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Commit 81b9282f authored by Christian Faber's avatar Christian Faber
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start from one patch

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2nbx.pdb 0 → 100644
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example_contact_mapping.py
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...@@ -8,13 +8,15 @@ from matplotlib.patches import Rectangle ...@@ -8,13 +8,15 @@ from matplotlib.patches import Rectangle
def main(): def main():
test_pdb = Cmap() test_pdb = Cmap()
test_pdb.load_native_pdb("1c2x.pdb") test_pdb.load_native_pdb("4gma.pdb", start_from_one=True)
test2_pdb = Cmap() print(test_pdb.positioning)
test2_pdb.load_native_pdb("4gma.pdb") print(test_pdb.num_to_id(1))
print(test_pdb.positioning, test_pdb.l, test_pdb.native_contacts.shape) print(test_pdb.positioning, test_pdb.l, test_pdb.native_contacts.shape)
test_pdb.load_contacts_from_restraints("simrna_1c2x_L0.5.res", "DCA") test_pdb.load_contacts_from_restraints("simrna_4gma_L0.5.res", "DCA")
test2_pdb.load_contacts_from_restraints("simrna_4gma_L0.5.res", "DCA") print(test_pdb.ppvs["DCA"])
print(test_pdb.get_unmodelled_regions(), test_pdb.ppvs["DCA"])
# print(test_pdb.get_unmodelled_regions(), test_pdb.ppvs["DCA"])
fig, ax = show_contact_map(test_pdb, ["DCA"], mark_match=True) fig, ax = show_contact_map(test_pdb, ["DCA"], mark_match=True)
plt.show() plt.show()
......
setup.py
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...@@ -5,7 +5,7 @@ with open("README.md", "r") as f: ...@@ -5,7 +5,7 @@ with open("README.md", "r") as f:
setup( setup(
name="BioHelpers_FABER", name="BioHelpers_FABER",
version="0.1.17", version="0.1.18",
description="Small collection of useful scripts for the computational work with RNA Data.", description="Small collection of useful scripts for the computational work with RNA Data.",
url="https://gitlab.jsc.fz-juelich.de/faber1/biohelpers", url="https://gitlab.jsc.fz-juelich.de/faber1/biohelpers",
package_dir={"": "src"}, package_dir={"": "src"},
......
simrna_2nbx_L0.5.res 0 → 100644
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src/BioHelpers_FABER/cmap.py
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...@@ -66,7 +66,7 @@ class Cmap: ...@@ -66,7 +66,7 @@ class Cmap:
if start_from_one: if start_from_one:
self.positioning.insert(0, 0) self.positioning.insert(0, 0)
self.positioning.insert(0, 0) self.positioning.insert(0, 0)
self.l = self.positioning[-1] - self.positioning[0] self.l = self.positioning[-1] - self.positioning[0] + 1 * (not start_from_one)
chain = next(pdb.PDBParser().get_structure(id, filename)[0].get_chains()) chain = next(pdb.PDBParser().get_structure(id, filename)[0].get_chains())
bm.cleanup_chain(chain) bm.cleanup_chain(chain)
self.native_contacts = np.zeros((len(chain), len(chain))) self.native_contacts = np.zeros((len(chain), len(chain)))
...@@ -77,8 +77,8 @@ class Cmap: ...@@ -77,8 +77,8 @@ class Cmap:
self.contacts["native"] = np.zeros((self.l, self.l)) self.contacts["native"] = np.zeros((self.l, self.l))
for c in bm.arr_to_contact_list(self.native_contacts): for c in bm.arr_to_contact_list(self.native_contacts):
self.contacts["native"][ self.contacts["native"][
self.num_to_id(c[0]) - self.positioning[0], self.num_to_id(c[0]) - self.positioning[0] - 1 * (not start_from_one),
self.num_to_id(c[1]) - self.positioning[0], self.num_to_id(c[1]) - self.positioning[0] - 1 * (not start_from_one),
] = 1 ] = 1
self.pdb_id = id self.pdb_id = id
...@@ -123,6 +123,7 @@ class Cmap: ...@@ -123,6 +123,7 @@ class Cmap:
with open(filename, "r") as file: with open(filename, "r") as file:
data = file.readlines() data = file.readlines()
list_of_contacts = self.simrna_restraints_to_contacts(data) list_of_contacts = self.simrna_restraints_to_contacts(data)
print(self.l)
matrix_of_contacts = np.zeros((self.l, self.l)) matrix_of_contacts = np.zeros((self.l, self.l))
for c in list_of_contacts: for c in list_of_contacts:
matrix_of_contacts[c[0] - 1, c[1] - 1] = 1 matrix_of_contacts[c[0] - 1, c[1] - 1] = 1
......
src/BioHelpers_FABER/visualisation.py
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...@@ -179,8 +179,8 @@ def show_contact_map( ...@@ -179,8 +179,8 @@ def show_contact_map(
**kwargs, **kwargs,
) )
ax.set_aspect("equal") ax.set_aspect("equal")
ax.set_ylim([0, cm.l]) ax.set_ylim([cm.positioning[0], cm.positioning[-1]])
ax.set_xlim([0, cm.l]) ax.set_xlim([cm.positioning[0], cm.positioning[-1]])
if mark_match: if mark_match:
tp = [] tp = []
fp = [] fp = []
......
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