calc_com¶
This class caluclates the center of mass of proteins from [dcd,pdb]-files.
| Editer: | Mogu |
|---|---|
| environment: | Pyton >= 3.5.1 |
| requirement: | Numpy >= 1.11 |
- example
-
class
cafepy.core.calc_com.CalcCOM(inputfile, *args, **kargs)[source]¶ Calculating the center of mass from [dcd,pdb]-files
- Examples:
tmp = CalcCom("filename") # both dcd-format and pdb-format are ok tmp.run() tmp.writeFile("outfile") or tmp.writeShow()
In Terminal.
pycafe.py com -f [dcd,pdb]-infile [optional: -o outfile, -nf index.file or -n int-value]
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read(filename)¶ read [pdb, dcd, index] files. This function define reading type from files suffix. you need to set a proper suffix with filename.
Inputs: filename(str) Returns: class [DCD, PDB, Index]
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run(atom_idx=[], unit_idx=[], traj_idx=[])[source]¶ Calculates the Center of mass from DCD-file or PDB-file.
Args: atom_idx (list), traj_idx (list)
atom_idx: You can select Atoms for calculating COM with idx[.ndx,.ninfo]-file [ from 0 to ~] unit_idx: You can select Units in pdb format. [from 1 to ~] traj_idx: You can extract trajectories for calculating COM.