Merge pull request #9 from AngelRuizMoreno/pre-release

v0.1.2

.gitignore

@@ -158,3 +158,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+.DS_Store
+example_files/.DS_Store
+example_files/analysis/.DS_Store

conphar/Pharmacophores.py

@@ -271,7 +271,7 @@ def save_pharmacophore_to_json (table:pd.DataFrame,out_file:str='pharmacophore.j
         f.write(data)
 
 
-def compute_concensus_pharmacophore (table:pd.DataFrame, save_data_per_descriptor:bool=True, out_folder:str='.', h_dist:float=0.17):
+def compute_concensus_pharmacophore (table:pd.DataFrame, save_data_per_descriptor:bool=True, out_folder:str='.', h_dist:float=0.17,cmap_plots:str='binary_r'):
     """
     Computes the concensus pharmacophore from a table of 3D coordinates and features of molecular descriptors.
 
@@ -373,10 +373,8 @@ def __save_pymol_cluster(table:pd.DataFrame,out_file:str='cluster.pse',cluster_c
             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),
+                               cmap=cmap_plots,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

conphar/Structures.py

@@ -139,8 +139,8 @@ def fetch_structure(target:str,target_chain:str,reference:str, reference_chain:s
     data=pd.DataFrame(arr.reshape(1,-1), columns=['refined_RMSD','refined_num_atoms','n_cycles','raw_RMSD','raw_num_atoms','aligment_score','n_residues_aligned'],index=[target])
 
     if extract_ligands:         
-        cmd.remove(f"solvent or inorganic or resn DMS or resn GOL or resn FTM or (not alt ''+{target_chain})")
-        n_lig=cmd.select('Ligand', state=1, selection=(f'byres ((chain {target_chain} and (resi 145 or resi 41) expand 10 and organic and not resn EDO or not chain {target_chain} and not chain B))'))
+        cmd.remove(f"solvent or inorganic or resn PEG or resn DMS or resn GOL or resn FTM or (not alt ''+{target_chain})")
+        n_lig=cmd.select('Ligand', state=1, selection=(f'byres chain {target_chain} and (organic or hetatm)'))
 
         data.loc[target,'lig_n_atoms']=n_lig
 

example_files/analysis/pharmacophore_all_descriptors.json

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example_files/analysis/pharmacophore_concensus.json

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