Class FragmentCreator
object --+
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FragmentCreator
This class will break up input structures into fragments
based on some simple rules. The basic rules are:
1. Cut one of these 2 types of bonds:
I. Bonds to rings
a. Do not cut bonds to hydrogens
b. Do not cut any in-ring bonds
c. Do not cut bonds between ring-carbon and a non-carbon atoms
(allowed with -c option)
II. Carbon-carbon bonds
a. Do not cut any bonds if either atom is in any ring
3. Refuse a fragment if any part of it matches a line in the SMARTS file
specified by -smarts.
4. Refuse a fragment if the number of broken bonds exceeds -bonds.
5. Refuse a fragment if the number of atoms is less than -atoms.
6. Do not attempt to fragment molecules with more than -maxatoms atoms.
For -recap option, here are the rules that are used:
1. [#6][C;X3](=O)!@[N;X3] Amide
2. [!#1][O;X2]!@[C;X3](=O)[C;X4;H2,H3] Ester
3. [#7;X3](!@[C,N&X3,#1])([C,N&X3,#1])[C,N&X3,#1] Amine
4. [#7;X3]!@[C;X3](=O)[#7;X3] Urea
5. [#6]!@[O;X2][#6] Ether
6. [#6]=!@[#6] Olefin
7. [#7;X4]!@[#6] Quarternary nitrogen
8. [n]!@[C] Aromatic nitrogen - aliphatic carbon
9. C!@N@C=O Lactam nitrogen - aliphatic carbon
10. c!@c Aromatic carbon - aromatic carbon
11. [#7][S;X4](=O)(=O) Sulphonamide
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__init__(self,
**kwargs)
Create a FragmentCreator object. |
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str
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checkArgs(self)
Check the input arguments for appropriate usage |
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list
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list
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Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
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__init__(self,
**kwargs)
(Constructor)
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Create a FragmentCreator object.
- Parameters:
atoms (int) - Minimum number of non-hydrogen atoms in a fragment (default=2)bonds (int) - Maximum number of broken bonds allowed in creating a fragment
(default=100)smarts (str) - Path to a file of SMARTS patterns (one per line) to identify and
eliminate fragments containing undesired features.carbon_hetero (bool) - Allows cutting of bonds between ring-carbon and hetero atoms
(default=False)maxatoms (int) - Maximum number of atoms allowed in molecule to be fragmented
(default=200).removedup (bool) - Keep only one copy of identical fragment but with different
coordinates. (default=False)murcko (bool) - Generate Murco Assembly scaffold instead of regular fragments.
(default=False)recap (bool) - Use RECAP rules to find bonds to break.recap_use (list of int) - Specify which RECAP rules to use (default is to use all). Value
must be a list of integers (example: [1, 2, 10, 11]).complete (bool) - Retain the complete list of fragments created, including
intermediates. Only works with RECAP rules. (Default: False)complete (bool) - Add hydrogens to complete lewis structures. I some calses, you do
not want to do this (Default: True)verbose (bool) - True if progress should be logged, False if notadd_h (bool) - Overrides:
object.__init__
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Get a string that describes the RECAP patterns
- Returns: str
- A string describing the RECAP patterns.
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fragmentStructure(self,
struct)
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Break the input structure into fragments.
- Parameters:
- Returns: list
- list of schrodinger.structure.Structure objects for the
fragments.
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fragmentStructureForEA(self,
struct)
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Break the input structure into fragments. Used for Event Analyis
(EA)
- Parameters:
- Returns: list
- list of schrodinger.structure.Structure objects for the
fragments
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