Skip to content
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

feat: take into account [ atomtype ] section when including itp files #24

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

feat: take into account [ atomtype ] section when including itp files #24

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
92 changes: 81 additions & 11 deletions biobb_gromacs/gromacs_extra/append_ligand.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ def launch(self) -> int:

forcefield_pattern = r"#include.*forcefield.itp\""
if top_lines:
for index, line in enumerate(top_lines):
for ff_index, line in enumerate(top_lines):
if re.search(forcefield_pattern, line):
break
else:
Expand All @@ -114,22 +114,88 @@ def launch(self) -> int:
self.global_log,
)
return 1

ligand_itp_path = self.io_dict["in"].get("input_itp_path")

# Read ligand itp contents
with open(ligand_itp_path, 'r') as itp_file:
ligand_itp_contents = itp_file.readlines()

# Separate ligand [ atomtypes ] section from the rest
lig_atomtypes_section = []
remaining_itp_contents = []
in_atomtypes_section = False
for line in ligand_itp_contents:
if line.strip().startswith("[ atomtypes ]"):
in_atomtypes_section = True
lig_atomtypes_section.append(line)
elif in_atomtypes_section:
if line.strip() == "" or line.startswith("["):
in_atomtypes_section = False
remaining_itp_contents.append(line)
else:
lig_atomtypes_section.append(line)
else:
remaining_itp_contents.append(line)

# If the ligand itp contains an [ atomtypes ] section, merge it into the main topology
if lig_atomtypes_section:

# Look for the [ atomtypes ] section in the main topology
top_atomtypes_section = []
in_atomtypes_section = False
for line in top_lines:
if line.strip().startswith("[ atomtypes ]"):
in_atomtypes_section = True
top_atomtypes_section.append(line)
elif in_atomtypes_section:
if line.strip() == "" or line.startswith("["):
in_atomtypes_section = False
else:
top_atomtypes_section.append(line)

# If there is already an [ atomtypes ] section in the main topology
if top_atomtypes_section:

# Remove the header and comments of the ligand [ atomtypes ] section
lig_atomtypes_section = lig_atomtypes_section[2:]

# Remove the [ atomtypes ] section from top_lines
top_lines = [line for line in top_lines if line not in top_atomtypes_section]

# NOTE: Check for repeated atoms in the [ atomtypes ] section
# NOTE: raise error if there are conflicts - atoms named equally with different parameters
# NOTE: raise error if there are different number of columns in the atomtypes sections

top_lines.insert(ff_index + 1, "\n")

# Merge both [ atomtypes ] sections
atomtype_section = top_atomtypes_section + lig_atomtypes_section

# Write the merged [ atomtypes ] section into the main topology after the forcefield include
for atomtype_index in range(len(atomtype_section)):
top_lines.insert(ff_index + atomtype_index + 2, atomtype_section[atomtype_index])

# Update the index for the remaining directives
at_index = ff_index + atomtype_index + 2
else:
at_index = ff_index

top_lines.insert(index + 1, "\n")
top_lines.insert(index + 2, "; Including ligand ITP\n")
top_lines.insert(index + 3, '#include "' + itp_name + '"\n')
top_lines.insert(index + 4, "\n")
top_lines.insert(at_index + 1, "\n")
top_lines.insert(at_index + 2, "; Including ligand ITP\n")
top_lines.insert(at_index + 3, '#include "' + itp_name + '"\n')
top_lines.insert(at_index + 4, "\n")
if self.io_dict["in"].get("input_posres_itp_path"):
top_lines.insert(index + 5, "; Ligand position restraints" + "\n")
top_lines.insert(index + 6, "#ifdef " + self.posres_name + "\n")
top_lines.insert(at_index + 5, "; Ligand position restraints" + "\n")
top_lines.insert(at_index + 6, "#ifdef " + self.posres_name + "\n")
top_lines.insert(
index + 7,
at_index + 7,
'#include "'
+ str(Path(self.io_dict["in"].get("input_posres_itp_path", "")).name)
+ '"\n',
)
top_lines.insert(index + 8, "#endif" + "\n")
top_lines.insert(index + 9, "\n")
top_lines.insert(at_index + 8, "#endif" + "\n")
top_lines.insert(at_index + 9, "\n")

inside_moleculetype_section = False
with open(self.io_dict["in"].get("input_itp_path", "")) as itp_file:
Expand Down Expand Up @@ -171,7 +237,11 @@ def launch(self) -> int:
with open(new_top, "w") as new_top_f:
new_top_f.write("".join(top_lines))

shutil.copy2(self.io_dict["in"].get("input_itp_path", ""), top_dir)
# Create a new itp ligand file without the [ atomtypes ] section
new_ligand_tip_path = str(Path(top_dir) / itp_name)
with open(new_ligand_tip_path, 'w') as new_itp_file:
new_itp_file.write("".join(remaining_itp_contents))

if self.io_dict["in"].get("input_posres_itp_path"):
shutil.copy2(self.io_dict["in"].get("input_posres_itp_path", ""), top_dir)

Expand Down