Remove MMTF usage

doc/examples/scripts/structure/adjacency_matrix.py

@@ -5,7 +5,7 @@
 In this example we create an adjacency matrix of the CA atoms in the
 lysozyme crystal structure (PDB: 1AKI).
 The values in the adjacency matrix ``m`` are
-``m[i,j] = 1 if distance(i,j) <= threshold else 0``. 
+``m[i,j] = 1 if distance(i,j) <= threshold else 0``.
 """
 
 # Code source: Patrick Kunzmann
@@ -16,12 +16,11 @@
 import biotite.structure as struc
 import biotite.structure.io as strucio
 import biotite.database.rcsb as rcsb
-import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.colors import ListedColormap
 
 
-file_name = rcsb.fetch("1aki", "mmtf", gettempdir())
+file_name = rcsb.fetch("1aki", "bcif", gettempdir())
 array = strucio.load_structure(file_name)
 # We only consider CA atoms
 ca = array[array.atom_name == "CA"]

doc/examples/scripts/structure/contact_sites.py

@@ -15,7 +15,7 @@
 
 import numpy as np
 import biotite.structure as struc
-import biotite.structure.io.mmtf as mmtf
+import biotite.structure.io.pdbx as pdbx
 import biotite.database.rcsb as rcsb
 
 
@@ -25,8 +25,8 @@
 
 
 # Fetch and load structure
-mmtf_file = mmtf.MMTFFile.read(rcsb.fetch("2or1", "mmtf"))
-structure = mmtf.get_structure(mmtf_file, model=1)
+pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("2or1", "bcif"))
+structure = pdbx.get_structure(pdbx_file, model=1)
 
 
 # Separate structure into the DNA and the two identical protein chains

doc/examples/scripts/structure/diameter.py

@@ -16,7 +16,7 @@
 import biotite.database.rcsb as rcsb
 
 def get_diameter(pdb_id):
-    file_name = rcsb.fetch(pdb_id, "mmtf", gettempdir())
+    file_name = rcsb.fetch(pdb_id, "bcif", gettempdir())
     atom_array = strucio.load_structure(file_name)
     # Remove all non-amino acids
     atom_array = atom_array[struc.filter_amino_acids(atom_array)]

doc/examples/scripts/structure/disulfide_bonds.py

@@ -17,14 +17,14 @@
 # Code source: Patrick Kunzmann
 # License: BSD 3 clause
 
+import io
 from tempfile import gettempdir
 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.patches as patches
 import biotite.sequence as seq
 import biotite.structure as struc
-import biotite.structure.io as strucio
-import biotite.structure.io.mmtf as mmtf
+import biotite.structure.io.pdbx as pdbx
 import biotite.database.rcsb as rcsb
 
 
@@ -96,18 +96,18 @@ def detect_disulfide_bonds(structure, distance=2.05, distance_tol=0.05,
 # (PDB: `2IT7 <http://www.rcsb.org/structure/2IT7>`_).
 # This motif is famous for its three characteristic disulfide bridges
 # forming a 'knot'.
-# However, the loaded MMTF file already has information about the
-# covalent bonds - including the disulfide bridges.
+# However, the loaded PDBx file already has information about the
+# the disulfide bridges.
 # To have a proper test case, all disulfide bonds are removed from the
 # structure and we pretend that the structure never had information
 # about the disulfide bonds.
-# For later verification that the implemented function wroks correctly,
+# For later verification that the implemented function works correctly,
 # the disulfide bonds, that are removed, are printed out.
 
-mmtf_file = mmtf.MMTFFile.read(
-    rcsb.fetch("2IT7", "mmtf", gettempdir())
+pdbx_file = pdbx.BinaryCIFFile.read(
+    rcsb.fetch("2IT7", "bcif", gettempdir())
 )
-knottin = mmtf.get_structure(mmtf_file, include_bonds=True, model=1)
+knottin = pdbx.get_structure(pdbx_file, include_bonds=True, model=1)
 sulfide_indices = np.where(
     (knottin.res_name == "CYS") & (knottin.atom_name == "SG")
 )[0]
@@ -175,8 +175,9 @@ def detect_disulfide_bonds(structure, distance=2.05, distance_tol=0.05,
     knottin.bonds.add_bond(sg1_index, sg2_index, struc.BondType.SINGLE)
 # The structure with added disulfide bonds
 # could now be written back into a structure file
-# At the moment, Biotite only supports bond input/outpout in MMTF files
 #
-# strucio.save_structure("structure_with_disulfide_bonds.mmtf", knottin)
+out_file = pdbx.BinaryCIFFile()
+pdbx.set_structure(out_file, knottin)
+out_file.write(io.BytesIO())
 
 plt.show()

doc/examples/scripts/structure/docking.py

@@ -33,18 +33,17 @@
 from scipy.stats import spearmanr
 import biotite.structure as struc
 import biotite.structure.info as info
-import biotite.structure.io.mmtf as mmtf
-import biotite.structure.graphics as graphics
+import biotite.structure.io.pdbx as pdbx
 import biotite.database.rcsb as rcsb
 import biotite.application.autodock as autodock
 
 
 # Get the receptor structure
 # and the original 'correct' conformation of the ligand
-mmtf_file = mmtf.MMTFFile.read(rcsb.fetch("2RTG", "mmtf"))
-structure = mmtf.get_structure(
+pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("2RTG", "bcif"))
+structure = pdbx.get_structure(
     # Include formal charge for accurate partial charge calculation
-    mmtf_file, model=1, include_bonds=True, extra_fields=["charge"]
+    pdbx_file, model=1, include_bonds=True, extra_fields=["charge"]
 )
 # The asymmetric unit describes a streptavidin homodimer
 # However, we are only interested in a single monomer

doc/examples/scripts/structure/domain_hbonds.py

@@ -20,7 +20,7 @@
 import biotite.database.rcsb as rcsb
 
 
-file_name = rcsb.fetch("2KB1", "mmtf", gettempdir())
+file_name = rcsb.fetch("2KB1", "bcif", gettempdir())
 stack = strucio.load_structure(file_name)
 # Four identical chains, consider only chain A
 chain_a = stack[:, stack.chain_id == "A"]

doc/examples/scripts/structure/gap_bars.py

@@ -16,7 +16,6 @@
 # License: BSD 3 clause
 
 from tempfile import gettempdir
-import biotite.structure as struc
 import biotite.structure.io as strucio
 import biotite.database.rcsb as rcsb
 import matplotlib.pyplot as plt
@@ -25,7 +24,7 @@
 
 def plot_gaps(pdb_id, chain_id, ax):
     # Download and parse structure file
-    path = rcsb.fetch(pdb_id, "mmtf", gettempdir())
+    path = rcsb.fetch(pdb_id, "bcif", gettempdir())
     atom_array = strucio.load_structure(path)
     # Consider only one chain
     atom_array = atom_array[atom_array.chain_id == chain_id]
@@ -43,7 +42,7 @@ def plot_gaps(pdb_id, chain_id, ax):
         else:
             # existing
             states[i] = 2
-    
+
     # Find the intervals for each state
     state_intervals = []
     curr_state = None
@@ -58,7 +57,7 @@ def plot_gaps(pdb_id, chain_id, ax):
                 curr_start = i
                 curr_state = states[i]
     state_intervals.append((curr_start, i, curr_state))
-    
+
     # Draw the state intervals as colored rectangles
     for interval in state_intervals:
         start = interval[0]

doc/examples/scripts/structure/glycan_visualization.py

@@ -25,8 +25,7 @@
 from networkx.drawing.nx_pydot import graphviz_layout
 import biotite.sequence as seq
 import biotite.structure as struc
-import biotite.structure.info as info
-import biotite.structure.io.mmtf as mmtf
+import biotite.structure.io.pdbx as pdbx
 import biotite.database.rcsb as rcsb
 
 
@@ -113,60 +112,60 @@
     "All": ("o", "purple"),
     "Tal": ("o", "lightsteelblue"),
     "Ido": ("o", "chocolate"),
-    
+
     "GlcNAc": ("s", "royalblue"),
     "ManNAc": ("s", "forestgreen"),
     "GalNAc": ("s", "gold"),
     "GulNAc": ("s", "darkorange"),
     "AllNAc": ("s", "purple"),
     "IdoNAc": ("s", "chocolate"),
-    
+
     "GlcN": ("1", "royalblue"),
     "ManN": ("1", "forestgreen"),
     "GalN": ("1", "gold"),
-    
+
     "GlcA": ("v", "royalblue"),
     "ManA": ("v", "forestgreen"),
     "GalA": ("v", "gold"),
     "GulA": ("v", "darkorange"),
     "TalA": ("v", "lightsteelblue"),
     "IdoA": ("v", "chocolate"),
-    
+
     "Qui": ("^", "royalblue"),
     "Rha": ("^", "forestgreen"),
     "6dGul": ("^", "darkorange"),
     "Fuc": ("^", "crimson"),
-    
+
     "QuiNAc": ("P", "royalblue"),
     "FucNAc": ("P", "crimson"),
-    
+
     "Oli": ("X", "royalblue"),
     "Tyv": ("X", "forestgreen"),
     "Abe": ("X", "darkorange"),
     "Par": ("X", "pink"),
     "Dig": ("X", "purple"),
-    
+
     "Ara": ("*", "forestgreen"),
     "Lyx": ("*", "gold"),
     "Xyl": ("*", "darkorange"),
     "Rib": ("*", "pink"),
-    
+
     "Kdn": ("D", "forestgreen"),
     "Neu5Ac": ("D", "mediumvioletred"),
     "Neu5Gc": ("D", "turquoise"),
-    
+
     "LDManHep": ("H", "forestgreen"),
     "Kdo": ("H", "gold"),
     "DDManHep": ("H", "pink"),
     "MurNAc": ("H", "purple"),
     "Mur": ("H", "chocolate"),
-    
+
     "Api": ("p", "royalblue"),
     "Fru": ("p", "forestgreen"),
     "Tag": ("p", "gold"),
     "Sor": ("p", "darkorange"),
     "Psi": ("p", "pink"),
-    
+
     # Default representation
     None: ("h", "black")
 }
@@ -183,8 +182,8 @@
 
 PDB_ID = "4CUO"
 
-mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf"))
-structure = mmtf.get_structure(mmtf_file, model=1, include_bonds=True)
+pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif"))
+structure = pdbx.get_structure(pdbx_file, model=1, include_bonds=True)
 
 # Create masks identifying whether an atom is part of a glycan...
 is_glycan = np.isin(structure.res_name, list(SACCHARIDE_NAMES.keys()))
@@ -239,7 +238,7 @@
 # So far, so good. We can already see glycans (red) on the long peptide
 # chain (blue).
 # The surrounding single nodes belong to water, ions etc.
-# In the final plot only the glycans should be highlighted. 
+# In the final plot only the glycans should be highlighted.
 # For this purpose the edges between all non-saccharides will be
 # removed.
 # The remaining subgraphs are either single nodes,
@@ -299,7 +298,7 @@
         [(min(atom_i, atom_j), max(atom_i, atom_j))
          for atom_i, atom_j in glycan_graph.edges()]
     )
-    
+
     # The 'root' is the amino acid
     root = [
         atom_i for atom_i in glycan_graph.nodes() if is_amino_acid[atom_i]
@@ -342,18 +341,18 @@
     pos_array[:,0] += structure.res_id[root]
     # Convert array back to dictionary
     pos = {node: tuple(coord) for node, coord in zip(nodes, pos_array)}
-    
+
     nx.draw_networkx_edges(
         glycan_graph, pos, ax=ax,
         arrows=False, node_size=0, width=LINE_WIDTH
     )
-    
+
     # Draw each node individually
     for atom_i in glycan_graph.nodes():
         # Only plot glycans, not amino acids
         if not is_glycan[atom_i]:
             continue
-        
+
         # Now the above data sets come into play
         common_name = SACCHARIDE_NAMES.get(structure.res_name[atom_i])
         shape, color = SACCHARIDE_REPRESENTATION[common_name]
@@ -388,7 +387,7 @@
 # Set the end of the axis to the last amino acid
 ax.set_xlim(1, np.max(structure.res_id[is_amino_acid]))
 ax.set_ylim(0, 7)
-ax.set_title(mmtf_file["title"])
+ax.set_title(pdbx_file.block["struct"]["title"].as_item())
 fig.tight_layout()
 
 # sphinx_gallery_thumbnail_number = 2