SSAGES
0.8.3
Software Suite for Advanced General Ensemble Simulations

Classes  
class  ABF 
Adaptive Biasing Force Algorithm. More...  
class  AlphaRMSDCV 
Collective variable to measure alpha helix secondary structure. More...  
class  AngleCV 
Collective variable to calculate angle. More...  
class  ANN 
Artificial Neural Network Method. More...  
class  AntiBetaRMSDCV 
Collective variable to measure antiparallel beta secondary structure. More...  
class  BasisEvaluator 
Calculates the inner product of all the basis functions and the histogram. More...  
class  BasisFunction 
Abstract class for all BasisFunction inheritance. More...  
struct  BasisLUT 
Lookup table for basis functions. More...  
class  BFS 
Basis Function Sampling Algorithm. More...  
class  BoxVolumeCV 
Collective variable on the volume of a box. More...  
class  BuildException 
Exception to be thrown when building the Driver fails. More...  
class  Chebyshev 
Defines the class of Chebyshev polynomials. More...  
class  CollectiveVariable 
Abstract class for a collective variable. More...  
class  Constraint 
Interface for Constraint implementations. More...  
class  COPSS 
Wrapper class for COPSS simulations. More...  
class  COPSSImage 
Image method. More...  
class  CVManager 
Collective variable manager. More...  
class  DirectForwardFlux 
ForwardFlux sampling method. More...  
class  ElasticBand 
Multiwalker Elastic Band. More...  
class  EventListener 
Base abstract class for listening in to events fired by "Hook". More...  
class  FiniteTempString 
Finite Temperature Spring Method. More...  
class  ForwardFlux 
ForwardFlux sampling method. More...  
class  Fourier 
Defines the class of Fourier polynomials. More...  
class  GaussianPK 
Gaussian Function. More...  
class  Grid 
Basic Grid. More...  
class  GridBase 
Base class for Grids. More...  
class  GyrationTensorCV 
Collective variable on components of the gyration tensor. More...  
struct  Hill 
Multidimensional hill. More...  
class  Hook 
Base class for hooks into the simultion engines. More...  
class  IncludePlugin 
Class for JSON loader include plugin. More...  
class  JSONLoader 
Class for loading JSON content from files. More...  
class  JSONLoaderPlugin 
Abstract class for JSON loader plugins. More...  
class  Legendre 
Defines the class of Legendre polynomials. More...  
class  Logger 
Base class for logging SSAGES data. More...  
struct  Map 
Map for histogram and coefficients. More...  
class  Meta 
"Vanilla" multidimensional Metadynamics. More...  
class  Method 
Interface for Method implementations. More...  
class  MockCV 
Mock collective variable for testing purposes. More...  
class  PairwiseCV 
Generalized collective variable based on pairwise properties of atoms. More...  
class  PairwiseKernel 
Pairwise kernel base class. More...  
class  ParallelBetaRMSDCV 
Collective variable to measure parallel beta sheet secondary structure. More...  
class  ParticleCoordinateCV 
Collective variable on a particle coordinate. More...  
class  ParticlePositionCV 
Collective variable on an particle position. More...  
class  ParticleSeparationCV 
Collective variable on the distance between two particles' centers of mass. More...  
class  RationalSwitchPK 
Rational Switching Function. More...  
class  ReadBackbone 
Utility class to read protein backbone atoms from a reference file. More...  
class  ReadFile 
Utility class to read file. More...  
class  ResourceHandler 
Class that handles SSAGES resources for a simulation. More...  
class  RMSDCV 
Collective variable to calculate root mean square displacement. More...  
class  RouseModeCV 
Collective variable is a Rouse mode for a polymer chain comprised of N particle groups. More...  
class  Snapshot 
Class containing a snapshot of the current simulation in time. More...  
class  StringMethod 
String base class for FTS, Swarm, and elastic band. More...  
class  Swarm 
Swarm of Trajectories String Method. More...  
class  TorsionalCV 
Collective variable on the torsion angles. More...  
class  Umbrella 
Umbrella sampling method. More...  
Typedefs  
using  ConstraintList = std::vector< Constraint * > 
List of Constraints.  
using  Vector = Eigen::VectorXd 
Arbitrary length vector.  
using  Vector3 = Eigen::Vector3d 
Threedimensional vector.  
using  Bool3 = Eigen::Matrix< bool, 3, 1 > 
Threedimensional boolean.  
using  Integer3 = Eigen::Vector3i 
Threedimensional integer vector.  
using  Matrix3 = Eigen::Matrix3d 
3x3 matrix.  
using  Matrix3N = Eigen::MatrixX3d 
nx3 matrix.  
using  Label = std::vector< int > 
List of integers.  
using  CVList = std::vector< CollectiveVariable * > 
List of Collective Variables.  
Enumerations  
enum  GyrationTensor { Rg = 0, principal1 = 1, principal2 = 2, principal3 = 3, asphericity = 4, acylindricity = 5, shapeaniso = 6 } 
Define components of gyration tensor. More...  
enum  Dimension { x = 0, y = 1, z = 2 } 
Enum for dimension.  
Functions  
void  PrintBoldNotice (const std::string ¬ice, int msgw) 
Print out Notice in bold text. More...  
int  DumpErrorsToConsole (const std::vector< std::string > &msgs, int notw) 
Print a list of errors. More...  
void  DumpNoticesToConsole (const std::vector< std::string > &msgs, std::string prefix, int notw) 
Print a list of notices. More...  
std::string  GetFileContents (const char *filename) 
Read contents from a file. More...  
std::string  GetFilePath (const std::string &str) 
Gets file path from filename. More...  
double  gaussian (double dx, double sigma) 
Evlauate Gaussian. Helper function. More...  
double  gaussianDerv (double dx, double sigma) 
Evaluate Gaussian derivative. Helper function. More...  
double  roundf (double x) 
Quick helper function to round a double.  
The global namespace for all SSAGES classes and functions.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Jiyuan Li jyli@ uchi cago. edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2017 Ashley Guo azguo @uch icago .edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Yamil Colon yamil Hythem Sidky colo n2015 @u.n orthw este rn.ed uhsidk y@nd .edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Hythem Sidky hsidk y@nd .edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ben Sikora bsiko Emre Sevgen ra90 6@gma il.c omsesev Yamil Colon gen@ uchic ago. eduyamil colo n2015 @u.n orthw este rn.ed u
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2017 Hythem Sidky hsidk y@nd .edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ben Sikora bsiko ra90 6@gma il.c om
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2017 Hythem Sidky hsidk Michael Quevillon y@nd .edumquev ill@ nd.ed u
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2017 Michael Webb xmweb b@gm ail.c om
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Hythem Sidky hsidk Ben Sikora y@nd .edubsiko Emre Sevgen ra90 6@gma il.c omsesev gen@ uchic ago. edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file has been obtained from SAPHRON  Statistical Applied PHysics through Random Onthefly Numerics https://github.com/hsidky/SAPHRON
Copyright 2017 Hythem Sidky
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 20162017 Julian Helfferich julia n.he lffer ich@ gmail .com
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2017 Julian Helfferich julia n.he lffer ich@ gmail .com
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ben Sikora bsiko Hythem Sidky ra90 6@gma il.c omhsidk y@nd .edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Hythem Sidky hsidk Ben Sikora y@nd .edubsiko ra90 6@gma il.c om
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file has been adapted from SAPHRON  Statistical Applied PHysics through Random Onthefly Numerics https://github.com/hsidky/SAPHRON
Copyright 2016 Hythem Sidky
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Emre Sevgen sesev Joshua Moller gen@ uchic ago. edujmoll Hythem Sidky er@u chica go.e duhsidk y@nd .edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Joshua Moller jmoll 2017 Julian Helfferich er@u chica go.e dujulia n.he lffer ich@ gmail .com
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ben Sikora bsiko Hythem Sidky ra90 6@gma il.c omhsidk Joshua Lequieu y@nd .edulequi Hadi RamezaniDakhel eu@u chica go.e duramez ani@ uchic ago. edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ben Sikora bsiko Joshua Lequieu ra90 6@gma il.c omlequi Hadi RamezaniDakhel eu@u chica go.e duramez ani@ uchic ago. edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ben Sikora bsiko Jonathan K. Whitmer ra90 6@gma il.c omjwhit me1@ nd.ed u
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ashley Guo azguo Ben Sikora @uch icago .edubsiko ra90 6@gma il.c om
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Hythem Sidky hsidk Jonathan K. Whitmer y@nd .edujwhit Ben Sikora me1@ nd.ed ubsiko ra90 6@gma il.c om
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Ben Sikora bsiko Ashley Guo ra90 6@gma il.c omazguo Cody Bezik @uch icago .edubezik @uch icago .edu
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2017 Hythem Sidky hsidk Ben Sikora y@nd .edubsiko ra90 6@gma il.c om
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
This file is part of SSAGES  Suite for Advanced Generalized Ensemble Simulations
Copyright 2016 Yamil Colon yamil colo n2015 @u.n orthw este rn.ed u
SSAGES is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SSAGES is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with SSAGES. If not, see http://www.gnu.org/licenses/.
Define components of gyration tensor.
Components of the gyration tensor. CV uses these definitions to determine what to calculate.
Definition at line 37 of file GyrationTensorCV.h.

inline 
Print a list of errors.
msgs  List of error messages. 
notw  Width of the messages. 
Write a list of error messages to the console.
Definition at line 102 of file DriverException.h.

inline 
Print a list of notices.
msgs  List of messages. 
prefix  Prefix to prepend to each message. 
notw  Width of the messages. 
Definition at line 123 of file DriverException.h.
double SSAGES::gaussian  (  double  dx, 
double  sigma  
) 
Evlauate Gaussian. Helper function.
dx  xvalue. 
sigma  Width of Gaussian 
Definition at line 42 of file Meta.cpp.
References gaussian().
Referenced by SSAGES::Meta::AddHill(), SSAGES::Meta::CalcBiasForce(), and gaussian().
double SSAGES::gaussianDerv  (  double  dx, 
double  sigma  
) 
Evaluate Gaussian derivative. Helper function.
dx  Value of x. 
sigma  Width of Gaussian. 
Definition at line 54 of file Meta.cpp.
References gaussianDerv().
Referenced by SSAGES::Meta::AddHill(), SSAGES::Meta::CalcBiasForce(), and gaussianDerv().

inline 
Read contents from a file.
filename  Name of the file to read from. 
Retrieves the contents of a file and returns them in a string. Throws exception on failure.
Definition at line 47 of file FileContents.h.
Referenced by SSAGES::IncludePlugin::ApplyFilter(), and SSAGES::JSONLoader::LoadFile().

inline 
Gets file path from filename.
str  String containing the absolute filename. 
Definition at line 73 of file FileContents.h.
Referenced by SSAGES::JSONLoader::LoadFile().

inline 
Print out Notice in bold text.
notice  Text to be written to console. 
msgw  Width of the message. 
Definition at line 82 of file DriverException.h.