(c) 2019, Dr. Ramil Nugmanov; Dr. Timur Madzhidov; Ravil Mukhametgaleev
Installation instructions of CGRtools package information and tutorial's files see on https://github.com/cimm-kzn/CGRtools
NOTE: Tutorial should be performed sequentially from the start. Random cell running will lead to unexpected results.
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import pkg_resources
if pkg_resources.get_distribution('CGRtools').version.split('.')[:2] != ['3', '1']:
print('WARNING. Tutorial was tested on 3.1 version of CGRtools')
else:
print('Welcome!')
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# load data for tutorial
from pickle import load
from traceback import format_exc
with open('molecules.dat', 'rb') as f:
molecules = load(f) # list of MoleculeContainer objects
with open('reactions.dat', 'rb') as f:
reactions = load(f) # list of ReactionContainer objects
m1, m2, m3, m4 = molecules # molecule
m12 = m3.copy()
r1 = reactions[0] # reaction
m1.reset_query_marks()
m1.atom(1).isotope = 16
m1.flush_cache()
m1.delete_atom(3)
m1.atom_implicit_h(1)
m1.atom_explicit_h(1)
m1.atom_total_h(1)
MoleculeContainer has standardize and aromatize methods.
Method aromatize transforms Kekule representation of rings into aromatized
Method standardize applies functional group standardization rules to molecules. The following rules are implemented (corresponding SMARTS are given):
• Aromatic N-Oxide [#7;a:1]=[O:2]>>[#7+:1]-[#8-:2]
• Azide [#7;A;X2-:1][N;X2+:2]#[N;X1:3]>>[#7:1]=[N+:2]=[#7-:3]
• Diazo [#6;X3-:1][N;X2+:2]#[N;X1:3]>>[#6;A:1]=[N+:2]=[#7-:3]
• Diazonium [#6]-[#7:1]=[#7+:2]>>[#6][N+:1]#[N:2]
• Iminium [#6;X3+:1]-[#7;X3:2]>>[#6;A:1]=[#7+:2]
• Isocyanate [#7+:1][#6;A-:2]=[O:3]>>[#7:1]=[C:2]=[O:3]
• Nitrilium [#6;A;X2+:1]=[#7;X2:2]>>[C:1]#[N+:2]
• Nitro [O:3]=[N:1]=[O:2]>>[#8-:2]-[#7+:1]=[O:3]
• Nitrone Nitronate [#6;A]=[N:1]=[O:2]>>[#8-:2]-[#7+:1]=[#6;A]
• Nitroso [#6]-[#7H2+:1]-[#8;X1-:2]>>[#6]-[#7:1]=[O:2]
• Phosphonic [#6][P+:1]([#8;X2])([#8;X2])[#8-:2]>>[#6][P:1]([#8])([#8])=[O:2]
• Phosphonium Ylide [#6][P-:1]([#6])([#6])[#6+:2]>>[#6][P:1]([#6])([#6])=[#6;A:2]
• Selenite [#8;X2][Se+:1]([#8;X2])[#8-:2]>>[#8][Se:1]([#8])=[O:2]
• Silicate [#8;X2]-[#14+:1](-[#8;X2])-[#8-:2]>>[#8]-[#14:1](-[#8])=[O:2]
• Sulfine [#6]-[#6](-[#6])=[S+:1][#8-:2]>>[#6]-[#6](-[#6])=[S:1]=[O:2]
• Sulfon [#6][S;X3+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
• Sulfonium Ylide [#6][S-:1]([#6])[#6+:2]>>[#6][S:1]([#6])=[#6;A:2]
• Sulfoxide [#6][S+:1]([#6])([#8-:2])=O>>[#6][S:1]([#6])(=[O:2])=O
• Sulfoxonium Ylide [#6][S+:1]([#6])([#8-:2])=[#6;A]>>[#6][S:1]([#6])(=[#6;A])=[O:2]
• Tertiary N-Oxide [#6]-[#7;X4:1]=[O:2]>>[#6]-[#7+:1]-[#8-:2]
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m12 # molecule with kekulized ring
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m12.aromatize() # aromatizes and returns number of transformed rings
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m12 # cleaned structure. Cache is flushed automatically
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m12.standardize() # apply standardization. Returns number of transformed groups
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m12
Molecules has explicify_hydrogens and implicify_hydrogens methods to handle hydrogens.
This methods is used to add or remove hydrogens in molecule.
Note that currently for pyrole-like molecules implicit hydrogens atoms are calculated incorrectly
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m1.explicify_hydrogens() # return number of added hydrogens
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m1 # for added hydrogen atoms coordinates are not calculated. Thus, it looks like hydrogen has the same position on image
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m1.implicify_hydrogens()
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m1
CGRtools has experimental algorithm for 2d geometry calcultaion. It works fine only for small molecules. Algorithm requires numpy and scipy packages
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m1.explicify_hydrogens() # add explicit hydrogens
m1.calculate2d() # experimental force field-based 2d geometry calculation.
m1
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reactions[2]
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reactions[2].standardize()
reactions[2].explicify_hydrogens()
reactions[2]