# API¶

## Package¶

The aesop submodule contains all relevant classes and functions for the AESOP package.

## AESOP contents¶

exception aesop.aesop.APBS_Exception

Bases: exceptions.Exception

class aesop.aesop.Alascan(pdb, pdb2pqr_exe='pdb2pqr', apbs_exe='apbs', coulomb_exe='coulomb', selstr=['protein'], jobname=None, region=None, grid=1, ion=0.15, pdie=20.0, sdie=78.54, ff='parse', cfac=1.5, dx=False, minim=False)

Summary Summary of internal varialbles in the Alascan class. All parameters are set in the Alascan.__init__(…) and the analysis is run with Alascan.run().

Attributes: apbs : str Full path to APBS executable. Must be compatible with OS. apbs_results : str Full path to output from APBS cfac : float Scaling factor for grid dimensions. We suggest to leave this unchanged. coulomb : str Full path to coulomb executable from APBS package. Must be compatible with OS. coulomb_results : str Full path to folder containing results from coulomb. dime : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ disu : bool, optional If True, Modeller will guess the patches for disulfide bridges within the provided protein structures. Only relevant if minim is set to Trueself. dx : bool Variable that specifies if potential files should be written to disk. Default is False. dx_files : list If written to disk, list of potential files written to disk. The folder containing these files is given by Alascan.apbs_results. E_ref : ndarray Description E_solv : ndarray Description ff : str Force-field to use for PDB2PQR file_pdb_template : TYPE Description gcent : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ Gcoul : ndarray Coulombic free energies, corresponding to Alascan.mutid. glen : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ Gref : ndarray Reference-state free energies, corresponding to Alascan.mutid. grid : numeric Distance spacing of grid points. If the grid dimensions are not divisible by three, resolution will be increased (smaller grid spacing) until grid dimensions are divisible by three. Gsolv : ndarray Solvated-state free energies, corresponding to Alascan.mutid. ion : numeric Ionic strength to be used in the solvated-state APBS calculations. jobdir : str [Optional] Path to folder containing results. If not specified, a directory will be generated. jobname : str [Optional] Name for current job, will be used to create the jobdir. list_chids : list Chain ID where mutation was made. Corresponds to Alascan.mutid. list_resnames : list Residue names where mutation was made. Corresponds to Alascan.mutid. list_resnums : list Residue numbers where mutation was made. Corresponds to Alascan.mutic. logs : list List of strings that represent the log files from every executable called (namely, PDB2PQR and APBS) logs_apbs_dir : str Folder in jobdir containing output from APBS (logs, input files, dx files) mask_by_sel : ndarray Matrix containing selection masks. The first column corresponds to the selection string for the parent and each column thereafter corresponds to an element of the selection string (selstr) in the same order. max_iter : integer, optional If minimization is to be performed, this parameter limits the maximum number of calls to the objective function before minimization is terminated. Default is 1000 iterations. min_atom_shift : float, optional If minimization is to be performed, this parameter will determine the convergence criteria. If the maximum atomic shift for all atoms between minimization steps is less than this value, then minimization is terminated. Default value is 0.1 angstroms. minim : bool, optional If True, minimization will be performed with Modeller’s conjugate gradient descent algorithm. Default is False for the Alanine scan class as no clashes should result from mutations. mutid : list List of mutant IDs. The first element corresponds to the parent. Subsequent elements correspond to each element of the selection string list (selstr). Please use Alascan.getMutids() to get vectorized version. output : string, optional If minimization is performed, this parameter deterimines what output to STDOUT Modeller will use. ‘NO_REPORT’ results in a minimal output to STDOUT, while ‘REPORT’ results in a more verbose output to STDOUT. pdb : str Path to PDB file with atomic coordinates. Must follow formatting conventions of the Protein Databank. pdb2pqr : str Full path to PDB2PQR executable. pdb_complex_dir : str Folder name in the job directory that contains the PDB file(s) of the complex structures. pdie : numeric Protein dielectric constant to be used in APBS. pqr_complex_dir : str Folder name in the job directory containing PQR files for each protein complex. pqr_sel_dir : list List of folder names in the job directory that contain PQR files for selection strings (selstr). Each element of pqr_sel_dir corresponds to the same element of selstr. region : list List of additional selection strings specifying the zone where mutations should occur. Generally unused, unless a region of interest is involved. Each element of region should correspond to the same element of selstr. That is, each region selection string will futher narrow down the initial selection string. sdie : numeric Solvent dielectric constant to be used in APBS. selstr : list List of selection strings. Typically each selection string will correspond to a chain in a protein complex. We advise users to specify two or more selection strings. (Ex: [‘chain A’, ‘chain B’])

Methods

 calcAPBS() Summary Run APBS on each structure in mutant library, in serial. calcAPBS_parallel([n_workers]) Summary Run APBS on each structure in mutant library, in parallel. calcCoulomb() Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox. calcCoulomb_parallel([n_workers]) Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox in a parallel manner. calcESI([idx]) Summary dGsolv_rel() Summary Calculates and returns the free energy of a solvation for each mutant relative to the parent free energy of solvation. ddGa_rel() Summary Calculates and returns the free energy of association relative to the parent free energy of association. find_grid() Summary genDirs() Summary This subroutine will generate all directories needed to contain structural files, logs, etc. genMutid() Summary This subroutine reads the input PDB, selects the structure where mutations will occur, and saves all mutant IDs in the class. genParent() Summary Reads PDB file specified in the constructor; applies and combines results from the selection strings; and saves the final template structure in the job directory. genTruncatedPQR() Summary Generate a structure for each mutant ID by truncating the side chain to form alanine. getMutids() Summary run() Summary Perform a compuational alanine scan on the initialized Alascan class. run_parallel([n_workers]) Summary Perform a computational alanine scan on the initialized Alascan class using multiple processes in parallel. set_grid(dime, glen, gcent) Summary In the case that the user wishes to manually specify grid dimension, this may be accomplished with the set_grid method. summary([filename]) Summary Summarize results from the computational alanine scan once complete.
 checkerrors checkwarnings viewLogs writeLogs
calcAPBS()

Summary Run APBS on each structure in mutant library, in serial.

Returns: None Stores energies from APBS in Gref and Gsolv class attributes.
calcAPBS_parallel(n_workers=None)

Summary Run APBS on each structure in mutant library, in parallel.

Parameters: n_workers : int Number of processes to run. If None, method will use all available threads. None Saves solvated-state and reference-state free energies as class attributes.
calcCoulomb()

Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox.

Returns: None Saves Coulombic free energies as a class attribute.
calcCoulomb_parallel(n_workers=None)

Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox in a parallel manner.

Parameters: n_workers : int Number of processes to run. If None, method will use all available threads. None Saves Coulombic free energies as a class attribute.
calcESI(idx=-1)

Summary

Compare potential files and calculate the similarity index. Values closer to 1 imply similarity while values closer to zero imply dissimilarity.

Parameters: method : str, optional This parameter will allow for other metrics to compare grid potentials; however, for now only ‘AND’ is implemented. idx : int Index of original PDB files supplied containing reference structure. Set to None to perform all pairwise comparisons. None Writes esi files to the esi_files directory within the job directory.
checkerrors()
checkwarnings()
dGsolv_rel()

Summary Calculates and returns the free energy of a solvation for each mutant relative to the parent free energy of solvation.

Returns: ndarray Array of solvation free energies corresponding to mutant IDs from the Alascan.getMutIDs() method.
ddGa_rel()

Summary Calculates and returns the free energy of association relative to the parent free energy of association.

Returns: ndarray Array of free energies corresponding to the mutant IDs from the Alascan.getMutIDs() method.
find_grid()

Summary Calculate grid dimensions for APBS (dime, glen, gcent)

Returns: TYPE Sets class attributes dime, glen, and gcent
genDirs()

Summary This subroutine will generate all directories needed to contain structural files, logs, etc. In the future we may implement a method to remove such files when outputs are more standardized.

Returns: None No output, operates on the class and generates folders in the job directory.
genMutid()

Summary This subroutine reads the input PDB, selects the structure where mutations will occur, and saves all mutant IDs in the class. If region is specified in the constructor, then the constraint will be applied here.

Returns: None Operates on the class to generate a list of mutant IDs for each selection string. The following class variables will be generated (see class description): mutid list_chids list_resnums list_resnames mask_by_sel
genParent()

Summary Reads PDB file specified in the constructor; applies and combines results from the selection strings; and saves the final template structure in the job directory.

Returns: None Template pdb written in job directory and location saved in Alascan.file_pdb_template.
genTruncatedPQR()

Summary Generate a structure for each mutant ID by truncating the side chain to form alanine.

Returns: None Write library of mutant structures to disk for subsequent analysis.
getMutids()

Summary

Returns: list Returns vectorized format of mutids.
run()

Summary Perform a compuational alanine scan on the initialized Alascan class.

Returns: None Outputs text to STDOUT when run is complete, will be made optional in the future.
run_parallel(n_workers=None)

Summary Perform a computational alanine scan on the initialized Alascan class using multiple processes in parallel.

Parameters: n_workers : int Number of processes to run. If None, method will use all available threads. None Outputs text to STDOUT when run is complete, will be made optional in the future.
set_grid(dime, glen, gcent)

Summary In the case that the user wishes to manually specify grid dimension, this may be accomplished with the set_grid method. Typically, this is used when grid space parameters must be consistent for many analyses. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ for description of parameters.

Parameters: dime : list List of three integers. glen : list List of three integers. gcent : list List of three integers. TYPE Description
summary(filename=None)

Summary Summarize results from the computational alanine scan once complete.

Parameters: filename : str, optional In order to write summary to a text file, supply the filename (full path). None Prints summary of residues and energies relative to the parent structure if no filename is provided. Otherwise, writes to text file.
viewLogs()
writeLogs(filename=None)
exception aesop.aesop.Complete_PDB_Exception

Bases: exceptions.Exception

class aesop.aesop.DirectedMutagenesis(pdb, target, mutation, pdb2pqr_exe='pdb2pqr', apbs_exe='apbs', coulomb_exe='coulomb', selstr=['protein'], jobname=None, grid=1, ion=0.15, pdie=20.0, sdie=78.54, ff='parse', cfac=1.5, dx=False, minim=True)

Summary

Attributes: apbs : str Full path to APBS executable. Must be compatible with OS. apbs_results : str Full path to output from APBS cfac : numeric Scaling factor for grid dimensions. We suggest to leave this unchanged. coulomb : str Full path to coulomb executable from APBS package. Must be compatible with OS. coulomb_results : str Full path to folder containing results from coulomb. dime : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ disu : bool, optional If true, Modeller will guess patches for disulfide bridges. Only relevant if minim is set to True. dx : bool Variable that specifies if potential files should be written to disk. Default is False. dx_files : list If written to disk, list of potential files written to disk. The folder containing these files is given by Alascan.apbs_results. E_ref : ndarray Reference state energy values for each structure from APBS. E_solv : ndarray Solvated state energy values for each structure from APBS. ff : string Force-field to use for PDB2PQR file_pdb_template : string Full path to template PDB file. gcent : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ Gcoul : ndarray Coulombic free energies, corresponding to Alascan.mutid. glen : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ Gref : ndarray Reference-state free energies, corresponding to Alascan.mutid. grid : numeric Distance spacing of grid points. If the grid dimensions are not divisible by three, resolution will be increased (smaller grid spacing) until grid dimensions are divisible by three. Gsolv : ndarray Solvated-state free energies, corresponding to Alascan.mutid. ion : numeric Ionic strength to be used in the solvated-state APBS calculations. jobdir : str [Optional] Path to folder containing results. If not specified, a directory will be generated. jobname : str [Optional] Name for current job, will be used to create the jobdir. list_chids : list Chain ID where mutation was made. Corresponds to Alascan.mutid. list_resnames : list Residue names where mutation was made. Corresponds to Alascan.mutid. list_resnums : list Residue numbers where mutation was made. Corresponds to Alascan.mutic. logs : list List of strings that represent the log files from every executable called (namely, PDB2PQR and APBS) logs_apbs_dir : str Folder in jobdir containing output from APBS (logs, input files, dx files) mask_by_sel : ndarray Matrix containing selection masks. The first column corresponds to the selection string for the parent and each column thereafter corresponds to an element of the selection string (selstr) in the same order. max_iter : integer, optional Maximum number of calls to the objective function. If this value is reached, then minimization is terminated. Default value is 1000 iterations. min_atom_shift : float, optional If the maximimum atomic shift between minimization steps is less thant this value, convergence is reached and minimization is terminated. Default value is 0.1 angstroms. minim : bool, optional If true, structures will be minimzed with Modeller’s conjugate gradient descent algorithm. mutation : list Identity of amino acid for mutation of corresponding target. Must be the same length as target and each residue must use the standard 3-letter amino acid code. mutid : list List of mutant IDs. The first element corresponds to the parent. Subsequent elements correspond to each element of the selection string list (selstr). Please use Alascan.getMutids() to get vectorized version. output : string, optional Modeller option specifying whether to print verbose output to STDOUT (‘REPORT’), or to print minimal output to STDOUT (‘NO_ REPORT’) pdb : str Path to PDB file with atomic coordinates. Must follow formatting conventions of the Protein Databank. pdb2pqr : str Full path to PDB2PQR executable. pdb_complex_dir : str Folder name in the job directory that contains the PDB file(s) of the complex structures. pdie : numeric Protein dielectric constant to be used in APBS. pqr_complex_dir : str Folder name in the job directory containing PQR files for each protein complex. pqr_sel_dir : list List of folder names in the job directory that contain PQR files for selection strings (selstr). Each element of pqr_sel_dir corresponds to the same element of selstr. sdie : numeric Solvent dielectric constant to be used in APBS. selstr : list List of selection strings. Typically each selection string will correspond to a chain in a protein complex. We advise users to specify two or more selection strings. (Ex: [‘chain A’, ‘chain B’]) target : list List of residue numbers to mutate. Must correspond element-wise to mutation attribute.

Methods

 calcAPBS() Summary Call apbs to calculate reference-state and solvation-state energies for all structures in library. calcAPBS_parallel([n_workers]) Summary Run APBS on each structure in mutant library, in parallel. calcCoulomb() Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox. calcCoulomb_parallel([n_workers]) Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox in a parallel manner. dGsolv_rel() Summary Calculates and returns the free energy of a solvation for each mutant relative to the parent free energy of solvation. ddGa_rel() Summary Calculates and returns the free energy of association relative to the parent free energy of association. find_grid() Summary genDirs() Summary This subroutine will generate all directories needed to contain structural files, logs, etc. genMutid() Summary This subroutine reads the input PDB, selects the structure where mutations will occur, and saves all mutant IDs in the class. genPDB([minim]) Summary genPQR() Summary Generates PQR for each PDB in library. genParent() Summary Reads PDB file specified in the constructor; applies and combines results from the selection strings; and saves the final template structure in the job directory. getMutids() Summary run() Summary Perform a directed mutagenesis scan on the initialized class. run_parallel([n_workers]) Summary Perform a computational directed mutagenesis scan on the initialized class using multiple processes in parallel. set_grid(dime, glen, gcent) Summary In the case that the user wishes to manually specify grid dimension, this may be accomplished with the set_grid method. summary([filename]) Summary Summarize results from the computational alanine scan once complete.
 checkerrors checkwarnings viewLogs writeLogs
calcAPBS()

Summary Call apbs to calculate reference-state and solvation-state energies for all structures in library.

Returns: None Sets class attributes Gsolv and Gref
calcAPBS_parallel(n_workers=None)

Summary Run APBS on each structure in mutant library, in parallel.

Parameters: n_workers : int Number of processes to run. If None, method will use all available threads. None Saves solvated-state and reference-state free energies as class attributes.
calcCoulomb()

Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox.

Returns: None Saves Coulombic free energies as a class attribute.
calcCoulomb_parallel(n_workers=None)

Summary Calculates Coulombic free energies with coulomb.exe from the APBS toolbox in a parallel manner.

Parameters: n_workers : int Number of processes to run. If None, method will use all available threads. None Saves Coulombic free energies as a class attribute.
checkerrors()
checkwarnings()
dGsolv_rel()

Summary Calculates and returns the free energy of a solvation for each mutant relative to the parent free energy of solvation.

Returns: ndarray Array of solvation free energies corresponding to mutant IDs from the Alascan.getMutIDs() method.
ddGa_rel()

Summary Calculates and returns the free energy of association relative to the parent free energy of association.

Returns: ndarray Array of free energies corresponding to the mutant IDs from the Alascan.getMutIDs() method.
find_grid()

Summary Calculate grid dimensions for APBS (dime, glen, gcent)

Returns: TYPE Sets class attributes dime, glen, and gcent
genDirs()

Summary This subroutine will generate all directories needed to contain structural files, logs, etc. In the future we may implement a method to remove such files when outputs are more standardized.

Returns: None No output, operates on the class and generates folders in the job directory.
genMutid()

Summary This subroutine reads the input PDB, selects the structure where mutations will occur, and saves all mutant IDs in the class. If region is specified in the constructor, then the constraint will be applied here.

Returns: None Operates on the class to generate a list of mutant IDs for each selection string. The following class variables will be generated (see class description): mutid list_chids list_resnums list_resnames mask_by_sel
genPDB(minim=True)

Summary Generates mutations by calling function to mutate PDB with modeller

Returns: None Write PDB library to expected path according to class attributes.
genPQR()

Summary Generates PQR for each PDB in library.

Returns: None Calls PDB2PQR and writes PQR to expected path according to class attributes.
genParent()

Summary Reads PDB file specified in the constructor; applies and combines results from the selection strings; and saves the final template structure in the job directory.

Returns: None Template pdb written in job directory and location saved in Alascan.file_pdb_template.
getMutids()

Summary

Returns: list Returns vectorized format of mutids.
run()

Summary Perform a directed mutagenesis scan on the initialized class.

Returns: None Outputs text to STDOUT when run is complete, will be made optional in the future.
run_parallel(n_workers=None)

Summary Perform a computational directed mutagenesis scan on the initialized class using multiple processes in parallel.

Parameters: n_workers : int Number of processes to run. If None, method will use all available threads. None Outputs text to STDOUT when run is complete, will be made optional in the future.
set_grid(dime, glen, gcent)

Summary In the case that the user wishes to manually specify grid dimension, this may be accomplished with the set_grid method. Typically, this is used when grid space parameters must be consistent for many analyses. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ for description of parameters.

Parameters: dime : list List of three integers. glen : list List of three integers. gcent : list List of three integers. TYPE Sets class attributes for dime, glen, gcent
summary(filename=None)

Summary Summarize results from the computational alanine scan once complete.

Parameters: filename : str, optional In order to write summary to a text file, supply the filename (full path). None Prints summary of residues and energies relative to the parent structure if no filename is provided. Otherwise, writes to text file.
viewLogs()
writeLogs(filename=None)
class aesop.aesop.ElecSimilarity(pdbfiles, pdb2pqr_exe='pdb2pqr', apbs_exe='apbs', selstr=None, jobname=None, grid=1, ion=0.15, pdie=20.0, sdie=78.54, ff='parse', cfac=1.5, minim=False)

Summary

Attributes: apbs : str Full path to APBS executable. Must be compatible with OS. cfac : numeric Scaling factor for grid dimensions. We suggest to leave this unchanged. dim_dx : list Dimensions of grid space dime : list List of three integers. Parameter required for APBS.Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ disu : bool, optional If True, Modeller will guess the patches for disulfide bridges within the provided protein structures. Only relevant if minim is set to True. dx : bool Variable that specifies if potential files should be written to disk. Default is False. dxdir : str Folder in job directory where potential files are stored. dxfiles : list List of all potential files. edges : ndarray Edges of grid space. esd : ndarray Matrix of pairwise electrostatic similarities. ff : str Forcefield to use in assigning charges to PDB files. gcent : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ glen : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ grid : int Desired grid spacing in Angstroms. Actual grid spacing may be slightly lower. ids : list List of IDs for each structure being compared with the ESD metric. ion : numeric Ionic strength to be used in the solvated-state APBS calculations. jobdir : TYPE Description jobname : str [Optional] Name for current job, will be used to create the jobdir. logs : list List of strings that represent the log files from every executable called (namely, PDB2PQR and APBS) max_iter : integer, optional Maximum number of calls to the objective function. If this value is reached, then minimization is terminated. Default value is 1000 iterations. midpoints : ndarray Midpoints of grid space min_atom_shift : float, optional If the maximimum atomic shift between minimization steps is less thant this value, convergence is reached and minimization is terminated. Default value is 0.1 angstroms. minim : bool, optional If true, structures will be minimzed with Modeller’s conjugate gradient descent algorithm. output : string, optional Modeller option specifying whether to print verbose output to STDOUT (‘REPORT’), or to print minimal output to STDOUT (‘NO_ REPORT’) pdb2pqr : str Full path to PDB2PQR executable. pdbdir : str Folder in job directory where PDB files are located. pdbfiles : list List of PDB file names. pdie : numeric Protein dielectric constant to be used in APBS. pqrdir : str Folder in job directory containing PQR files. pqrfiles : list List of PQR files in pqrdir sdie : numeric Solvent dielectric constant to be used in APBS.

Methods

 calcESD([method]) Summary Compare potential files and calculate the similarity distance. calcESI([method, idx]) Summary centerPDB() Summary genDX() Summary Generates potential files using APBS. genDX_parallel([n_workers]) Summary Generates multiple potential files in parallel by calling APBS multiple times according to how many threads are available/specified. genPQR() Summary initializeGrid() Summary Method to find grid parameters and ensure that the product of dimensions is divisible by three. minimPDB() Summary Re-reads PDB files in pdbdir and performs energy minimization. mutatePQR([selstr, minim, ff]) Summary superposePDB() Summary Superpose each structure in pdbfiles with first element in pdbfiles list.
 checkerrors checkwarnings run run_parallel viewLogs writeLogs
calcESD(method='AND')

Summary Compare potential files and calculate the similarity distance. Smaller distances imply similarity.

Parameters: method : str, optional This parameter will allow for other metrics to compare grid potentials; however, for now only ‘AND’ is implemented. None Stores esd matrix as class attribute.
calcESI(method='AND', idx=0)

Summary

Compare potential files and calculate the similarity index. Values closer to 1 imply similarity while values closer to zero imply dissimilarity.

Parameters: method : str, optional This parameter will allow for other metrics to compare grid potentials; however, for now only ‘AND’ is implemented. idx : int Index of original PDB files supplied containing reference structure. Set to None to perform all pairwise comparisons. None Writes esi files to the esi_files directory within the job directory.
centerPDB()

Summary Re-reads PDB file in pdbdir and centers coordinates at (0, 0, 0)

Returns: TYPE Overwrites previous PDB files in pdbdir
checkerrors()
checkwarnings()
genDX()

Summary Generates potential files using APBS.

Returns: None Generates DX files in dxdir
genDX_parallel(n_workers=None)

Summary Generates multiple potential files in parallel by calling APBS multiple times according to how many threads are available/specified.

Parameters: n_workers : int Number of processes to run. If None, method will use all available threads. TYPE Generates DX files in dxdir.
genPQR()

Summary Convert all PDB files to PQR files with charges allocated according to a compatible force-field

Returns: None Generates PQR files in the pqrdir
initializeGrid()

Summary Method to find grid parameters and ensure that the product of dimensions is divisible by three.

Returns: None Sets class attributes dime, glen, gcent.
minimPDB()

Summary Re-reads PDB files in pdbdir and performs energy minimization.

Returns: TYPE Overwrites previous PDB files in pdbdir
mutatePQR(selstr=['protein'], minim=False, ff='parse')

Summary Mutate all PQR files, optional method

Returns: None Generates PQR files in the pqrdir
run(center=False, superpose=False, esi=False, esd=True, selstr=None, idx=0, minim=False)
run_parallel(n_workers=None, center=False, superpose=False, esi=False, esd=True, selstr=None, idx=0, minim=False)
superposePDB()

Summary Superpose each structure in pdbfiles with first element in pdbfiles list. This uses Modeller to perform the superpositioning.

Returns: TYPE Overwrites PDB files in pdbdir with new coordinate information.
viewLogs()
writeLogs(filename=None)
class aesop.aesop.Grid(filename=None)

Summary

The grid class facilitates parsing and writing of OpenDX file formats. In the current state, the class is quite rudimentary and only supports changing vectors for the grid data.

Attributes: filename : string DX file to import pot : ndarray Vectors at each grid point. For AESOP, these will typically be electrostatic potentials or an electrostatic similarity index. header : list List of grid parameters from the OpenDX format prior to vectors. footer : list List of grid parameters from the OpenDX format subsequent to the vectors.

Methods

 readDX([filename]) Summary writeDX([filename]) Summary
re = <module 're' from '/home/docs/checkouts/readthedocs.org/user_builds/aesop/envs/latest/lib/python2.7/re.pyc'>
readDX(filename=None)

Summary

Method to parse a DX file

Parameters: filename : string Name for the OpenDX file to be imported. If unspecified, this parameter defaults to the class attribute.
writeDX(filename=None)

Summary

Function to write OpenDX files

Parameters: filename : string Name for OpenDX file that will be written. This should be a full path if you wish to place the file somewhere other than the current working directory.
exception aesop.aesop.Minimize_CG_Exception

Bases: exceptions.Exception

exception aesop.aesop.PDB2PQR_Exception

Bases: exceptions.Exception

aesop.aesop.batchAPBS(kernel)

Summary Function required to run multiple APBS jobs simultaneously. Not intended for general use.

Parameters: kernel : tuple Tuple of parameters required for APBS. ndarray i, j represent the index in the matrix with which the calculated energies correspond. The last two elements are the solvation and reference energies, respectively.
aesop.aesop.batchCalcDX(kernel)

Summary Function required to run multiple APBS jobs simultaneously. Not intended for general use.

Parameters: kernel : tuple Tuple of parameters required for APBS. None Writes files according to calcDX function.
aesop.aesop.batchCoulomb(kernel)

Summary Function required to run multiple Coulomb jobs simultaneously. Not intended for general use.

Parameters: kernel : tuple Tuple of parameters required for APBS. ndarray i, j represent the index in the matrix with which the calculated energies correspond. The last element is the Coulombic energy.
aesop.aesop.calcDX(path_apbs_exe, pqrfile, prefix=None, grid=1.0, ion=0.15, pdie=20.0, sdie=78.54, cfac=1.5, glen=None, gcent=array([ 0., 0., 0.]), dime=None)

Summary Calls the APBS executable after generating the APBS inputfile. Generates a potential file (DX).

Parameters: path_apbs_exe : str Full path to APBS executable, EX: ‘C:APBSapbs.exe’. pqrfile : str The PQR file that will be used to generate a grid of electrostatic potentials. Must be a full path if file is not in current path. prefix : str, optional Phrase to prepend before any file that is generated before writing. grid : float, optional Distance spacing of grid points. If the grid dimensions are not divisible by three, resolution will be increased (smaller grid spacing) until grid dimensions are divisible by three. ion : float, optional Ionic strength for APBS calculation. pdie : float, optional Protein dielectric constant for APBS calculation. sdie : float, optional Solvent dielectric constant for APBS calculation. cfac : float, optional Scaling factor for grid dimensions. We suggest to leave this unchanged. glen : None, optional List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ gcent : TYPE, optional List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ dime : None, optional List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ (log, err) : tuple When APBS runs, outputs that would have been sent to STDOUT are captured. Log contains the run log and err contains errors.
aesop.aesop.complete_structure(pdb, dest=None, disu=False)

Summary Function to fill in residues with missing atoms. This method simply calls complete_pdb from Modeller.

Parameters: pdb : str Full path to pdbfile that will be modified. dest : str (optional) Full path to destination where completed pdb will be written. If not specified, the model object from Modeller will be returned. disu : bool (optional) If True, complete_pdb will predict and patch all disulfide bridges. Default is False.
aesop.aesop.execAPBS(path_apbs_exe, pqr_chain, dime, glen, gcent, prefix=None, ion=0.15, pdie=20.0, sdie=78.54, dx=False)

Summary Calls the APBS executable after generating the APBS inputfile. Calculates solvation and reference energies.

Parameters: path_apbs_exe : str Full path to APBS executable, EX: ‘C:APBSapbs.exe’. pqr_chain : str PQR file name containing the segment that will undergo electrostatic calculations. dime : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ glen : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ gcent : list List of three integers. Parameter required for APBS. Please see description at: http://www.poissonboltzmann.org/docs/apbs-overview/ prefix : str, optional Phrase to prepend before any file that is generated before writing. ion : float, optional Ionic strength for APBS calculation. pdie : float, optional Protein dielectric constant for APBS calculation. sdie : float, optional Solvent dielectric constant for APBS calculation. dx : bool, optional If true, potential files are written. file_apbs_log : str File name for the log file that APBS generates. This file contains results from performed calculations.
aesop.aesop.execCoulomb(path_coulomb_exe, pqr)

Summary Call Coulomb from APBS tools to calculate Coulombic energies.

Parameters: path_coulomb_exe : str Full path to coulomb executable. pqr : TYPE Filename for PQR to use for Coulombic energy calculation. Must be full path if not in current path. float Coulombic energy associated with input PQR file.
aesop.aesop.execPDB2PQR(path_pdb2pqr_exe, pdbfile, outfile=None, ff='parse')

Summary Calls the APBS executable according to: <path to pdb2pqr appropriate for OS> –ff=parse –chain inputfile outputfile

Parameters: path_pdb2pqr_exe : str Full path to pdb2pqr executable pdbfile : str PDB file to be converted to a PQR. Should be a full path if not in current working directory. outfile : str, optional File name for PQR file that will be generated. May be a full path if desired output is not in current working directory. ff : str, optional String instructing PDB2PQR what force field to employ. For more information visit: http://www.poissonboltzmann.org/docs/pdb2pqr-usage/ (log, err) : tuple When PDB2PQR runs, outputs that would have been sent to STDOUT are captured. Log contains the run log and err contains errors.
aesop.aesop.minimize_cg(struct, dest=None, disu=True, min_atom_shift=0.1, max_iter=1000, output='NO_REPORT', log=None, report_iter=10)

Summary Function to perform conjugate gradient descent minimization in Modeller on a user-provided structural file (PDB).

Parameters: struct : str String for path to PDB file dest : str String for path to location where minimized structure will be written disu : bool If true, positions of disulfide bridges will be automatically detected min_atom_shift : float If the max atomic shift between minimization steps is less than this value, then convergence is reached and minimization is terminated max_iter : int Maximum number of calls of objective function before minimization is terminated output : str Valid options are ‘NO_REPORT’ and ‘REPORT’. If set to ‘REPORT’, then a log file during minimation will be printed to screen log : str or None String for path to location where minimization report will be saved. If None, no report will be saved. Report contains only values of objective function at after each report interval. report_iter : int Integer that describes the number of minimization steps to perform before reporting the objective function. mdl : Model object from Modeller If dest is None, the function will return the minimized model. If dest is specified, then no model will be returned but the minimized model will be written to file.
aesop.aesop.mutatePDB(pdb, mutid, resnum, chain=None, resid='ALA')

Summary Function to generate a mutant structure given a local PDB file using MODELLER.

Parameters: pdb : str Full path to pdbfile that will be modified. mutid : str Prefix for mutated structure that will be written. May be a full path without file extension if desired output path is not in working directory. resnum : int, or type that can be forced to int Integer number specifying residue number to be mutated. chain : str, optional Chain ID where specified residue number is to be mutated. This is necessary to specify if residue numbers are not unique on each chain. resid : str, optional Three letter amino acid code specifying the type of mutation. Default mutation is to alanine (‘ALA’). None Writes mutated structure to file.
aesop.aesop.mutatePQR(pqrfile, mutid, resnum, chain=None, ff='parse')

Summary Mutate PQR file via side-chain truncation scheme (mutate to Alanine)

Parameters: pqrfile : str Full path to PQR file mutid : str Prefix to use when writing mutated PQR. Should be a full path if destination is not in working directory. resnum : int Residue number to mutate to alanine. chain : str, optional Chain where residue that will be mutated is located. None Writes mutated PQR to file specified by the prefix mutid.
aesop.aesop.plotDend(esd, filename=None)

Summary Function to display an electrostatic similarity dendrogram from a previously run ElecSimilarity class.

Parameters: esd : ElecSimilarity class ElecSimilarity class containing final esd matrix. filename : str, optional If the resulting plot should be written to disk, specify a filename. Otherwise, the image will only be saved. None Writes image to disk, if desired.
aesop.aesop.plotESD(esd, filename=None, cmap='hot')

Summary Function to display an electrostatic similarity heatmap from a previously run ElecSimilarity class.

Parameters: esd : ndarray ESD matrix from ElecSimilarity class (ElecSimilarity.esd). filename : str, optional If the resulting plot should be written to disk, specify a filename. Otherwise, the image will only be saved. cmap : str, optional Colormap from matplotlib to use. None Writes image to disk, if desired.
aesop.aesop.plotESD_interactive(esd, filename=None, cmap='YIGnBu', display_output='external')

Summary Function to display an electrostatic similarity heatmap from a previously run ElecSimilarity class. Figure is more interactive that the standard matplotlib figure.

Parameters: esd : ElecSimilarity class ElecSimilarity class containing final esd matrix. filename : str, optional If the resulting plot should be written to disk, specify a filename. Otherwise, the image will only be saved. cmap : str, optional Colormap from matplotlib to use. display_output : str Set output to either open local html file in browser or inline plot in notebook. None Writes image to disk, if desired.
aesop.aesop.plotNetwork(scan, filename=None, title='', dpi=300, cutoff=5.0, E=2.5, node_size=1500, font_size=12, alpha=0.8, edge_color='g', edge_width=3.0, layout=None, **kwargs)

Summary Function to visualize electrostatic interactions from a scan class (Alascan or Directed Mutagenesis). Requires networkx to be installed.

Parameters: scan : Alascan or DirectedMutagenesis class Scan class where calculation of free energies is complete. filename : str or None Full path to file where figure will be saved. If None, no figure is saved, but the plot is displayed and the graph is returned. title : str Matplotlib style title for plot. dpi : int Integer specifying the dots per inch, or image resolution. cutoff : float Distance cutoff in Angstroms for determining if a electrostatic interaction occurs. Default value is 5 Angstroms. E : float Threshold for determing those nodes that should be included in the network based on the value of the free energy perturbation that results from mutating the amino acid. If the magnitude of the free energy of association relative to the parent structure is greater than E, then the node is included. Default is 2.5 kJ/mol. node_size : int Parameter to scale size of nodes in network. Larger values result in nodes with larger diameter. font_size : int Font size for text within network. 12 pt font is default. alpha : float Set transparency of nodes. Default is 0.8. Accepted range is [0, 1]. edge_color : str Matplotlib-style specification of line color. Default is ‘g’ (green). edge_width : int Set the line width for edges. Default is 3 pt font. layout : Networkx layout kernel or None Network layout from networkx. Extra arguments for this layout may be passed as key word arguments to plotNetwork.
aesop.aesop.plotNetwork_interactive(scan, filename=None, title='', cutoff=5.0, E=2.5, font_size=14, node_size=20, edge_color='#888', edge_width=0.5, display_output='external', layout=None, **kwargs)

Summary Function to visualize electrostatic interactions from a scan class (Alascan or Directed Mutagenesis). Figure is more interactive than the standard matplotlib figure. Requires networkx to be installed.

Parameters: scan : Alascan or DirectedMutagenesis class Scan class where calculation of free energies is complete. filename : str or None Full path to file where figure will be saved. If None, no figure is saved, but the plot is displayed and the graph is returned. title : str Matplotlib style title for plot. cutoff : float Distance cutoff in Angstroms for determining if a electrostatic interaction occurs. Default value is 5 Angstroms. E : float Threshold for determing those nodes that should be included in the network based on the value of the free energy perturbation that results from mutating the amino acid. If the magnitude of the free energy of association relative to the parent structure is greater than E, then the node is included. Default is 2.5 kJ/mol. node_size : int Parameter to scale size of nodes in network. Larger values result in nodes with larger diameter. font_size : int Font size for text within network. 12 pt font is default. edge_color : str Matplotlib-style specification of line color. Default is ‘g’ (green). edge_width : int Set the line width for edges. Default is 3 pt font. display_output : str Set output to either open local html file in browser or inline plot in notebook. layout : Networkx layout kernel or None Network layout from networkx. Extra arguments for this layout may be passed as key word arguments to plotNetwork.
aesop.aesop.plotScan(Alascan, filename=None)

Summary Function to display results from the computational alanine or directed mutagenesis scan.

Parameters: Alascan : scan class Alascan or DirectedMutagenesis class after running the complete analysis. filename : None, optional If the resulting plot should be written to disk, specify a filename. Otherwise, the image will only be saved. tuple Handles to generated figure.
aesop.aesop.plotScan_interactive(Alascan, display_output='external', filename=None)

Summary Function to display results from the computational alanine or directed mutagenesis scan. Figure is more interactive than the standard matplotlib figure.

Parameters: Alascan : scan class Alascan or DirectedMutagenesis class after running the complete analysis. display_output : str Set output to either open local html file in browser or inline plot in notebook. filename : None, optional If the resulting plot should be written to disk, specify a filename. Otherwise, the image will only be saved. None Saves image of figure, if desired.
aesop.aesop.runProcess(command)

Summary Simple function intended to capture outputs from processes that write to STDOUT.

Parameters: command : list Lists of strings where each element is a part of the entire command. Ex: [‘script’,’arg1’,’arg2’,…] tuple return tuple where first element is output that would have been sent to STDOUT and the second element captures errors.
exception aesop.aesop.runProcess_Exception

Bases: exceptions.Exception

aesop.aesop.superpose(ref, pdb, atype='CA', output=None)

Summary Uses Modeller to superpose a PDB file (pdb) to a reference PDB (ref).

Parameters: ref : str Full path to PDB file (or name of file in working directory) that will be used as the reference for superpositioning. pdb : str Full path to PDB file (or name of file in working directory) that will be used as the mobile structure for superpositioning. atype : str Modeller-compatible string selection for atoms to be used in superpositioning. We suggest using ‘CA’. output : str or None If output is None, the file specified by pdb will be updated with the superposed structure. If specified, output should be a full path where the superposed structure will be saved.
aesop.aesop.writePDB(alascan, filename=None)

Summary Function to write free energies of association/solvation into B-factor column of PDB for easy visualization of results.

Parameters: alascan : scan class Alascan or DirectedMutagenesis class after running the complete analysis. filename : str, optional Full path to file where PDB file will be written. Defaults to job directory.