Skip to content

Use one-based indexing in final PDB output #6

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ray-berkeley wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Use one-based indexing in final PDB output #6

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 9 additions & 10 deletions dodo/pdb_tools.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -607,30 +607,30 @@ def save_pdb_from_PDBParserObj(PDBParserObj, out_path,
if atom=='CA':
xyz_list.append(all_coords[aa][atom])
residue_names.append(PDBParserObj.sequence_3aa_by_index[aa]['CA'])
residue_indices.append(aa)
atom_indices.append(aa)
residue_indices.append(aa + 1)
atom_indices.append(len(atom_indices) + 1)
atom_names.append('CA')
beta_vals.append(PDBParserObj.beta_vals_by_index[aa])
if aa < len(PDBParserObj.sequence)-1:
CONECT_COORDS.append([aa, aa+1])
if aa != aa_range[-1]:
CONECT_COORDS.append([len(atom_indices), len(atom_indices) + 1])
else:
cur_atoms = all_coords[aa]
for atom in cur_atoms:

xyz_list.append(all_coords[aa][atom])
residue_names.append(PDBParserObj.sequence_3aa_by_index[aa][atom])
residue_indices.append(aa)
atom_indices.append(atom_count)
residue_indices.append(aa + 1)
atom_indices.append(atom_count + 1)
atom_names.append(atom)
beta_vals.append(PDBParserObj.beta_vals_by_index[aa])
# only conect N-CA-C because this is for the IDR.
if atom_count < PDBParserObj.number_atoms:
if atom == 'CA':
all_connect_atoms[atom_count]=atom
all_connect_atoms[atom_count + 1]=atom
if atom == 'C':
all_connect_atoms[atom_count]=atom
all_connect_atoms[atom_count + 1]=atom
if atom=='N':
all_connect_atoms[atom_count]=atom
all_connect_atoms[atom_count + 1]=atom
atom_count+=1


Expand Down Expand Up @@ -666,4 +666,3 @@ def save_pdb_from_PDBParserObj(PDBParserObj, out_path,
atom_names=atom_names, residue_indices=residue_indices,
residue_names=residue_names, beta=beta_vals,CONECT_LINES=None,
add_mode='w', model_num=1, last_model=True)