From 7325eddc31d7d0ef95e892a33c2e45473618e9d8 Mon Sep 17 00:00:00 2001 From: AngelRuizMoreno Date: Fri, 1 Sep 2023 14:17:24 +0200 Subject: [PATCH 1/2] library restructured --- conphar/Pharmacophores.py | 79 ++++++++++++++++++++++++--------------- conphar/__init__.py | 10 +++++ 2 files changed, 58 insertions(+), 31 deletions(-) diff --git a/conphar/Pharmacophores.py b/conphar/Pharmacophores.py index eba523b..9145b3b 100644 --- a/conphar/Pharmacophores.py +++ b/conphar/Pharmacophores.py @@ -10,14 +10,6 @@ __PHARMIT_LIC = files("conphar.bin").joinpath("README") -''' -################### TOOLBOX ################### -''' - -__all__= -['get_ligand_receptor_pharmacophore','get_molecule_pharmacophore','parse_json_pharmacophore','show_pharmacophoric_descriptors','save_pharmacophore_to_pymol','compute_concensus_pharmacophore'] - - import os, subprocess, json import pandas as pd @@ -34,6 +26,7 @@ import numpy as np import seaborn as sns +__all__=['get_ligand_receptor_pharmacophore','get_molecule_pharmacophore','parse_json_pharmacophore','show_pharmacophoric_descriptors','save_pharmacophore_to_pymol','compute_concensus_pharmacophore'] def get_ligand_receptor_pharmacophore (receptor:str,ligand:str,out:str,out_format:str='json',cmd:str='pharma'): @@ -217,7 +210,7 @@ def save_pharmacophore_to_pymol (table:pd.DataFrame,out_file:str='pharmacophore. Args: table (pd.DataFrame): A DataFrame with the columns 'name', 'center', 'radius', 'color', 'cluster', 'weight', 'balance', and 'svector' for each pharmacophore point. out_file (str, optional): The file name of the PyMOL session file to be written. Defaults to 'pharmacophore.pse'. - select (str, optional): A string indicating how to group the points in PyMOL. It can be 'cluster', 'concensus', or 'all'. Defaults to 'all'. + select (str, optional): A string indicating how to group the points in PyMOL. It can be 'concensus' or 'all'. Defaults to 'all'. Returns: None: The function does not return anything, but writes the PyMOL session file. @@ -227,17 +220,7 @@ def save_pharmacophore_to_pymol (table:pd.DataFrame,out_file:str='pharmacophore. >>> save_pharmacophore_to_pymol(table, out_file='pharmacophore.pse', select='cluster') # A PyMOL session file with the pharmacophore points grouped by cluster is written. """ - - if select=='cluster': - for point in table.index: - cmd.pseudoatom(object=int(table.loc[point,'cluster']),resn=table.loc[point,'name'], - resi=point, chain='P', elem='PS',label=int(table.loc[point,'cluster']), - vdw=table.loc[point,'radius'], hetatm=1, color=table.loc[point,'color'],b=table.loc[point,'weight'], - q=table.loc[point,'balance'],pos=[table.loc[point,'x'],table.loc[point,'y'],table.loc[point,'z']]) - - cmd.group(table.loc[point,'name'], '*') - - elif select=='concensus': + if select=='concensus': for point in table.index: cmd.pseudoatom(object=table.loc[point,'name'],resn=table.loc[point,'name'], resi=point, chain='P', elem='PS',label=table.loc[point,'name'], @@ -287,6 +270,7 @@ def save_pharmacophore_to_json (table:pd.DataFrame,out_file:str='pharmacophore.j with open(out_file,'w') as f: f.write(data) + def compute_concensus_pharmacophore (table:pd.DataFrame, save_data_per_descriptor:bool=True, out_folder:str='.', h_dist:float=0.17): """ Computes the concensus pharmacophore from a table of 3D coordinates and features of molecular descriptors. @@ -326,11 +310,11 @@ def __compute_cluster(table:pd.DataFrame): matrix=distance_matrix(x=table[['x','y','z']],y=table[['x','y','z']]) dm = sch.distance.pdist(matrix) linkage = sch.linkage(dm, method='complete') - clusters = sch.fcluster(linkage, 0.17*dm.max(), 'distance') + clusters = sch.fcluster(linkage, h_dist*dm.max(), 'distance') table['cluster']=clusters - + weight=[] for row in matrix: weight.append(len([distance for distance in row if distance <= 1.5])) @@ -338,7 +322,8 @@ def __compute_cluster(table:pd.DataFrame): table['weight']=weight table['balance']=normalize([weight], norm="l1")[0] - + + return linkage,matrix,table def __compute_center_of_mass_and_radius(table:pd.DataFrame): @@ -353,6 +338,24 @@ def __compute_center_of_mass_and_radius(table:pd.DataFrame): return center_of_mass,radius + def __save_pymol_cluster(table:pd.DataFrame,out_file:str='cluster.pse',cluster_color_map:dict={}): + for point in table.index: + cmd.pseudoatom(object=int(table.loc[point,'cluster']),resn=table.loc[point,'name'], + resi=point, chain='P', elem='PS',label=int(table.loc[point,'cluster']), + vdw=table.loc[point,'radius'], hetatm=1, color=table.loc[point,'color'],b=table.loc[point,'weight'], + q=table.loc[point,'balance'],pos=[table.loc[point,'x'],table.loc[point,'y'],table.loc[point,'z']]) + + cmd.group(table.loc[point,'name'], '*') + + for clus_idx,color in cluster_color_map.items(): + cmd.set_color(f"clus_{clus_idx}", color) + cmd.color(f"clus_{clus_idx}", clus_idx) + + cmd.show(representation='spheres') + cmd.center(selection='all') + cmd.save(out_file,format='pse') + cmd.remove('all') + cmd.reinitialize(what='everything') Concensus=pd.DataFrame() Links={} @@ -360,17 +363,31 @@ def __compute_center_of_mass_and_radius(table:pd.DataFrame): index=1 for group in Descriptors.groups: linkage,matrix,descriptor_cluster=__compute_cluster(Descriptors.get_group(group)) - Links[group]={'matrix':matrix,'linkage':linkage} + Links[group]={'matrix':matrix,'linkage':linkage,'table':descriptor_cluster} if save_data_per_descriptor==True: - save_pharmacophore_to_pymol(table=descriptor_cluster,out_file=f"{out_folder}/{group}_clusters.pse",select='cluster') - fig=sns.clustermap (matrix,method='complete',figsize=(10,10),xticklabels=descriptor_cluster.index, yticklabels=descriptor_cluster.index, - cmap='RdBu',cbar_kws=dict(label='Distance',shrink=1,orientation='vertical',spacing='uniform',pad=0.02), - row_linkage=linkage, col_linkage=linkage, rasterized=True) - fig.savefig(f"{out_folder}/{group}_clusters.png",dpi=300) - + + lut = dict(zip(descriptor_cluster.cluster.unique(), sns.color_palette('Set3',len(descriptor_cluster.cluster.unique())))) + row_colors = descriptor_cluster.cluster.map(lut).to_numpy() + + + + + ax=sns.clustermap (matrix,method='complete',figsize=(6,6),xticklabels=0, yticklabels=0, + cmap='binary_r',cbar_kws=dict(label='Distance',shrink=1,orientation='vertical',spacing='uniform',pad=0.02), + row_linkage=linkage, col_linkage=linkage, rasterized=True,row_colors=row_colors,tree_kws=dict(linewidths=1)) + + x0, _y0, _w, _h = ax.cbar_pos + ax.ax_cbar.set_position([0.1, 0.8, _w/1, _h/1.2]) + ax.ax_cbar.set_ylabel('Distance Å',fontsize=10,fontweight='bold') + ax.ax_cbar.tick_params(axis='y', length=3,width=1,labelsize=10) + + ax.savefig(f"{out_folder}/{group}_clusters.svg",dpi=300,bbox_inches="tight") + + __save_pymol_cluster(table=descriptor_cluster,out_file=f"{out_folder}/{group}_clusters.pse",cluster_color_map=lut) + else: pass @@ -386,7 +403,7 @@ def __compute_center_of_mass_and_radius(table:pd.DataFrame): Concensus.loc[index,'radius']=radius Concensus.loc[index,'color']=clus.loc[clus.index[0],'color'] Concensus.loc[index,'weight']=int(len(clus.index)) - Concensus.loc[index,'balance']=clus['balance'].mean() + Concensus.loc[index,'balance']=clus['balance'].sum() index=index+1 return Concensus, Links \ No newline at end of file diff --git a/conphar/__init__.py b/conphar/__init__.py index 5a3142b..71c581b 100644 --- a/conphar/__init__.py +++ b/conphar/__init__.py @@ -1,2 +1,12 @@ +""" +ConPhar: Python library to work and generate concensus pharmacophores +""" + __version__ = "0.1.0" __author__ = "https://github.com/AngelRuizMoreno" + + +from .Structures import * +from .Pharmacophores import * + +print("ConPhar tools imported successfully") \ No newline at end of file From b04cfce18756f19aba5578ec6b2aa0b5ba6dccbf Mon Sep 17 00:00:00 2001 From: AngelRuizMoreno Date: Fri, 1 Sep 2023 14:18:06 +0200 Subject: [PATCH 2/2] patch applied to correct installation issue --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index dd80fd8..e27ccb6 100644 --- a/setup.py +++ b/setup.py @@ -7,7 +7,7 @@ with codecs.open(os.path.join(here, "README.md"), encoding="utf-8") as fh: long_description = "\n" + fh.read() -VERSION = 'v0.1.0' +VERSION = 'v0.1.1' DESCRIPTION = 'PyPharmer' #LONG_DESCRIPTION = ''