenses.
Copyright (c) 2003-2007. Washington University in St. Louis.
All Rights Reserved.
This file is part of PDB2PQR.
PDB2PQR is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
PDB2PQR is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with PDB2PQR; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
----------------------------`

Modules
`` |  |
copy math | os string | sys |

Classes
`` |  | 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)`
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)`
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)`
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)`

Data
`` |  | BACKBONE = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN'] DIHEDRAL = 57.2958 SMALL = 9.9999999999999995e-08 __author__ = 'Todd Dolinsky' __date__ = '28 February 2006'

Author
`` |  | Todd Dolinsky