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fix: fix: Add fingerprint, radius commands #21

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fix: fix: Add fingerprint, radius commands #21

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caa13e1
fix: revert linter changes
Kohulan Apr 21, 2023
870a351
fix: loosen up the versions
Kohulan Apr 26, 2023
d5e3526
Update setup.py
Kohulan Apr 26, 2023
1253c8e
fix: explicit conversion to a numpy array tsne
Kohulan Sep 18, 2024
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24 changes: 15 additions & 9 deletions chemplot/chemplot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ class Plotter(object):

_target_types = {'R', 'C'}

def __init__(self, encoding_list, target, target_type, sim_type, get_desc, get_fingerprints):
def __init__(self, encoding_list, target, target_type, sim_type, get_desc, get_fingerprints, radius, nBits):

# Error handeling sym_type
if sim_type not in self._sim_types:
Expand Down Expand Up @@ -136,7 +136,7 @@ def __init__(self, encoding_list, target, target_type, sim_type, get_desc, get_f
raise Exception("Descriptors could not be computed for given molecules")
self.__df_descriptors, self.__target = desc.select_descriptors_lasso(df_descriptors,target,kind=self.__target_type)
elif self.__sim_type == "structural":
self.__mols, self.__df_descriptors, self.__target = get_fingerprints(encoding_list,target,2,2048)
self.__mols, self.__df_descriptors, self.__target = get_fingerprints(encoding_list,target, radius, nBits)

if len(self.__mols) < 2 or len(self.__df_descriptors.columns) < 2:
raise Exception("Plotter object cannot be instantiated for given molecules")
Expand All @@ -146,14 +146,16 @@ def __init__(self, encoding_list, target, target_type, sim_type, get_desc, get_f


@classmethod
def from_smiles(cls, smiles_list, target=[], target_type=None, sim_type=None):
def from_smiles(cls, smiles_list, target=[], target_type=None, sim_type=None, radius=2, nBits=2048):
"""
Class method to construct a Plotter object from a list of SMILES.

:param smile_list: List of the SMILES representation of the molecules to plot.
:param target: target values
:param target_type: target type R (regression) or C (classificatino)
:param sim_type: similarity type structural or tailored
:param sim_type: similarity type structural or tailored
:param radius: The ECPF fingerprints radius.
:param nBits: The number of bits of the fingerprint vector.
:type smile_list: list
:type target: list
:type target_type: string
Expand All @@ -162,11 +164,11 @@ def from_smiles(cls, smiles_list, target=[], target_type=None, sim_type=None):
:rtype: Plotter
"""

return cls(smiles_list, target, target_type, sim_type, desc.get_mordred_descriptors, desc.get_ecfp)
return cls(smiles_list, target, target_type, sim_type, desc.get_mordred_descriptors, desc.get_ecfp, radius, nBits)


@classmethod
def from_inchi(cls, inchi_list, target=[], target_type=None, sim_type=None):
def from_inchi(cls, inchi_list, target=[], target_type=None, sim_type=None, radius=2, nBits=2048):
"""
Class method to construct a Plotter object from a list of InChi.

Expand All @@ -178,11 +180,15 @@ def from_inchi(cls, inchi_list, target=[], target_type=None, sim_type=None):
:type target_type: string
:param sim_type: similarity type structural or tailored
:type sim_type: string
:param radius: The ECPF fingerprints radius.
:type radius: int
:param nBits: The number of bits of the fingerprint vector.
:type nBits: int
:returns: A Plotter object for the molecules given as input.
:rtype: Plotter
"""

return cls(inchi_list, target, target_type, sim_type, desc.get_mordred_descriptors_from_inchi, desc.get_ecfp_from_inchi)
return cls(inchi_list, target, target_type, sim_type, desc.get_mordred_descriptors_from_inchi, desc.get_ecfp_from_inchi, radius, nBits)


def pca(self, **kwargs):
Expand Down Expand Up @@ -257,7 +263,7 @@ def tsne(self, perplexity=None, pca=False, random_state=None, **kwargs):

# Embed the data in two dimensions
self.tsne_fit = TSNE(n_components=2, perplexity=perplexity, random_state=random_state, **kwargs)
ecfp_tsne_embedding = self.tsne_fit.fit_transform(self.__data)
ecfp_tsne_embedding = self.tsne_fit.fit_transform(np.array(self.__data))
# Create a dataframe containinting the first 2 TSNE components of ECFP
self.__df_2_components = pd.DataFrame(data = ecfp_tsne_embedding
, columns = ['t-SNE-1', 't-SNE-2'])
Expand Down Expand Up @@ -722,4 +728,4 @@ def __open_plot(self, p):
show(p)

def get_target(self):
return self.__target
return self.__target
8 changes: 4 additions & 4 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

setup(
name="chemplot",
version="1.2.1",
version="1.2.2",
author="Murat Cihan Sorkun, Dajt Mullaj",
author_email="[email protected], [email protected]",
description="A python library for chemical space visualization.",
Expand Down Expand Up @@ -35,10 +35,10 @@
install_requires=[
"pandas>=1.1.3",
"numpy>=1.19.2",
"matplotlib==3.3.2",
"seaborn==0.11.1",
"matplotlib>=3.3.2",
"seaborn>=0.11.1",
"umap-learn>=0.5.1",
"scikit-learn==0.24.2",
"scikit-learn>=0.24.2",
"bokeh>=2.2.3",
"scipy>=1.5.2",
"mordred>=1.2.0",
Expand Down