Merge pull request #145 from talagayev/fix_last_frame

Fix last frame modified

Author: talagayev

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,15 @@
+---
+name: Bug report
+about: Create a report to tell about a bug or problem you encountered
+
+---
+
+## Bug Behavior ##
+
+<!-- A description of what happens. (Code to reproduce the behavior can be added below). Please check that your bug is consistently reproducable -->
+
+## Additional Information ##
+
+- Which OpenMMDL version are you using? (version displayed in `conda list` of your environment as `openmmdl`)
+- Which version of Python (`python -V`)?
+- Which operating system do you use?

.github/ISSUE_TEMPLATE/feature_suggestion.md

@@ -0,0 +1,14 @@
+---
+name: Feature request
+about: Suggest an idea or feature for OpenMMDL
+
+---
+
+## Describe the feature you would like to have ##
+<!-- A description of the feature you want to have. For example, I'd like to be able to do [...]. 
+You can also add code snippets how it can look like. -->
+
+
+## Additional context ##
+<!-- Add any other context, links of repositories that can be used for the feature 
+or screenshots about the feature request here. -->

.github/pull_request_template.md

@@ -0,0 +1,17 @@
+<!-- 
+Insert issue number that this PR fixes (if any) just after 'Fixes #'.
+If this PR does not fix an existing issue, consider opening one or remove 'Fixes #' from the PR description.
+-->
+Fixes #
+
+Changes made:
+<!-- Describe the changes that this PR makes. --> 
+-
+
+## PR Checklist
+<!-- Please use the following checklist to ensure the PR is ready to be reviewed/merged. -->
+ - [ ] Issue raised/referenced?
+ - [ ] Tests updated/added?
+ - [ ] Documentation updated/added?
+ - [ ] `CHANGELOG` file updated?
+ - [ ] Is your name in `AUTHORS`?

openmmdl/openmmdl_analysis/interaction_gathering.py

@@ -13,14 +13,15 @@
 
 class InteractionAnalyzer:
     def __init__(
-        self, pdb_md, dataframe, num_processes, lig_name, special_ligand, peptide
+        self, pdb_md, dataframe, num_processes, lig_name, special_ligand, peptide, md_len
     ):
         self.pdb_md = pdb_md
         self.dataframe = dataframe
         self.num_processes = num_processes
         self.lig_name = lig_name
         self.special = special_ligand
         self.peptide = peptide
+        self.md_len = md_len
         self.ineraction_list = self.process_trajectory()
 
     def characterize_complex(
@@ -386,15 +387,14 @@ def fill_missing_frames(self, df):
             pandas dataframe: DataFrame with placeholder values in the frames with no interactions.
         """
 
-        md_len = len(self.pdb_md.trajectory) - 1
         # Create a set containing all unique values in the 'FRAME' column
         existing_frames = set(df["FRAME"])
 
         # Create a list to store new rows for missing numbers
         missing_rows = []
 
         # Iterate through numbers from 0 to md_len
-        for frame_number in range(1, md_len):
+        for frame_number in range(1, self.md_len):
             if frame_number not in existing_frames:
                 # Create a new row with 'FRAME' set to the missing number and other columns set to "skip"
                 missing_row = {"FRAME": frame_number}
@@ -428,17 +428,16 @@ def process_trajectory(self):
         if self.dataframe is None:
             print("\033[1mProcessing protein-ligand trajectory\033[0m")
             print(f"\033[1mUsing {self.num_processes} CPUs\033[0m")
-            total_frames = len(self.pdb_md.trajectory) - 1
 
             with Pool(processes=self.num_processes) as pool:
                 frame_args = [
                     (i, self.pdb_md, self.lig_name, self.special, self.peptide)
-                    for i in range(1, total_frames + 1)
+                    for i in range(1, self.md_len)
                 ]
 
                 # Initialize the progress bar with the total number of frames
                 pbar = tqdm(
-                    total=total_frames,
+                    total=self.md_len - 1,
                     ascii=True,
                     desc="\033[1mAnalyzing frames\033[0m",
                 )

openmmdl/openmmdl_analysis/openmmdlanalysis.py

@@ -268,14 +268,6 @@ def main():
     if not pdb_md:
         pdb_md = mda.Universe(topology, trajectory)
 
-    if frames != None:
-        print(f"\033[1mWriting out the first {frames} out for the analysis\033[0m")
-        ag = pdb_md.select_atoms("all")
-        with DCDWriter(f"{frames}.dcd", ag.n_atoms) as w:
-            for ts in pdb_md.trajectory[: int(frames) + 1]:
-                w.write(ag)
-        pdb_md = mda.Universe(topology, f"{frames}.dcd")
-
     trajsaver = TrajectorySaver(pdb_md, ligand, special_ligand, receptor_nucleic)
 
     # TODO maybe put this part into a function possibly in visualization_functions.py TrajectorySaver
@@ -382,8 +374,17 @@ def main():
     if peptide != None:
         config.PEPTIDES = [peptide]
 
+    md_len = args.frames
+    if md_len is None:
+        md_len = len(pdb_md.trajectory)
+        print(type(md_len))
+        print(f"\033[1mThe whole trajectory consisting of {len(pdb_md.trajectory) - 1} frames will be analyzed\033[0m")
+    else:
+        md_len = int(md_len) + 1
+        print(f"\033[1mThe trajectory until frame {md_len - 1} will be analyzed\033[0m")
+
     interaction_analysis = InteractionAnalyzer(
-        pdb_md, dataframe, cpu_count, ligand, special_ligand, peptide
+        pdb_md, dataframe, cpu_count, ligand, special_ligand, peptide, md_len
     )
     interaction_list = interaction_analysis.ineraction_list
     interaction_list.to_csv("missing_frames_filled.csv")
@@ -823,8 +824,6 @@ def main():
             topology, "representative_waters.pdb", water_eps
         )
 
-    if frames != None:
-        os.remove(f"{frames}.dcd")
 
 if __name__ == "__main__":
     main()