diff --git a/.gitignore b/.gitignore
index 68bc17f..26e5680 100644
--- a/.gitignore
+++ b/.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
diff --git a/conphar/Pharmacophores.py b/conphar/Pharmacophores.py
index 9145b3b..1b49f4b 100644
--- a/conphar/Pharmacophores.py
+++ b/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
diff --git a/conphar/Structures.py b/conphar/Structures.py
index 434f30e..f910d21 100644
--- a/conphar/Structures.py
+++ b/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
diff --git a/example_files/analysis/HydrogenAcceptor_clusters.png b/example_files/analysis/HydrogenAcceptor_clusters.png
deleted file mode 100644
index 563c63c..0000000
Binary files a/example_files/analysis/HydrogenAcceptor_clusters.png and /dev/null differ
diff --git a/example_files/analysis/HydrogenAcceptor_clusters.pse b/example_files/analysis/HydrogenAcceptor_clusters.pse
index 1e68949..ca25909 100644
Binary files a/example_files/analysis/HydrogenAcceptor_clusters.pse and b/example_files/analysis/HydrogenAcceptor_clusters.pse differ
diff --git a/example_files/analysis/HydrogenAcceptor_clusters.svg b/example_files/analysis/HydrogenAcceptor_clusters.svg
new file mode 100644
index 0000000..329784f
--- /dev/null
+++ b/example_files/analysis/HydrogenAcceptor_clusters.svg
@@ -0,0 +1,554 @@
+
+
+
diff --git a/example_files/analysis/HydrogenDonor_clusters.png b/example_files/analysis/HydrogenDonor_clusters.png
deleted file mode 100644
index 0266b92..0000000
Binary files a/example_files/analysis/HydrogenDonor_clusters.png and /dev/null differ
diff --git a/example_files/analysis/HydrogenDonor_clusters.pse b/example_files/analysis/HydrogenDonor_clusters.pse
index f6c7e42..9965c1a 100644
Binary files a/example_files/analysis/HydrogenDonor_clusters.pse and b/example_files/analysis/HydrogenDonor_clusters.pse differ
diff --git a/example_files/analysis/HydrogenDonor_clusters.svg b/example_files/analysis/HydrogenDonor_clusters.svg
new file mode 100644
index 0000000..90f0be0
--- /dev/null
+++ b/example_files/analysis/HydrogenDonor_clusters.svg
@@ -0,0 +1,464 @@
+
+
+
diff --git a/example_files/analysis/Hydrophobic_clusters.png b/example_files/analysis/Hydrophobic_clusters.png
deleted file mode 100644
index f8afb9b..0000000
Binary files a/example_files/analysis/Hydrophobic_clusters.png and /dev/null differ
diff --git a/example_files/analysis/Hydrophobic_clusters.pse b/example_files/analysis/Hydrophobic_clusters.pse
index 3fc6551..f0b48e4 100644
Binary files a/example_files/analysis/Hydrophobic_clusters.pse and b/example_files/analysis/Hydrophobic_clusters.pse differ
diff --git a/example_files/analysis/Hydrophobic_clusters.svg b/example_files/analysis/Hydrophobic_clusters.svg
new file mode 100644
index 0000000..44422a0
--- /dev/null
+++ b/example_files/analysis/Hydrophobic_clusters.svg
@@ -0,0 +1,477 @@
+
+
+
diff --git a/example_files/analysis/pharmacophore_all_descriptors.json b/example_files/analysis/pharmacophore_all_descriptors.json
index 3be68b2..ae181e5 100644
--- a/example_files/analysis/pharmacophore_all_descriptors.json
+++ b/example_files/analysis/pharmacophore_all_descriptors.json
@@ -1 +1 @@
-{"points":[{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.2347041033,"y":-0.303889268,"z":0.9233446251},"vector":[{"x":0.804,"y":-1.041,"z":3.163}],"x":8.507,"y":-3.446,"z":27.187,"color":"orange","ligand":"5R7Y"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":9.948,"y":-5.5,"z":26.143,"color":"green","ligand":"5R7Y"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":-0.3557676211,"y":-0.2541865084,"z":-0.8993434376},"vector":[{"x":-0.9894,"y":-0.7069,"z":-2.5011}],"x":11.6174,"y":5.2669,"z":22.6831,"color":"white","ligand":"5R7Z"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.3889030718,"y":-0.0847055981,"z":-0.9173763472},"vector":[{"x":1.1625,"y":-0.2532,"z":-2.7422}],"x":9.0505,"y":5.0012,"z":22.9142,"color":"white","ligand":"5R80"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.921293364,"y":0.224728907,"z":0.3173569847},"vector":[{"x":2.8078,"y":0.6849,"z":0.9672}],"x":14.1192,"y":-0.5219,"z":22.5378,"color":"orange","ligand":"5R80"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":-0.1009322475,"y":-0.3740126207,"z":0.9219149858},"vector":[{"x":-0.3709,"y":-1.3744,"z":3.3878}],"x":10.1989,"y":5.3444,"z":25.2512,"color":"orange","ligand":"5R80"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":13.7965,"y":-2.5469,"z":24.2454,"color":"green","ligand":"5R80"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.9738090202,"y":0.1135155434,"z":0.1970030802},"vector":[{"x":3.8235,"y":0.4457,"z":0.7735}],"x":11.6325,"y":6.0783,"z":23.5055,"color":"white","ligand":"5R81"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":-0.0748364864,"y":-0.3374237647,"z":0.9383734349},"vector":[{"x":-0.295,"y":-1.3301,"z":3.699}],"x":10.232,"y":4.6831,"z":25.275,"color":"orange","ligand":"5R81"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.2251563148,"y":0.9712168385,"z":0.0777334322},"vector":[{"x":0.599,"y":2.5838,"z":0.2068}],"x":10.203,"y":0.2472,"z":25.7112,"color":"white","ligand":"5R82"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.777398938,"y":0.3513900659,"z":0.5217048139},"vector":[{"x":2.9765,"y":1.3454,"z":1.9975}],"x":12.0815,"y":0.4206,"z":24.2915,"color":"orange","ligand":"5R82"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":-0.812759597,"y":-0.1132362419,"z":0.5714887497},"vector":[{"x":-3.1086,"y":-0.4331,"z":2.1858}],"x":7.4526,"y":-0.7409,"z":20.9042,"color":"white","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.8401167956,"y":0.4831898238,"z":0.2464373428},"vector":[{"x":3.2703,"y":1.8809,"z":0.9593}],"x":6.6617,"y":0.6271,"z":17.6257,"color":"orange","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.2047406877,"y":0.6360206896,"z":-0.7440154119},"vector":[{"x":0.6152,"y":1.9111,"z":-2.2356}],"x":9.3168,"y":0.5969,"z":20.8206,"color":"orange","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.7578753537,"y":0.6238569658,"z":0.1908597246},"vector":[{"x":2.7653,"y":2.2763,"z":0.6964}],"x":7.1817,"y":0.3027,"z":17.8106,"color":"orange","ligand":"5R84"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.1644883933,"y":0.5587550249,"z":-0.8128569312},"vector":[{"x":0.5011,"y":1.7022,"z":-2.4763}],"x":9.4459,"y":0.8768,"z":20.9833,"color":"orange","ligand":"5R84"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.8058199881,"y":0.5635066944,"z":0.181973493},"vector":[{"x":3.125,"y":2.1853,"z":0.7057}],"x":6.817,"y":0.2747,"z":17.7783,"color":"orange","ligand":"5RE4"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.1011082636,"y":0.5416635826,"z":-0.8344924699},"vector":[{"x":0.2967,"y":1.5895,"z":-2.4488}],"x":9.6453,"y":0.8705,"z":20.9328,"color":"orange","ligand":"5RE4"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":10.2243,"y":-0.7737,"z":22.5041,"color":"green","ligand":"5RE4"}]}
\ No newline at end of file
+{"points":[{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":-0.812759597,"y":-0.1132362419,"z":0.5714887497},"vector":[{"x":-3.1086,"y":-0.4331,"z":2.1858}],"x":7.4526,"y":-0.7409,"z":20.9042,"color":"white","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.8401167956,"y":0.4831898238,"z":0.2464373428},"vector":[{"x":3.2703,"y":1.8809,"z":0.9593}],"x":6.6617,"y":0.6271,"z":17.6257,"color":"orange","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.2047406877,"y":0.6360206896,"z":-0.7440154119},"vector":[{"x":0.6152,"y":1.9111,"z":-2.2356}],"x":9.3168,"y":0.5969,"z":20.8206,"color":"orange","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.2347041033,"y":-0.303889268,"z":0.9233446251},"vector":[{"x":0.804,"y":-1.041,"z":3.163}],"x":8.507,"y":-3.446,"z":27.187,"color":"orange","ligand":"5R7Y"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":9.948,"y":-5.5,"z":26.143,"color":"green","ligand":"5R7Y"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.2251563148,"y":0.9712168385,"z":0.0777334322},"vector":[{"x":0.599,"y":2.5838,"z":0.2068}],"x":10.203,"y":0.2472,"z":25.7112,"color":"white","ligand":"5R82"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.777398938,"y":0.3513900659,"z":0.5217048139},"vector":[{"x":2.9765,"y":1.3454,"z":1.9975}],"x":12.0815,"y":0.4206,"z":24.2915,"color":"orange","ligand":"5R82"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.7578753537,"y":0.6238569658,"z":0.1908597246},"vector":[{"x":2.7653,"y":2.2763,"z":0.6964}],"x":7.1817,"y":0.3027,"z":17.8106,"color":"orange","ligand":"5R84"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.1644883933,"y":0.5587550249,"z":-0.8128569312},"vector":[{"x":0.5011,"y":1.7022,"z":-2.4763}],"x":9.4459,"y":0.8768,"z":20.9833,"color":"orange","ligand":"5R84"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.8058199881,"y":0.5635066944,"z":0.181973493},"vector":[{"x":3.125,"y":2.1853,"z":0.7057}],"x":6.817,"y":0.2747,"z":17.7783,"color":"orange","ligand":"5RE4"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.1011082636,"y":0.5416635826,"z":-0.8344924699},"vector":[{"x":0.2967,"y":1.5895,"z":-2.4488}],"x":9.6453,"y":0.8705,"z":20.9328,"color":"orange","ligand":"5RE4"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":10.2243,"y":-0.7737,"z":22.5041,"color":"green","ligand":"5RE4"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.9738090202,"y":0.1135155434,"z":0.1970030802},"vector":[{"x":3.8235,"y":0.4457,"z":0.7735}],"x":11.6325,"y":6.0783,"z":23.5055,"color":"white","ligand":"5R81"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":-0.0748364864,"y":-0.3374237647,"z":0.9383734349},"vector":[{"x":-0.295,"y":-1.3301,"z":3.699}],"x":10.232,"y":4.6831,"z":25.275,"color":"orange","ligand":"5R81"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":-0.3557676211,"y":-0.2541865084,"z":-0.8993434376},"vector":[{"x":-0.9894,"y":-0.7069,"z":-2.5011}],"x":11.6174,"y":5.2669,"z":22.6831,"color":"white","ligand":"5R7Z"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.3889030718,"y":-0.0847055981,"z":-0.9173763472},"vector":[{"x":1.1625,"y":-0.2532,"z":-2.7422}],"x":9.0505,"y":5.0012,"z":22.9142,"color":"white","ligand":"5R80"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.921293364,"y":0.224728907,"z":0.3173569847},"vector":[{"x":2.8078,"y":0.6849,"z":0.9672}],"x":14.1192,"y":-0.5219,"z":22.5378,"color":"orange","ligand":"5R80"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":-0.1009322475,"y":-0.3740126207,"z":0.9219149858},"vector":[{"x":-0.3709,"y":-1.3744,"z":3.3878}],"x":10.1989,"y":5.3444,"z":25.2512,"color":"orange","ligand":"5R80"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":13.7965,"y":-2.5469,"z":24.2454,"color":"green","ligand":"5R80"}]}
\ No newline at end of file
diff --git a/example_files/analysis/pharmacophore_all_descriptors.pse b/example_files/analysis/pharmacophore_all_descriptors.pse
index 69789ed..f669593 100644
Binary files a/example_files/analysis/pharmacophore_all_descriptors.pse and b/example_files/analysis/pharmacophore_all_descriptors.pse differ
diff --git a/example_files/analysis/pharmacophore_concensus.json b/example_files/analysis/pharmacophore_concensus.json
index 3be68b2..937d8f1 100644
--- a/example_files/analysis/pharmacophore_concensus.json
+++ b/example_files/analysis/pharmacophore_concensus.json
@@ -1 +1 @@
-{"points":[{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.2347041033,"y":-0.303889268,"z":0.9233446251},"vector":[{"x":0.804,"y":-1.041,"z":3.163}],"x":8.507,"y":-3.446,"z":27.187,"color":"orange","ligand":"5R7Y"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":9.948,"y":-5.5,"z":26.143,"color":"green","ligand":"5R7Y"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":-0.3557676211,"y":-0.2541865084,"z":-0.8993434376},"vector":[{"x":-0.9894,"y":-0.7069,"z":-2.5011}],"x":11.6174,"y":5.2669,"z":22.6831,"color":"white","ligand":"5R7Z"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.3889030718,"y":-0.0847055981,"z":-0.9173763472},"vector":[{"x":1.1625,"y":-0.2532,"z":-2.7422}],"x":9.0505,"y":5.0012,"z":22.9142,"color":"white","ligand":"5R80"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.921293364,"y":0.224728907,"z":0.3173569847},"vector":[{"x":2.8078,"y":0.6849,"z":0.9672}],"x":14.1192,"y":-0.5219,"z":22.5378,"color":"orange","ligand":"5R80"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":-0.1009322475,"y":-0.3740126207,"z":0.9219149858},"vector":[{"x":-0.3709,"y":-1.3744,"z":3.3878}],"x":10.1989,"y":5.3444,"z":25.2512,"color":"orange","ligand":"5R80"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":13.7965,"y":-2.5469,"z":24.2454,"color":"green","ligand":"5R80"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.9738090202,"y":0.1135155434,"z":0.1970030802},"vector":[{"x":3.8235,"y":0.4457,"z":0.7735}],"x":11.6325,"y":6.0783,"z":23.5055,"color":"white","ligand":"5R81"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":-0.0748364864,"y":-0.3374237647,"z":0.9383734349},"vector":[{"x":-0.295,"y":-1.3301,"z":3.699}],"x":10.232,"y":4.6831,"z":25.275,"color":"orange","ligand":"5R81"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":0.2251563148,"y":0.9712168385,"z":0.0777334322},"vector":[{"x":0.599,"y":2.5838,"z":0.2068}],"x":10.203,"y":0.2472,"z":25.7112,"color":"white","ligand":"5R82"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.777398938,"y":0.3513900659,"z":0.5217048139},"vector":[{"x":2.9765,"y":1.3454,"z":1.9975}],"x":12.0815,"y":0.4206,"z":24.2915,"color":"orange","ligand":"5R82"},{"enabled":true,"name":"HydrogenDonor","radius":0.5,"size":1,"svector":{"x":-0.812759597,"y":-0.1132362419,"z":0.5714887497},"vector":[{"x":-3.1086,"y":-0.4331,"z":2.1858}],"x":7.4526,"y":-0.7409,"z":20.9042,"color":"white","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.8401167956,"y":0.4831898238,"z":0.2464373428},"vector":[{"x":3.2703,"y":1.8809,"z":0.9593}],"x":6.6617,"y":0.6271,"z":17.6257,"color":"orange","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.2047406877,"y":0.6360206896,"z":-0.7440154119},"vector":[{"x":0.6152,"y":1.9111,"z":-2.2356}],"x":9.3168,"y":0.5969,"z":20.8206,"color":"orange","ligand":"5R83"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.7578753537,"y":0.6238569658,"z":0.1908597246},"vector":[{"x":2.7653,"y":2.2763,"z":0.6964}],"x":7.1817,"y":0.3027,"z":17.8106,"color":"orange","ligand":"5R84"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.1644883933,"y":0.5587550249,"z":-0.8128569312},"vector":[{"x":0.5011,"y":1.7022,"z":-2.4763}],"x":9.4459,"y":0.8768,"z":20.9833,"color":"orange","ligand":"5R84"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.8058199881,"y":0.5635066944,"z":0.181973493},"vector":[{"x":3.125,"y":2.1853,"z":0.7057}],"x":6.817,"y":0.2747,"z":17.7783,"color":"orange","ligand":"5RE4"},{"enabled":true,"name":"HydrogenAcceptor","radius":0.5,"size":1,"svector":{"x":0.1011082636,"y":0.5416635826,"z":-0.8344924699},"vector":[{"x":0.2967,"y":1.5895,"z":-2.4488}],"x":9.6453,"y":0.8705,"z":20.9328,"color":"orange","ligand":"5RE4"},{"enabled":true,"name":"Hydrophobic","radius":1.0,"size":1,"svector":null,"vector":null,"x":10.2243,"y":-0.7737,"z":22.5041,"color":"green","ligand":"5RE4"}]}
\ No newline at end of file
+{"points":[{"name":"HydrogenAcceptor","cluster":1.0,"x":9.4693333333,"y":0.7814,"z":20.9122333333,"radius":0.5,"color":"orange","weight":3.0,"balance":0.36},{"name":"HydrogenAcceptor","cluster":2.0,"x":6.8868,"y":0.4015,"z":17.7382,"radius":0.5,"color":"orange","weight":3.0,"balance":0.36},{"name":"HydrogenAcceptor","cluster":3.0,"x":10.21545,"y":5.01375,"z":25.2631,"radius":0.5,"color":"orange","weight":2.0,"balance":0.16},{"name":"HydrogenAcceptor","cluster":4.0,"x":12.0815,"y":0.4206,"z":24.2915,"radius":0.5,"color":"orange","weight":1.0,"balance":0.04},{"name":"HydrogenAcceptor","cluster":5.0,"x":14.1192,"y":-0.5219,"z":22.5378,"radius":0.5,"color":"orange","weight":1.0,"balance":0.04},{"name":"HydrogenAcceptor","cluster":6.0,"x":8.507,"y":-3.446,"z":27.187,"radius":0.5,"color":"orange","weight":1.0,"balance":0.04},{"name":"HydrogenDonor","cluster":1.0,"x":11.62495,"y":5.6726,"z":23.0943,"radius":0.5,"color":"white","weight":2.0,"balance":0.5714285714},{"name":"HydrogenDonor","cluster":2.0,"x":9.0505,"y":5.0012,"z":22.9142,"radius":0.5,"color":"white","weight":1.0,"balance":0.1428571429},{"name":"HydrogenDonor","cluster":3.0,"x":7.4526,"y":-0.7409,"z":20.9042,"radius":0.5,"color":"white","weight":1.0,"balance":0.1428571429},{"name":"HydrogenDonor","cluster":4.0,"x":10.203,"y":0.2472,"z":25.7112,"radius":0.5,"color":"white","weight":1.0,"balance":0.1428571429},{"name":"Hydrophobic","cluster":1.0,"x":10.2243,"y":-0.7737,"z":22.5041,"radius":1.0,"color":"green","weight":1.0,"balance":0.3333333333},{"name":"Hydrophobic","cluster":2.0,"x":13.7965,"y":-2.5469,"z":24.2454,"radius":1.0,"color":"green","weight":1.0,"balance":0.3333333333},{"name":"Hydrophobic","cluster":3.0,"x":9.948,"y":-5.5,"z":26.143,"radius":1.0,"color":"green","weight":1.0,"balance":0.3333333333}]}
\ No newline at end of file
diff --git a/example_files/analysis/pharmacophore_concensus.pse b/example_files/analysis/pharmacophore_concensus.pse
index d6b3916..96b6ba1 100644
Binary files a/example_files/analysis/pharmacophore_concensus.pse and b/example_files/analysis/pharmacophore_concensus.pse differ
diff --git a/example_files/ligand/5R7Y_lig.sdf b/example_files/ligand/5R7Y_lig.sdf
index 315fb39..836f7ab 100644
--- a/example_files/ligand/5R7Y_lig.sdf
+++ b/example_files/ligand/5R7Y_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
13 13 0 0 0 0 0 0 0 0999 V2000
9.9480 -5.5000 26.1430 C 0 0 0 0 0 0 0 0 0 0 0 0
@@ -29,4 +29,101 @@ target
8 13 4 0 0 0 0
12 13 4 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF COVID-19 MAIN
+TITLE 2 PROTEASE IN COMPLEX WITH Z45617795
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,A.J.POWELL,A.DOUANGAMATH,C.D.OWEN,C.WILD,T.KROJER,P.LUKACIK,
+AUTHOR 2 C.M.STRAIN-DAMERELL,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM JFM N-(2-PHENYLETHYL)METHANESULFONAMIDE
+HETNAM DMS DIMETHYL SULFOXIDE
+HETNAM CL CHLORIDE ION
+FORMUL 2 JFM C9 H13 N O2 S
+FORMUL 3 DMS 4(C2 H6 O S)
+FORMUL 7 CL CL 1-
+FORMUL 8 HOH *321(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 GLU A 47 ASN A 51 5 5
+HELIX 4 AA4 ASN A 53 ARG A 60 1 8
+HELIX 5 AA5 LYS A 61 HIS A 64 5 4
+HELIX 6 AA6 ILE A 200 ASN A 214 1 15
+HELIX 7 AA7 THR A 226 TYR A 237 1 12
+HELIX 8 AA8 THR A 243 LEU A 250 1 8
+HELIX 9 AA9 LEU A 250 GLY A 258 1 9
+HELIX 10 AB1 ALA A 260 GLY A 275 1 16
+HELIX 11 AB2 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N GLN A 83 O VAL A 86
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162
+SITE 1 AC1 8 HIS A 41 CYS A 44 SER A 46 MET A 49
+SITE 2 AC1 8 HIS A 164 MET A 165 ARG A 188 GLN A 189
+SITE 1 AC2 6 GLN A 74 LEU A 75 ARG A 76 THR A 224
+SITE 2 AC2 6 ASP A 263 HOH A1196
+SITE 1 AC3 4 MET A 6 SER A 123 GLN A 127 ARG A 298
+SITE 1 AC4 2 GLY A 15 MET A 17
+SITE 1 AC5 5 PHE A 140 LEU A 141 HIS A 163 MET A 165
+SITE 2 AC5 5 GLU A 166
+SITE 1 AC6 4 GLY A 143 SER A 144 CYS A 145 HOH A1319
+CRYST1 112.463 52.731 44.299 90.00 102.81 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008892 0.000000 0.002022 0.00000
+SCALE2 0.000000 0.018964 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023150 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5R7Z_lig.sdf b/example_files/ligand/5R7Z_lig.sdf
index ff75d80..3470824 100644
--- a/example_files/ligand/5R7Z_lig.sdf
+++ b/example_files/ligand/5R7Z_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
16 17 0 0 0 0 0 0 0 0999 V2000
9.1852 6.1013 22.6414 C 0 0 0 0 0 0 0 0 0 0 0 0
@@ -13,7 +13,7 @@ target
11.1312 2.5927 24.1987 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2295 0.4437 23.6963 C 0 0 0 0 0 0 0 0 0 0 0 0
12.3103 1.0362 23.0881 C 0 0 0 0 0 0 0 0 0 0 0 0
- 13.2023 0.2372 22.3230 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.2022 0.2372 22.3230 C 0 0 0 0 0 0 0 0 0 0 0 0
12.9775 -1.1322 22.1896 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8767 -1.7277 22.8149 C 0 0 0 0 0 0 0 0 0 0 0 0
10.9997 -0.9517 23.5678 C 0 0 0 0 0 0 0 0 0 0 0 0
@@ -36,4 +36,100 @@ target
13 16 1 0 0 0 0
14 15 4 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2
+TITLE 2 MAIN PROTEASE IN COMPLEX WITH Z1220452176
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,A.J.POWELL,A.DOUANGAMATH,C.D.OWEN,C.WILD,T.KROJER,P.LUKACIK,
+AUTHOR 2 C.M.STRAIN-DAMERELL,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM DMS DIMETHYL SULFOXIDE
+HETNAM HWH ~{N}-[2-(5-FLUORANYL-1~{H}-INDOL-3-YL)ETHYL]ETHANAMIDE
+FORMUL 2 DMS 4(C2 H6 O S)
+FORMUL 5 HWH C12 H13 F N2 O
+FORMUL 7 HOH *328(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 GLU A 47 ASN A 51 5 5
+HELIX 4 AA4 ASN A 53 ARG A 60 1 8
+HELIX 5 AA5 LYS A 61 HIS A 64 5 4
+HELIX 6 AA6 ILE A 200 ASN A 214 1 15
+HELIX 7 AA7 THR A 226 TYR A 237 1 12
+HELIX 8 AA8 THR A 243 GLY A 258 1 16
+HELIX 9 AA9 ALA A 260 GLY A 275 1 16
+HELIX 10 AB1 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N GLY A 149 O TYR A 161
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
+SITE 1 AC1 8 GLN A 74 LEU A 75 ARG A 76 PHE A 223
+SITE 2 AC1 8 THR A 224 ASP A 263 HOH A 516 HOH A 564
+SITE 1 AC2 5 MET A 6 PHE A 8 SER A 123 GLN A 127
+SITE 2 AC2 5 ARG A 298
+SITE 1 AC3 3 GLY A 15 MET A 17 LYS A 97
+SITE 1 AC4 13 HIS A 41 MET A 49 MET A 165 GLU A 166
+SITE 2 AC4 13 LEU A 167 PRO A 168 ASP A 187 ARG A 188
+SITE 3 AC4 13 GLN A 189 THR A 190 GLY A 251 PRO A 252
+SITE 4 AC4 13 HOH A 627
+SITE 1 AC5 6 PHE A 140 LEU A 141 CYS A 145 HIS A 163
+SITE 2 AC5 6 MET A 165 GLU A 166
+CRYST1 112.090 52.513 44.384 90.00 102.94 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008921 0.000000 0.002049 0.00000
+SCALE2 0.000000 0.019043 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023117 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5R80_lig.sdf b/example_files/ligand/5R80_lig.sdf
index 18c4ca4..794b976 100644
--- a/example_files/ligand/5R80_lig.sdf
+++ b/example_files/ligand/5R80_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
14 14 0 0 0 0 0 0 0 0999 V2000
13.7965 -2.5469 24.2454 C 0 0 0 0 0 0 0 0 0 0 0 0
@@ -31,4 +31,96 @@ target
11 13 2 0 0 0 0
11 14 1 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2
+TITLE 2 MAIN PROTEASE IN COMPLEX WITH Z18197050
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,A.J.POWELL,A.DOUANGAMATH,C.D.OWEN,C.WILD,T.KROJER,P.LUKACIK,
+AUTHOR 2 C.M.STRAIN-DAMERELL,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM DMS DIMETHYL SULFOXIDE
+HETNAM RZG METHYL 4-SULFAMOYLBENZOATE
+FORMUL 2 DMS 3(C2 H6 O S)
+FORMUL 5 RZG C8 H9 N O4 S
+FORMUL 6 HOH *330(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 ASN A 53 ARG A 60 1 8
+HELIX 4 AA4 LYS A 61 HIS A 64 5 4
+HELIX 5 AA5 ILE A 200 ASN A 214 1 15
+HELIX 6 AA6 THR A 226 TYR A 237 1 12
+HELIX 7 AA7 THR A 243 GLY A 258 1 16
+HELIX 8 AA8 ALA A 260 GLY A 275 1 16
+HELIX 9 AA9 THR A 292 CYS A 300 1 9
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N GLN A 83 O VAL A 86
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O CYS A 128 N PHE A 112
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
+SITE 1 AC1 8 GLN A 74 ARG A 76 PHE A 223 THR A 224
+SITE 2 AC1 8 ASP A 263 HOH A 587 HOH A 637 HOH A 798
+SITE 1 AC2 5 MET A 6 PHE A 8 SER A 123 GLN A 127
+SITE 2 AC2 5 ARG A 298
+SITE 1 AC3 3 GLY A 15 MET A 17 HOH A 681
+SITE 1 AC4 12 HIS A 41 TYR A 54 GLU A 166 PRO A 168
+SITE 2 AC4 12 ASP A 187 ARG A 188 GLN A 189 ASP A 248
+SITE 3 AC4 12 GLY A 251 PRO A 252 HOH A 518 HOH A 675
+CRYST1 112.891 53.030 44.352 90.00 102.46 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008858 0.000000 0.001957 0.00000
+SCALE2 0.000000 0.018857 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023090 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5R81_lig.sdf b/example_files/ligand/5R81_lig.sdf
index 965fed3..a0ad582 100644
--- a/example_files/ligand/5R81_lig.sdf
+++ b/example_files/ligand/5R81_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
15 16 0 0 0 0 0 0 0 0999 V2000
10.0015 -0.5220 25.0692 C 0 0 0 0 0 0 0 0 0 0 0 0
@@ -34,4 +34,100 @@ target
12 14 2 0 0 0 0
12 15 1 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF COVID-19 MAIN
+TITLE 2 PROTEASE IN COMPLEX WITH Z1367324110
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,A.J.POWELL,A.DOUANGAMATH,C.D.OWEN,C.WILD,T.KROJER,P.LUKACIK,
+AUTHOR 2 C.M.STRAIN-DAMERELL,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM RZJ 1-METHYL-3,4-DIHYDRO-2~{H}-QUINOLINE-7-SULFONAMIDE
+HETNAM DMS DIMETHYL SULFOXIDE
+FORMUL 2 RZJ C10 H14 N2 O2 S
+FORMUL 3 DMS 4(C2 H6 O S)
+FORMUL 7 HOH *334(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 ASN A 53 ILE A 59 1 7
+HELIX 4 AA4 ARG A 60 LYS A 61 5 2
+HELIX 5 AA5 SER A 62 HIS A 64 5 3
+HELIX 6 AA6 ILE A 200 ASN A 214 1 15
+HELIX 7 AA7 THR A 226 TYR A 237 1 12
+HELIX 8 AA8 THR A 243 LEU A 250 1 8
+HELIX 9 AA9 LEU A 250 GLY A 258 1 9
+HELIX 10 AB1 ALA A 260 GLY A 275 1 16
+HELIX 11 AB2 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O CYS A 128 N PHE A 112
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
+SITE 1 AC1 10 HIS A 41 MET A 49 GLU A 166 PRO A 168
+SITE 2 AC1 10 ASP A 187 ARG A 188 GLN A 189 PRO A 252
+SITE 3 AC1 10 HOH A1159 HOH A1259
+SITE 1 AC2 8 GLN A 74 ARG A 76 ARG A 222 PHE A 223
+SITE 2 AC2 8 THR A 224 ASP A 263 HOH A1158 HOH A1283
+SITE 1 AC3 6 MET A 6 PHE A 8 SER A 123 GLN A 127
+SITE 2 AC3 6 ARG A 298 HOH A1235
+SITE 1 AC4 2 GLY A 15 MET A 17
+SITE 1 AC5 5 PHE A 140 LEU A 141 HIS A 163 MET A 165
+SITE 2 AC5 5 GLU A 166
+CRYST1 113.780 53.490 44.450 90.00 101.70 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008789 0.000000 0.001820 0.00000
+SCALE2 0.000000 0.018695 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.022975 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5R82_lig.sdf b/example_files/ligand/5R82_lig.sdf
index 15735bc..ba4261c 100644
--- a/example_files/ligand/5R82_lig.sdf
+++ b/example_files/ligand/5R82_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
11 11 0 0 0 0 0 0 0 0999 V2000
9.0161 -0.0370 27.7721 C 0 0 0 0 0 0 0 0 0 0 0 0
@@ -25,4 +25,99 @@ target
7 10 4 0 0 0 0
10 11 4 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF COVID-19 MAIN
+TITLE 2 PROTEASE IN COMPLEX WITH Z219104216
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,A.J.POWELL,A.DOUANGAMATH,C.D.OWEN,C.WILD,T.KROJER,P.LUKACIK,
+AUTHOR 2 C.M.STRAIN-DAMERELL,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM RZS 6-(ETHYLAMINO)PYRIDINE-3-CARBONITRILE
+HETNAM DMS DIMETHYL SULFOXIDE
+FORMUL 2 RZS C8 H9 N3
+FORMUL 3 DMS 4(C2 H6 O S)
+FORMUL 7 HOH *332(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 GLU A 47 ASN A 51 5 5
+HELIX 4 AA4 ASN A 53 ARG A 60 1 8
+HELIX 5 AA5 LYS A 61 HIS A 64 5 4
+HELIX 6 AA6 ILE A 200 ASN A 214 1 15
+HELIX 7 AA7 THR A 226 TYR A 237 1 12
+HELIX 8 AA8 THR A 243 LEU A 250 1 8
+HELIX 9 AA9 LEU A 250 GLY A 258 1 9
+HELIX 10 AB1 ALA A 260 GLY A 275 1 16
+HELIX 11 AB2 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N ALA A 70 O VAL A 73
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N GLN A 83 O VAL A 86
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
+SITE 1 AC1 8 HIS A 41 MET A 49 HIS A 164 MET A 165
+SITE 2 AC1 8 ASP A 187 GLN A 189 DMS A1005 HOH A1171
+SITE 1 AC2 7 GLN A 74 LEU A 75 ARG A 76 THR A 224
+SITE 2 AC2 7 ASP A 263 HOH A1182 HOH A1257
+SITE 1 AC3 5 MET A 6 PHE A 8 SER A 123 GLN A 127
+SITE 2 AC3 5 ARG A 298
+SITE 1 AC4 4 GLY A 15 MET A 17 LYS A 97 HOH A1256
+SITE 1 AC5 8 GLU A 166 PRO A 168 ARG A 188 GLN A 189
+SITE 2 AC5 8 THR A 190 GLN A 192 RZS A1001 HOH A1175
+CRYST1 112.665 52.848 44.468 90.00 102.97 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008876 0.000000 0.002044 0.00000
+SCALE2 0.000000 0.018922 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023076 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5R83_lig.sdf b/example_files/ligand/5R83_lig.sdf
index 3651b91..9918bb8 100644
--- a/example_files/ligand/5R83_lig.sdf
+++ b/example_files/ligand/5R83_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
16 17 0 0 0 0 0 0 0 0999 V2000
9.4094 -1.0606 22.3873 N 0 0 0 0 0 0 0 0 0 0 0 0
@@ -36,4 +36,97 @@ target
14 15 4 0 0 0 0
7 16 4 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2
+TITLE 2 MAIN PROTEASE IN COMPLEX WITH Z44592329
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,A.J.POWELL,A.DOUANGAMATH,C.D.OWEN,C.WILD,T.KROJER,P.LUKACIK,
+AUTHOR 2 C.M.STRAIN-DAMERELL,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM DMS DIMETHYL SULFOXIDE
+HETNAM K0G N-PHENYL-N'-PYRIDIN-3-YLUREA
+FORMUL 2 DMS 3(C2 H6 O S)
+FORMUL 5 K0G C12 H11 N3 O
+FORMUL 6 HOH *328(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 GLU A 47 ASN A 51 5 5
+HELIX 4 AA4 ASN A 53 ARG A 60 1 8
+HELIX 5 AA5 LYS A 61 HIS A 64 5 4
+HELIX 6 AA6 ILE A 200 ASN A 214 1 15
+HELIX 7 AA7 THR A 226 TYR A 237 1 12
+HELIX 8 AA8 THR A 243 LEU A 250 1 8
+HELIX 9 AA9 LEU A 250 GLY A 258 1 9
+HELIX 10 AB1 ALA A 260 GLY A 275 1 16
+HELIX 11 AB2 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N GLN A 83 O VAL A 86
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
+SITE 1 AC1 8 GLN A 74 LEU A 75 ARG A 76 PHE A 223
+SITE 2 AC1 8 THR A 224 ASP A 263 HOH A 528 HOH A 608
+SITE 1 AC2 4 MET A 6 SER A 123 GLN A 127 ARG A 298
+SITE 1 AC3 4 GLY A 15 MET A 17 LYS A 97 HOH A 647
+SITE 1 AC4 11 MET A 49 PHE A 140 LEU A 141 ASN A 142
+SITE 2 AC4 11 HIS A 163 HIS A 164 MET A 165 GLU A 166
+SITE 3 AC4 11 ARG A 188 GLN A 189 HOH A 547
+CRYST1 112.267 52.583 44.535 90.00 102.95 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008907 0.000000 0.002048 0.00000
+SCALE2 0.000000 0.019018 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023040 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5R84_lig.sdf b/example_files/ligand/5R84_lig.sdf
index 1cd8b46..66379cd 100644
--- a/example_files/ligand/5R84_lig.sdf
+++ b/example_files/ligand/5R84_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
16 17 0 0 0 0 0 0 0 0999 V2000
7.5974 -0.3658 21.3429 N 0 0 0 0 0 0 0 0 0 0 0 0
@@ -36,4 +36,97 @@ target
13 14 4 0 0 0 0
14 15 4 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF COVID-19 MAIN
+TITLE 2 PROTEASE IN COMPLEX WITH Z31792168
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,A.J.POWELL,A.DOUANGAMATH,C.D.OWEN,C.WILD,T.KROJER,P.LUKACIK,
+AUTHOR 2 C.M.STRAIN-DAMERELL,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM GWS 2-CYCLOHEXYL-~{N}-PYRIDIN-3-YL-ETHANAMIDE
+HETNAM DMS DIMETHYL SULFOXIDE
+FORMUL 2 GWS C13 H18 N2 O
+FORMUL 3 DMS 3(C2 H6 O S)
+FORMUL 6 HOH *324(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 ASN A 53 ARG A 60 1 8
+HELIX 4 AA4 LYS A 61 PHE A 66 5 6
+HELIX 5 AA5 ILE A 200 ASN A 214 1 15
+HELIX 6 AA6 THR A 226 TYR A 237 1 12
+HELIX 7 AA7 THR A 243 LEU A 250 1 8
+HELIX 8 AA8 LEU A 250 GLY A 258 1 9
+HELIX 9 AA9 ALA A 260 GLY A 275 1 16
+HELIX 10 AB1 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASP A 153 O CYS A 156
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O TYR A 126 N VAL A 114
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162
+SITE 1 AC1 11 HIS A 41 PHE A 140 LEU A 141 ASN A 142
+SITE 2 AC1 11 CYS A 145 HIS A 163 HIS A 164 MET A 165
+SITE 3 AC1 11 GLU A 166 ARG A 188 GLN A 189
+SITE 1 AC2 8 GLN A 74 LEU A 75 ARG A 76 THR A 224
+SITE 2 AC2 8 ASP A 263 HOH A1225 HOH A1254 HOH A1410
+SITE 1 AC3 5 MET A 6 PHE A 8 SER A 123 GLN A 127
+SITE 2 AC3 5 ARG A 298
+SITE 1 AC4 3 GLY A 15 MET A 17 LYS A 97
+CRYST1 113.146 53.167 44.267 90.00 101.66 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008838 0.000000 0.001824 0.00000
+SCALE2 0.000000 0.018809 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023066 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5RE4_lig.sdf b/example_files/ligand/5RE4_lig.sdf
index 1f7b3c6..370d801 100644
--- a/example_files/ligand/5RE4_lig.sdf
+++ b/example_files/ligand/5RE4_lig.sdf
@@ -1,5 +1,5 @@
target
- PyMOL2.1 3D 0
+ PyMOL3.0 3D 0
11 11 0 0 0 0 0 0 0 0999 V2000
10.2243 -0.7737 22.5041 C 0 0 0 0 0 0 0 0 0 0 0 0
@@ -25,4 +25,98 @@ target
9 10 4 0 0 0 0
10 11 1 0 0 0 0
M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 15-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2
+TITLE 2 MAIN PROTEASE IN COMPLEX WITH Z1129283193
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,C.D.OWEN,A.DOUANGAMATH,P.LUKACIK,A.J.POWELL,C.M.STRAIN-
+AUTHOR 2 DAMERELL,E.RESNICK,T.KROJER,P.GEHRTZ,C.WILD,A.AIMON,J.BRANDAO-NETO,
+AUTHOR 3 A.CARBERY,L.DUNNETT,R.SKYNER,M.SNEE,N.LONDON,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM DMS DIMETHYL SULFOXIDE
+HETNAM SZY N-(4-METHYLPYRIDIN-3-YL)ACETAMIDE
+FORMUL 2 DMS 3(C2 H6 O S)
+FORMUL 5 SZY C8 H10 N2 O
+FORMUL 6 HOH *335(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 GLU A 47 ASN A 51 5 5
+HELIX 4 AA4 ASN A 53 ARG A 60 1 8
+HELIX 5 AA5 LYS A 61 HIS A 64 5 4
+HELIX 6 AA6 ILE A 200 ASN A 214 1 15
+HELIX 7 AA7 THR A 226 TYR A 237 1 12
+HELIX 8 AA8 THR A 243 GLY A 258 1 16
+HELIX 9 AA9 ALA A 260 GLY A 275 1 16
+HELIX 10 AB1 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N GLN A 83 O VAL A 86
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
+SITE 1 AC1 10 GLN A 74 LEU A 75 ARG A 76 ARG A 222
+SITE 2 AC1 10 PHE A 223 THR A 224 ASP A 263 HOH A 567
+SITE 3 AC1 10 HOH A 575 HOH A 773
+SITE 1 AC2 6 MET A 6 PHE A 8 SER A 123 GLN A 127
+SITE 2 AC2 6 ARG A 298 HOH A 662
+SITE 1 AC3 4 GLY A 15 MET A 17 LYS A 97 HOH A 612
+SITE 1 AC4 7 PHE A 140 LEU A 141 ASN A 142 CYS A 145
+SITE 2 AC4 7 HIS A 163 MET A 165 GLU A 166
+CRYST1 111.643 52.352 44.369 90.00 103.08 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008957 0.000000 0.002082 0.00000
+SCALE2 0.000000 0.019101 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023139 0.00000
+
+
$$$$
diff --git a/example_files/ligand/5RE5_lig.sdf b/example_files/ligand/5RE5_lig.sdf
index e69de29..00f3c9f 100644
--- a/example_files/ligand/5RE5_lig.sdf
+++ b/example_files/ligand/5RE5_lig.sdf
@@ -0,0 +1,138 @@
+target
+ PyMOL3.0 3D 0
+
+ 18 19 0 0 0 0 0 0 0 0999 V2000
+ 23.8838 -16.7138 25.7799 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 24.6744 -17.8396 25.2968 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 25.7632 -17.9821 25.7329 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 24.1564 -18.8778 24.2895 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 24.8987 -18.9081 23.0096 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 24.4988 -20.1279 22.1720 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 23.0970 -20.6876 22.3578 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.2822 -20.0907 23.4673 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.7343 -18.7273 23.9612 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.4883 -21.7609 21.5722 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 21.3834 -22.1166 21.8297 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 23.1970 -22.3911 20.4762 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.5921 -23.4454 19.6948 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.4911 -23.2674 18.3282 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 21.9273 -24.2607 17.5396 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 21.4674 -25.4339 18.1276 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 21.5703 -25.6119 19.5022 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.1332 -24.6177 20.2868 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 4 9 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 7 10 1 0 0 0 0
+ 10 11 2 0 0 0 0
+ 10 12 1 0 0 0 0
+ 12 13 1 0 0 0 0
+ 13 14 4 0 0 0 0
+ 13 18 4 0 0 0 0
+ 14 15 4 0 0 0 0
+ 15 16 4 0 0 0 0
+ 16 17 4 0 0 0 0
+ 17 18 4 0 0 0 0
+M END
+>
+HEADER HYDROLASE/HYDROLASE INHIBITOR 15-MAR-20 XXXX
+TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2
+TITLE 2 MAIN PROTEASE IN COMPLEX WITH Z33545544
+KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER,
+KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.FEARON,C.D.OWEN,A.DOUANGAMATH,P.LUKACIK,A.J.POWELL,C.M.STRAIN-
+AUTHOR 2 DAMERELL,E.RESNICK,T.KROJER,P.GEHRTZ,C.WILD,A.AIMON,J.BRANDAO-NETO,
+AUTHOR 3 A.CARBERY,L.DUNNETT,R.SKYNER,M.SNEE,N.LONDON,M.A.WALSH,F.VON DELFT
+JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN,
+JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH,
+JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES,
+JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY,
+JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN,
+JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD,
+JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH
+JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE
+JRNL TITL 2 SARS-COV-2 MAIN PROTEASE.
+JRNL REF NAT COMMUN V. 11 5047 2020
+JRNL REFN ESSN 2041-1723
+JRNL PMID 33028810
+JRNL DOI 10.1038/S41467-020-18709-W
+SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL
+SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR
+SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO
+SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO
+SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN
+SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE
+SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL
+SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL
+SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS
+SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET
+SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY
+SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS
+SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR
+SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR
+SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY
+SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU
+SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN
+SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA
+SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL
+SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA
+SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN
+SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU
+SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN
+SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN
+HETNAM DMS DIMETHYL SULFOXIDE
+HETNAM T0J N~1~-PHENYLPIPERIDINE-1,4-DICARBOXAMIDE
+FORMUL 2 DMS 3(C2 H6 O S)
+FORMUL 5 T0J C13 H17 N3 O2
+FORMUL 6 HOH *330(H2 O)
+HELIX 1 AA1 SER A 10 GLY A 15 1 6
+HELIX 2 AA2 HIS A 41 CYS A 44 5 4
+HELIX 3 AA3 GLU A 47 ASN A 51 5 5
+HELIX 4 AA4 ASN A 53 ARG A 60 1 8
+HELIX 5 AA5 LYS A 61 HIS A 64 5 4
+HELIX 6 AA6 ILE A 200 ASN A 214 1 15
+HELIX 7 AA7 THR A 226 TYR A 237 1 12
+HELIX 8 AA8 THR A 243 GLY A 258 1 16
+HELIX 9 AA9 ALA A 260 GLY A 275 1 16
+HELIX 10 AB1 THR A 292 GLY A 302 1 11
+SHEET 1 AA1 7 VAL A 73 LEU A 75 0
+SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75
+SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69
+SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20
+SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30
+SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36
+SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N ILE A 78 O LYS A 90
+SHEET 1 AA2 5 LYS A 100 PHE A 103 0
+SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N GLY A 149 O TYR A 161
+SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
+SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O CYS A 128 N PHE A 112
+SHEET 1 AA3 3 LYS A 100 PHE A 103 0
+SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102
+SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
+SITE 1 AC1 9 GLN A 74 ARG A 76 ARG A 222 PHE A 223
+SITE 2 AC1 9 THR A 224 ASP A 263 HOH A 514 HOH A 581
+SITE 3 AC1 9 HOH A 809
+SITE 1 AC2 6 MET A 6 PHE A 8 SER A 123 GLN A 127
+SITE 2 AC2 6 ARG A 298 HOH A 668
+SITE 1 AC3 4 GLY A 15 MET A 17 LYS A 97 HOH A 614
+SITE 1 AC4 10 ILE A 78 HIS A 80 PRO A 184 VAL A 186
+SITE 2 AC4 10 ARG A 188 ALA A 193 HOH A 508 HOH A 529
+SITE 3 AC4 10 HOH A 568 HOH A 658
+CRYST1 112.530 52.810 44.520 90.00 102.15 90.00 C 1 2 1 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008887 0.000000 0.001913 0.00000
+SCALE2 0.000000 0.018936 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.022976 0.00000
+
+
+$$$$
diff --git a/example_files/receptor/5R7Y_A.pdb b/example_files/receptor/5R7Y_A.pdb
index aeea056..6b551b3 100644
--- a/example_files/receptor/5R7Y_A.pdb
+++ b/example_files/receptor/5R7Y_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 112.463 52.731 44.299 90.00 102.81 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.551 4.208 -17.081 1.00 31.04 N
ATOM 2 CA SER A 1 -2.151 5.509 -16.492 1.00 30.79 C
ATOM 3 C SER A 1 -2.458 5.531 -14.988 1.00 29.60 C
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 5.965 -10.009 -10.128 1.00 50.10 O
ATOM 2345 CB THR A 304 4.391 -9.282 -12.698 1.00 50.75 C
ATOM 2346 CG2 THR A 304 3.299 -8.384 -13.235 1.00 48.40 C
ATOM 2347 OG1 THR A 304 5.086 -9.911 -13.775 1.00 51.21 O
+TER
END
diff --git a/example_files/receptor/5R7Z_A.pdb b/example_files/receptor/5R7Z_A.pdb
index fc672b5..153544f 100644
--- a/example_files/receptor/5R7Z_A.pdb
+++ b/example_files/receptor/5R7Z_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 112.090 52.513 44.384 90.00 102.94 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.253 4.513 -16.964 1.00 36.71 N
ATOM 2 CA SER A 1 -2.036 5.839 -16.336 1.00 38.02 C
ATOM 3 C SER A 1 -2.457 5.782 -14.858 1.00 34.86 C
@@ -2269,7 +2270,7 @@ ATOM 2268 O PHE A 294 11.405 1.243 -10.604 1.00 21.72 O
ATOM 2269 CB PHE A 294 14.458 1.108 -9.105 1.00 27.55 C
ATOM 2270 CG PHE A 294 15.925 1.216 -9.471 1.00 36.34 C
ATOM 2271 CD1 PHE A 294 16.366 0.960 -10.766 1.00 40.69 C
-ATOM 2272 CD2 PHE A 294 16.885 1.573 -8.527 1.00 42.51 C
+ATOM 2272 CD2 PHE A 294 16.885 1.573 -8.526 1.00 42.51 C
ATOM 2273 CE1 PHE A 294 17.712 1.058 -11.107 1.00 39.89 C
ATOM 2274 CE2 PHE A 294 18.228 1.681 -8.877 1.00 42.66 C
ATOM 2275 CZ PHE A 294 18.641 1.409 -10.163 1.00 38.68 C
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.280 -10.020 -10.296 1.00 48.15 O
ATOM 2345 CB THR A 304 4.411 -9.142 -12.655 1.00 52.70 C
ATOM 2346 CG2 THR A 304 3.273 -8.250 -13.102 1.00 52.97 C
ATOM 2347 OG1 THR A 304 4.979 -9.756 -13.812 1.00 52.97 O
+TER
END
diff --git a/example_files/receptor/5R80_A.pdb b/example_files/receptor/5R80_A.pdb
index f6bf877..390fa8e 100644
--- a/example_files/receptor/5R80_A.pdb
+++ b/example_files/receptor/5R80_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 112.891 53.030 44.352 90.00 102.46 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.200 4.307 -16.794 1.00 46.95 N
ATOM 2 CA SER A 1 -1.990 5.656 -16.222 1.00 45.24 C
ATOM 3 C SER A 1 -2.444 5.678 -14.758 1.00 44.79 C
@@ -346,7 +347,7 @@ ATOM 345 CB SER A 46 7.389 -3.660 30.829 0.64 66.87 C
ATOM 346 OG SER A 46 7.200 -2.252 30.822 0.64 68.89 O
ATOM 347 N GLU A 47 10.627 -3.070 32.427 0.64 72.65 N
ATOM 348 CA GLU A 47 11.447 -2.700 33.620 0.64 74.91 C
-ATOM 349 C GLU A 47 12.921 -3.039 33.346 0.64 72.02 C
+ATOM 349 C GLU A 47 12.921 -3.039 33.345 0.64 72.02 C
ATOM 350 O GLU A 47 13.795 -2.389 33.949 0.64 75.08 O
ATOM 351 CB GLU A 47 10.988 -3.410 34.897 0.64 77.65 C
ATOM 352 CG GLU A 47 11.105 -4.922 34.827 0.64 79.97 C
@@ -1170,7 +1171,7 @@ ATOM 1169 N ASP A 153 12.132 -9.029 -6.100 1.00 55.73 N
ATOM 1170 CA ASP A 153 12.664 -9.101 -7.491 1.00 58.61 C
ATOM 1171 C ASP A 153 12.233 -10.442 -8.109 1.00 57.78 C
ATOM 1172 O ASP A 153 12.830 -11.497 -7.766 1.00 55.79 O
-ATOM 1173 CB ASP A 153 14.183 -8.902 -7.511 1.00 66.34 C
+ATOM 1173 CB ASP A 153 14.183 -8.902 -7.512 1.00 66.34 C
ATOM 1174 CG ASP A 153 14.783 -8.732 -8.901 1.00 74.79 C
ATOM 1175 OD1 ASP A 153 15.599 -7.793 -9.086 1.00 76.74 O
ATOM 1176 OD2 ASP A 153 14.454 -9.552 -9.786 1.00 82.51 O1-
@@ -1869,7 +1870,7 @@ ATOM 1868 C GLU A 240 20.765 16.238 -1.328 1.00 38.46 C
ATOM 1869 O GLU A 240 20.129 16.503 -2.348 1.00 31.92 O
ATOM 1870 CB GLU A 240 19.798 14.173 -0.292 1.00 46.94 C
ATOM 1871 CG GLU A 240 19.285 13.478 0.954 1.00 53.56 C
-ATOM 1872 CD GLU A 240 20.346 13.216 2.016 1.00 63.84 C
+ATOM 1872 CD GLU A 240 20.345 13.216 2.016 1.00 63.84 C
ATOM 1873 OE1 GLU A 240 21.321 12.495 1.701 1.00 69.51 O
ATOM 1874 OE2 GLU A 240 20.205 13.739 3.153 1.00 63.01 O1-
ATOM 1875 N PRO A 241 22.106 16.414 -1.287 1.00 40.92 N
@@ -1879,7 +1880,7 @@ ATOM 1878 O PRO A 241 22.571 14.652 -3.247 1.00 40.94 O
ATOM 1879 CB PRO A 241 24.286 17.013 -1.977 1.00 43.30 C
ATOM 1880 CG PRO A 241 24.172 17.023 -0.465 1.00 42.08 C
ATOM 1881 CD PRO A 241 23.008 16.104 -0.168 1.00 42.20 C
-ATOM 1882 N LEU A 242 22.497 16.301 -4.792 1.00 35.46 N
+ATOM 1882 N LEU A 242 22.498 16.301 -4.792 1.00 35.46 N
ATOM 1883 CA LEU A 242 22.388 15.460 -6.012 1.00 37.69 C
ATOM 1884 C LEU A 242 23.791 15.275 -6.609 1.00 35.64 C
ATOM 1885 O LEU A 242 24.514 16.261 -6.746 1.00 32.62 O
@@ -2273,7 +2274,7 @@ ATOM 2272 CD2 PHE A 294 16.875 1.363 -8.714 1.00 81.42 C
ATOM 2273 CE1 PHE A 294 17.594 1.231 -11.371 1.00 76.06 C
ATOM 2274 CE2 PHE A 294 18.214 1.439 -9.088 1.00 82.38 C
ATOM 2275 CZ PHE A 294 18.573 1.368 -10.415 1.00 76.40 C
-ATOM 2276 N ASP A 295 11.418 2.508 -8.725 1.00 35.15 N
+ATOM 2276 N ASP A 295 11.418 2.508 -8.724 1.00 35.15 N
ATOM 2277 CA ASP A 295 9.964 2.406 -8.429 1.00 36.27 C
ATOM 2278 C ASP A 295 9.177 3.058 -9.566 1.00 36.79 C
ATOM 2279 O ASP A 295 8.138 2.499 -9.981 1.00 34.74 O
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.516 -9.859 -10.406 1.00 69.72 O
ATOM 2345 CB THR A 304 4.475 -9.064 -12.612 1.00 60.95 C
ATOM 2346 CG2 THR A 304 3.390 -8.217 -13.244 1.00 54.96 C
ATOM 2347 OG1 THR A 304 5.048 -9.901 -13.617 1.00 57.55 O
+TER
END
diff --git a/example_files/receptor/5R81_A.pdb b/example_files/receptor/5R81_A.pdb
index b0d302e..ed4935d 100644
--- a/example_files/receptor/5R81_A.pdb
+++ b/example_files/receptor/5R81_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 113.780 53.490 44.450 90.00 101.70 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.486 4.326 -16.804 1.00 47.25 N
ATOM 2 CA SER A 1 -2.096 5.622 -16.223 1.00 47.20 C
ATOM 3 C SER A 1 -2.520 5.679 -14.752 1.00 47.41 C
@@ -1454,7 +1455,7 @@ ATOM 1453 NE ARG A 188 19.737 2.599 28.590 1.00 67.65 N
ATOM 1454 CZ ARG A 188 20.434 3.606 29.103 1.00 68.10 C
ATOM 1455 NH1 ARG A 188 21.282 4.295 28.355 1.00 73.70 N1+
ATOM 1456 NH2 ARG A 188 20.260 3.923 30.374 1.00 68.85 N
-ATOM 1457 N GLN A 189 15.099 1.580 26.095 1.00 44.54 N
+ATOM 1457 N GLN A 189 15.100 1.580 26.095 1.00 44.54 N
ATOM 1458 CA GLN A 189 14.096 2.641 26.374 1.00 46.16 C
ATOM 1459 C GLN A 189 14.823 3.842 26.990 1.00 47.11 C
ATOM 1460 O GLN A 189 14.860 3.965 28.233 1.00 45.49 O
@@ -2289,7 +2290,7 @@ ATOM 2288 CB VAL A 296 9.382 6.393 -11.402 1.00 37.03 C
ATOM 2289 CG1 VAL A 296 8.614 7.130 -12.498 1.00 41.75 C
ATOM 2290 CG2 VAL A 296 9.374 7.182 -10.110 1.00 37.30 C
ATOM 2291 N VAL A 297 10.067 3.617 -12.819 1.00 39.87 N
-ATOM 2292 CA VAL A 297 10.233 2.758 -14.031 1.00 43.37 C
+ATOM 2292 CA VAL A 297 10.233 2.758 -14.030 1.00 43.37 C
ATOM 2293 C VAL A 297 9.330 1.524 -13.887 1.00 44.82 C
ATOM 2294 O VAL A 297 8.592 1.223 -14.825 1.00 43.13 O
ATOM 2295 CB VAL A 297 11.692 2.316 -14.231 1.00 43.52 C
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.385 -9.895 -10.613 1.00 86.68 O
ATOM 2345 CB THR A 304 4.377 -9.001 -12.801 1.00 81.99 C
ATOM 2346 CG2 THR A 304 3.354 -8.159 -13.532 1.00 73.88 C
ATOM 2347 OG1 THR A 304 4.956 -9.905 -13.743 1.00 80.19 O
+TER
END
diff --git a/example_files/receptor/5R82_A.pdb b/example_files/receptor/5R82_A.pdb
index 4e795bd..69ec974 100644
--- a/example_files/receptor/5R82_A.pdb
+++ b/example_files/receptor/5R82_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 112.665 52.848 44.468 90.00 102.97 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.425 4.371 -16.996 1.00 27.76 N
ATOM 2 CA SER A 1 -2.098 5.674 -16.363 1.00 27.12 C
ATOM 3 C SER A 1 -2.423 5.635 -14.866 1.00 26.29 C
@@ -44,7 +45,7 @@ ATOM 43 CA MET A 6 2.341 0.845 -4.237 1.00 18.37 C
ATOM 44 C MET A 6 3.307 0.029 -3.388 1.00 16.52 C
ATOM 45 O MET A 6 4.515 0.249 -3.524 1.00 16.69 O
ATOM 46 CB MET A 6 2.537 0.509 -5.719 1.00 22.51 C
-ATOM 47 CG MET A 6 1.985 -0.802 -6.100 1.00 29.50 C
+ATOM 47 CG MET A 6 1.985 -0.802 -6.099 1.00 29.50 C
ATOM 48 SD MET A 6 2.217 -0.953 -7.883 1.00 35.52 S
ATOM 49 CE MET A 6 0.869 0.062 -8.460 1.00 31.18 C
ATOM 50 N ALA A 7 2.772 -0.930 -2.635 1.00 16.51 N
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 5.996 -10.120 -10.203 1.00 38.46 O
ATOM 2345 CB THR A 304 4.313 -9.340 -12.683 1.00 38.12 C
ATOM 2346 CG2 THR A 304 3.324 -8.444 -13.393 1.00 34.89 C
ATOM 2347 OG1 THR A 304 5.036 -10.136 -13.628 1.00 36.00 O
+TER
END
diff --git a/example_files/receptor/5R83_A.pdb b/example_files/receptor/5R83_A.pdb
index 0b41ce9..fb4a07e 100644
--- a/example_files/receptor/5R83_A.pdb
+++ b/example_files/receptor/5R83_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 112.267 52.583 44.535 90.00 102.95 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.364 4.464 -16.840 1.00 28.73 N
ATOM 2 CA SER A 1 -2.150 5.799 -16.280 1.00 30.74 C
ATOM 3 C SER A 1 -2.493 5.810 -14.782 1.00 28.33 C
@@ -1474,7 +1475,7 @@ ATOM 1473 N ALA A 191 16.144 8.320 25.839 1.00 41.53 N
ATOM 1474 CA ALA A 191 16.214 9.507 24.954 1.00 44.62 C
ATOM 1475 C ALA A 191 17.118 9.194 23.773 1.00 38.69 C
ATOM 1476 O ALA A 191 18.341 9.094 23.959 1.00 44.00 O
-ATOM 1477 CB ALA A 191 16.749 10.717 25.697 1.00 46.61 C
+ATOM 1477 CB ALA A 191 16.749 10.717 25.698 1.00 46.61 C
ATOM 1478 N GLN A 192 16.518 9.056 22.600 1.00 34.69 N
ATOM 1479 CA GLN A 192 17.261 9.010 21.324 1.00 31.02 C
ATOM 1480 C GLN A 192 16.565 9.955 20.348 1.00 32.39 C
@@ -1799,7 +1800,7 @@ ATOM 1798 CA LEU A 232 23.092 25.370 -3.229 1.00 24.22 C
ATOM 1799 C LEU A 232 21.648 25.563 -2.760 1.00 24.79 C
ATOM 1800 O LEU A 232 21.421 25.715 -1.534 1.00 23.19 O
ATOM 1801 CB LEU A 232 23.546 26.624 -3.973 1.00 28.36 C
-ATOM 1802 CG LEU A 232 25.031 26.747 -4.285 1.00 31.18 C
+ATOM 1802 CG LEU A 232 25.030 26.747 -4.285 1.00 31.18 C
ATOM 1803 CD1 LEU A 232 25.292 28.145 -4.843 1.00 34.80 C
ATOM 1804 CD2 LEU A 232 25.886 26.475 -3.054 1.00 31.94 C
ATOM 1805 N VAL A 233 20.699 25.544 -3.700 1.00 25.72 N
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.239 -10.045 -10.478 1.00 48.62 O
ATOM 2345 CB THR A 304 4.333 -9.166 -12.740 1.00 43.23 C
ATOM 2346 CG2 THR A 304 3.264 -8.286 -13.347 1.00 40.12 C
ATOM 2347 OG1 THR A 304 4.962 -9.915 -13.782 1.00 42.40 O
+TER
END
diff --git a/example_files/receptor/5R84_A.pdb b/example_files/receptor/5R84_A.pdb
index db63b4e..eae6e86 100644
--- a/example_files/receptor/5R84_A.pdb
+++ b/example_files/receptor/5R84_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 113.146 53.167 44.267 90.00 101.66 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.317 4.286 -16.861 1.00 45.33 N
ATOM 2 CA SER A 1 -2.008 5.592 -16.274 1.00 43.61 C
ATOM 3 C SER A 1 -2.396 5.608 -14.795 1.00 43.25 C
@@ -471,7 +472,7 @@ ATOM 470 O LYS A 61 18.023 -19.635 27.839 1.00 35.49 O
ATOM 471 CB LYS A 61 16.041 -17.156 27.808 1.00 36.26 C
ATOM 472 CG LYS A 61 15.438 -15.889 28.381 1.00 39.16 C
ATOM 473 CD LYS A 61 13.993 -16.011 28.770 1.00 38.62 C
-ATOM 474 CE LYS A 61 13.586 -14.963 29.778 1.00 40.98 C
+ATOM 474 CE LYS A 61 13.586 -14.963 29.777 1.00 40.98 C
ATOM 475 NZ LYS A 61 12.114 -14.811 29.835 1.00 44.46 N1+
ATOM 476 N SER A 62 15.902 -20.460 27.993 1.00 36.41 N
ATOM 477 CA SER A 62 16.121 -21.791 27.401 1.00 36.48 C
@@ -881,7 +882,7 @@ ATOM 880 CZ PHE A 112 12.010 0.062 5.590 1.00 37.91 C
ATOM 881 N SER A 113 8.550 -2.297 1.093 1.00 30.41 N
ATOM 882 CA SER A 113 7.209 -2.634 1.618 1.00 31.63 C
ATOM 883 C SER A 113 7.339 -3.169 3.051 1.00 33.39 C
-ATOM 884 O SER A 113 8.281 -3.980 3.337 1.00 32.47 O
+ATOM 884 O SER A 113 8.281 -3.981 3.337 1.00 32.47 O
ATOM 885 CB SER A 113 6.527 -3.570 0.721 1.00 32.58 C
ATOM 886 OG SER A 113 6.280 -2.923 -0.507 1.00 37.14 O
ATOM 887 N VAL A 114 6.479 -2.652 3.929 1.00 29.79 N
@@ -1487,7 +1488,7 @@ ATOM 1486 OE1 GLN A 192 18.680 4.917 20.345 1.00 39.21 O
ATOM 1487 N ALA A 193 17.332 11.122 19.963 1.00 55.71 N
ATOM 1488 CA ALA A 193 16.889 12.084 18.935 1.00 59.01 C
ATOM 1489 C ALA A 193 17.383 11.549 17.586 1.00 56.40 C
-ATOM 1490 O ALA A 193 18.478 10.957 17.551 1.00 50.74 O
+ATOM 1490 O ALA A 193 18.479 10.957 17.551 1.00 50.74 O
ATOM 1491 CB ALA A 193 17.391 13.471 19.266 1.00 66.38 C
ATOM 1492 N ALA A 194 16.547 11.641 16.553 1.00 54.69 N
ATOM 1493 CA ALA A 194 16.917 11.369 15.144 1.00 55.38 C
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.656 -10.084 -10.471 1.00 81.27 O
ATOM 2345 CB THR A 304 4.638 -9.043 -12.588 1.00 65.59 C
ATOM 2346 CG2 THR A 304 3.549 -8.097 -13.046 1.00 64.47 C
ATOM 2347 OG1 THR A 304 5.125 -9.758 -13.727 1.00 66.86 O
+TER
END
diff --git a/example_files/receptor/5R8T_A.pdb b/example_files/receptor/5R8T_A.pdb
index 5c67d7f..efc2876 100644
--- a/example_files/receptor/5R8T_A.pdb
+++ b/example_files/receptor/5R8T_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 112.207 52.596 44.631 90.00 102.99 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.449 4.397 -16.868 1.00 27.40 N
ATOM 2 CA SER A 1 -2.136 5.703 -16.309 1.00 26.70 C
ATOM 3 C SER A 1 -2.457 5.701 -14.811 1.00 24.24 C
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.246 -10.030 -10.356 1.00 42.41 O
ATOM 2345 CB THR A 304 4.370 -9.297 -12.783 1.00 36.28 C
ATOM 2346 CG2 THR A 304 3.272 -8.414 -13.332 1.00 33.34 C
ATOM 2347 OG1 THR A 304 5.026 -9.963 -13.865 1.00 36.52 O
+TER
END
diff --git a/example_files/receptor/5RE4_A.pdb b/example_files/receptor/5RE4_A.pdb
index 7dfd6eb..c43c538 100644
--- a/example_files/receptor/5RE4_A.pdb
+++ b/example_files/receptor/5RE4_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 111.643 52.352 44.369 90.00 103.08 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.271 4.450 -16.793 1.00 45.33 N
ATOM 2 CA SER A 1 -1.992 5.778 -16.186 1.00 45.41 C
ATOM 3 C SER A 1 -2.492 5.815 -14.737 1.00 42.53 C
@@ -512,7 +513,7 @@ ATOM 511 O PHE A 66 9.731 -20.877 22.271 1.00 30.37 O
ATOM 512 CB PHE A 66 11.868 -18.870 22.381 1.00 25.60 C
ATOM 513 CG PHE A 66 12.987 -18.078 22.986 1.00 24.51 C
ATOM 514 CD1 PHE A 66 12.934 -16.689 22.993 1.00 24.30 C
-ATOM 515 CD2 PHE A 66 14.075 -18.715 23.560 1.00 24.29 C
+ATOM 515 CD2 PHE A 66 14.075 -18.715 23.559 1.00 24.29 C
ATOM 516 CE1 PHE A 66 13.971 -15.943 23.532 1.00 24.12 C
ATOM 517 CE2 PHE A 66 15.097 -17.967 24.130 1.00 24.83 C
ATOM 518 CZ PHE A 66 15.043 -16.586 24.106 1.00 24.76 C
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.432 -9.925 -10.150 1.00 59.34 O
ATOM 2345 CB THR A 304 4.530 -9.026 -12.404 1.00 64.99 C
ATOM 2346 CG2 THR A 304 3.494 -8.147 -13.071 1.00 66.19 C
ATOM 2347 OG1 THR A 304 5.095 -9.886 -13.391 1.00 69.62 O
+TER
END
diff --git a/example_files/receptor/5RE5_A.pdb b/example_files/receptor/5RE5_A.pdb
index 64b0708..984facd 100644
--- a/example_files/receptor/5RE5_A.pdb
+++ b/example_files/receptor/5RE5_A.pdb
@@ -1,3 +1,4 @@
+CRYST1 112.530 52.810 44.520 90.00 102.15 90.00 C 1 2 1 1
ATOM 1 N SER A 1 -2.155 4.211 -16.970 1.00 50.34 N
ATOM 2 CA SER A 1 -1.965 5.570 -16.400 1.00 51.09 C
ATOM 3 C SER A 1 -2.379 5.581 -14.921 1.00 48.55 C
@@ -1499,7 +1500,7 @@ ATOM 1498 CA GLY A 195 19.233 13.985 12.935 1.00 44.59 C
ATOM 1499 C GLY A 195 18.179 14.654 12.078 1.00 39.02 C
ATOM 1500 O GLY A 195 16.999 14.285 12.178 1.00 36.31 O
ATOM 1501 N THR A 196 18.611 15.617 11.272 1.00 36.27 N
-ATOM 1502 CA THR A 196 17.794 16.314 10.257 1.00 34.69 C
+ATOM 1502 CA THR A 196 17.795 16.314 10.257 1.00 34.69 C
ATOM 1503 C THR A 196 17.157 15.277 9.325 1.00 34.93 C
ATOM 1504 O THR A 196 17.902 14.434 8.805 1.00 32.97 O
ATOM 1505 CB THR A 196 18.663 17.282 9.446 1.00 33.97 C
@@ -2345,4 +2346,5 @@ ATOM 2344 O THR A 304 6.898 -9.514 -10.309 1.00 85.19 O
ATOM 2345 CB THR A 304 4.382 -9.062 -12.625 1.00 85.85 C
ATOM 2346 CG2 THR A 304 3.504 -8.205 -13.517 1.00 79.27 C
ATOM 2347 OG1 THR A 304 4.920 -10.144 -13.388 1.00 89.83 O
+TER
END
diff --git a/setup.py b/setup.py
index 11f39b2..3c8f64f 100644
--- a/setup.py
+++ b/setup.py
@@ -7,8 +7,8 @@
with codecs.open(os.path.join(here, "README.md"), encoding="utf-8") as fh:
long_description = "\n" + fh.read()
-VERSION = 'v0.1.1'
-DESCRIPTION = 'PyPharmer'
+VERSION = 'v0.1.2'
+DESCRIPTION = 'ConPhar'
#LONG_DESCRIPTION = ''
# Setting up
diff --git a/tutorials/ConsensusPharmacophore.ipynb b/tutorials/ConsensusPharmacophore.ipynb
index 9404680..b9cc7ed 100644
--- a/tutorials/ConsensusPharmacophore.ipynb
+++ b/tutorials/ConsensusPharmacophore.ipynb
@@ -7,7 +7,15 @@
"metadata": {
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "ConPhar tools imported successfully\n"
+ ]
+ }
+ ],
"source": [
"from conphar.Pharmacophores import parse_json_pharmacophore, show_pharmacophoric_descriptors, save_pharmacophore_to_pymol, save_pharmacophore_to_json, compute_concensus_pharmacophore\n",
"\n",
@@ -111,13 +119,13 @@
}
],
"source": [
- "t,l,r=parse_json_pharmacophore(\"Example/pharmacophores/5R7Y.json\")\n",
+ "t,l,r=parse_json_pharmacophore(\"example_files/pharmacophores/5R7Y.json\")\n",
"t"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 3,
"id": "3d2d4f63-8aa3-4ded-9ec2-be47afab1d40",
"metadata": {
"tags": []
@@ -125,10 +133,10 @@
"outputs": [],
"source": [
"p4_table=pd.DataFrame()\n",
- "for file in os.listdir('Example/pharmacophores/'):\n",
+ "for file in os.listdir('example_files/pharmacophores/'):\n",
" if '.json' in file:\n",
" try:\n",
- " p4,lig,rec=parse_json_pharmacophore(f\"Example/pharmacophores/{file}\")\n",
+ " p4,lig,rec=parse_json_pharmacophore(f\"example_files/pharmacophores/{file}\")\n",
" p4['ligand']=file.replace('.json','')\n",
" p4_table=pd.concat([p4_table,p4],ignore_index=True)\n",
" except Exception:\n",
@@ -137,7 +145,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 4,
"id": "221142e3-acc1-4665-8b10-0c862313f95c",
"metadata": {
"tags": []
@@ -181,6 +189,48 @@
"