Testing at lower seqID

PDBeurope · Jun 11, 2024 · 7d619ce · 7d619ce
1 parent 09cf897
commit 7d619ce
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Showing 4 changed files with 96 additions and 23 deletions.
diff --git a/cluster_conformers/cluster_monomers.py b/cluster_conformers/cluster_monomers.py
@@ -222,6 +222,7 @@ def _generate_ca_matx(self, pdbe_chain_id: str) -> "tuple(dict)":
         if not path_save_this_ca_matx.with_suffix(".npz").exists() or self.force:
 
             pdbe_chain_id_split = pdbe_chain_id.split("_")
+
             # Extract x, y, z, and UNP index info from mmCIF/chain
             mmcif = io_utils.load_mmcif(self.mmcif_paths[pdbe_chain_id_split[0]])
             xyz_unp_dict = parsing_utils.parse_mmcif(mmcif, pdbe_chain_id_split[1])
@@ -278,7 +279,7 @@ def ca_distance(self, path_save: PosixPath = None) -> None:
 
         # Dir to save the raw UniProt residue IDs as 1D np.array()s
         self.path_save_unps = path_save.joinpath("unp_residue_ids")
-        self.path_save_unps.mkdir(exist_ok=True)
+        self.path_save_unps.mkdir(parents=True, exist_ok=True)
 
         self.path_save_base_ca = path_save
 
@@ -464,6 +465,10 @@ def cluster(
         """
 
         logger.info("Generating distance difference matrices...")
+        if not path_save_dd_matx:
+            raise ValueError("Path to save distance difference matrices not specified.")
+
+        path_save_dd_matx.mkdir(parents=True, exist_ok=True)
         self.score_matx, self.label_matx = self.build_clustering_inputs(
             path_save_dd_matx
         )
@@ -518,6 +523,8 @@ def cluster(
         # Write out clustering results if path specified
         if path_save_cluster_results:
 
+            path_save_cluster_results.mkdir(parents=True, exist_ok=True)
+
             # Save clustering results
             path_save_all_conf = path_save_cluster_results.joinpath(
                 f"{self.unp}_sum_based_clustering_results.csv"
@@ -710,7 +717,7 @@ def render_dendrogram(
 
         fig, ax = plt.subplots(1, 1)
 
-        logger.info("Rendering dendogram")
+        logger.info("Rendering dendrogram")
         cluster_chains.plot_dendrogram(
             unp,
             ax,

diff --git a/examples/run_O34926.sh b/examples/run_O34926.sh
@@ -1,27 +1,29 @@
 #!/bin/sh
 
-rm benchmark_data/examples/O34926/O34926_ca_distances/*
-rm benchmark_data/examples/O34926/O34926_ca_distances/unp_residue_ids/*
-rm benchmark_data/examples/O34926/O34926_distance_differences/*
-rm benchmark_data/examples/O34926/O34926_cluster_results/*
+path_mmcifs="benchmark_data/examples/O34926/O34926_updated_mmcif"
+path_ca_distances="benchmark_data/examples/O34926/O34926_ca_distances"
+path_distance_differences="benchmark_data/examples/O34926/O34926_distance_differences"
+path_cluster_results="benchmark_data/examples/O34926/O34926_cluster_results"
 
-# mprof run --python
+rm $path_ca_distances/*
+rm $path_ca_distances/unp_residue_ids/*
+rm $path_distance_differences/*
+rm $path_cluster_results/*
 
-python3 find_conformers.py -u "O34926" \
-    -m benchmark_data/examples/O34926/O34926_updated_mmcif/3nc7_updated.cif A B \
-    -m benchmark_data/examples/O34926/O34926_updated_mmcif/3nc5_updated.cif A B \
-    -m benchmark_data/examples/O34926/O34926_updated_mmcif/3nc3_updated.cif A B \
-    -c benchmark_data/examples/O34926/O34926_ca_distances/ \
-    -s benchmark_data/examples/O34926/O34926_cluster_results/ \
-    -d benchmark_data/examples/O34926/O34926_distance_differences/ \
-    -m benchmark_data/examples/O34926/O34926_updated_mmcif/3nc6_updated.cif A B \
-    -i 3nc6 \
-    -f \
-    -g benchmark_data/examples/O34926/O34926_cluster_results/ png svg \
+python3 find_conformers.py \
+    -u "O34926" \
+    -m $path_mmcifs/3nc7_updated.cif A B \
+    -m $path_mmcifs/3nc5_updated.cif A B \
+    -m $path_mmcifs/3nc3_updated.cif A B \
+    -m $path_mmcifs/3nc6_updated.cif A B \
+    -c $path_ca_distances \
+    -d $path_distance_differences \
+    -s $path_cluster_results \
+    -g $path_cluster_results png svg \
     -0 1 \
-    -1 405
+    -1 405 \
+    -f \
     # -v \
-    # -a benchmark_data/examples/O34926/O34926_alpha_fold_mmcifs
-
-# -o benchmark_data/examples/O34926/O34926_distance_difference_maps/ \
-# -w benchmark_data/examples/O34926/O34926_cluster_results/ png svg \
+    # -a benchmark_data/examples/O34926/O34926_alpha_fold_mmcifs \
+    # -o benchmark_data/examples/O34926/O34926_distance_difference_maps/ \
+    # -w benchmark_data/examples/O34926/O34926_cluster_results/ png svg \
diff --git a/examples/run_P15291.sh b/examples/run_P15291.sh
@@ -1,5 +1,7 @@
 #!/bin/sh
 
+
+
 python3 find_conformers.py -u "P15291" \
     -m benchmark_data/examples/P15291/P15291_updated_mmcif/2fyb_updated.cif A \
     -m benchmark_data/examples/P15291/P15291_updated_mmcif/2fyd_updated.cif B D \

diff --git a/run_uniref50.sh b/run_uniref50.sh
@@ -0,0 +1,62 @@
+#!/bin/sh
+
+path_base="/media/jellaway/FlashData/EMBL-EBI/funclan_work/clustering_w_uniref"
+path_cluster_results="$path_base/cluster_results_uniref50"
+
+
+path_mmcifs="$path_base/reindexed_mmcifs_combined/uniref50_mmcifs"
+path_ca_distances="$path_cluster_results/ca_distances"
+path_distance_differences="$path_cluster_results/distance_differences"
+path_cluster_results="$path_cluster_results/cluster_results"
+
+rm $path_ca_distances/*
+rm $path_ca_distances/unp_residue_ids/*
+rm $path_distance_differences/*
+rm $path_cluster_results/*
+
+python3 find_conformers.py \
+    -u "uniref50" \
+    -m $path_mmcifs/6mkh_updated.cif A \
+    -m $path_mmcifs/6bsr_updated.cif A \
+    -m $path_mmcifs/8f3v_updated.cif A \
+    -m $path_mmcifs/6g88_updated.cif A B C \
+    -m $path_mmcifs/6mki_updated.cif A \
+    -m $path_mmcifs/5dvy_updated.cif A \
+    -m $path_mmcifs/8f3t_updated.cif A \
+    -m $path_mmcifs/8f3x_updated.cif A \
+    -m $path_mmcifs/8f3f_updated.cif A \
+    -m $path_mmcifs/8u55_updated.cif A \
+    -m $path_mmcifs/8f3l_updated.cif A \
+    -m $path_mmcifs/8f67_updated.cif A B C \
+    -m $path_mmcifs/8f3s_updated.cif A \
+    -m $path_mmcifs/6g0k_updated.cif A B C \
+    -m $path_mmcifs/8f3n_updated.cif A \
+    -m $path_mmcifs/8f3i_updated.cif A \
+    -m $path_mmcifs/8f3o_updated.cif A \
+    -m $path_mmcifs/8f3y_updated.cif A \
+    -m $path_mmcifs/8f3p_updated.cif A \
+    -m $path_mmcifs/8f3q_updated.cif A \
+    -m $path_mmcifs/8f3m_updated.cif A \
+    -m $path_mmcifs/6mkf_updated.cif A \
+    -m $path_mmcifs/8f3z_updated.cif A \
+    -m $path_mmcifs/6bsq_updated.cif A \
+    -m $path_mmcifs/6mkj_updated.cif A \
+    -m $path_mmcifs/6mkg_updated.cif A \
+    -m $path_mmcifs/8f3g_updated.cif A \
+    -m $path_mmcifs/8f3h_updated.cif A \
+    -m $path_mmcifs/8f3r_updated.cif A \
+    -m $path_mmcifs/8f3w_updated.cif A \
+    -m $path_mmcifs/6mka_updated.cif A \
+    -m $path_mmcifs/8f3j_updated.cif A \
+    -m $path_mmcifs/8f3u_updated.cif A \
+    -m $path_mmcifs/5e31_updated.cif A \
+    -c $path_ca_distances \
+    -d $path_distance_differences \
+    -s $path_cluster_results \
+    -g $path_cluster_results png svg \
+    -f \
+    -n 8 \
+    # -v \
+    # -a benchmark_data/examples/O34926/O34926_alpha_fold_mmcifs \
+    # -o benchmark_data/examples/O34926/O34926_distance_difference_maps/ \
+    # -w benchmark_data/examples/O34926/O34926_cluster_results/ png svg \