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RDK props #398

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RDK props #398

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Description

generate cheminformatics descriptors with properties driver in RDKit

Changelog description

Added DescriptorConstructor class that returns a dictionary of molecular descriptors

Status

  • Code base linted
  • Ready to go

1eyedt0ad added 23 commits January 12, 2023 16:51
added testing module for RDKit
e47748a
variable holders for AtomicInput in compute function
22b33ec
properties driver will return canonical SMILES property
a634296
amino acids in stock molecules, incomplete changes to rdkit.py and
1635c8e 
test_rdkit.py
working on testing module and molecular descriptors in rdkit
e929759
removed amino acids from stock, added Ala w explicit Hs and 3D coords,
53c4e06 
smiles string contains stereochemistry
test smiles in test_rdkit.py
4a65fd9
linted prior changes with (Black)
9472450
rdkit compute returns calcinfo_natoms, linted stock_mols
d958743
fixed properties dict new entry syntax error
827a076
calcinfo_natom not calcinfo_natoms
fbd080e
gradient driver with rdkit includes return_energy property
2379c66
minor refactoring with MolecularDescriptors class for new descriptors
1afa545 
property in AtomicResultProperties
complete bond types dictionary for connectivity in rdkit
46e1d69
Merge branch 'RDK_props' of https://github.com/dr-marsmm/QCEngine int…
4239c68 
…o RDK_props
all rdkit bond types can be accessed
b9df2fa
3D amino acids with explicit hydrogens in stock_mols
3474896
correctly formatted optimized amino acids in stock_mols
0474c57
return_bondtype is static function, compute descriptors with
d4706d8 
DescriptorConstructor
explicit valence fix for some amino acids, sanitization flags
94ec7c8
no 1.5 bonds in stock_mols, no stereochemistry returns None
c9680cc
better molecule processing, partial ring info, gasteiger charges
0d28ad6
full set of descriptors in rdkit
a340728
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codecov bot commented Feb 23, 2023 •
edited
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Codecov Report

Merging #398 (a340728) into master (1887e71) will decrease coverage by 26.36%.
The diff coverage is 12.72%.

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@dr-marsmm