6.7. ligandparam.multiresp.respfunctions
- ligandparam.multiresp.respfunctions.GetAtomsBondedToIdx(parm, idx)[source]
Get the atoms bonded to a given atom index
- Parameters:
parm (parmed structure) – The parmed structure
idx (int) – The atom index
- Returns:
cats – The indices of the atoms bonded to the given atom
- Return type:
list of int
- ligandparam.multiresp.respfunctions.GetAvgStdDevAndErr(x)[source]
Get the average, standard deviation, and standard error of the mean of a list of numbers
- Parameters:
x (list of float) – The list of numbers
TODO (Check why this isn't just done with numpy)
- ligandparam.multiresp.respfunctions.GetEquivHydrogens(parm, sele)[source]
Get the equivalent hydrogens bonded to a given atom
- Parameters:
parm (parmed structure) – The parmed structure
sele (list of int) – The atom indices
- Returns:
hpairs – The indices of the equivalent hydrogens
- Return type:
list of list of int
- ligandparam.multiresp.respfunctions.GetEquivNonbridgeOxygens(parm, sele)[source]
Get the equivalent non-bridge oxygens bonded to a given atom
- Parameters:
parm (parmed structure) – The parmed structure
sele (list of int) – The atom indices
- Returns:
hpairs – The indices of the equivalent non-bridge oxygens
- Return type:
list of list of int
- ligandparam.multiresp.respfunctions.ReadGauEsp(fname)[source]
Read the ESP from a Gaussian output file
- Parameters:
fname (str) – The Gaussian output file
- Returns:
crds – The coordinates of the atoms
- Return type:
list of float
- ligandparam.multiresp.respfunctions.ReadGauOutput(fname)[source]
Read the atomic coordinates, charge, and multiplicity from a Gaussian output file
- Parameters:
fname (str) – The Gaussian output file
- Returns:
atn (list of str) – The atomic symbols
crds (list of float) – The atomic coordinates
charge (int) – The charge
mult (int) – The multiplicity
- ligandparam.multiresp.respfunctions.ReadNextRespCharges(fh)[source]
Read the next set of RESP charges from the file handle
- Parameters:
fh (file handle) – The file handle to read the charges from
- Returns:
qs – The list of charges
- Return type:
list of float
- ligandparam.multiresp.respfunctions.ReadOrMakeGauEsp(mdout, nproc=4)[source]
Read the ESP from a Gaussian output file, or generate it if it doesn’t exist
- Parameters:
mdout (str) – The Gaussian output file
nproc (int) – The number of processors to use
- Returns:
crds (list of list of float) – The coordinates of the atoms
pts (list of list of float) – The coordinates of the grid points
esp (list of float) – The ESP values
- ligandparam.multiresp.respfunctions.RunGauEsp(atn, crds, charge, mult, basename, nproc)[source]
Run Gaussian to calculate the ESP
- Parameters:
atn (list of str) – The atomic symbols
crds (list of float) – The atomic coordinates
charge (int) – The charge
mult (int) – The multiplicity
basename (str) – The base name for the output files
nproc (int) – The number of processors to use