From 61416f2a86982c744e672084ae40076807a403b0 Mon Sep 17 00:00:00 2001 From: JHKru Date: Fri, 27 Sep 2024 17:27:31 +0200 Subject: [PATCH] Switched mmtf -> bcif in examples --- doc/examples/scripts/basic_nma.py | 8 ++++---- doc/examples/scripts/normal_mode.py | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/doc/examples/scripts/basic_nma.py b/doc/examples/scripts/basic_nma.py index 2b35732..0d55168 100644 --- a/doc/examples/scripts/basic_nma.py +++ b/doc/examples/scripts/basic_nma.py @@ -12,15 +12,15 @@ import biotite import biotite.database.rcsb as rcsb import biotite.structure as struc -import biotite.structure.io.mmtf as mmtf +import biotite.structure.io.pdbx as pdbx import matplotlib.pyplot as plt import numpy as np import springcraft # Fetch G:T/U Mismatch-specific DNA glycosylase from E. coli PDB_ID = "1MUG" -mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf")) -whole_structure = mmtf.get_structure(mmtf_file, model=1, include_bonds=True) +bcif_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif")) +whole_structure = pdbx.get_structure(bcif_file, model=1, include_bonds=True) protein = whole_structure[struc.filter_amino_acids(whole_structure)] ca = protein[(protein.atom_name == "CA") & (protein.element == "C")] @@ -39,7 +39,7 @@ freq = eanm.frequencies()[6:106] ## Plot -fig = plt.figure(figsize=(8.0, 8.0), constrained_layout=True) +fig = plt.figure(figsize=(8.0, 8.0), constrained_layout=True, dpi=300) grid = fig.add_gridspec(nrows=2, ncols=2) ax00 = fig.add_subplot(grid[0, 0]) diff --git a/doc/examples/scripts/normal_mode.py b/doc/examples/scripts/normal_mode.py index cbb8a7a..f2a7f26 100644 --- a/doc/examples/scripts/normal_mode.py +++ b/doc/examples/scripts/normal_mode.py @@ -12,7 +12,7 @@ import ammolite import biotite.database.rcsb as rcsb import biotite.structure as struc -import biotite.structure.io.mmtf as mmtf +import biotite.structure.io.pdbx as pdbx import numpy as np import springcraft @@ -31,8 +31,8 @@ # Load structure -mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf")) -structure = mmtf.get_structure(mmtf_file, model=1, include_bonds=True) +bcif_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif")) +structure = pdbx.get_structure(bcif_file, model=1, include_bonds=True) # Filter first peptide chain protein_chain = structure[