diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 434f8f7..38415ed 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,7 +11,7 @@ jobs: strategy: max-parallel: 4 matrix: - python-version: [3.10.12] + python-version: [3.10.14] steps: - uses: actions/checkout@v2 @@ -56,7 +56,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.10.12] + python-version: [3.10.14] needs: build steps: diff --git a/README.md b/README.md index 272cdeb..b56f005 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ For intructions on importing `protein-cluster-conformers` into your own Python c `protein-cluster-conformers` requires >=Python3.10 to run. Initialise virtual environment and install dependencies with: ```shell -$ cd contact_map_difference +$ cd protein-cluster-conformers] $ python3.10 -m venv cluster_venv $ source cluster_venv/bin/activate $ python -m pip install -r requirements.txt @@ -31,6 +31,7 @@ $ python find_conformers.py [-h] [-v] -u UNIPROT -m MMCIF [MMCIF ...] [-g PATH_DENDROGRAM [PATH_DENDROGRAM ...]] [-w PATH_SWARM [PATH_SWARM ...]] [-o PATH_HISTOGRAM] [-a PATH_ALPHA_FOLD] + [-0 FIRST_RESIDUE_POSITION] [-1 LAST_RESIDUE_POSITION] ``` The following parameters can be parsed: @@ -58,6 +59,10 @@ optional arguments: Path to save histograms of distance difference maps -a PATH_ALPHA_FOLD, --path_alpha_fold PATH_ALPHA_FOLD Path to save AlphaFold Database structure + -0 FIRST_RESIDUE_POSITION, --first_residue_position FIRST_RESIDUE_POSITION + First residue position in (UniProt) sequence + -1 LAST_RESIDUE_POSITION, --last_residue_position LAST_RESIDUE_POSITION + Last residue position in (UniProt) sequence ``` @@ -148,7 +153,7 @@ The resulting plots are saved in PNG format (to save render time). E.g: **Example**: O34926 ```shell -$ python run_find_clusters.py -u "O34926" \ +$ python find_clusters.py -u "O34926" \ -m benchmark_data/examples/O34926/O34926_updated_mmcif/3nc3_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/3nc6_updated.cif A B \ @@ -163,7 +168,7 @@ $ python run_find_clusters.py -u "O34926" \ From the clustering results, a dendrogram can be rendered to show the relationships between all clustered chains. To save a dendrogram of the hierarchical clustering results, run: ```shell -$ python run_find_clusters.py -u "A12345" \ +$ python find_clusters.py -u "A12345" \ -m /path/to/structure_1.cif [chains] \ -m ... \ -g /path/to/save/dendrogram/ [png svg] @@ -171,14 +176,16 @@ $ python run_find_clusters.py -u "A12345" \ where either a `png` or `svg` file type is saved. E.g. -Dendrogram of clustered UniProt:P14902 chains, via UPGMA agglomerative clustering +Dendrogram of clustered UniProt:P14902 chains, via UPGMA agglomerative clustering + +Dendrogram of clustered UniProt:P14902 chains, via UPGMA agglomerative clustering
**Example**: O34926 ```shell -$ python run_find_clusters.py -u "O34926" \ +$ python find_clusters.py -u "O34926" \ -m benchmark_data/examples/O34926/O34926_updated_mmcif/3nc3_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/3nc6_updated.cif A B \ @@ -193,7 +200,7 @@ $ python run_find_clusters.py -u "O34926" \ The scores generated between pairwise structure comparisons can be plotted as a swarm plot by parsing the `-w` flag: ```shell -$ python run_find_clusters.py -u "A12345" \ +$ python find_clusters.py -u "A12345" \ -m /path/to/structure_1.cif [chains] \ -m ... \ -w /path/to/save/swarm_plot/ [png svg] @@ -269,7 +276,7 @@ $ ./run_O34926.sh **Example #2:** P15291 ``` shell -python3 run_find_conformers.py -u "P15291" \ +python3 find_conformers.py -u "P15291" \ -m benchmark_data/examples/P15291/P15291_updated_mmcif/2fy7_updated.cif A \ -m benchmark_data/examples/P15291/P15291_updated_mmcif/2fya_updated.cif A \ -m benchmark_data/examples/P15291/P15291_updated_mmcif/2fyb_updated.cif A \ diff --git a/__version__.py b/__version__.py index 6849410..c68196d 100644 --- a/__version__.py +++ b/__version__.py @@ -1 +1 @@ -__version__ = "1.1.0" +__version__ = "1.2.0" diff --git a/benchmark_data/figures/O34926_1_405_agglomerative_dendrogram.png b/benchmark_data/figures/O34926_1_405_agglomerative_dendrogram.png new file mode 100644 index 0000000..4fc1366 Binary files /dev/null and b/benchmark_data/figures/O34926_1_405_agglomerative_dendrogram.png differ diff --git a/benchmark_data/figures/P15291_122_398_agglomerative_dendrogram.png b/benchmark_data/figures/P15291_122_398_agglomerative_dendrogram.png new file mode 100644 index 0000000..a7cde22 Binary files /dev/null and b/benchmark_data/figures/P15291_122_398_agglomerative_dendrogram.png differ diff --git a/cluster_conformers/cluster_chains.py b/cluster_conformers/cluster_chains.py index e7a55ec..341da64 100644 --- a/cluster_conformers/cluster_chains.py +++ b/cluster_conformers/cluster_chains.py @@ -105,7 +105,8 @@ def plot_dendrogram( unp: str, axis, linkage_matrix: ndarray = None, cutoff: float = None, **kwargs ) -> "tuple(Figure, Axes)": """ - Create linkage matrix from SKLearn model and plot the dendrogram of nodes. + Create linkage matrix from SKLearn model and plot the dendrogram of nodes. Applies + this to parsed Matplotlib axis, inplace. :param unp: UniProt accession :type unp: str @@ -123,26 +124,48 @@ def plot_dendrogram( """ # Plot the corresponding dendrogram - dn = dendrogram(linkage_matrix, ax=axis, **kwargs) - del dn + dendrogram_plot = dendrogram(linkage_matrix, ax=axis, **kwargs) + + hline_props = { + "colors": ["black"], + "linestyles": ["dashed"], + "linewidths": 1, + "alpha": 0.5, + } # Add horizontal line where cutoff is placed if cutoff: - max_parent = max(linkage_matrix[:, 2]) + max_parent = linkage_matrix[:, 2].max() axis_xlimits = axis.get_xlim() axis.hlines( y=max_parent * cutoff, xmin=axis_xlimits[0], xmax=axis_xlimits[1], - colors=["black"], - linestyles=["dashed"], - linewidths=1, - alpha=0.5, + **hline_props, ) - axis.set_title(f"Agglomerative clustering dendrogram: {unp}", fontweight="bold") + axis.set_title(f"Agglomerative clustering results: {unp}", fontweight="bold") axis.set_ylabel("Score (\u212B)") + # Set the y-axis limits + rock_bottom = -max_parent * 0.025 + axis.set_ylim(rock_bottom, max_parent * 1.05) + + # Add vlines for each leaf below the x-axis + axis.vlines( + x=axis.get_xticks(), + ymin=rock_bottom, + ymax=0, + colors=dendrogram_plot["leaves_color_list"], + linestyles=["solid"], + linewidths=1, + # alpha=0.5, + ) + + axis.hlines(y=0, xmin=axis_xlimits[0], xmax=axis_xlimits[1], **hline_props) + + del dendrogram_plot + def plot_swarmplot(y_data: Iterable, unp: str) -> "tuple(Figure, Axes)": """Creates a strip plot of non-overlapping data points for a given list of data. The diff --git a/cluster_conformers/cluster_monomers.py b/cluster_conformers/cluster_monomers.py index 563a970..a18e600 100644 --- a/cluster_conformers/cluster_monomers.py +++ b/cluster_conformers/cluster_monomers.py @@ -672,6 +672,7 @@ def render_dendrogram( path_save: PosixPath = None, png: bool = False, svg: bool = False, + unp_range: "tuple[int, int]" = None, ) -> None: """ Plot hierachical dendrogram from clustering results. Must have a linkage matrix and @@ -684,6 +685,7 @@ def render_dendrogram( :type png: bool, optional :param svg: Save dendrogram image in SVG format, defaults to False :type svg: bool, optional + :param unp_range: Range of UniProt residues used for clustering """ # Set matplotlib global formatting @@ -718,14 +720,24 @@ def render_dendrogram( leaf_rotation=90, ) # p=3 + # UniProt residue range specified, make modifications (optional) + if unp_range: + ax.set_title( + f"Agglomerative clustering results: {unp} ({unp_range[0]}-{unp_range[1]})", + fontweight="bold", + ) + fname = f"{unp}_{unp_range[0]}_{unp_range[1]}_agglomerative_dendrogram" + else: + fname = f"{unp}_agglomerative_dendrogram" + + # Save file io_utils.save_figure( path_save, - save_fname=f"{unp}_agglomerative_dendrogram", + save_fname=fname, png=png, svg=svg, ) - # plt.clf() plt.close(fig=fig) else: diff --git a/cluster_conformers/utils/appearance_utils.py b/cluster_conformers/utils/appearance_utils.py index 0f10199..1ab45b2 100644 --- a/cluster_conformers/utils/appearance_utils.py +++ b/cluster_conformers/utils/appearance_utils.py @@ -11,5 +11,5 @@ def init_plot_appearance(): """ # Figure parameters and formatting - plt.style.use("seaborn-v0_8-colorblind") + # plt.style.use("seaborn-v0_8-colorblind") plt.style.use("fast") diff --git a/examples/run_O34926.sh b/examples/run_O34926.sh index c9b3bac..216dafa 100755 --- a/examples/run_O34926.sh +++ b/examples/run_O34926.sh @@ -7,7 +7,7 @@ rm benchmark_data/examples/O34926/O34926_cluster_results/* # mprof run --python -python find_conformers.py -u "O34926" \ +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 \ @@ -18,6 +18,8 @@ python find_conformers.py -u "O34926" \ -i 3nc6 \ -f \ -g benchmark_data/examples/O34926/O34926_cluster_results/ png svg \ + -0 1 \ + -1 405 # -v \ # -a benchmark_data/examples/O34926/O34926_alpha_fold_mmcifs diff --git a/examples/run_P00519_merged_segms.sh b/examples/run_P00519_merged_segms.sh deleted file mode 100755 index 75b5afb..0000000 --- a/examples/run_P00519_merged_segms.sh +++ /dev/null @@ -1,143 +0,0 @@ -#!/bin/sh - -python3 find_conformers.py -u "P00519" \ - -m ../P00519_updated_mmcifs/2fo0_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4xey_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5mo4_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4wa9_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/7n9g_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4yc8_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2hz4_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4wa9_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2g1t_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2g1t_updated.cif.gz D \ - -m ../P00519_updated_mmcifs/3qri_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2f4j_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5hu9_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2gqg_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2gqg_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/6xrg_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/6xr7_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2hiw_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2hiw_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/6xr6_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3qrk_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/1opl_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/1opl_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3cs9_updated.cif.gz D \ - -m ../P00519_updated_mmcifs/3cs9_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3cs9_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/3cs9_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/2hz0_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2hz0_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2hyy_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2hyy_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2hyy_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/2hyy_updated.cif.gz D \ - -m ../P00519_updated_mmcifs/2g1t_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2g1t_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/3qri_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/4yc8_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/3pyy_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/3pyy_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2hz4_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2hz4_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/4zog_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4zog_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/3ue4_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3ue4_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2g2h_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2g2h_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2hzi_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2hzi_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/7dt2_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/7dt2_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2e2b_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2e2b_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/6bl8_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/6bl8_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2g2i_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2g2i_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/3qrj_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3qrj_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/4twp_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4twp_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2v7a_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2v7a_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/6npe_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/6npe_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/7cc2_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/7cc2_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/4xey_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/2g2f_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2g2f_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/6npu_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/6npu_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/6npv_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/6npv_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/7w7y_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/7w7y_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/7w7x_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/7w7x_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/7n9g_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/7n9g_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/6amv_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2abl_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5dc0_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/1ab2_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3t04_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3k2m_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/3k2m_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/6amw_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5dc9_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3uyo_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5dc4_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3eg3_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9f_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3eg2_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9h_updated.cif.gz E \ - -m ../P00519_updated_mmcifs/4j9h_updated.cif.gz F \ - -m ../P00519_updated_mmcifs/4j9h_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/4j9h_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9h_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4j9h_updated.cif.gz D \ - -m ../P00519_updated_mmcifs/4j9g_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9g_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4j9g_updated.cif.gz E \ - -m ../P00519_updated_mmcifs/3eg1_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3eg1_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/3eg0_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5np2_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5np2_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/1ju5_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/1awo_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4jjb_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4jjd_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2o88_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/2o88_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/1bbz_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/1bbz_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/1bbz_updated.cif.gz E \ - -m ../P00519_updated_mmcifs/1bbz_updated.cif.gz G \ - -m ../P00519_updated_mmcifs/4j9d_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4j9d_updated.cif.gz E \ - -m ../P00519_updated_mmcifs/4j9d_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/3egu_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9f_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4j9f_updated.cif.gz E \ - -m ../P00519_updated_mmcifs/4j9b_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9i_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9i_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4j9i_updated.cif.gz E \ - -m ../P00519_updated_mmcifs/4j9c_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5oaz_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/5oaz_updated.cif.gz B \ - -m ../P00519_updated_mmcifs/4jjc_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9e_updated.cif.gz A \ - -m ../P00519_updated_mmcifs/4j9e_updated.cif.gz C \ - -m ../P00519_updated_mmcifs/4j9e_updated.cif.gz E \ - -c examples/P00519/P00519_ca_distances/ \ - -d examples/P00519/P00519_distance_differences/ \ - -s examples/P00519/P00519_cluster_results/ \ - -g examples/P00519/P00519_cluster_results/ png svg - # -a benchmark_data/examples/O34926/O34926_alpha_fold_mmcifs diff --git a/examples/run_P02787.sh b/examples/run_P02787.sh deleted file mode 100755 index e3205bf..0000000 --- a/examples/run_P02787.sh +++ /dev/null @@ -1,70 +0,0 @@ -#!/bin/sh - -mkdir -p ~/EMBL-EBI/funclan_work/P02787/ca_distances -mkdir -p ~/EMBL-EBI/funclan_work/P02787/distance_differences -mkdir -p ~/EMBL-EBI/funclan_work/P02787/distance_difference_maps -mkdir -p ~/EMBL-EBI/funclan_work/P02787/cluster_results -# Remove files from previous executions -rm ~/EMBL-EBI/funclan_work/P02787/ca_distances/* -rm ~/EMBL-EBI/funclan_work/P02787/distance_differences/* -rm ~/EMBL-EBI/funclan_work/P02787/distance_difference_maps/* -rm ~/EMBL-EBI/funclan_work/P02787/cluster_results/* - -python3 run_find_conformers.py -u "P02787" \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1a8e_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1a8f_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1b3e_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1bp5_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1btj_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1d3k_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1d4n_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1dtg_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1fqe_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1fqf_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1jqf_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1n7w_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1n7x_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1n84_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1oqg_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1oqh_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1ryo_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1suv_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2hau_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2hav_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2o7u_updated.cif B A C D E F G H I \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2o84_updated.cif X \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3fgs_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3qyt_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3s9l_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3s9m_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3s9n_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3skp_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3v83_updated.cif A B C D E F \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3v89_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3v8x_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3ve1_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/4h0w_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/4x1b_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/4x1d_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5dyh_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5h52_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5wtd_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5x5p_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5y6k_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6ctc_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6d03_updated.cif A B C D E \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6d04_updated.cif A B C D E F \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6d05_updated.cif A B C D E F \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6jas_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6soy_updated.cif A B C \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6soz_updated.cif A B C \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6uj6_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/7ffm_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/7ffu_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/7q1l_updated.cif A B \ - -c ~/EMBL-EBI/funclan_work/P02787/ca_distances/ \ - -d ~/EMBL-EBI/funclan_work/P02787/distance_differences/ \ - -s ~/EMBL-EBI/funclan_work/P02787/cluster_results/ \ - -g ~/EMBL-EBI/funclan_work/P02787/cluster_results/ png svg - -# -o ~/EMBL-EBI/funclan_work/P02787/distance_difference_maps/ \ diff --git a/examples/run_P02787_seg1.sh b/examples/run_P02787_seg1.sh deleted file mode 100755 index a4963e8..0000000 --- a/examples/run_P02787_seg1.sh +++ /dev/null @@ -1,46 +0,0 @@ -#!/bin/sh - -mkdir -p ~/EMBL-EBI/funclan_work/P02787_1/ca_distances -mkdir -p ~/EMBL-EBI/funclan_work/P02787_1/distance_differences -mkdir -p ~/EMBL-EBI/funclan_work/P02787_1/distance_difference_maps -mkdir -p ~/EMBL-EBI/funclan_work/P02787_1/cluster_results -# Remove files from previous executions -rm ~/EMBL-EBI/funclan_work/P02787_1/ca_distances/* -rm ~/EMBL-EBI/funclan_work/P02787_1/distance_differences/* -rm ~/EMBL-EBI/funclan_work/P02787_1/distance_difference_maps/* -rm ~/EMBL-EBI/funclan_work/P02787_1/cluster_results/* - -python3 run_find_conformers.py -u "P02787" \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2hau_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2hav_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3qyt_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3s9l_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3s9m_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3s9n_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3skp_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3v83_updated.cif A B C D E F \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3v89_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3v8x_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3ve1_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/4h0w_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/4x1b_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/4x1d_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5dyh_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5h52_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5wtd_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5x5p_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/5y6k_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6ctc_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6d03_updated.cif A B C D E \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6d04_updated.cif A B C D E F \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6d05_updated.cif A B C D E F \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6jas_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6soy_updated.cif A B C \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6soz_updated.cif A B C \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/6uj6_updated.cif A \ - -c ~/EMBL-EBI/funclan_work/P02787_1/ca_distances/ \ - -d ~/EMBL-EBI/funclan_work/P02787_1/distance_differences/ \ - -s ~/EMBL-EBI/funclan_work/P02787_1/cluster_results/ \ - -g ~/EMBL-EBI/funclan_work/P02787_1/cluster_results/ png svg - -# -o ~/EMBL-EBI/funclan_work/P02787/distance_difference_maps/ \ diff --git a/examples/run_P02787_seg2.sh b/examples/run_P02787_seg2.sh deleted file mode 100755 index 39a8b2c..0000000 --- a/examples/run_P02787_seg2.sh +++ /dev/null @@ -1,40 +0,0 @@ -#!/bin/sh - -mkdir -p ~/EMBL-EBI/funclan_work/P02787_2/ca_distances -mkdir -p ~/EMBL-EBI/funclan_work/P02787_2/distance_differences -mkdir -p ~/EMBL-EBI/funclan_work/P02787_2/distance_difference_maps -mkdir -p ~/EMBL-EBI/funclan_work/P02787_2/cluster_results -# Remove files from previous executions -rm ~/EMBL-EBI/funclan_work/P02787_2/ca_distances/* -rm ~/EMBL-EBI/funclan_work/P02787_2/distance_differences/* -rm ~/EMBL-EBI/funclan_work/P02787_2/distance_difference_maps/* -rm ~/EMBL-EBI/funclan_work/P02787_2/cluster_results/* - -python3 run_find_conformers.py -u "P02787" \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1a8e_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1a8f_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1b3e_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1bp5_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1btj_updated.cif A B \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1d3k_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1d4n_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1dtg_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1fqe_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1fqf_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1jqf_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1n7w_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1n7x_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1n84_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1oqg_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1oqh_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1ryo_updated.cif A \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/1suv_updated.cif A B C D \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2o7u_updated.cif B A C D E F G H I \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/2o84_updated.cif X \ - -m /home/jellaway/EMBL-EBI/funclan_work/P02787_updated/3fgs_updated.cif A \ - -c ~/EMBL-EBI/funclan_work/P02787_2/ca_distances/ \ - -d ~/EMBL-EBI/funclan_work/P02787_2/distance_differences/ \ - -s ~/EMBL-EBI/funclan_work/P02787_2/cluster_results/ \ - -g ~/EMBL-EBI/funclan_work/P02787_2/cluster_results/ png svg - -# -o ~/EMBL-EBI/funclan_work/P02787/distance_difference_maps/ \ diff --git a/examples/run_P15291.sh b/examples/run_P15291.sh index f7c7751..58b1c73 100755 --- a/examples/run_P15291.sh +++ b/examples/run_P15291.sh @@ -1,6 +1,6 @@ #!/bin/sh -python3.7 find_conformers.py -u "P15291" \ +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 \ -m benchmark_data/examples/P15291/P15291_updated_mmcif/6fwu_updated.cif A B \ @@ -11,6 +11,8 @@ python3.7 find_conformers.py -u "P15291" \ -d benchmark_data/examples/P15291/P15291_distance_differences/ \ -s benchmark_data/examples/P15291/P15291_cluster_results/ \ -g benchmark_data/examples/P15291/P15291_cluster_results/ png svg \ + -0 122 \ + -1 398 # -a benchmark_data/examples/P15291/P15291_alpha_fold_mmcifs \ diff --git a/examples/run_P69905.sh b/examples/run_P69905.sh deleted file mode 100755 index 447a29c..0000000 --- a/examples/run_P69905.sh +++ /dev/null @@ -1,336 +0,0 @@ -#!/bin/sh - -# rm benchmark_data/examples/O34926/O34926_ca_distances/* -# rm benchmark_data/examples/O34926/O34926_distance_differences/* -# rm benchmark_data/examples/O34926/O34926_cluster_results/* - -rm /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/ca_distances/* -rm /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/ca_distances/unp_residue_ids/* -rm -r /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/dd_matrices/ -mkdir /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/dd_matrices/ -rm /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/cluster_results/* - -# mprof run -- - - -python /home/jellaway/EMBL-EBI/funclan_work/contact_map_difference/find_conformers.py -u "P69905" \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a00_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a01_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a0u_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a0z_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a3n_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a3o_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a9w_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1abw_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1aby_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1aj9_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1b86_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bab_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bbb_updated.cif.gz A C \ - 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-s /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/cluster_results/ \ - -n 6 \ - # -g /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/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_P69905_variable_cores.sh b/examples/run_P69905_variable_cores.sh deleted file mode 100755 index 551f1c2..0000000 --- a/examples/run_P69905_variable_cores.sh +++ /dev/null @@ -1,345 +0,0 @@ -#!/bin/sh - -# rm benchmark_data/examples/O34926/O34926_ca_distances/* -# rm benchmark_data/examples/O34926/O34926_distance_differences/* -# rm benchmark_data/examples/O34926/O34926_cluster_results/* - - - - -# mprof run -- -for nproc in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 -do - for repeat in 1 2 3 - do - echo "repeat = $repeat, nproc = $nproc, nchains = 310, remaking matxs each time" - # rm /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/ca_distances/* - # rm /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/ca_distances/unp_residue_ids/* - # rm -r /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/dd_matrices/ - # mkdir /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/dd_matrices/ - rm /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/cluster_results/* - - { time python /home/jellaway/EMBL-EBI/funclan_work/contact_map_difference/find_conformers.py -u "P69905" \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a00_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a01_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a0u_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a0z_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a3n_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a3o_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1a9w_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1abw_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1aby_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1aj9_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1b86_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bab_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bbb_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bij_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1buw_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bz0_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bz1_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1bzz_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1c7b_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1c7c_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1c7d_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1cls_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1cmy_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1coh_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1dke_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1dxt_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1dxu_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1dxv_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1fdh_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1fn3_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1g9v_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1gbu_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1gbv_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1gli_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1gzx_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hab_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hac_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hba_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hbb_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hbs_updated.cif.gz A C E G \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hco_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hdb_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hga_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hgb_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hgc_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1hho_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1ird_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1j3y_updated.cif.gz A C E G \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1j3z_updated.cif.gz A C E G \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1j40_updated.cif.gz A C E G \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1j41_updated.cif.gz A C E G \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1j7s_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1j7w_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1j7y_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1jy7_updated.cif.gz A C E G I K \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1k0y_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1k1k_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1kd2_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1lfl_updated.cif.gz A C E G \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1lfq_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1lft_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1lfv_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1lfy_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1lfz_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1ljw_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1m9p_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1mko_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1nej_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1nih_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1nqp_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1i_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1j_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1k_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1l_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1m_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1n_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1o_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1o1p_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1qi8_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1qsh_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1qsi_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1qxd_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1qxe_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1r1x_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1r1y_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1rps_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1rq3_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1rq4_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1rqa_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1rvw_updated.cif.gz A \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1sdk_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1sdl_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1shr_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1si4_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1thb_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1uiw_updated.cif.gz A C E G \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1vwt_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xxt_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xy0_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xye_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xz2_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xz4_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xz5_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xz7_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xzu_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1xzv_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y01_updated.cif.gz B \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y09_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y0a_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y0c_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y0d_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y0t_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y0w_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y22_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y2z_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y31_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y35_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y45_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y46_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y4b_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y4f_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y4g_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y4p_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y4q_updated.cif.gz A C \ - -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/1y4r_updated.cif.gz A C \ - 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# -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/7qu4_updated.cif.gz C D \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/7ud7_updated.cif.gz A C \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/7ud8_updated.cif.gz A C \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/7uf6_updated.cif.gz A C \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/7uf7_updated.cif.gz A C \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/7vde_updated.cif.gz A C \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/7xgy_updated.cif.gz A C \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/8dov_updated.cif.gz A C E G \ - # -m /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/updated_mmcifs/8egi_updated.cif.gz A C \ - -# -g /home/jellaway/EMBL-EBI/funclan_work/many-chain-unps/P69905/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/find_conformers.py b/find_conformers.py index 5687772..a76842e 100644 --- a/find_conformers.py +++ b/find_conformers.py @@ -178,6 +178,22 @@ def create_parser(input_args=None): default=None, ) + parser.add_argument( + "-0", + "--first_residue_position", + help="First residue position in (UniProt) sequence", + type=int, + default=None, + ) + + parser.add_argument( + "-1", + "--last_residue_position", + help="Last residue position in (UniProt) sequence", + type=int, + default=None, + ) + args = parser.parse_args(input_args) # Add parsed list of mmCIFs to dictionary @@ -195,6 +211,12 @@ def main(): # Initialise logger logging_utils.init_logger(verbose=args.verbose) + # End early if only one residue parsed + if bool(args.first_residue_position) != bool(args.last_residue_position): + raise NameError( + "Must parse in BOTH first (-0) and last (-1) residue positions in sequence" + ) + # Create object for clustering unp_cluster = cluster_monomers.ClusterConformations( unp=args.uniprot, @@ -246,12 +268,19 @@ def main(): path_save, png_bool, svg_bool = extract_image_format(args.path_dendrogram) + # Define residue range if parsed in + if args.first_residue_position and args.last_residue_position: + this_unp_range = (args.first_residue_position, args.last_residue_position) + else: + this_unp_range = None + cluster_monomers.render_dendrogram( unp=args.uniprot, path_results=path_save, path_save=path_save, png=png_bool, svg=svg_bool, + unp_range=this_unp_range, ) diff --git a/tests/test_cluster_monomers.py b/tests/test_cluster_monomers.py index c952d92..a1f3b38 100644 --- a/tests/test_cluster_monomers.py +++ b/tests/test_cluster_monomers.py @@ -275,6 +275,9 @@ def test_render_dendrogram(self): executing ClusterConformations().cluster() """ + # Remove remnants from previous tests + remove_files_in_dir(self.path_save) + # Input data here is a copy of clustering results for UniProt=O34926 test_unp = "B12345"