Clean up and automated testing

.gitlab-ci.yml

 image: "registry.jsc.fz-juelich.de/faber1/gitlab-container/testing:python311"
 
+
+test:
+  tags:
+  - public-docker
+  script:
+  - pip install numpy biopython matplotlib scikit-learn
+  - pytest
+
+
 pages:
   tags:
   - public-docker

arc_test.txt

-Sequence:
-GGGGGCCACAGCAGAAGCGTTCACGTCGCGGCCCCTGTCAGATTCTGGTGAATCTGCGAATTCTGCTGT
-Secondary:
-.........((((((((((.......)))......((.(((((........)))))))..)))))))..
-Weights:
-[1.6604664325714111, 2.90354323387146, 2.1825625896453857, 0.5971742272377014, 0.8108296990394592, 1.7135246992111206, 1.102308988571167, 1.0844101905822754, 0.9618269205093384, 0.19237223267555237, 1.1943042278289795, 1.3098340034484863, 1.6046257019042969, 0.8343143463134766, 1.839804768562317, 0.994997501373291, -0.31095585227012634]

example1.py

-from src.BioHelpers_FABER.cmap import Cmap
-from src.BioHelpers_FABER.gmap import gaussWeightMap
-from src.BioHelpers_FABER.bio_mod import arrToList
-from src.BioHelpers_FABER.visualisation import show_contact_map
-import matplotlib.pyplot as plt
-
-
-if __name__ == "__main__":
-    c1 = Cmap(68)
-    c1.load_native_pdb(
-        filename="tests/4pqv_A.pdb",
-        id="4pqv",
-        reference="nearest",
-        contact_threshold=10,
-    )
-    c1.load_contacts_from_restraints("simrna_dca_4pqv_A.res", "DCA_Restraints")
-    c1.load_contacts_from_restraints("simrna_coconet_4pqv_A.res", "COCONET_Restraints")
-    print(
-        c1.l,
-        c1.contacts["DCA_Restraints"].sum(),
-        c1.ppvs["DCA_Restraints"],
-        c1.gauss["DCA_Restraints"],
-    )
-    print(
-        c1.l,
-        c1.contacts["COCONET_Restraints"].sum(),
-        c1.ppvs["COCONET_Restraints"],
-        c1.gauss["COCONET_Restraints"],
-    )
-    fig, ax = show_contact_map(c1, ["DCA_Restraints"], mark_match=True)
-    plt.show()

example2.py

-import Bio.PDB
-import Bio.PDB.Atom
-import numpy as np
-
-
-def main():
-    structure = Bio.PDB.PDBParser().get_structure("4pqv", "tests/4pqv_A.pdb")
-    residues = list(structure.get_residues())
-    res1 = residues[8]
-    res2 = residues[3]
-    atoms1 = list(res1.get_atoms())
-    atoms2 = list(res2.get_atoms())
-    min_dist = 999
-    min_atom1 = Bio.PDB.Atom.Atom("dummy", np.zeros(3), 0, 1, 1, "dummy", 0)
-    min_atom2 = Bio.PDB.Atom.Atom("dummy", np.zeros(3), 0, 1, 1, "dummy", 0)
-    for a1 in atoms1:
-        for a2 in atoms2:
-            if np.linalg.norm(a1.get_coord() - a2.get_coord()) < min_dist:
-                min_dist = np.linalg.norm(a1.get_coord() - a2.get_coord())
-                min_atom1 = a1
-                min_atom2 = a2
-
-    print(
-        f"Minimal distance: {min_dist:.2f}, Coordinate1: {min_atom1}, Coordinate2: {min_atom2}"
-    )
-
-
-if __name__ == "__main__":
-    main()

example_arc.py → examples/example_arc.py

+import sys, os
+
+sys.path.insert(0, os.path.abspath("../src"))
+
 import matplotlib.pyplot as plt
-from src.BioHelpers_FABER.visualisation import RNA_Arc
+from BioHelpers_FABER.visualisation import RNA_Arc
 
 
 def main() -> None:

examples/example_contact_mapping.py

-from src.BioHelpers_FABER.cmap import Cmap
-from src.BioHelpers_FABER.bio_mod import renumber_pdb
-from src.BioHelpers_FABER.visualisation import show_contact_map
-import src.BioHelpers_FABER.bio_mod as bm
+import sys, os
+
+sys.path.insert(0, os.path.abspath("../src"))
+
+from BioHelpers_FABER.cmap import Cmap
+from BioHelpers_FABER.bio_mod import renumber_pdb
+from BioHelpers_FABER.visualisation import show_contact_map
+import BioHelpers_FABER.bio_mod as bm
 import Bio.PDB as PDB
 import matplotlib.pyplot as plt
 from matplotlib.patches import Rectangle

example_rmsd.py → examples/example_rmsd.py

-import src.BioHelpers_FABER.rmsd as rmsd
-import src.BioHelpers_FABER.bio_mod as bm
+import sys, os
+
+sys.path.insert(0, os.path.abspath("../src"))
+
+import BioHelpers_FABER.rmsd as rmsd
+import BioHelpers_FABER.bio_mod as bm
 import Bio.PDB as pdb
 import numpy as np
 from Bio.SVDSuperimposer import SVDSuperimposer

pixi.toml

 [workspace]
-authors = ["c.faber <c.faber@fz-juelich.de>"]
+authors = ["Christian Faber <c.faber@fz-juelich.de>"]
 channels = ["conda-forge"]
 name = "biohelpers"
 platforms = ["linux-64"]

simrna_1l9a_L0.5.res

-WELL A/15/N A/113/N 3.5 9.5 1.0 
-SLOPE A/15/N A/113/N 3.5 9.5 1.0 
-SLOPE A/15/N A/113/N 0 25 -1.0 
-WELL A/34/N A/41/N 3.5 9.5 1.0 
-SLOPE A/34/N A/41/N 3.5 9.5 1.0 
-SLOPE A/34/N A/41/N 0 25 -1.0 
-WELL A/33/N A/42/N 3.5 9.5 1.0 
-SLOPE A/33/N A/42/N 3.5 9.5 1.0 
-SLOPE A/33/N A/42/N 0 25 -1.0 
-WELL A/12/N A/116/N 3.5 9.5 1.0 
-SLOPE A/12/N A/116/N 3.5 9.5 1.0 
-SLOPE A/12/N A/116/N 0 25 -1.0 
-WELL A/23/N A/52/N 3.5 9.5 1.0 
-SLOPE A/23/N A/52/N 3.5 9.5 1.0 
-SLOPE A/23/N A/52/N 0 25 -1.0 
-WELL A/11/N A/117/N 3.5 9.5 1.0 
-SLOPE A/11/N A/117/N 3.5 9.5 1.0 
-SLOPE A/11/N A/117/N 0 25 -1.0 
-WELL A/16/N A/112/N 3.5 9.5 1.0 
-SLOPE A/16/N A/112/N 3.5 9.5 1.0 
-SLOPE A/16/N A/112/N 0 25 -1.0 
-WELL A/35/N A/40/N 3.5 9.5 1.0 
-SLOPE A/35/N A/40/N 3.5 9.5 1.0 
-SLOPE A/35/N A/40/N 0 25 -1.0 
-WELL A/19/N A/56/N 3.5 9.5 1.0 
-SLOPE A/19/N A/56/N 3.5 9.5 1.0 
-SLOPE A/19/N A/56/N 0 25 -1.0 
-WELL A/9/N A/119/N 3.5 9.5 1.0 
-SLOPE A/9/N A/119/N 3.5 9.5 1.0 
-SLOPE A/9/N A/119/N 0 25 -1.0 
-WELL A/30/N A/45/N 3.5 9.5 1.0 
-SLOPE A/30/N A/45/N 3.5 9.5 1.0 
-SLOPE A/30/N A/45/N 0 25 -1.0 
-WELL A/4/N A/125/N 3.5 9.5 1.0 
-SLOPE A/4/N A/125/N 3.5 9.5 1.0 
-SLOPE A/4/N A/125/N 0 25 -1.0 
-WELL A/20/N A/55/N 3.5 9.5 1.0 
-SLOPE A/20/N A/55/N 3.5 9.5 1.0 
-SLOPE A/20/N A/55/N 0 25 -1.0 
-WELL A/6/N A/123/N 3.5 9.5 1.0 
-SLOPE A/6/N A/123/N 3.5 9.5 1.0 
-SLOPE A/6/N A/123/N 0 25 -1.0 
-WELL A/14/N A/114/N 3.5 9.5 1.0 
-SLOPE A/14/N A/114/N 3.5 9.5 1.0 
-SLOPE A/14/N A/114/N 0 25 -1.0 
-WELL A/26/N A/49/N 3.5 9.5 1.0 
-SLOPE A/26/N A/49/N 3.5 9.5 1.0 
-SLOPE A/26/N A/49/N 0 25 -1.0 
-WELL A/27/N A/48/N 3.5 9.5 1.0 
-SLOPE A/27/N A/48/N 3.5 9.5 1.0 
-SLOPE A/27/N A/48/N 0 25 -1.0 
-WELL A/10/N A/118/N 3.5 9.5 1.0 
-SLOPE A/10/N A/118/N 3.5 9.5 1.0 
-SLOPE A/10/N A/118/N 0 25 -1.0 
-WELL A/7/N A/122/N 3.5 9.5 1.0 
-SLOPE A/7/N A/122/N 3.5 9.5 1.0 
-SLOPE A/7/N A/122/N 0 25 -1.0 
-WELL A/24/N A/51/N 3.5 9.5 1.0 
-SLOPE A/24/N A/51/N 3.5 9.5 1.0 
-SLOPE A/24/N A/51/N 0 25 -1.0 
-WELL A/5/N A/124/N 3.5 9.5 1.0 
-SLOPE A/5/N A/124/N 3.5 9.5 1.0 
-SLOPE A/5/N A/124/N 0 25 -1.0 
-WELL A/29/N A/46/N 3.5 9.5 1.0 
-SLOPE A/29/N A/46/N 3.5 9.5 1.0 
-SLOPE A/29/N A/46/N 0 25 -1.0 
-WELL A/17/N A/111/N 3.5 9.5 1.0 
-SLOPE A/17/N A/111/N 3.5 9.5 1.0 
-SLOPE A/17/N A/111/N 0 25 -1.0 
-WELL A/28/N A/47/N 3.5 9.5 1.0 
-SLOPE A/28/N A/47/N 3.5 9.5 1.0 
-SLOPE A/28/N A/47/N 0 25 -1.0 
-WELL A/21/N A/54/N 3.5 9.5 1.0 
-SLOPE A/21/N A/54/N 3.5 9.5 1.0 
-SLOPE A/21/N A/54/N 0 25 -1.0 
-WELL A/13/N A/115/N 3.5 9.5 1.0 
-SLOPE A/13/N A/115/N 3.5 9.5 1.0 
-SLOPE A/13/N A/115/N 0 25 -1.0 
-WELL A/32/N A/43/N 3.5 9.5 1.0 
-SLOPE A/32/N A/43/N 3.5 9.5 1.0 
-SLOPE A/32/N A/43/N 0 25 -1.0 
-WELL A/31/N A/44/N 3.5 9.5 1.0 
-SLOPE A/31/N A/44/N 3.5 9.5 1.0 
-SLOPE A/31/N A/44/N 0 25 -1.0 
-WELL A/18/N A/57/N 3.5 9.5 1.0 
-SLOPE A/18/N A/57/N 3.5 9.5 1.0 
-SLOPE A/18/N A/57/N 0 25 -1.0 
-WELL A/25/N A/50/N 3.5 9.5 1.0 
-SLOPE A/25/N A/50/N 3.5 9.5 1.0 
-SLOPE A/25/N A/50/N 0 25 -1.0 
-WELL A/78/N A/99/N 3.5 9.5 1.0 
-SLOPE A/78/N A/99/N 3.5 9.5 1.0 
-SLOPE A/78/N A/99/N 0 25 -1.0 
-WELL A/3/N A/126/N 3.5 9.5 1.0 
-SLOPE A/3/N A/126/N 3.5 9.5 1.0 
-SLOPE A/3/N A/126/N 0 25 -1.0 
-WELL A/1/N A/128/N 3.5 9.5 1.0 
-SLOPE A/1/N A/128/N 3.5 9.5 1.0 
-SLOPE A/1/N A/128/N 0 25 -1.0 
-WELL A/70/N A/105/N 3.5 9.5 1.0 
-SLOPE A/70/N A/105/N 3.5 9.5 1.0 
-SLOPE A/70/N A/105/N 0 25 -1.0 
-WELL A/8/N A/120/N 3.5 9.5 1.0 
-SLOPE A/8/N A/120/N 3.5 9.5 1.0 
-SLOPE A/8/N A/120/N 0 25 -1.0 
-WELL A/22/N A/53/N 3.5 9.5 1.0 
-SLOPE A/22/N A/53/N 3.5 9.5 1.0 
-SLOPE A/22/N A/53/N 0 25 -1.0 
-WELL A/66/N A/109/N 3.5 9.5 1.0 
-SLOPE A/66/N A/109/N 3.5 9.5 1.0 
-SLOPE A/66/N A/109/N 0 25 -1.0 
-WELL A/67/N A/108/N 3.5 9.5 1.0 
-SLOPE A/67/N A/108/N 3.5 9.5 1.0 
-SLOPE A/67/N A/108/N 0 25 -1.0 
-WELL A/84/N A/93/N 3.5 9.5 1.0 
-SLOPE A/84/N A/93/N 3.5 9.5 1.0 
-SLOPE A/84/N A/93/N 0 25 -1.0 
-WELL A/69/N A/106/N 3.5 9.5 1.0 
-SLOPE A/69/N A/106/N 3.5 9.5 1.0 
-SLOPE A/69/N A/106/N 0 25 -1.0 
-WELL A/85/N A/92/N 3.5 9.5 1.0 
-SLOPE A/85/N A/92/N 3.5 9.5 1.0 
-SLOPE A/85/N A/92/N 0 25 -1.0 
-WELL A/77/N A/100/N 3.5 9.5 1.0 
-SLOPE A/77/N A/100/N 3.5 9.5 1.0 
-SLOPE A/77/N A/100/N 0 25 -1.0 
-WELL A/68/N A/107/N 3.5 9.5 1.0 
-SLOPE A/68/N A/107/N 3.5 9.5 1.0 
-SLOPE A/68/N A/107/N 0 25 -1.0 
-WELL A/86/N A/91/N 3.5 9.5 1.0 
-SLOPE A/86/N A/91/N 3.5 9.5 1.0 
-SLOPE A/86/N A/91/N 0 25 -1.0 
-WELL A/65/N A/110/N 3.5 9.5 1.0 
-SLOPE A/65/N A/110/N 3.5 9.5 1.0 
-SLOPE A/65/N A/110/N 0 25 -1.0 
-WELL A/58/N A/64/N 3.5 9.5 1.0 
-SLOPE A/58/N A/64/N 3.5 9.5 1.0 
-SLOPE A/58/N A/64/N 0 25 -1.0 
-WELL A/79/N A/98/N 3.5 9.5 1.0 
-SLOPE A/79/N A/98/N 3.5 9.5 1.0 
-SLOPE A/79/N A/98/N 0 25 -1.0 
-WELL A/2/N A/127/N 3.5 9.5 1.0 
-SLOPE A/2/N A/127/N 3.5 9.5 1.0 
-SLOPE A/2/N A/127/N 0 25 -1.0 
-WELL A/71/N A/104/N 3.5 9.5 1.0 
-SLOPE A/71/N A/104/N 3.5 9.5 1.0 
-SLOPE A/71/N A/104/N 0 25 -1.0 
-WELL A/76/N A/101/N 3.5 9.5 1.0 
-SLOPE A/76/N A/101/N 3.5 9.5 1.0 
-SLOPE A/76/N A/101/N 0 25 -1.0 
-WELL A/82/N A/87/N 3.5 9.5 1.0 
-SLOPE A/82/N A/87/N 3.5 9.5 1.0 
-SLOPE A/82/N A/87/N 0 25 -1.0 
-WELL A/32/N A/41/N 3.5 9.5 1.0 
-SLOPE A/32/N A/41/N 3.5 9.5 1.0 
-SLOPE A/32/N A/41/N 0 25 -1.0 
-WELL A/8/N A/17/N 3.5 9.5 1.0 
-SLOPE A/8/N A/17/N 3.5 9.5 1.0 
-SLOPE A/8/N A/17/N 0 25 -1.0 
-WELL A/117/N A/122/N 3.5 9.5 1.0 
-SLOPE A/117/N A/122/N 3.5 9.5 1.0 
-SLOPE A/117/N A/122/N 0 25 -1.0 
-WELL A/93/N A/100/N 3.5 9.5 1.0 
-SLOPE A/93/N A/100/N 3.5 9.5 1.0 
-SLOPE A/93/N A/100/N 0 25 -1.0 
-WELL A/81/N A/97/N 3.5 9.5 1.0 
-SLOPE A/81/N A/97/N 3.5 9.5 1.0 
-SLOPE A/81/N A/97/N 0 25 -1.0 
-WELL A/75/N A/102/N 3.5 9.5 1.0 
-SLOPE A/75/N A/102/N 3.5 9.5 1.0 
-SLOPE A/75/N A/102/N 0 25 -1.0 
-WELL A/118/N A/123/N 3.5 9.5 1.0 
-SLOPE A/118/N A/123/N 3.5 9.5 1.0 
-SLOPE A/118/N A/123/N 0 25 -1.0 
-WELL A/90/N A/96/N 3.5 9.5 1.0 
-SLOPE A/90/N A/96/N 3.5 9.5 1.0 
-SLOPE A/90/N A/96/N 0 25 -1.0 
-WELL A/23/N A/53/N 3.5 9.5 1.0 
-SLOPE A/23/N A/53/N 3.5 9.5 1.0 
-SLOPE A/23/N A/53/N 0 25 -1.0 
-WELL A/77/N A/84/N 3.5 9.5 1.0 
-SLOPE A/77/N A/84/N 3.5 9.5 1.0 
-SLOPE A/77/N A/84/N 0 25 -1.0 
-WELL A/34/N A/42/N 3.5 9.5 1.0 
-SLOPE A/34/N A/42/N 3.5 9.5 1.0 
-SLOPE A/34/N A/42/N 0 25 -1.0 
-WELL A/33/N A/41/N 3.5 9.5 1.0 
-SLOPE A/33/N A/41/N 3.5 9.5 1.0 
-SLOPE A/33/N A/41/N 0 25 -1.0 
-WELL A/84/N A/100/N 3.5 9.5 1.0 
-SLOPE A/84/N A/100/N 3.5 9.5 1.0 
-SLOPE A/84/N A/100/N 0 25 -1.0 
-WELL A/26/N A/48/N 3.5 9.5 1.0 
-SLOPE A/26/N A/48/N 3.5 9.5 1.0 
-SLOPE A/26/N A/48/N 0 25 -1.0 
-WELL A/11/N A/17/N 3.5 9.5 1.0 
-SLOPE A/11/N A/17/N 3.5 9.5 1.0 
-SLOPE A/11/N A/17/N 0 25 -1.0 
-WELL A/77/N A/88/N 3.5 9.5 1.0 
-SLOPE A/77/N A/88/N 3.5 9.5 1.0 
-SLOPE A/77/N A/88/N 0 25 -1.0 
-WELL A/35/N A/49/N 3.5 9.5 1.0 
-SLOPE A/35/N A/49/N 3.5 9.5 1.0 
-SLOPE A/35/N A/49/N 0 25 -1.0 
-WELL A/6/N A/14/N 3.5 9.5 1.0 
-SLOPE A/6/N A/14/N 3.5 9.5 1.0 
-SLOPE A/6/N A/14/N 0 25 -1.0 
-WELL A/51/N A/57/N 3.5 9.5 1.0 
-SLOPE A/51/N A/57/N 3.5 9.5 1.0 
-SLOPE A/51/N A/57/N 0 25 -1.0 
-WELL A/31/N A/46/N 3.5 9.5 1.0 
-SLOPE A/31/N A/46/N 3.5 9.5 1.0 
-SLOPE A/31/N A/46/N 0 25 -1.0 
-WELL A/72/N A/99/N 3.5 9.5 1.0 
-SLOPE A/72/N A/99/N 3.5 9.5 1.0 
-SLOPE A/72/N A/99/N 0 25 -1.0 
-WELL A/112/N A/120/N 3.5 9.5 1.0 
-SLOPE A/112/N A/120/N 3.5 9.5 1.0 
-SLOPE A/112/N A/120/N 0 25 -1.0 
-WELL A/120/N A/128/N 3.5 9.5 1.0 
-SLOPE A/120/N A/128/N 3.5 9.5 1.0 
-SLOPE A/120/N A/128/N 0 25 -1.0 
-WELL A/74/N A/79/N 3.5 9.5 1.0 
-SLOPE A/74/N A/79/N 3.5 9.5 1.0 
-SLOPE A/74/N A/79/N 0 25 -1.0