Package schrodinger :: Module structure :: Class _StructureAtom

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Class _StructureAtom

Access of mmct atoms properties pythonically.

Instance Methods

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__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)

__str__(self)

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)

vdw_radius(self)

_isHalogen(self)

is_halogen(self)

_getAtomMoleculeNumber(self)

molecule_number(self)

_getAtomNumberByMolecule(self)

number_by_molecule(self)

_getAtomNumberByEntry(self)

number_by_entry(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)

Class Variables

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_index = property(__int__, doc= "The atom index. I{Read only.}")

index = property(__int__, doc= "The atom index. I{Read only.}")

bond_total = property(_getBondTotal, doc= "Number of bonds to ...

bond = property(_getAtomBondContainer, doc= "List of bonds to ...

bonded_atoms = property(_getBondedAtoms, doc= "Iterator for at...

atomic_weight = property(_getAtomicWeight, doc= ...

growname = property(_getGrowName, _setGrowName, doc= "Maestro ...

pdbname = property(_getPdbname, _setPdbname, doc= "PDB atom na...

pdbres = property(_getPdbres, _setPdbres, doc= "PDB residue na...

pdbcode = property(_getPdbCode, doc= "One-letter PDB residue c...

resnum = property(_getResnum, _setResnum, doc= "PDB residue nu...

inscode = property(_getInscode, _setInscode, doc= "PDB residue...

atom_type = property(_getAtomType, _setAtomType, doc= "MacroMo...

atom_type_name = property(_getAtomTypeName, doc= "MacroModel a...

color = property(_getAtomColor, _setAtomColor, doc= "Atom colo...

chain = property(_getAtomChain, _setAtomChain, doc= "Atom chai...

atom_name = property(_getAtomNameWarning, _setAtomNameWarning,...

name = property(_getAtomName, _setAtomName, doc= "Name of the ...

entry_id = property(_getAtomEntryID, doc= "Maestro entry ID")

element = property(_getAtomElement, _setAtomElement, doc= "Ele...

partial_charge = property(_getAtomPartialCharge, _setAtomParti...

solvation_charge = property(_getAtomSolvationCharge, _setAtomS...

formal_charge = property(_getAtomFormalCharge, _setAtomFormalC...

isotope = property(_getAtomIsotope, _setAtomIsotope, doc= "Mas...

secondary_structure = property(_getAtomSecondaryStructure, _se...

temperature_factor = property(_getAtomTemperatureFactor, _setA...

atomic_number = property(_getAtomicNumber, _setAtomicNumber, d...

x = property(_getX, _setX, doc= "X-coordinate of the atom.")

y = property(_getY, _setY, doc= "Y-coordinate of the atom.")

z = property(_getZ, _setZ, doc= "Z-coordinate of the atom.")

xyz = property(_getXYZ, _setXYZ, doc= "XYZ-coordinates of the ...

alt_xyz = property(_getAltXYZ, _setAltXYZ, doc= "Alternative X...

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

chirality = property(_getAtomChirality, doc= _doc)

atom_style = property(_getAtomStyle, _setAtomStyle)

style = property(_getStyle, _setStyle)

visible = property(_getAtomVisible, _setAtomVisible)

label_format = property(_getAtomLabelFormat, _setAtomLabelFormat)

label_color = property(_getAtomLabelColor, _setAtomLabelColor)

label_user_text = property(_getAtomLabelUserText, _setAtomLabe...

property = property(_getAtomProperty, doc= "Dictionary-like co...

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.

int(self)

The atom index. Read only.

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

Class Variable Details

[hide private]

bond_total

Value:

property(_getBondTotal, doc= "Number of bonds to the atom.")

bond

Value:

property(_getAtomBondContainer, doc= "List of bonds to the atom (L{_St
ructureBond} objects).")

bonded_atoms

Value:

property(_getBondedAtoms, doc= "Iterator for atoms bonded to this atom
 (L{_StructureAtom} objects).")

atomic_weight

Value:

property(_getAtomicWeight, doc= """
        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.
        """)

growname

Value:

property(_getGrowName, _setGrowName, doc= "Maestro grow name.")

pdbname

Value:

property(_getPdbname, _setPdbname, doc= "PDB atom name.")

pdbres

Value:

property(_getPdbres, _setPdbres, doc= "PDB residue name.")

pdbcode

Value:

property(_getPdbCode, doc= "One-letter PDB residue code.")

resnum

Value:

property(_getResnum, _setResnum, doc= "PDB residue number.")

inscode

Value:

property(_getInscode, _setInscode, doc= "PDB residue insertion code.")

atom_type

Value:

property(_getAtomType, _setAtomType, doc= "MacroModel atom type. Note 
that changing the atom type does " "not automatically update the charg
e. See " "L{schrodinger.structure.Structure.retype}.")

atom_type_name

Value:

property(_getAtomTypeName, doc= "MacroModel atom type name.")

color

Value:

property(_getAtomColor, _setAtomColor, doc= "Atom color.")

chain

Value:

property(_getAtomChain, _setAtomChain, doc= "Atom chain.")

atom_name

Value:

property(_getAtomNameWarning, _setAtomNameWarning, doc= "Name of the a
tom.")

name

Value:

property(_getAtomName, _setAtomName, doc= "Name of the atom.")

element

Value:

property(_getAtomElement, _setAtomElement, doc= "Element character of 
the atom.")

partial_charge

Value:

property(_getAtomPartialCharge, _setAtomPartialCharge, doc= "Partial c
harge of the atom.")

solvation_charge

Value:

property(_getAtomSolvationCharge, _setAtomSolvationCharge)

formal_charge

Value:

property(_getAtomFormalCharge, _setAtomFormalCharge, doc= "Formal char
ge of the atom.")

isotope

Value:

property(_getAtomIsotope, _setAtomIsotope, doc= "Mass number charge of
 the atom.")

secondary_structure

Value:

property(_getAtomSecondaryStructure, _setAtomSecondaryStructure)

temperature_factor

Value:

property(_getAtomTemperatureFactor, _setAtomTemperatureFactor)

atomic_number

Value:

property(_getAtomicNumber, _setAtomicNumber, doc= "Atomic number of th
e atom's element.")

xyz

Value:

property(_getXYZ, _setXYZ, doc= "XYZ-coordinates of the atom.")

alt_xyz

Value:

property(_getAltXYZ, _setAltXYZ, doc= "Alternative XYZ-coordinates of 
the atom, if available, otherwise returns None.")

label_user_text

Value:

property(_getAtomLabelUserText, _setAtomLabelUserText)

property

Value:

property(_getAtomProperty, doc= "Dictionary-like container of Atom-lev
el " "properties.  Keys are strings of the form " "C{type_family_name}
 as described in the " "L{PropertyName} documentation.")

Class _StructureAtom

__init__(self, ct, index) (Constructor)

__int__(self)

addBond(self, atom2, bond_order)

retype(self)

getColorRGB(self)

setColorRGB(self, red, green, blue)

_getCtEntryId(self)

bond_total

bond

bonded_atoms

atomic_weight

growname

pdbname

pdbres

pdbcode

resnum

inscode

atom_type

atom_type_name

color

chain

atom_name

name

element

partial_charge

solvation_charge

formal_charge

isotope

secondary_structure

temperature_factor

atomic_number

xyz

alt_xyz

label_user_text

property

init(self, ct, index)
(Constructor)

int(self)