Class _StructureAtom

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__

The atom index. Read only.

hash(x)

Overrides: object.__hash__

(inherited documentation)

str(x)

Overrides: object.__str__

(inherited documentation)

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

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.

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

index

The atom index. Read only.

Get Method:

__int__(self) - The atom index.

structure

Return the parent Structure object for this atom.

Get Method:

unreachable.structure(self) - Return the parent Structure object for this atom.

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)

molecule_number

Get Method:

_getAtomMoleculeNumber(self)

number_by_molecule

Get Method:

_getAtomNumberByMolecule(self)

number_by_entry

Get Method:

_getAtomNumberByEntry(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)