parmed.amber.mask module¶
Module for evaluating Amber Mask strings and translating them into lists in which a selected atom is 1 and one that’s not is 0.
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class
parmed.amber.mask.AmberMask(parm, mask)[source]¶ Bases:
objectWhat is hopefully a fully-fledged Amber mask parser implemented in Python.
- Parameters
- parmStructure
The topology structure for which to select atoms
- maskstr
The mask string that selects a subset of atoms
Methods
Selected([invert])Generator that returns the indexes of selected atoms
Selection([prnlev, invert])Parses the mask and analyzes the result to return an atom selection array
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Selected(invert=False)[source]¶ Generator that returns the indexes of selected atoms
- Parameters
- invertbool, optional
If True, all atoms not selected by the mask will be returned
- Returns
- generator of int
Each iteration will yield the index of the next atom that has been selected by the mask. Atom indices are 0-based
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Selection(prnlev=0, invert=False)[source]¶ Parses the mask and analyzes the result to return an atom selection array
- Parameters
- prnlevint, optional
Print debug information on the processing of the Amber mask string. This is mainly useful if you are modifying the mask parser. Default value is 0 (no printout), values between 1 and 8 control the level of output (larger values produce more output). Default 0
- invertbool, optional
If True, the returned array will invert the selection of the mask (i.e., selected atoms will not be selected and vice-versa)
- Returns
- masklist of int
A list with length equal to the number of atoms in the assigned
Structureinstance. Selected atoms will have a value of 1 placed in the corresponding slot in the return list while atoms not selected will be assigned 0.