Answers.Body: <p>The PDB module in Biopython is worth checking out for obtaining angles, distances, torsion angles. It is described from p208 at <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf" rel="nofollow noreferrer">http://biopython.org/DIST/docs/tutorial/Tutorial.pdf</a>. It doesn't do van der Waal interactions.</p>
  <p>For example,</p>
  <pre><code>from Bio.PDB.PDBParser import PDBParser
  from Bio.PDB.Chain import Chain
  from Bio.PDB.internal_coords import *
  from Bio.PDB.PICIO import write_PIC, read_PIC, read_PIC_seq
  from Bio.PDB.ic_rebuild import write_PDB, IC_duplicate, structure_rebuild_test
  from Bio.PDB.SCADIO import write_SCAD
  from Bio.PDB.PDBIO import PDBIO
  
  parser = PDBParser(PERMISSIVE=1)
  myProtein = parser.get_structure(&quot;1a8o&quot;, &quot;1A8O.pdb&quot;)
  myChain = myProtein[0][&quot;A&quot;]
  IC_Chain.MaxPeptideBond = 4.0
  myChain.internal_coord = None
  myChain.atom_to_internal_coordinates(verbose=True)
  r2 = myChain.child_list[1]
  r2ic = r2.internal_coord
  r2chi1 = r2ic.get_angle(&quot;chi1&quot;)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-10T13:32:07.390Z
Answers.Text: I wanted to compute the 3D structures of the peptides (i.e) x,y,z coordinates of the atoms for the given set of input Ramachandran angles for a fixed bond lengths and bond angles. I don't require to compute the Ramachandran angles of a given PDB file.
Answers.UserDisplayName: vigneshwaran kannan
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Answers.CreationDate: 2023-05-10T14:27:52.387Z
Answers.Text: @vigneshwarankannan thanks for the feedback. What you want is simply to extend the Biopython module with appropriate code for the trigonometric calculation, i.e. angles and distances. It's not my area - but it would be doable.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-10T13:05:01.123Z
Answers.LastActivityDate: 2023-05-10T13:05:01.123Z
Answers.UserDisplayName: M__
Body: <p>I wanted to generate 3D Cartesian coordinates of a peptide sequence for fixed bond lengths and bond angles for a given set of backbone dihedral angles and side dihedral angles. I also wanted to compute non-bonded van der Waal interactions (1-4 atoms) for each of the peptide generated from the dihedral angles. I initially tried frag builder module in python although it works fine. There are few issues,</p>
  <ol>
  <li><p>I could not fix bond length and bond angle of my own choice.</p>
  </li>
  <li><p>It generates PDB file and save it inside the hard disk. So I need to read it again and parse it to compute non-bonded van der Waal interactions (1-4 atom). It consumes lot of time</p>
  </li>
  <li><p>Also I find fragbuilder is not that fast in generating peptides.</p>
  </li>
  <li><p>Reading , parsing and computing the interactions takes around 30 mins to complete the task for 200,000 3D ensemble of structures of given peptide sequence of length 18.</p>
  </li>
  </ol>
  <p>Kindly suggest me a better module in python which does the job faster and also give reference to it.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-09T15:58:21.567Z
Comments.Text: Don't ask multiple questions in a single post. Focus on solving one problem at a time.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-10T08:58:02.563Z
Comments.Text: @M__    Yes Fragbuilder has many shortcomings as pointed out in the questing itself. So I am looking for better alternative. Yes, I am limited to python. Is there any other modules which could handle this inside python ?  Yet, I want to know whether there is any other method outside python as well. Thanks in advance !
Comments.UserDisplayName: vigneshwaran kannan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-10T12:42:04.483Z
Comments.Text: Thanks @vigneshwarankannan updating the question would be cool.
Comments.UserDisplayName: M__
Tags: <python><protein-structure><pdb><molecular-dynamics>
Title: Generating 3D cartesian coordinates of a peptide and computing van der Waal interactions (1-4 atoms) for a given set of dihedral angles?
ThreadText: # Generating 3D cartesian coordinates of a peptide and computing van der Waal interactions (1-4 atoms) for a given set of dihedral angles?
  
  (Asked by: username_0 on 2023-05-09)
  
  I wanted to generate 3D Cartesian coordinates of a peptide sequence for fixed bond lengths and bond angles for a given set of backbone dihedral angles and side dihedral angles. I also wanted to compute non-bonded van der Waal interactions (1-4 atoms) for each of the peptide generated from the dihedral angles. I initially tried frag builder module in python although it works fine. There are few issues,
  
  1. I could not fix bond length and bond angle of my own choice.
  2. It generates PDB file and save it inside the hard disk. So I need to read it again and parse it to compute non-bonded van der Waal interactions (1-4 atom). It consumes lot of time
  3. Also I find fragbuilder is not that fast in generating peptides.
  4. Reading , parsing and computing the interactions takes around 30 mins to complete the task for 200,000 3D ensemble of structures of given peptide sequence of length 18.
  
  Kindly suggest me a better module in python which does the job faster and also give reference to it.
  
  **Tags:** python, protein-structure, pdb, molecular-dynamics
  
  > **Comments:**
  > **username_1**: Don't ask multiple questions in a single post. Focus on solving one problem at a time.  
  > **username_0**: @username_2    Yes Fragbuilder has many shortcomings as pointed out in the questing itself. So I am looking for better alternative. Yes, I am limited to python. Is there any other modules which could handle this inside python ?  Yet, I want to know whether there is any other method outside python as well. Thanks in advance !  
  > **username_2**: Thanks @username_0 updating the question would be cool.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-05-10. Score: 1
  
  The PDB module in Biopython is worth checking out for obtaining angles, distances, torsion angles. It is described from p208 at <http://biopython.org/DIST/docs/tutorial/Tutorial.pdf>. It doesn't do van der Waal interactions.
  
  For example,
  
  ```
  from Bio.PDB.PDBParser import PDBParser
  from Bio.PDB.Chain import Chain
  from Bio.PDB.internal_coords import *
  from Bio.PDB.PICIO import write_PIC, read_PIC, read_PIC_seq
  from Bio.PDB.ic_rebuild import write_PDB, IC_duplicate, structure_rebuild_test
  from Bio.PDB.SCADIO import write_SCAD
  from Bio.PDB.PDBIO import PDBIO
  
  parser = PDBParser(PERMISSIVE=1)
  myProtein = parser.get_structure("1a8o", "1A8O.pdb")
  myChain = myProtein[0]["A"]
  IC_Chain.MaxPeptideBond = 4.0
  myChain.internal_coord = None
  myChain.atom_to_internal_coordinates(verbose=True)
  r2 = myChain.child_list[1]
  r2ic = r2.internal_coord
  r2chi1 = r2ic.get_angle("chi1")
  
  ```
  
  > **Comments:**
  > **username_0**: I wanted to compute the 3D structures of the peptides (i.e) x,y,z coordinates of the atoms for the given set of input Ramachandran angles for a fixed bond lengths and bond angles. I don't require to compute the Ramachandran angles of a given PDB file.  
  > **username_2**: @username_0 thanks for the feedback. What you want is simply to extend the Biopython module with appropriate code for the trigonometric calculation, i.e. angles and distances. It's not my area - but it would be doable.  
  
  ---
  
  