inputgen
¶
Create an APBS input file using psize
data.
Code author: Todd Dolinsky
Code author: Nathan Baker
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class
pdb2pqr.inputgen.
Elec
(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ An object for the ELEC section of an APBS input file.
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__init__
(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ Initialize object.
Todo
Remove hard-coded parameters.
Parameters: - pqrpath (str) – path to PQR file
- size (Psize) – parameter sizing object
- method (str) – solution method (e.g., mg-para, mg-auto, etc.)
- asyncflag (bool) – perform an asynchronous parallel focusing calculation
- istrng – ionic strength/concentration (M)
- potdx (bool) – whether to write out potential information in DX format
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class
pdb2pqr.inputgen.
Input
(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ Each object of this class is one APBS input file.
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__init__
(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ Initialize the input file class.
Each input file contains a PQR name, a list of elec objects, and a list of strings containing print statements. For starters, assume two ELEC statements are needed, one for the inhomgenous and the other for the homogenous dielectric calculations.
Note
This assumes you have already run psize, either by
size.run_psize(...)()
orsize.parse_string(...)()
followed bysize.set_all()
.Parameters: - pqrpath (str) – path to PQR file
- size (Psize) – parameter sizing object
- method (str) – solution method (e.g., mg-para, mg-auto, etc.)
- asyncflag (bool) – perform an asynchronous parallel focusing calculation
- istrng – ionic strength/concentration (M)
- potdx (bool) – whether to write out potential information in DX format
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