6.2. ligandparam.multiresp.parmhelper

class ligandparam.multiresp.parmhelper.BASH(numnodes)[source]

Bases: Computer

Generates a bash script

Methods

`get_num_cores`()	Get the number of cores
`open`(fname)	Open the bash file
`set_exclude`(x)	Set the exclude variable
`unset_amberhome`()	Unset the amberhome variable
`use_gpu`([x])	Use the gpu
`write_array`(fh)	Write the array to the file handle

get_array

Initialize the bash object

Parameters:: numnodes (int) – The number of nodes to use

Methods

`get_num_cores`()	Get the number of cores
`open`(fname)	Open the bash file
`set_exclude`(x)	Set the exclude variable
`unset_amberhome`()	Unset the amberhome variable
`use_gpu`([x])	Use the gpu
`write_array`(fh)	Write the array to the file handle

get_array

open(fname)[source]

Open the bash file

Parameters:: fname (str) – The name of the file to open

class ligandparam.multiresp.parmhelper.Computer(numnodes)[source]

Bases: object

Base class for computer objects

Methods

`get_num_cores`()	Get the number of cores
`set_exclude`(x)	Set the exclude variable
`unset_amberhome`()	Unset the amberhome variable
`use_gpu`([x])	Use the gpu
`write_array`(fh)	Write the array to the file handle

get_array

Initialize the computer object

Parameters:: numnodes (int) – The number of nodes to use

Methods

`get_num_cores`()	Get the number of cores
`set_exclude`(x)	Set the exclude variable
`unset_amberhome`()	Unset the amberhome variable
`use_gpu`([x])	Use the gpu
`write_array`(fh)	Write the array to the file handle

get_array

get_array()[source]

get_num_cores()[source]: Get the number of cores

set_exclude(x)[source]: Set the exclude variable

unset_amberhome()[source]: Unset the amberhome variable

use_gpu(x=True)[source]

Use the gpu

Parameters:: x (bool, optional) – If True, use the gpu

write_array(fh)[source]

Write the array to the file handle

Parameters:: fh (file handle) – The file handle to write to

ligandparam.multiresp.parmhelper.CopyParm(parm)[source]

Copy the parmed object

Parameters:: parm (parmed object) – The parmed object to copy
Returns:: The copied parmed object
Return type:: parmed object

class ligandparam.multiresp.parmhelper.Fragment(parmobj, ambmask, coef0=None, coef1=None, method='AM1D')[source]

Bases: object

A fragment

Methods

`GetAtomsBondedToIdx`(idx)	Get the atoms bonded to the index
`GetConnectionAtoms`()	Get the connection atoms
`GetLinkPairs`()	Get the link pairs
`GetMMBoundaryTerms`()	Get the MM boundary terms
`funkify_residue_name`(ires)	Funkify the residue name for the given residue index
`get_coef`([lam])	Get the coefficient
`get_funkified_residue_name`(origname)	Get the funkified residue name
`get_selected_mmcharge_from_each_touched_residue`()	Get the selected mm charge from each touched residue
`get_touched_residues`()	Get the touched residues
`redistribute_residue_charges`()	Redistribute the residue charges

Initialize the fragment

Parameters:

parmobj (parmed object) – The parmed object
ambmask (str) – The ambmask
coef0 (float, optional) – The coefficient for lambda=0. Default is None
coef1 (float, optional) – The coefficient for lambda=1. Default is None
method (str, optional) – The method. Default is AM1D

Methods

`GetAtomsBondedToIdx`(idx)	Get the atoms bonded to the index
`GetConnectionAtoms`()	Get the connection atoms
`GetLinkPairs`()	Get the link pairs
`GetMMBoundaryTerms`()	Get the MM boundary terms
`funkify_residue_name`(ires)	Funkify the residue name for the given residue index
`get_coef`([lam])	Get the coefficient
`get_funkified_residue_name`(origname)	Get the funkified residue name
`get_selected_mmcharge_from_each_touched_residue`()	Get the selected mm charge from each touched residue
`get_touched_residues`()	Get the touched residues
`redistribute_residue_charges`()	Redistribute the residue charges

GetAtomsBondedToIdx(idx)[source]

Get the atoms bonded to the index

Parameters:: idx (int) – The index

GetConnectionAtoms()[source]: Get the connection atoms

GetLinkPairs()[source]: Get the link pairs

GetMMBoundaryTerms()[source]: Get the MM boundary terms

funkify_residue_name(ires)[source]

Funkify the residue name for the given residue index

Parameters:: ires (int) – The residue index

get_coef(lam=0)[source]

Get the coefficient

Parameters:: lam (int, optional) – The lambda value. Default is 0
Returns:: The coefficient
Return type:: float

get_funkified_residue_name(origname)[source]

Get the funkified residue name

Parameters:: origname (str) – The original name
Returns:: The funkified residue name
Return type:: str

get_selected_mmcharge_from_each_touched_residue()[source]: Get the selected mm charge from each touched residue

get_touched_residues()[source]: Get the touched residues

redistribute_residue_charges()[source]: Redistribute the residue charges

class ligandparam.multiresp.parmhelper.FragmentedSys(parmobj, compobj)[source]

Bases: object

A fragmented system

Methods

`GetMMTermsForQMRegion`()	Get the MM terms for the QM region
`GetQMAtoms`()	Get the QM atoms
`MakeNewMMBoundaryTerms`()	Make new MM boundary terms
`add_fragment`(ambmask, coef0[, coef1, method])	Add a fragment
`add_mm`()	Add the MM fragment
`check_overlaps`()	Check for overlaps
`get_coefs`([lam])	Get the coefficients
`get_dvdl`(fragenes)	Get the dvdl
`get_dvdl_coefs`()	Get the dvdl coefficients
`get_energy`(fragenes[, lam])	Get the energy
`get_mbar`(fragenes[, nlam])	Get the mbar
`get_noshake_selection`()	Get the no shake selection
`has_ab_initio`()	Check if there is ab initio
`mdouts_to_pymbar`([name, nlam, datadir])	Convert the mdouts to pymbar
`read_mdout`([prefix, lam, nlam])	Read the mdout file
`redistribute_cores`()	Redistribute the cores
`redistribute_residue_charges`()	Redistribute the residue charges
`set_mm_parm`(fname)	Set the MM parm file
`sort`()	Sort the fragments
`write_mdin`([prefix, init, lam, ...])	Write the mdin file
`write_parm`([parmname, overwrite])	Write the parameter file

GetMMTermsForQMRegionAsDict
write_mm_optimization

Initialize the fragmented system

Parameters:

parmobj (parmed object) – The parmed object
compobj (BASH) – The computer object

Methods

`GetMMTermsForQMRegion`()	Get the MM terms for the QM region
`GetQMAtoms`()	Get the QM atoms
`MakeNewMMBoundaryTerms`()	Make new MM boundary terms
`add_fragment`(ambmask, coef0[, coef1, method])	Add a fragment
`add_mm`()	Add the MM fragment
`check_overlaps`()	Check for overlaps
`get_coefs`([lam])	Get the coefficients
`get_dvdl`(fragenes)	Get the dvdl
`get_dvdl_coefs`()	Get the dvdl coefficients
`get_energy`(fragenes[, lam])	Get the energy
`get_mbar`(fragenes[, nlam])	Get the mbar
`get_noshake_selection`()	Get the no shake selection
`has_ab_initio`()	Check if there is ab initio
`mdouts_to_pymbar`([name, nlam, datadir])	Convert the mdouts to pymbar
`read_mdout`([prefix, lam, nlam])	Read the mdout file
`redistribute_cores`()	Redistribute the cores
`redistribute_residue_charges`()	Redistribute the residue charges
`set_mm_parm`(fname)	Set the MM parm file
`sort`()	Sort the fragments
`write_mdin`([prefix, init, lam, ...])	Write the mdin file
`write_parm`([parmname, overwrite])	Write the parameter file

GetMMTermsForQMRegionAsDict
write_mm_optimization

GetMMTermsForQMRegion()[source]

Get the MM terms for the QM region

Returns:

bonds (list) – The bonds
angles (list) – The angles
dihes (list) – The dihedrals

GetMMTermsForQMRegionAsDict()[source]

GetQMAtoms()[source]

Get the QM atoms

Returns:: The QM atoms
Return type:: list

MakeNewMMBoundaryTerms()[source]: Make new MM boundary terms

add_fragment(ambmask, coef0, coef1=None, method='AM1D')[source]

Add a fragment

Parameters:

ambmask (str) – The ambmask
coef0 (float) – The coefficient for lambda=0
coef1 (float, optional) – The coefficient for lambda=1. Default is None
method (str, optional) – The method. Default is AM1D

add_mm()[source]: Add the MM fragment

check_overlaps()[source]

Check for overlaps

Raises:: Exception – If an overlap is found

get_coefs(lam=0)[source]

Get the coefficients

Parameters:: lam (int, optional) – The lambda value. Default is 0

get_dvdl(fragenes)[source]

Get the dvdl

Parameters:: fragenes (list) – The list of fragment energies
Returns:: The dvdl
Return type:: float

get_dvdl_coefs()[source]: Get the dvdl coefficients

get_energy(fragenes, lam=0)[source]

Get the energy

Parameters:

fragenes (list) – The list of fragment energies
lam (int, optional) – The lambda value. Default is 0

get_mbar(fragenes, nlam=11)[source]

Get the mbar

Parameters:

fragenes (list) – The list of fragment energies
nlam (int, optional) – The number of lambdas. Default is 11

Returns:

The mbar

Return type:

list

get_noshake_selection()[source]: Get the no shake selection

has_ab_initio()[source]: Check if there is ab initio

mdouts_to_pymbar(name='frag', nlam=11, datadir='mbar/data')[source]

Convert the mdouts to pymbar

Parameters:

name (str, optional) – The name. Default is “frag”
nlam (int, optional) – The number of lambdas. Default is 11
datadir (str, optional) – The data directory. Default is “mbar/data”

Raises:

Exception – If no files match the glob ‘prod*.%s%s’

read_mdout(prefix='frag', lam=0, nlam=11)[source]

Read the mdout file

Parameters:

prefix (str, optional) – The prefix. Default is “frag”
lam (int, optional) – The lambda value. Default is 0
nlam (int, optional) – The number of lambdas. Default is 11

Returns:

float – The time step
list – The dvdl
list – The mbar

redistribute_cores()[source]: Redistribute the cores

redistribute_residue_charges()[source]: Redistribute the residue charges

set_mm_parm(fname)[source]: Set the MM parm file

sort()[source]: Sort the fragments

write_mdin(prefix='frag', init='init', lam=0, init_from_same_rst=False, directory=None, dipout=False, same_ntpr=False)[source]

Write the mdin file

Parameters:

prefix (str, optional) – The prefix. Default is “frag”
init (str, optional) – The initialization. Default is “init”
lam (int, optional) – The lambda value. Default is 0
init_from_same_rst (bool, optional) – If True, initialize from the same restart. Default is False
directory (str, optional) – The directory. Default is None
dipout (bool, optional) – If True, output the dipole. Default is False
same_ntpr (bool, optional) – If True, use the same ntpr. Default is False

write_mm_optimization(reftraj, refmdin=None)[source]

write_parm(parmname='frag.parm7', overwrite=True)[source]

Write the parameter file

Parameters:

parmname (str, optional) – The parameter name. Default is “frag.parm7”
overwrite (bool, optional) – If True, overwrite the file. Default is True

ligandparam.multiresp.parmhelper.GetSelectedAtomIndices(param, maskstr)[source]

Get the selected atom indices

Parameters:

param (parmed object) – The parmed object
maskstr (str) – The mask string

ligandparam.multiresp.parmhelper.GetSelectedResidueIndices(param, maskstr)[source]

Get the selected residue indices

Parameters:

param (parmed object) – The parmed object
maskstr (str) – The mask string

ligandparam.multiresp.parmhelper.ListToSelection(atomlist)[source]

Convert a list to a selection

Parameters:: atomlist (list) – The list of atoms
Returns:: The selection
Return type:: str

ligandparam.multiresp.parmhelper.MakeUniqueAngleParams(p, xlist, scale=1.0)[source]

Make unique angle parameters

Parameters:

p (parmed object) – The parmed object
xlist (list) – The list of angles
scale (float, optional) – The scale factor. Default is 1.0

ligandparam.multiresp.parmhelper.MakeUniqueBondParams(p, xlist, scale=1.0)[source]

Make unique bond parameters

Parameters:

p (parmed object) – The parmed object
xlist (list) – The list of bonds
scale (float, optional) – The scale factor. Default is 1.0

ligandparam.multiresp.parmhelper.MakeUniqueDihedralParams(p, xlist, scale=1.0)[source]

Make unique dihedral parameters

Parameters:

p (parmed object) – The parmed object
xlist (list) – The list of dihedrals
scale (float, optional) – The scale factor. Default is 1.0

ligandparam.multiresp.parmhelper.OpenParm(fname, xyz=None)[source]

Open a file with parmed.

Parameters:

fname (str) – The name of the file to open
xyz (str, optional) – The name of the xyz file to open

Returns:

The parmed object

Return type:

parmed object