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Basic support for phosphorylated residues

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Jérôme Tubiana
2021-10-25 12:32:14 +03:00
parent 4b54b5de99
commit 8cb616a6ee
2 changed files with 8 additions and 6 deletions
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10
preprocessing/PDB_processing.py
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@@ -9,14 +9,14 @@ from Bio.PDB.ResidueDepth import _read_vertex_array, _get_atom_radius
import tempfile
from utilities.paths import structures_folder,path_to_dssp,path_to_msms
from preprocessing.protein_chemistry import list_atoms,list_atoms_types,VanDerWaalsRadii,atom_mass,atom_type_to_index,atom_to_index,index_to_type,atom_type_mass
from preprocessing.protein_chemistry import residue_dictionary
from preprocessing.protein_chemistry import residue_dictionary,hetresidue_field
from preprocessing import PDBio
#%% Functions for parsing PDB files.
def is_residue(residue):
try:
return (residue.get_id()[0] == ' ') & (residue.resname in residue_dictionary.keys())
return (residue.get_id()[0] in hetresidue_field) & (residue.resname in residue_dictionary.keys())
except:
return False
@@ -24,7 +24,7 @@ def is_residue(residue):
def is_heavy_atom(atom):
# Second condition for Rosetta-generated files.
try:
return (atom.get_id()[0] in atom_type_to_index.keys()) & (atom.get_id() != 'CEN')
return (atom.get_id() in atom_to_index.keys() )
except:
return False
@@ -57,9 +57,9 @@ def process_chain(chain):
residue_atom_coordinates = np.array(
[atom.get_coord() for atom in residue if is_heavy_atom(atom)])
residue_atoms = [atom_to_index[atom.get_id()]
for atom in residue if is_heavy_atom(atom)]
for atom in residue if is_heavy_atom(atom) ]
residue_atom_type = [atom_type_to_index[atom.get_id()[0]]
for atom in residue if is_heavy_atom(atom)]
for atom in residue if is_heavy_atom(atom) ]
residue_backbone_coordinates = []
for atom in ['N', 'C', 'CA', 'O', 'CB']:
try:

4
preprocessing/protein_chemistry.py
View File

@@ -78,12 +78,14 @@ residue_dictionary = {'CYS': 'C', 'ASP': 'D', 'SER': 'S', 'GLN': 'Q', 'LYS': 'K'
'ALA': 'A', 'VAL': 'V', 'GLU': 'E', 'TYR': 'Y', 'MET': 'M',
'MSE': 'M',
'PTR':'Y',
'TYS':'Y',
'SEP':'S',
'TPO':'T',
'HIP':'H',
'MSE':'M'
}
hetresidue_field = [' '] + ['H_%s'%name for name in residue_dictionary.keys()]
aa_to_index = dict([(list_aa[i],i) for i in range(20)])
'''