Package schrodinger :: Module structure :: Class _StructureAtom

Class _StructureAtom

  object --+    
           |    
_NotSortable --+
               |
              _StructureAtom

Access of mmct atoms properties pythonically.

Instance Methods

[hide private]

__init__(self, ct, index)
Create an instance from the Structure object and the atom index.

__int__(self)
The atom index.

__eq__(self, that)
Compare on mmct handle and index.

__ne__(self, other)
Check for inequality based on mmct handle and index.

__hash__(self)
hash(x)

__str__(self)
str(x)

addBond(self, atom2, bond_order)
Add a bond between the current atom and atom2.

deleteBond(self, atom2)
Delete the bond between the current atom and atom2.

retype(self)
Reassign the MacroModel atom type based on the bond orders and formal charge.

getResidue(self)
Return a _Residue object for the residue that this atom is part of.

getMolecule(self)
Return a _Molecule object for the molecule that this atom is part of.

getChain(self)
Return a _Chain object for the molecule that this atom is part of.

_getBondTotal(self)
Get total number of bonds to this atom.

_getAtomBondContainer(self)

_getBondedAtoms(self)

_getAtomicWeight(self)

_getGrowName(self)

_setGrowName(self, value)

_getPdbname(self)

_setPdbname(self, value)

_getPdbres(self)

_setPdbres(self, value)

_getPdbCode(self)

_getResnum(self)

_setResnum(self, rnum)

_getInscode(self)

_setInscode(self, icode)

_getAtomType(self)

_setAtomType(self, type)

_getAtomTypeName(self)

_getAtomColor(self)

_setAtomColor(self, co)

getColorRGB(self)
Return the RGB color of this atom as a tuple (R,G.B).

setColorRGB(self, red, green, blue)
Set the RGB color of this atom as a tuple (R,G.B).

setColorRGBString(self, rgb_string)
Set the atom color as RGB using a string in the form #FFFFFF or FFFFFF

getColorRGBString(self)
Get the atom color as an RGB string in the form #FFFFFF

_getAtomChain(self)

_setAtomChain(self, chain)

_atomNameWarning(self)

_getAtomNameWarning(self)

_setAtomNameWarning(self, name)

_getAtomName(self)

_setAtomName(self, name)

_getAtomEntryID(self)

str or NoneType

_getCtEntryId(self)
Return the entry id from the structure's property dictionary

_getAtomElement(self)

_setAtomElement(self, element)

_getAtomPartialCharge(self)

_setAtomPartialCharge(self, pcharge)

_getAtomSolvationCharge(self)

_setAtomSolvationCharge(self, scharge)

_getAtomFormalCharge(self)

_setAtomFormalCharge(self, fcharge)

_getAtomIsotope(self)

_setAtomIsotope(self, mass_number)

_getAtomSecondaryStructure(self)

_setAtomSecondaryStructure(self, secondary_struct)

_getAtomTemperatureFactor(self)

_setAtomTemperatureFactor(self, tfactor)

_getVDWRadius(self)

_isHalogen(self)

_getAtomMoleculeNumber(self)

_getAtomNumberByMolecule(self)

_getAtomNumberByEntry(self)

_getAtomicNumber(self)

_setAtomicNumber(self, value)

_getX(self)

_setX(self, value)

_getY(self)

_setY(self, value)

_getZ(self)

_setZ(self, value)

_getXYZ(self)

_setXYZ(self, xyz)

_getAltXYZ(self)

_setAltXYZ(self, xyz)

_getAtomChirality(self)

_atomStyleWarning(self)

_getAtomStyle(self)

_setAtomStyle(self, style)

_getStyle(self)

_setStyle(self, style)

_getAtomVisible(self)

_setAtomVisible(self, visible)

_getAtomLabelFormat(self)

_setAtomLabelFormat(self, fmt)

_getAtomLabelColor(self)

_setAtomLabelColor(self, col)

_getAtomLabelUserText(self)

_setAtomLabelUserText(self, utext)

_getAtomProperty(self)

Inherited from _NotSortable: __ge__, __gt__, __le__, __lt__

Inherited from object: __delattr__, __format__, __getattribute__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Variables

[hide private]

_doc = 'Chirality of the atom. R, S, ANR, ANS, undef, or None.'

Properties

[hide private]

_index
The atom index.

index
The atom index.

bond_total
Number of bonds to the atom.

bond
List of bonds to the atom (_StructureBond objects).

bonded_atoms
Iterator for atoms bonded to this atom (_StructureAtom objects).

atomic_weight
Return the atomic weight of the atom.

growname
Maestro grow name.

pdbname
PDB atom name.

pdbres
PDB residue name.

pdbcode
One-letter PDB residue code.

resnum
PDB residue number.

inscode
PDB residue insertion code.

atom_type
MacroModel atom type.

atom_type_name
MacroModel atom type name.

color
Atom color.

chain
Atom chain.

atom_name
Name of the atom.

name
Name of the atom.

entry_id
Maestro entry ID

element
Element character of the atom.

partial_charge
Partial charge of the atom.

solvation_charge

formal_charge
Formal charge of the atom.

isotope
Mass number charge of the atom.

secondary_structure

temperature_factor

vdw_radius

is_halogen

molecule_number

number_by_molecule

number_by_entry

atomic_number
Atomic number of the atom's element.

x
X-coordinate of the atom.

y
Y-coordinate of the atom.

z
Z-coordinate of the atom.

xyz
XYZ-coordinates of the atom.

alt_xyz
Alternative XYZ-coordinates of the atom, if available, otherwise returns None.

chirality
Chirality of the atom.

atom_style

style

visible

label_format

label_color

label_user_text

property
Dictionary-like container of Atom-level properties.

Inherited from object: __class__

Method Details

[hide private]

init(self, ct, index)
(Constructor)

Create an instance from the Structure object and the atom index. Note that the index used starts at 1 as per the underlying mmct lib.

Overrides: object.__init__

int(self)

The atom index. Read only.

hash(self)
(Hashing function)

hash(x)

Overrides: object.__hash__: (inherited documentation)

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

addBond(self, atom2, bond_order)

Add a bond between the current atom and atom2. @param bond_order Takes an integer bond order or a BondType

retype(self)

Reassign the MacroModel atom type based on the bond orders and formal charge. This function should be called after either of these have been changed.

getColorRGB(self)

Return the RGB color of this atom as a tuple (R,G.B). The color values have a range between 0 and 255.

setColorRGB(self, red, green, blue)

Set the RGB color of this atom as a tuple (R,G.B). Each color value should be an integer between 0 and 255.

_getCtEntryId(self)

Return the entry id from the structure's property dictionary

Returns: str or NoneType: The structure entry id, or None if no entry id was found

Property Details

[hide private]

_index

The atom index. Read only.

Get Method:: __int__(self) - The atom index.

index

The atom index. Read only.

Get Method:: __int__(self) - The atom index.

bond_total

Number of bonds to the atom.

Get Method:: _getBondTotal(self) - Get total number of bonds to this atom.

bond

List of bonds to the atom (_StructureBond objects).

Get Method:: _getAtomBondContainer(self)

bonded_atoms

Iterator for atoms bonded to this atom (_StructureAtom objects).

Get Method:: _getBondedAtoms(self)

atomic_weight

Return the atomic weight of the atom.

If implicit hydrogens are present, these are included with the weight of the atom they are attached to.

Get Method:: _getAtomicWeight(self)

growname

Maestro grow name.

Get Method:: _getGrowName(self)
Set Method:: _setGrowName(self, value)

pdbname

PDB atom name.

Get Method:: _getPdbname(self)
Set Method:: _setPdbname(self, value)

pdbres

PDB residue name.

Get Method:: _getPdbres(self)
Set Method:: _setPdbres(self, value)

pdbcode

One-letter PDB residue code.

Get Method:: _getPdbCode(self)

resnum

PDB residue number.

Get Method:: _getResnum(self)
Set Method:: _setResnum(self, rnum)

inscode

PDB residue insertion code.

Get Method:: _getInscode(self)
Set Method:: _setInscode(self, icode)

atom_type

MacroModel atom type. Note that changing the atom type does not automatically update the charge. See schrodinger.structure.Structure.retype.

Get Method:: _getAtomType(self)
Set Method:: _setAtomType(self, type)

atom_type_name

MacroModel atom type name.

Get Method:: _getAtomTypeName(self)

color

Atom color.

Get Method:: _getAtomColor(self)
Set Method:: _setAtomColor(self, co)

chain

Atom chain.

Get Method:: _getAtomChain(self)
Set Method:: _setAtomChain(self, chain)

atom_name

Name of the atom.

Get Method:: _getAtomNameWarning(self)
Set Method:: _setAtomNameWarning(self, name)

name

Name of the atom.

Get Method:: _getAtomName(self)
Set Method:: _setAtomName(self, name)

entry_id

Maestro entry ID

Get Method:: _getAtomEntryID(self)

element

Element character of the atom.

Get Method:: _getAtomElement(self)
Set Method:: _setAtomElement(self, element)

partial_charge

Partial charge of the atom.

Get Method:: _getAtomPartialCharge(self)
Set Method:: _setAtomPartialCharge(self, pcharge)

solvation_charge

Get Method:: _getAtomSolvationCharge(self)
Set Method:: _setAtomSolvationCharge(self, scharge)

formal_charge

Formal charge of the atom.

Get Method:: _getAtomFormalCharge(self)
Set Method:: _setAtomFormalCharge(self, fcharge)

isotope

Mass number charge of the atom.

Get Method:: _getAtomIsotope(self)
Set Method:: _setAtomIsotope(self, mass_number)

secondary_structure

Get Method:: _getAtomSecondaryStructure(self)
Set Method:: _setAtomSecondaryStructure(self, secondary_struct)

temperature_factor

Get Method:: _getAtomTemperatureFactor(self)
Set Method:: _setAtomTemperatureFactor(self, tfactor)

vdw_radius

Get Method:: _getVDWRadius(self)

is_halogen

Get Method:: _isHalogen(self)

atomic_number

Atomic number of the atom's element.

Get Method:: _getAtomicNumber(self)
Set Method:: _setAtomicNumber(self, value)

x

X-coordinate of the atom.

Get Method:: _getX(self)
Set Method:: _setX(self, value)

y

Y-coordinate of the atom.

Get Method:: _getY(self)
Set Method:: _setY(self, value)

z

Z-coordinate of the atom.

Get Method:: _getZ(self)
Set Method:: _setZ(self, value)

xyz

XYZ-coordinates of the atom.

Get Method:: _getXYZ(self)
Set Method:: _setXYZ(self, xyz)

alt_xyz

Alternative XYZ-coordinates of the atom, if available, otherwise returns None.

Get Method:: _getAltXYZ(self)
Set Method:: _setAltXYZ(self, xyz)

chirality

Chirality of the atom. R, S, ANR, ANS, undef, or None.

Get Method:: _getAtomChirality(self)

atom_style

Get Method:: _getAtomStyle(self)
Set Method:: _setAtomStyle(self, style)

style

Get Method:: _getStyle(self)
Set Method:: _setStyle(self, style)

visible

Get Method:: _getAtomVisible(self)
Set Method:: _setAtomVisible(self, visible)

label_format

Get Method:: _getAtomLabelFormat(self)
Set Method:: _setAtomLabelFormat(self, fmt)

label_color

Get Method:: _getAtomLabelColor(self)
Set Method:: _setAtomLabelColor(self, col)

label_user_text

Get Method:: _getAtomLabelUserText(self)
Set Method:: _setAtomLabelUserText(self, utext)

property

Dictionary-like container of Atom-level properties. Keys are strings of the form type_family_name as described in the PropertyName documentation.

Get Method:: _getAtomProperty(self)

Class _StructureAtom

__init__(self, ct, index) (Constructor)

__int__(self)

__hash__(self) (Hashing function)

__str__(self) (Informal representation operator)

addBond(self, atom2, bond_order)

retype(self)

getColorRGB(self)

setColorRGB(self, red, green, blue)

_getCtEntryId(self)

_index

index

bond_total

bond

bonded_atoms

atomic_weight

growname

pdbname

pdbres

pdbcode

resnum

inscode

atom_type

atom_type_name

color

chain

atom_name

name

entry_id

element

partial_charge

solvation_charge

formal_charge

isotope

secondary_structure

temperature_factor

vdw_radius

is_halogen

molecule_number

number_by_molecule

number_by_entry

atomic_number

x

y

z

xyz

alt_xyz

chirality

atom_style

style

visible

label_format

label_color

label_user_text

property

init(self, ct, index)
(Constructor)

int(self)

hash(self)
(Hashing function)

str(self)
(Informal representation operator)