The PyBabel package is a Python re-implementation of some of Babel
v1.6 functionalities, including:
I- ATOM HYBRIDIZATION ASSIGNMENT:
The AtomHybridization class allows to assign atom types.
example:
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> babel = AtomHybridization()
>>> babel.assignHybridization(allAtoms)
- allAtoms is a list of 'Atom' objects having the following members:
-
a.element : atom's chemical element symbol (string, 2 character max, second character lower case)
a.coords : 3-sequence of floats (tuple, float or array)
a.bonds : list of Bond objects
-
Bond are objects having the following members:
-
b.atom1 : instance of Atom
b.atom2 : instance of Atom
After completion each atom has the following additional members:
-
babel_type : string
babel_atomic_number : int
babel_organic : 0/1
II- GASTEIGER CHARGES CALCULATIONS:
Before Gasteiger charges can be calculated, babel AtomHybridization has
to be assigned (see I).
example:
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> babel = AtomHybridization()
>>> babel.assignHybridization(allAtoms)
>>>
>>> from PyBabel.gasteiger import Gasteiger
>>> Gast = Gasteiger()
>>> Gast.compute(allAtoms)
-
allAtoms is a list of 'Atom' objects having the following members:
-
a.babel_type
a.babel_atomic_number
a.bonds
After completion each atom has a gast_charge member.
III - TYPES CONVERSION :
Before atom types can be obtained, babel's internal types have to be
assigned (see I).
example:
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> babel = AtomHybridization()
>>> babel.assignHybridization(allAtoms)
>>>
>>> from PyBabel.atomTypes import AtomHybridization
>>> converter = TypeConverter('SYB')
>>> newTypes = map( converter.convert, allAtoms.babel_type)
IV - PROPERTIES FROM ATOM ELEMENT NAME:
Before atom properties can be obtained, babel's internal types have to
be assigned (see I).
example:
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> babel = AtomHybridization()
>>> babel.assignHybridization(allAtoms)
>>>
>>> rad = babel.getProperty('vdw_rad', allAtoms.element)
-
valid property names are:
-
'num'
'cov_rad'
'bond_ord_rad'
'vdw_rad'
'bs_rad'
'max_bonds'
'rgb'
V - FINDING RINGS :
This algorithm is different from the one used in Babel to avoid the N^2
complexity in number of bonds.
When rings are nested the smalest rings are reported.
The algorithms might fail to report all rings if all the atoms in some
rings belong to multiple rings.
example:
>>> #create an instance of RingFinder object
>>> from PyBabel.cycle import RingFinder
>>> r = RingFinder()
>>> r.findRings(atoms, bonds)
>>> r.printRings()
atoms has to be a list of Atom objects-
- Atom:
- a.coords: 3-sequence of floats
- a.bonds : list of Bond objects
- Bond:
- b.atom1 : instance of Atom
- b.atom2 :instance of Atom
After completion the RingFinder object has the following members:
- ringCount: number of rings
- rings : a list of rings. A ring is a dictionary with 2 keys 'atoms' and 'bonds'
- allRingAtoms: list of atoms that are in rings(atoms may appear twice)
- allRingBonds: list of bonds that are in rings(bonds may appear twice)
In addition:
- atoms involved in rings have a member ring that is a list of rings they belong to (0-based list of integers)
VI - ASSIGNING BOND ORDERS:
Before a BondOrder object can be used, atoms must have been assigned a
type (see I).
Bond order can be calculated using 2 different methods depending on
whether rings have been identified previously or not.
Babel decides to use the first method for molecules with more than 200
atoms and the second one else.
example:
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> atype = AtomHybridization()
>>> atype.assignHybridization(atoms)
>>> #create an instance of BondOrder object
>>> from PyBabel.bo import BondOrder
>>> bo = BondOrder()
>>> bo.assignBondOrder( atoms, bonds )
or
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> atype = AtomHybridization()
>>> atype.assignHybridization(atoms)
>>> from PyBabel.cycle import RingFinder
>>> rings = RingFinder()
>>> rings.findRings(allAtoms, bonds)
>>> from PyBabel.bo import BondOrder
>>> bo = BondOrder()
>>> bo.assignBondOrder( atoms, bonds, rings )
atoms has to be a list of atom objects
- Atom:
- a.coords : 3-sequence of floats
- a.bonds : list of Bond objects
- babel_type: string
- babel_atomic_number: int
- Bond:
- b.atom1 : instance of Atom
- b.atom2 : instance of Atom
After completion each bond has a bondOrder attribute (integer)
VII -IDENTIFYING AROMATIC RINGS:
Before this Aromatic object can be used to identify aromatic rings,
several steps have to be completed before:
- 1.atoms must have been assigned a type
(see I)
- 2.rings must have been identified
(see V)
- 3.bond orders must have been defined
(see VI)
example:
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> atype = AtomHybridization()
>>> atype.assignHybridization(atoms)
>>> from PyBabel.cycle import RingFinder
>>> rings = RingFinder()
>>> rings.findRings(atoms, bonds)
>>> from PyBabel.bo import BondOrder
>>> bo = BondOrder()
>>> bo.assignBondOrder(atoms, bonds, rings)
>>> from PyBabel.aromatic import Aromatic
>>> arom = Aromatic(rings)
>>> arom.find_aromatic_atoms(atoms)
atoms has to be a list of atom objects
- Atom:
- a.coords : 3-sequence of floats
- a.bonds : list of Bond objects
- babel_type: string
- babel_atomic_number: int
- b.atom1 : instance of Atom
- b.atom2 : instance of Atom
After completion the bondOrder member of bonds in aromatic bonds is
aromatic.
The aromatic rings has a new key called aromatic set to 1 or 0.
VIII - ADDING HYDROGEN ATOMS :
Before this AddHydrogens object can be used, atoms must have been
assigned a type (see I)
Hydrogen atoms can be added using 2 different methods. The first one
requires bondOrders to have been calculated previousely.
example:
>>> #create an instance of AtomHybridization
>>> from PyBabel.atomTypes import AtomHybridization
>>> atype = AtomHybridization()
>>> atype.assignHybridization(atoms)
>>> from PyBabel.addh import AddHydrogens
>>> addh = AddHydrogens()
>>> hat = addh.addHydrogens(atoms)
>>> from PyBabel.addh import AddHydrogens
>>> addh = AddHydrogens()
>>> hat = addh.addHydrogens(atoms, method='withBondOrder')
atoms has to be a list of atom objects:
- Atoms:
- a.coords : 3-sequence of floats
- a.bonds : list of Bond objects
- babel_type : string
- babel_atomic_number : int
- Bond:
- b.atom1 : instance of Atom
- b.atom2 : instance of Atom
atoms has to be a list of atom objects as above and
- Bond:
- b.atom1 : instance of Atom
- b.atom2 : instance of Atom
- b.bondOrder : integer
- These calls return a list hat containing a tuple for each Hydrogen
atom to be added. This tuple provides:
- coordsH : 3-float coordinates of the H atom
- atom : the atom to which the H atom is to be connected
- atomic_number : the babel_atomic_number of the H atom
- type : tyhe babel_type of the H atom
