calc_distance¶
| Editer: | Mogu |
|---|---|
| Version: | 0.0.1dev |
| environment: | Pyton3.5.1 |
contants
- CalcDistance: provide calculating the distance.
This class caluclates the distance between atoms from [dcd, pdb]-files.
- example:
- cafepy distance -f test.dcd[.pdb]
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class
cafepy.core.calc_distance.CalcDistance(filename, index='')[source]¶ Calculating the distance between atoms.
Examples
# filename = [pdb, dcd]-file tmp = CalcDistance(filename) tmp.calcDist() tmp.dist_data()
Members
Self.index: Index class. Self.filename: dcd or pdb file path. Self.pairlist: this values is came from self.index. Self.dist_data: contains result after calculating pair distances. -
_calcDistDCD()[source]¶ calculate distances between given pairs from PDB files. this class is called from self.calcDist()
Args: Returns: Distances (list)
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_calcDistPDB()[source]¶ calculate distances between given pairs from PDB files. this class is called from self.calcDist() :args: :return: Distances (list)
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getIndex(index)[source]¶ get indexes from file for list. :Args: index (filename or list-format) :return: self.index ( list-format )
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makePair(index_list)[source]¶ make pairs from index[list-foarmat] :Args: index_list (list) :return: pairs (list)
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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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