SSAGES Namespace Reference

Classes
class	AlphaRMSDCV
	Collective variable to measure alpha helix secondary structure. More...
class	AngleCV
	Collective variable to calculate angle. More...
class	ANNCV
	ANN (artifical neural network) collective variables. More...
class	AntiBetaRMSDCV
	Collective variable to measure antiparallel beta secondary structure. More...
class	BoxVolumeCV
	Collective variable on the volume of a box. More...
class	CollectiveVariable
	Abstract class for a collective variable. More...
class	CVManager
	Collective variable manager. More...
class	GyrationTensorCV
	Collective variable on components of the gyration tensor. More...
class	MockCV
	Mock collective variable for testing purposes. More...
class	PairwiseCV
	Generalized collective variable based on pairwise properties of atoms. 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	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	TorsionalCV
	Collective variable on the torsion angles. More...
class	BuildException
	Exception to be thrown when building the Driver fails. More...
class	EventListener
	Base abstract class for listening in to events fired by "Hook". More...
class	Grid
	Basic Grid. More...
class	GridBase
	Base class for Grids. More...
class	Hook
	Base class for hooks into the simultion engines. More...
class	JSONLoader
	Class for loading JSON content from files. More...
class	JSONLoaderPlugin
	Abstract class for JSON loader plugins. More...
class	IncludePlugin
	Class for JSON loader include plugin. More...
class	Logger
	Base class for logging SSAGES data. More...
class	ABF
	Adaptive Biasing Force Algorithm. More...
class	ANN
	Artificial Neural Network Method. More...
class	BFS
	Basis Function Sampling Algorithm. More...
class	CFF
	Combined Force Frequency (CFF) Algorithm. More...
class	DirectForwardFlux
	ForwardFlux sampling method. More...
class	ElasticBand
	Multi-walker Elastic Band. More...
class	FiniteTempString
	Finite Temperature Spring Method. More...
class	ForwardFlux
	ForwardFlux sampling method. More...
struct	Hill
	Multidimensional hill. More...
class	Meta
	"Vanilla" multi-dimensional Metadynamics. More...
class	Method
	Interface for Method implementations. More...
class	StringMethod
	String base class for FTS, Swarm, and elastic band. More...
class	Swarm
	Swarm of Trajectories String Method. More...
class	Umbrella
	Umbrella sampling method. More...
class	ResourceHandler
	Class that handles SSAGES resources for a simulation. More...
class	Snapshot
	Class containing a snapshot of the current simulation in time. More...
struct	BasisLUT
	Look-up table for basis functions. More...
struct	Map
	Map for histogram and coefficients. More...
class	BasisFunction
	Abstract class for all BasisFunction inheritance. More...
class	Chebyshev
	Defines the class of Chebyshev polynomials. More...
class	Legendre
	Defines the class of Legendre polynomials. More...
class	Fourier
	Defines the class of Fourier polynomials. More...
class	BasisEvaluator
	Calculates the inner product of all the basis functions and the histogram. More...
class	PairwiseKernel
	Pairwise kernel base class. More...
class	GaussianPK
	Gaussian Function. 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...

Typedefs
using	Vector = Eigen::VectorXd
	Arbitrary length vector.
using	Vector3 = Eigen::Vector3d
	Three-dimensional vector.
using	Bool3 = Eigen::Matrix< bool, 3, 1 >
	Three-dimensional boolean.
using	Integer3 = Eigen::Vector3i
	Three-dimensional 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 class	Dimension { x = 0 , y = 1 , z = 2 }
	Enum for dimension.

Functions
void	PrintBoldNotice (const std::string &notice, 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 std::string filename)
	Read contents from a file. More...
std::string	GetFilePath (const std::string filename)
	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. More...

Detailed Description

The global namespace for all SSAGES classes and functions.

This file is part of SSAGES - Software Suite for Advanced General Ensemble Simulations

Copyright 2017 Ashley Guo azguo.nosp@m.@uch.nosp@m.icago.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Yamil Colon yamil.nosp@m.colo.nosp@m.n2015.nosp@m.@u.n.nosp@m.orthw.nosp@m.este.nosp@m.rn.ed.nosp@m.u Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2020 Wei Chen wei.h.nosp@m.erbe.nosp@m.rt.ch.nosp@m.en@g.nosp@m.mail..nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.om Emre Sevgen sesev.nosp@m.gen@.nosp@m.uchic.nosp@m.ago..nosp@m.edu Yamil Colon yamil.nosp@m.colo.nosp@m.n2015.nosp@m.@u.n.nosp@m.orthw.nosp@m.este.nosp@m.rn.ed.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2017 Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2017 Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..edu Michael Quevillon mquev.nosp@m.ill@.nosp@m.nd.ed.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2017 Michael Webb xmweb.nosp@m.b@gm.nosp@m.ail.c.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..edu Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.om Emre Sevgen sesev.nosp@m.gen@.nosp@m.uchic.nosp@m.ago..nosp@m.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 On-the-fly 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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016-2017 Julian Helfferich julia.nosp@m.n.he.nosp@m.lffer.nosp@m.ich@.nosp@m.gmail.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2017 Julian Helfferich julia.nosp@m.n.he.nosp@m.lffer.nosp@m.ich@.nosp@m.gmail.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.om Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..edu Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.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 On-the-fly 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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Emre Sevgen sesev.nosp@m.gen@.nosp@m.uchic.nosp@m.ago..nosp@m.edu Joshua Moller jmoll.nosp@m.er@u.nosp@m.chica.nosp@m.go.e.nosp@m.du Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Joshua Moller jmoll.nosp@m.er@u.nosp@m.chica.nosp@m.go.e.nosp@m.du 2017 Julian Helfferich julia.nosp@m.n.he.nosp@m.lffer.nosp@m.ich@.nosp@m.gmail.nosp@m..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 - Software Suite for Advanced Generalized Ensemble Simulations

Copyright 2018 Emre Sevgen sesev.nosp@m.gen@.nosp@m.uchic.nosp@m.ago..nosp@m.edu and Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..edu 2020 Elizabeth M.Y. Lee emlee.nosp@m.@uch.nosp@m.icago.nosp@m..edu and Boyuan Yu boyua.nosp@m.nyu@.nosp@m.uchic.nosp@m.ago..nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.om Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..edu Joshua Lequieu lequi.nosp@m.eu@u.nosp@m.chica.nosp@m.go.e.nosp@m.du Hadi Ramezani-Dakhel ramez.nosp@m.ani@.nosp@m.uchic.nosp@m.ago..nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.om Joshua Lequieu lequi.nosp@m.eu@u.nosp@m.chica.nosp@m.go.e.nosp@m.du Hadi Ramezani-Dakhel ramez.nosp@m.ani@.nosp@m.uchic.nosp@m.ago..nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.om Jonathan K. Whitmer jwhit.nosp@m.me1@.nosp@m.nd.ed.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ashley Guo azguo.nosp@m.@uch.nosp@m.icago.nosp@m..edu Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..edu Jonathan K. Whitmer jwhit.nosp@m.me1@.nosp@m.nd.ed.nosp@m.u Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.om Ashley Guo azguo.nosp@m.@uch.nosp@m.icago.nosp@m..edu Cody Bezik bezik.nosp@m.@uch.nosp@m.icago.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations
  
• *
  
• * Copyright 2016 Cody Bezik bezik.nosp@m.@uch.nosp@m.icago.nosp@m..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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2017 Hythem Sidky hsidk.nosp@m.y@nd.nosp@m..edu Ben Sikora bsiko.nosp@m.ra90.nosp@m.6@gma.nosp@m.il.c.nosp@m.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 - Software Suite for Advanced General Ensemble Simulations

Copyright 2016 Yamil Colon yamil.nosp@m.colo.nosp@m.n2015.nosp@m.@u.n.nosp@m.orthw.nosp@m.este.nosp@m.rn.ed.nosp@m.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/.

Enumeration Type Documentation

GyrationTensor

enum SSAGES::GyrationTensor

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.

    {
        Rg = 0, // Radius of gyration (squared)
        principal1 = 1, // First (largest) principal moment 
        principal2 = 2, // Second (middle) principal moment 
        principal3 = 3, // Third (smallest) principal moment
        asphericity = 4, // Asphericity 
        acylindricity = 5, // Acylindricity
        shapeaniso = 6 // Relative shape anisotropy
    };

Function Documentation

DumpErrorsToConsole()

int SSAGES::DumpErrorsToConsole ( const std::vector< std::string > &  msgs, int  notw  )

inline

Print a list of errors.

Parameters

msgs	List of error messages.
notw	Width of the messages.

Returns

-1 always.

Write a list of error messages to the console.

Definition at line 103 of file DriverException.h.

    {
        if(isatty(fileno(stdout)))
        {
            std::cout << std::setw(notw) << std::right << "\033[1;31mError(s)! See below.\033[0m\n";
        }
        else
        {
            std::cout << std::setw(notw) << std::right << "Error(s)! See below.\n";
        }
        for(auto& msg : msgs)
                std::cout << " * " << msg << "\n";
        return -1;
    }

DumpNoticesToConsole()

void SSAGES::DumpNoticesToConsole ( const std::vector< std::string > &  msgs, std::string  prefix, int  notw  )

inline

Print a list of notices.

Parameters

msgs	List of messages.
prefix	Prefix to prepend to each message.
notw	Width of the messages.

Definition at line 124 of file DriverException.h.

    {
        if(isatty(fileno(stdout)))
        {
            std::cout << std::setw(notw) << std::right << "\033[32mOK!\033[0m\n";
        }
        else
        {
            std::cout << std::setw(notw) << std::right << "OK!\n";
        }
        if(msgs.size() == 0)
            return;
        
        for(auto& msg : msgs)
            std::cout << prefix << " * " << msg << "\n";
    }

gaussian()

double SSAGES::gaussian	(	double	dx,
		double	sigma
	)

Evlauate Gaussian. Helper function.

Parameters

dx	x-value.
sigma	Width of Gaussian

Returns

Value at x of Gaussian with center at zero and width sigma.

Definition at line 42 of file Meta.cpp.

    {
        double arg = (dx * dx) / (2. * sigma * sigma);
        return exp(-arg);
    }

References gaussian().

Referenced by SSAGES::Meta::AddHill(), SSAGES::Meta::CalcBiasForce(), and gaussian().

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gaussianDerv()

double SSAGES::gaussianDerv	(	double	dx,
		double	sigma
	)

Evaluate Gaussian derivative. Helper function.

Parameters

dx	Value of x.
sigma	Width of Gaussian.

Returns

Derivative at x of Gaussian with center at zero and width sigma.

Definition at line 54 of file Meta.cpp.

    {
        double arg =  (dx * dx) / (2. * sigma * sigma);
        double pre = - dx / (sigma * sigma);
        return pre * exp(-arg);
    }

References gaussianDerv().

Referenced by SSAGES::Meta::AddHill(), SSAGES::Meta::CalcBiasForce(), and gaussianDerv().

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GetFileContents()

std::string SSAGES::GetFileContents ( const std::string  filename )

inline

Read contents from a file.

Parameters

filename

Name of the file to read from.

Returns

String containing the contents of the file.

Retrieves the contents of a file and returns them in a string. Throws exception on failure.

Definition at line 46 of file FileContents.h.

    {
        std::ifstream ifs(filename);
        if(ifs.is_open()) {
            std::string contents( (std::istreambuf_iterator<char>(ifs) ),
                                  (std::istreambuf_iterator<char>()    ) );
            return contents;
        }
        throw std::runtime_error("File " + filename + " does not exist.");
    }

Referenced by SSAGES::IncludePlugin::ApplyFilter(), and SSAGES::JSONLoader::LoadFile().

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GetFilePath()

std::string SSAGES::GetFilePath ( const std::string  filename )

inline

Gets file path from filename.

Parameters

filename

String containing the absolute filename.

Returns

String containing only the directory path.

Definition at line 62 of file FileContents.h.

    {
        size_t found;
        found = filename.find_last_of("/\\");
        if(found == filename.npos)
            return "./";
        return filename.substr(0, found);
    }

Referenced by SSAGES::JSONLoader::LoadFile().

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PrintBoldNotice()

void SSAGES::PrintBoldNotice ( const std::string &  notice, int  msgw  )

inline

Print out Notice in bold text.

Parameters

notice	Text to be written to console.
msgw	Width of the message.

Definition at line 83 of file DriverException.h.

    {
        if(isatty(fileno(stdout)))
        {
            std::cout << std::setw(msgw + 8) << std::left << "\033[1m" + notice + "\033[0m";
        }
        else
        {
            std::cout << std::setw(msgw + 8) << std::left << notice;
        }
    }

roundf()

double SSAGES::roundf ( double  x )

inline

Quick helper function to round a double.

Parameters

x	Double to be rounded.

Returns

Rounded number as a double.

Definition at line 35 of file Snapshot.h.

    {
        return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
    }

Referenced by SSAGES::Snapshot::ApplyMinimumImage().

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