Hi Frido,

these are the methods I implemented so far in a new class Morse.h.

The first one returns a constant score if *feature* is greater then * threshold*. At the moment the returned score is the Harmonic potential calculated when feature >= threshold (i.e. when feature is >= threshold, the returned score will always be Harmonic::evaluate(threshold) ). The second one implements the Morse potential as described by Marc.

These methods are still in a development phase since there are some parameters which need to be better defined, such as the threshold to be applied and the parameters that define the Morse potential.

Regards, Davide

// 1. a function that is a Harmonic for x<std and constant for x>std

> /** If the feature is greater than or equal to the threshold, the score > is constant. > \param[in] feature Value of feature being tested. > \return Score > */ > virtual Float evaluate(Float feature) const {

Float k = Harmonic::get_k(); > Float mean = Harmonic::get_mean(); > Float threshold = 1.0 * mean + XYZRDecorator::get_radius();

> if ( feature <= threshold ) { > return Harmonic::evaluate(feature); > } else { > return evaluate_with_derivative(threshold, k).first; > } > } >

// 2. a function that is a Harmonic for x<std and asymptotically approaches a constant value for x-> inf:

> /** If the feature is greater than or equal to the threshold, apply the > Morse potential. > \param[in] feature Value of feature being tested. > \return Score > */ > virtual Float evaluate(Float feature) const { > Float mean = Harmonic::get_mean(); > Float k = Harmonic::get_k();

Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >

> // MORSE POTENTIAL PARAMETERS > Float var = 1.0/k; > Float alpha = 2.0; > Float De = 40.0; > Float beta = 1.0; > Float swf = 0.0; > > if ( feature <= threshold ) { > return Harmonic::evaluate(feature); > } else { > swf = beta * pow( ( 1.0 - exp( - sqrt( alpha/De ) * ( feature - > threshold )/2.0 ) ), 2 ); // MORSE POTENTIAL > return swf; > } > } >

On Thu, Jan 8, 2009 at 10:20 AM, Marc A. Marti-Renom mmarti@cipf.es wrote:

> Hi Frido, > Indeed we are also in need of similar stuff. Davide Bau (a postdoc in my > lab and also in the IMP-Dev list) has already implemented a sort of a MORSE > potential in IMP restraints, which is not what you ask but may be similar. I > implemented many many many years ago something similar in CHARMM ( > http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf, Chapter 4 > page 86). > > Unfortunately, we are NOT yet ready to commit the changes in the code to > the SVN since we are in the middle of production phase (ie, making models) > thus would prefer not to update IMP. But I am sure we could do soon. > > Davide, any comments? :-) > > m > > ------- > *Marc A. Marti-Renom, **Head of the Structural Genomics Unit* > Bioinformatics & Genomics Department, Prince Felipe Research Center > Avda. Autopista del Saler, 16 , 46012 Valencia, Spain > Tel +34 96 328 96 80 (ext. 1015) Fax +34 96 328 97 01 > email mmarti@cipf.es web http://sgu.bioinfo.cipf.es > > *** Consider the environment. Print responsibly. *** > > On Jan 8, 2009, at 10:00 AM, Friedrich Foerster wrote: > > hi all, > > when dealing with experimental restraints i often feel that harmonic > restraints are somewhat unsatisfactory: > experimental data can be wrong and thus there is not necessarily a solution > that fulfills all restraints (score=0). in those cases, a model with a lower > score is not necessarily any more correct than a higher scoring one. thus, i > think it'd be good to have an additional scoring function that levels off if > the feature exceeds a certain value. for example, i'd suggest the following > two functions alternatively to Harmonic: > 1. a function that is a Harmonic for x<std and constant for x>std > 2. a function that is a Harmonic for x<std and asymptotically approaches a > constant value for x-> inf: > e.g.: f=x^2 for x<1 and f=2-x^-2 for x>1 (would even be continuous in > 1st derivative) > > is anyone else also interested in something like that? > any better suggestions? > is any IMP core expert interested and willing to code that (including > analogous functions for Upper and Lower Harmonic)? probably i'd be one of > the slowest and clumsiest persons in doing that... > > thanks > > frido > > > -- > > Friedrich Foerster > Max-Planck Institut fuer Biochemie > Am Klopferspitz 18 > D-82152 Martinsried > > Tel: +49 89 8578 2651 > Fax: +49 89 8578 2641 > > foerster@biochem.mpg.de > > www.tomotronic.org > > > > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >

It's the exp() function of the standard cmath. Performance is indeed another thing to be improved.

Davide

On Thu, Jan 8, 2009 at 12:37 PM, Friedrich Foerster <foerster@biochem.mpg.de > wrote:

> thanks. > > just for info: isn't the exp() a bit slow, or are you using some dodgy > macro? > > best > > frido > > > On Jan 8, 2009, at 12:05 PM, Davide Baú wrote: > > Hi Frido, >> >> these are the methods I implemented so far in a new class Morse.h. >> >> The first one returns a constant score if feature is greater then >> threshold. At the moment the returned score is the Harmonic potential >> calculated when feature >= threshold (i.e. when feature is >= threshold, the >> returned score will always be Harmonic::evaluate(threshold) ). >> The second one implements the Morse potential as described by Marc. >> >> These methods are still in a development phase since there are some >> parameters which need to be better defined, such as the threshold to be >> applied and the parameters that define the Morse potential. >> >> Regards, >> Davide >> >> >> // 1. a function that is a Harmonic for x<std and constant for x>std >> /** If the feature is greater than or equal to the threshold, the score >> is constant. >> \param[in] feature Value of feature being tested. >> \return Score >> */ >> virtual Float evaluate(Float feature) const { >> Float k = Harmonic::get_k(); >> Float mean = Harmonic::get_mean(); >> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >> if ( feature <= threshold ) { >> return Harmonic::evaluate(feature); >> } else { >> return evaluate_with_derivative(threshold, k).first; >> } >> } >> >> >> // 2. a function that is a Harmonic for x<std and asymptotically >> approaches a constant value for x-> inf: >> /** If the feature is greater than or equal to the threshold, apply the >> Morse potential. >> \param[in] feature Value of feature being tested. >> \return Score >> */ >> virtual Float evaluate(Float feature) const { >> Float mean = Harmonic::get_mean(); >> Float k = Harmonic::get_k(); >> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >> >> // MORSE POTENTIAL PARAMETERS >> Float var = 1.0/k; >> Float alpha = 2.0; >> Float De = 40.0; >> Float beta = 1.0; >> Float swf = 0.0; >> >> if ( feature <= threshold ) { >> return Harmonic::evaluate(feature); >> } else { >> swf = beta * pow( ( 1.0 - exp( - sqrt( alpha/De ) * ( feature - >> threshold )/2.0 ) ), 2 ); // MORSE POTENTIAL >> return swf; >> } >> } >> >> >> >> >> >> On Thu, Jan 8, 2009 at 10:20 AM, Marc A. Marti-Renom mmarti@cipf.es >> wrote: >> Hi Frido, >> >> Indeed we are also in need of similar stuff. Davide Bau (a postdoc in my >> lab and also in the IMP-Dev list) has already implemented a sort of a MORSE >> potential in IMP restraints, which is not what you ask but may be similar. I >> implemented many many many years ago something similar in CHARMM ( >> http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf, Chapter 4 >> page 86). >> >> Unfortunately, we are NOT yet ready to commit the changes in the code to >> the SVN since we are in the middle of production phase (ie, making models) >> thus would prefer not to update IMP. But I am sure we could do soon. >> >> Davide, any comments? :-) >> >> m >> >> ------- >> Marc A. Marti-Renom, Head of the Structural Genomics Unit >> Bioinformatics & Genomics Department, Prince Felipe Research Center >> Avda. Autopista del Saler, 16 , 46012 Valencia, Spain >> Tel +34 96 328 96 80 (ext. 1015) Fax +34 96 328 97 01 >> email mmarti@cipf.es web http://sgu.bioinfo.cipf.es >> >> *** Consider the environment. Print responsibly. *** >> >> On Jan 8, 2009, at 10:00 AM, Friedrich Foerster wrote: >> >> hi all, >>> >>> when dealing with experimental restraints i often feel that harmonic >>> restraints are somewhat unsatisfactory: >>> experimental data can be wrong and thus there is not necessarily a >>> solution that fulfills all restraints (score=0). in those cases, a model >>> with a lower score is not necessarily any more correct than a higher scoring >>> one. thus, i think it'd be good to have an additional scoring function that >>> levels off if the feature exceeds a certain value. for example, i'd suggest >>> the following two functions alternatively to Harmonic: >>> 1. a function that is a Harmonic for x<std and constant for x>std >>> 2. a function that is a Harmonic for x<std and asymptotically approaches >>> a constant value for x-> inf: >>> e.g.: f=x^2 for x<1 and f=2-x^-2 for x>1 (would even be continuous in >>> 1st derivative) >>> >>> is anyone else also interested in something like that? >>> any better suggestions? >>> is any IMP core expert interested and willing to code that (including >>> analogous functions for Upper and Lower Harmonic)? probably i'd be one of >>> the slowest and clumsiest persons in doing that... >>> >>> thanks >>> >>> frido >>> >>> >>> -- >>> >>> Friedrich Foerster >>> Max-Planck Institut fuer Biochemie >>> Am Klopferspitz 18 >>> D-82152 Martinsried >>> >>> Tel: +49 89 8578 2651 >>> Fax: +49 89 8578 2641 >>> >>> foerster@biochem.mpg.de >>> >>> www.tomotronic.org >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> > > -- > > Friedrich Foerster > Max-Planck Institut fuer Biochemie > Am Klopferspitz 18 > D-82152 Martinsried > > Tel: +49 89 8578 2651 > Fax: +49 89 8578 2641 > > foerster@biochem.mpg.de > > www.tomotronic.org > > > > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >

___________ *Carpe diem.*

Chi non ride non è una persona seria. Who does not laugh is not a serious person.

*"Di solito non sono un uomo religioso, ma se tu sei lassu', salvami, Superman!"* > Homer Simpson

On Thu, Jan 8, 2009 at 7:58 PM, Daniel Russel drussel@gmail.com wrote:

> Having such a general function in IMP would be very nice (I was using a > non-smooth truncated harmonic before). Such a function should not be > dependent on the parameter tuning (since the parameters would simply be > passes by a user). > Davide, if you have a version of your code which allows the user to pass in > the threshold and cutoff, we can put a version into core for people to look > at as a starting point. Otherwise, it would only take me a few minutes to > throw something together. > > It sounds like we would like something like: > > class TruncatedHarmonicLowerBound { > /** threshold > center, capped_value > .5*k*(center-threshold)^2 */ > TruncatedHarmonicLowerBound(Float center, Float k, Float threshold, > Float capped_value) > } > that'd be great. for me that'd help a lot

> > If we use Frido's smooth function, capped_value could default to > k*(threshold-center)^2, i.e. 2x the value at the threshold to give it space > to go smoothly to the value. And we could have Upper and symmetric versions > too (as that is little more code). > also fine with me. for the specific function: i just came up with 2-x^(-2) spontaneously. i'd also be happy with another solution (morse, fermi, ...) if that is advantageous. if anyone has a probabilistic reasoning for a specific function, that'd be nice.

thanks

frido

> > > On Jan 8, 2009, at 3:44 AM, Davide Baú wrote: > > It's the exp() function of the standard cmath. > Performance is indeed another thing to be improved. > > Davide > > > > On Thu, Jan 8, 2009 at 12:37 PM, Friedrich Foerster < > foerster@biochem.mpg.de> wrote: > >> thanks. >> >> just for info: isn't the exp() a bit slow, or are you using some dodgy >> macro? >> >> best >> >> frido >> >> >> On Jan 8, 2009, at 12:05 PM, Davide Baú wrote: >> >> Hi Frido, >>> >>> these are the methods I implemented so far in a new class Morse.h. >>> >>> The first one returns a constant score if feature is greater then >>> threshold. At the moment the returned score is the Harmonic potential >>> calculated when feature >= threshold (i.e. when feature is >= threshold, the >>> returned score will always be Harmonic::evaluate(threshold) ). >>> The second one implements the Morse potential as described by Marc. >>> >>> These methods are still in a development phase since there are some >>> parameters which need to be better defined, such as the threshold to be >>> applied and the parameters that define the Morse potential. >>> >>> Regards, >>> Davide >>> >>> >>> // 1. a function that is a Harmonic for x<std and constant for x>std >>> /** If the feature is greater than or equal to the threshold, the score >>> is constant. >>> \param[in] feature Value of feature being tested. >>> \return Score >>> */ >>> virtual Float evaluate(Float feature) const { >>> Float k = Harmonic::get_k(); >>> Float mean = Harmonic::get_mean(); >>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>> if ( feature <= threshold ) { >>> return Harmonic::evaluate(feature); >>> } else { >>> return evaluate_with_derivative(threshold, k).first; >>> } >>> } >>> >>> >>> // 2. a function that is a Harmonic for x<std and asymptotically >>> approaches a constant value for x-> inf: >>> /** If the feature is greater than or equal to the threshold, apply the >>> Morse potential. >>> \param[in] feature Value of feature being tested. >>> \return Score >>> */ >>> virtual Float evaluate(Float feature) const { >>> Float mean = Harmonic::get_mean(); >>> Float k = Harmonic::get_k(); >>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>> >>> // MORSE POTENTIAL PARAMETERS >>> Float var = 1.0/k; >>> Float alpha = 2.0; >>> Float De = 40.0; >>> Float beta = 1.0; >>> Float swf = 0.0; >>> >>> if ( feature <= threshold ) { >>> return Harmonic::evaluate(feature); >>> } else { >>> swf = beta * pow( ( 1.0 - exp( - sqrt( alpha/De ) * ( feature - >>> threshold )/2.0 ) ), 2 ); // MORSE POTENTIAL >>> return swf; >>> } >>> } >>> >>> >>> >>> >>> >>> On Thu, Jan 8, 2009 at 10:20 AM, Marc A. Marti-Renom mmarti@cipf.es >>> wrote: >>> Hi Frido, >>> >>> Indeed we are also in need of similar stuff. Davide Bau (a postdoc in my >>> lab and also in the IMP-Dev list) has already implemented a sort of a MORSE >>> potential in IMP restraints, which is not what you ask but may be similar. I >>> implemented many many many years ago something similar in CHARMM ( >>> http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf, Chapter 4 >>> page 86). >>> >>> Unfortunately, we are NOT yet ready to commit the changes in the code to >>> the SVN since we are in the middle of production phase (ie, making models) >>> thus would prefer not to update IMP. But I am sure we could do soon. >>> >>> Davide, any comments? :-) >>> >>> m >>> >>> ------- >>> Marc A. Marti-Renom, Head of the Structural Genomics Unit >>> Bioinformatics & Genomics Department, Prince Felipe Research Center >>> Avda. Autopista del Saler, 16 , 46012 Valencia, Spain >>> Tel +34 96 328 96 80 (ext. 1015) Fax +34 96 328 97 01 >>> email mmarti@cipf.es web http://sgu.bioinfo.cipf.es >>> >>> *** Consider the environment. Print responsibly. *** >>> >>> On Jan 8, 2009, at 10:00 AM, Friedrich Foerster wrote: >>> >>> hi all, >>>> >>>> when dealing with experimental restraints i often feel that harmonic >>>> restraints are somewhat unsatisfactory: >>>> experimental data can be wrong and thus there is not necessarily a >>>> solution that fulfills all restraints (score=0). in those cases, a model >>>> with a lower score is not necessarily any more correct than a higher scoring >>>> one. thus, i think it'd be good to have an additional scoring function that >>>> levels off if the feature exceeds a certain value. for example, i'd suggest >>>> the following two functions alternatively to Harmonic: >>>> 1. a function that is a Harmonic for x<std and constant for x>std >>>> 2. a function that is a Harmonic for x<std and asymptotically approaches >>>> a constant value for x-> inf: >>>> e.g.: f=x^2 for x<1 and f=2-x^-2 for x>1 (would even be continuous in >>>> 1st derivative) >>>> >>>> is anyone else also interested in something like that? >>>> any better suggestions? >>>> is any IMP core expert interested and willing to code that (including >>>> analogous functions for Upper and Lower Harmonic)? probably i'd be one of >>>> the slowest and clumsiest persons in doing that... >>>> >>>> thanks >>>> >>>> frido >>>> >>>> >>>> -- >>>> >>>> Friedrich Foerster >>>> Max-Planck Institut fuer Biochemie >>>> Am Klopferspitz 18 >>>> D-82152 Martinsried >>>> >>>> Tel: +49 89 8578 2651 >>>> Fax: +49 89 8578 2641 >>>> >>>> foerster@biochem.mpg.de >>>> >>>> www.tomotronic.org >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> >> -- >> >> Friedrich Foerster >> Max-Planck Institut fuer Biochemie >> Am Klopferspitz 18 >> D-82152 Martinsried >> >> Tel: +49 89 8578 2651 >> Fax: +49 89 8578 2641 >> >> foerster@biochem.mpg.de >> >> www.tomotronic.org >> >> >> >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> > > > ___________ > *Carpe diem.* > > Chi non ride non è una persona seria. > Who does not laugh is not a serious person. > > *"Di solito non sono un uomo religioso, ma se tu sei lassu', salvami, > Superman!"* > > Homer Simpson > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >

Hi Daniel,

would it be possible to check in the Morse potential too, so that to test if it works fine?

Cheers, Davide

On Mon, Jan 12, 2009 at 2:14 AM, Daniel Russel drussel@gmail.com wrote:

> I checked in a truncated harmonic (IMP.core.TruncatedHarmonicBound, > TruncatedHarmonicLowerBound, TruncatedHarmonicUpperBound) for people to look > at. It currently uses Frido's function, but can be easily changed to > something else. I deliberately kept the documentation vague on the details > of the internal function as I am not sure we want the exact nature to be > important (at least until we come up with a function which we have a strong > justification for). Anyway, let me know if you have comments. > > > On Jan 8, 2009, at 11:11 AM, Friedrich Foerster wrote: > > > > On Thu, Jan 8, 2009 at 7:58 PM, Daniel Russel drussel@gmail.com wrote: > >> Having such a general function in IMP would be very nice (I was using a >> non-smooth truncated harmonic before). Such a function should not be >> dependent on the parameter tuning (since the parameters would simply be >> passes by a user). >> Davide, if you have a version of your code which allows the user to pass >> in the threshold and cutoff, we can put a version into core for people to >> look at as a starting point. Otherwise, it would only take me a few minutes >> to throw something together. >> >> It sounds like we would like something like: >> >> class TruncatedHarmonicLowerBound { >> /** threshold > center, capped_value > .5*k*(center-threshold)^2 */ >> TruncatedHarmonicLowerBound(Float center, Float k, Float threshold, >> Float capped_value) >> } >> > that'd be great. for me that'd help a lot > >> >> If we use Frido's smooth function, capped_value could default to >> k*(threshold-center)^2, i.e. 2x the value at the threshold to give it space >> to go smoothly to the value. And we could have Upper and symmetric versions >> too (as that is little more code). >> > also fine with me. > for the specific function: i just came up with 2-x^(-2) spontaneously. i'd > also be happy with another solution (morse, fermi, ...) if that is > advantageous. if anyone has a probabilistic reasoning for a specific > function, that'd be nice. > > thanks > > frido > >> >> >> On Jan 8, 2009, at 3:44 AM, Davide Baú wrote: >> >> It's the exp() function of the standard cmath. >> Performance is indeed another thing to be improved. >> >> Davide >> >> >> >> On Thu, Jan 8, 2009 at 12:37 PM, Friedrich Foerster < >> foerster@biochem.mpg.de> wrote: >> >>> thanks. >>> >>> just for info: isn't the exp() a bit slow, or are you using some dodgy >>> macro? >>> >>> best >>> >>> frido >>> >>> >>> On Jan 8, 2009, at 12:05 PM, Davide Baú wrote: >>> >>> Hi Frido, >>>> >>>> these are the methods I implemented so far in a new class Morse.h. >>>> >>>> The first one returns a constant score if feature is greater then >>>> threshold. At the moment the returned score is the Harmonic potential >>>> calculated when feature >= threshold (i.e. when feature is >= threshold, the >>>> returned score will always be Harmonic::evaluate(threshold) ). >>>> The second one implements the Morse potential as described by Marc. >>>> >>>> These methods are still in a development phase since there are some >>>> parameters which need to be better defined, such as the threshold to be >>>> applied and the parameters that define the Morse potential. >>>> >>>> Regards, >>>> Davide >>>> >>>> >>>> // 1. a function that is a Harmonic for x<std and constant for x>std >>>> /** If the feature is greater than or equal to the threshold, the score >>>> is constant. >>>> \param[in] feature Value of feature being tested. >>>> \return Score >>>> */ >>>> virtual Float evaluate(Float feature) const { >>>> Float k = Harmonic::get_k(); >>>> Float mean = Harmonic::get_mean(); >>>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>>> if ( feature <= threshold ) { >>>> return Harmonic::evaluate(feature); >>>> } else { >>>> return evaluate_with_derivative(threshold, k).first; >>>> } >>>> } >>>> >>>> >>>> // 2. a function that is a Harmonic for x<std and asymptotically >>>> approaches a constant value for x-> inf: >>>> /** If the feature is greater than or equal to the threshold, apply the >>>> Morse potential. >>>> \param[in] feature Value of feature being tested. >>>> \return Score >>>> */ >>>> virtual Float evaluate(Float feature) const { >>>> Float mean = Harmonic::get_mean(); >>>> Float k = Harmonic::get_k(); >>>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>>> >>>> // MORSE POTENTIAL PARAMETERS >>>> Float var = 1.0/k; >>>> Float alpha = 2.0; >>>> Float De = 40.0; >>>> Float beta = 1.0; >>>> Float swf = 0.0; >>>> >>>> if ( feature <= threshold ) { >>>> return Harmonic::evaluate(feature); >>>> } else { >>>> swf = beta * pow( ( 1.0 - exp( - sqrt( alpha/De ) * ( feature - >>>> threshold )/2.0 ) ), 2 ); // MORSE POTENTIAL >>>> return swf; >>>> } >>>> } >>>> >>>> >>>> >>>> >>>> >>>> On Thu, Jan 8, 2009 at 10:20 AM, Marc A. Marti-Renom mmarti@cipf.es >>>> wrote: >>>> Hi Frido, >>>> >>>> Indeed we are also in need of similar stuff. Davide Bau (a postdoc in my >>>> lab and also in the IMP-Dev list) has already implemented a sort of a MORSE >>>> potential in IMP restraints, which is not what you ask but may be similar. I >>>> implemented many many many years ago something similar in CHARMM ( >>>> http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf, Chapter 4 >>>> page 86). >>>> >>>> Unfortunately, we are NOT yet ready to commit the changes in the code to >>>> the SVN since we are in the middle of production phase (ie, making models) >>>> thus would prefer not to update IMP. But I am sure we could do soon. >>>> >>>> Davide, any comments? :-) >>>> >>>> m >>>> >>>> ------- >>>> Marc A. Marti-Renom, Head of the Structural Genomics Unit >>>> Bioinformatics & Genomics Department, Prince Felipe Research Center >>>> Avda. Autopista del Saler, 16 , 46012 Valencia, Spain >>>> Tel +34 96 328 96 80 (ext. 1015) Fax +34 96 328 97 01 >>>> email mmarti@cipf.es web http://sgu.bioinfo.cipf.es >>>> >>>> *** Consider the environment. Print responsibly. *** >>>> >>>> On Jan 8, 2009, at 10:00 AM, Friedrich Foerster wrote: >>>> >>>> hi all, >>>>> >>>>> when dealing with experimental restraints i often feel that harmonic >>>>> restraints are somewhat unsatisfactory: >>>>> experimental data can be wrong and thus there is not necessarily a >>>>> solution that fulfills all restraints (score=0). in those cases, a model >>>>> with a lower score is not necessarily any more correct than a higher scoring >>>>> one. thus, i think it'd be good to have an additional scoring function that >>>>> levels off if the feature exceeds a certain value. for example, i'd suggest >>>>> the following two functions alternatively to Harmonic: >>>>> 1. a function that is a Harmonic for x<std and constant for x>std >>>>> 2. a function that is a Harmonic for x<std and asymptotically >>>>> approaches a constant value for x-> inf: >>>>> e.g.: f=x^2 for x<1 and f=2-x^-2 for x>1 (would even be continuous >>>>> in 1st derivative) >>>>> >>>>> is anyone else also interested in something like that? >>>>> any better suggestions? >>>>> is any IMP core expert interested and willing to code that (including >>>>> analogous functions for Upper and Lower Harmonic)? probably i'd be one of >>>>> the slowest and clumsiest persons in doing that... >>>>> >>>>> thanks >>>>> >>>>> frido >>>>> >>>>> >>>>> -- >>>>> >>>>> Friedrich Foerster >>>>> Max-Planck Institut fuer Biochemie >>>>> Am Klopferspitz 18 >>>>> D-82152 Martinsried >>>>> >>>>> Tel: +49 89 8578 2651 >>>>> Fax: +49 89 8578 2641 >>>>> >>>>> foerster@biochem.mpg.de >>>>> >>>>> www.tomotronic.org >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>> >>> -- >>> >>> Friedrich Foerster >>> Max-Planck Institut fuer Biochemie >>> Am Klopferspitz 18 >>> D-82152 Martinsried >>> >>> Tel: +49 89 8578 2651 >>> Fax: +49 89 8578 2641 >>> >>> foerster@biochem.mpg.de >>> >>> www.tomotronic.org >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> >> >> ___________ >> *Carpe diem.* >> >> Chi non ride non è una persona seria. >> Who does not laugh is not a serious person. >> >> *"Di solito non sono un uomo religioso, ma se tu sei lassu', salvami, >> Superman!"* >> > Homer Simpson >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >

Daniel,

here is the code for the Morse potential.

Thanks a lot! Davide

/** * \file Morse.h \brief Morse potential function. * * */

#ifndef __IMP_MORSE_H #define __IMP_MORSE_H

#include "Harmonic.h" #include <cmath>

namespace IMP {

//! Morse potential function /** \ingroup unaryf */ class Morse : public Harmonic { public: Morse(Float mean, Float k, Float threshold, Float alpha, Float De) : Harmonic(mean, k) {} virtual ~Morse() {}

//! Calculate Morse potential with respect to the given feature. /** If the feature is greater than threshold, the Morse function is applied. \param[in] feature Value of feature being tested. \param[in] threshold Value for feature being tested. \param[in] smoothly constant alpha (amplitude of the curve). \param[in] bond energy dissociation De (depth of the curve). \return mscore */ virtual Float evaluate(Float feature, Float threshold, Float alpha, Float De) const { Float Kb = 173; // Kcal/mol. K bond Extracted from MacKerell et al., 1998 Float mscore = 0.0;

if ( feature <= threshold ) { return evaluate_with_derivative(feature).first; } else { mscore = De * pow( ( 1.0 - exp( - sqrt( alpha * Kb /De ) * ( feature - Harmonic::get_mean() )/2.0 ) ), 2 ); // MORSE return mscore; } }

//! Calculate harmonic score and derivative with respect to the given feature. /** \param[in] feature Value of feature being tested. \return Score */ virtual FloatPair evaluate_with_derivative(Float feature) const { Float e = (feature - mean_); Float deriv = k_ * e; return std::make_pair(0.5 * k_ * e * e, deriv); }

void show(std::ostream &out=std::cout) const { out << "Morse: " << Harmonic::get_mean() << " and " << Harmonic::get_k() << std::endl; } };

} // namespace IMP

#endif /* __IMP_MORSE_H */

On Mon, Jan 12, 2009 at 2:21 PM, Daniel Russel drussel@gmail.com wrote:

> Sure. Send it to me. Or, better yet, commit a patch in the patches die > which adds it to core. > > > > On Jan 12, 2009, at 7:42 AM, "Davide Baú" davide.bau@gmail.com wrote: > > Hi Daniel, > > would it be possible to check in the Morse potential too, so that to test > if it works fine? > > Cheers, > Davide > > > > On Mon, Jan 12, 2009 at 2:14 AM, Daniel Russel < drussel@gmail.com > drussel@gmail.com> wrote: > >> I checked in a truncated harmonic (IMP.core.TruncatedHarmonicBound, >> TruncatedHarmonicLowerBound, TruncatedHarmonicUpperBound) for people to look >> at. It currently uses Frido's function, but can be easily changed to >> something else. I deliberately kept the documentation vague on the details >> of the internal function as I am not sure we want the exact nature to be >> important (at least until we come up with a function which we have a strong >> justification for). Anyway, let me know if you have comments. >> >> >> On Jan 8, 2009, at 11:11 AM, Friedrich Foerster wrote: >> >> >> >> On Thu, Jan 8, 2009 at 7:58 PM, Daniel Russel < drussel@gmail.com >> drussel@gmail.com> wrote: >> >>> Having such a general function in IMP would be very nice (I was using a >>> non-smooth truncated harmonic before). Such a function should not be >>> dependent on the parameter tuning (since the parameters would simply be >>> passes by a user). >>> Davide, if you have a version of your code which allows the user to pass >>> in the threshold and cutoff, we can put a version into core for people to >>> look at as a starting point. Otherwise, it would only take me a few minutes >>> to throw something together. >>> >>> It sounds like we would like something like: >>> >>> class TruncatedHarmonicLowerBound { >>> /** threshold > center, capped_value > .5*k*(center-threshold)^2 */ >>> TruncatedHarmonicLowerBound(Float center, Float k, Float threshold, >>> Float capped_value) >>> } >>> >> that'd be great. for me that'd help a lot >> >>> >>> If we use Frido's smooth function, capped_value could default to >>> k*(threshold-center)^2, i.e. 2x the value at the threshold to give it space >>> to go smoothly to the value. And we could have Upper and symmetric versions >>> too (as that is little more code). >>> >> also fine with me. >> for the specific function: i just came up with 2-x^(-2) spontaneously. i'd >> also be happy with another solution (morse, fermi, ...) if that is >> advantageous. if anyone has a probabilistic reasoning for a specific >> function, that'd be nice. >> >> thanks >> >> frido >> >>> >>> >>> On Jan 8, 2009, at 3:44 AM, Davide Baú wrote: >>> >>> It's the exp() function of the standard cmath. >>> Performance is indeed another thing to be improved. >>> >>> Davide >>> >>> >>> >>> On Thu, Jan 8, 2009 at 12:37 PM, Friedrich Foerster <foerster@biochem.mpg.de >>> foerster@biochem.mpg.de> wrote: >>> >>>> thanks. >>>> >>>> just for info: isn't the exp() a bit slow, or are you using some dodgy >>>> macro? >>>> >>>> best >>>> >>>> frido >>>> >>>> >>>> On Jan 8, 2009, at 12:05 PM, Davide Baú wrote: >>>> >>>> Hi Frido, >>>>> >>>>> these are the methods I implemented so far in a new class Morse.h. >>>>> >>>>> The first one returns a constant score if feature is greater then >>>>> threshold. At the moment the returned score is the Harmonic potential >>>>> calculated when feature >= threshold (i.e. when feature is >= threshold, the >>>>> returned score will always be Harmonic::evaluate(threshold) ). >>>>> The second one implements the Morse potential as described by Marc. >>>>> >>>>> These methods are still in a development phase since there are some >>>>> parameters which need to be better defined, such as the threshold to be >>>>> applied and the parameters that define the Morse potential. >>>>> >>>>> Regards, >>>>> Davide >>>>> >>>>> >>>>> // 1. a function that is a Harmonic for x<std and constant for x>std >>>>> /** If the feature is greater than or equal to the threshold, the >>>>> score is constant. >>>>> \param[in] feature Value of feature being tested. >>>>> \return Score >>>>> */ >>>>> virtual Float evaluate(Float feature) const { >>>>> Float k = Harmonic::get_k(); >>>>> Float mean = Harmonic::get_mean(); >>>>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>>>> if ( feature <= threshold ) { >>>>> return Harmonic::evaluate(feature); >>>>> } else { >>>>> return evaluate_with_derivative(threshold, k).first; >>>>> } >>>>> } >>>>> >>>>> >>>>> // 2. a function that is a Harmonic for x<std and asymptotically >>>>> approaches a constant value for x-> inf: >>>>> /** If the feature is greater than or equal to the threshold, apply >>>>> the Morse potential. >>>>> \param[in] feature Value of feature being tested. >>>>> \return Score >>>>> */ >>>>> virtual Float evaluate(Float feature) const { >>>>> Float mean = Harmonic::get_mean(); >>>>> Float k = Harmonic::get_k(); >>>>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>>>> >>>>> // MORSE POTENTIAL PARAMETERS >>>>> Float var = 1.0/k; >>>>> Float alpha = 2.0; >>>>> Float De = 40.0; >>>>> Float beta = 1.0; >>>>> Float swf = 0.0; >>>>> >>>>> if ( feature <= threshold ) { >>>>> return Harmonic::evaluate(feature); >>>>> } else { >>>>> swf = beta * pow( ( 1.0 - exp( - sqrt( alpha/De ) * ( feature - >>>>> threshold )/2.0 ) ), 2 ); // MORSE POTENTIAL >>>>> return swf; >>>>> } >>>>> } >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, Jan 8, 2009 at 10:20 AM, Marc A. Marti-Renom <mmarti@cipf.es >>>>> mmarti@cipf.es> wrote: >>>>> Hi Frido, >>>>> >>>>> Indeed we are also in need of similar stuff. Davide Bau (a postdoc in >>>>> my lab and also in the IMP-Dev list) has already implemented a sort of a >>>>> MORSE potential in IMP restraints, which is not what you ask but may be >>>>> similar. I implemented many many many years ago something similar in CHARMM >>>>> ( http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf >>>>> http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf, Chapter 4 >>>>> page 86). >>>>> >>>>> Unfortunately, we are NOT yet ready to commit the changes in the code >>>>> to the SVN since we are in the middle of production phase (ie, making >>>>> models) thus would prefer not to update IMP. But I am sure we could do soon. >>>>> >>>>> Davide, any comments? :-) >>>>> >>>>> m >>>>> >>>>> ------- >>>>> Marc A. Marti-Renom, Head of the Structural Genomics Unit >>>>> Bioinformatics & Genomics Department, Prince Felipe Research Center >>>>> Avda. Autopista del Saler, 16 , 46012 Valencia, Spain >>>>> Tel +34 96 328 96 80 (ext. 1015) Fax +34 96 328 97 01 >>>>> email mmarti@cipf.esmmarti@cipf.es web http://sgu.bioinfo.cipf.es >>>>> http://sgu.bioinfo.cipf.es >>>>> >>>>> *** Consider the environment. Print responsibly. *** >>>>> >>>>> On Jan 8, 2009, at 10:00 AM, Friedrich Foerster wrote: >>>>> >>>>> hi all, >>>>>> >>>>>> when dealing with experimental restraints i often feel that harmonic >>>>>> restraints are somewhat unsatisfactory: >>>>>> experimental data can be wrong and thus there is not necessarily a >>>>>> solution that fulfills all restraints (score=0). in those cases, a model >>>>>> with a lower score is not necessarily any more correct than a higher scoring >>>>>> one. thus, i think it'd be good to have an additional scoring function that >>>>>> levels off if the feature exceeds a certain value. for example, i'd suggest >>>>>> the following two functions alternatively to Harmonic: >>>>>> 1. a function that is a Harmonic for x<std and constant for x>std >>>>>> 2. a function that is a Harmonic for x<std and asymptotically >>>>>> approaches a constant value for x-> inf: >>>>>> e.g.: f=x^2 for x<1 and f=2-x^-2 for x>1 (would even be continuous >>>>>> in 1st derivative) >>>>>> >>>>>> is anyone else also interested in something like that? >>>>>> any better suggestions? >>>>>> is any IMP core expert interested and willing to code that (including >>>>>> analogous functions for Upper and Lower Harmonic)? probably i'd be one of >>>>>> the slowest and clumsiest persons in doing that... >>>>>> >>>>>> thanks >>>>>> >>>>>> frido >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Friedrich Foerster >>>>>> Max-Planck Institut fuer Biochemie >>>>>> Am Klopferspitz 18 >>>>>> D-82152 Martinsried >>>>>> >>>>>> Tel: +49 89 8578 2651 >>>>>> Fax: +49 89 8578 2641 >>>>>> >>>>>> foerster@biochem.mpg.defoerster@biochem.mpg.de >>>>>> >>>>>> http://www.tomotronic.orgwww.tomotronic.org >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.orgIMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.orgIMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.orgIMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>> >>>> -- >>>> >>>> Friedrich Foerster >>>> Max-Planck Institut fuer Biochemie >>>> Am Klopferspitz 18 >>>> D-82152 Martinsried >>>> >>>> Tel: +49 89 8578 2651 >>>> Fax: +49 89 8578 2641 >>>> >>>> foerster@biochem.mpg.defoerster@biochem.mpg.de >>>> >>>> http://www.tomotronic.orgwww.tomotronic.org >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.orgIMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>> >>> >>> ___________ >>> *Carpe diem.* >>> >>> Chi non ride non è una persona seria. >>> Who does not laugh is not a serious person. >>> >>> *"Di solito non sono un uomo religioso, ma se tu sei lassu', salvami, >>> Superman!"* >>> > Homer Simpson >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.orgIMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.orgIMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.orgIMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.orgIMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> https://salilab.org/mailman/listinfo/imp-ZGV2PC9hPjxicj4KPGJyPjwvYmxvY2txdW9... >> https://salilab.org/mailman/listinfo/imp-dev >> https://salilab.org/mailman/listinfo/imp-ZGV2PC9hPjxicj4KPGJyPjwvYmxvY2txdW9... > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >

Hi Daniel,

this is the class I implemented to use the Morse potential as described in Marc's thesis (see http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf , Chapter 4 page 86):

mscore = De * pow( ( 1.0 - exp( - sqrt( alpha * Kb /De ) * ( feature - Harmonic::get_mean() )/2.0 ) ), 2 );

where: feature = value of feature being tested. alpha = smoothly constant (amplitude of the curve). De =bond energy dissociation (depth of the curve). Kb = K bond Extracted from MacKerell et al., 1998

Davide

On Thu, Jan 8, 2009 at 7:58 PM, Daniel Russel drussel@gmail.com wrote:

> Having such a general function in IMP would be very nice (I was using a > non-smooth truncated harmonic before). Such a function should not be > dependent on the parameter tuning (since the parameters would simply be > passes by a user). > Davide, if you have a version of your code which allows the user to pass in > the threshold and cutoff, we can put a version into core for people to look > at as a starting point. Otherwise, it would only take me a few minutes to > throw something together. > > It sounds like we would like something like: > > class TruncatedHarmonicLowerBound { > /** threshold > center, capped_value > .5*k*(center-threshold)^2 */ > TruncatedHarmonicLowerBound(Float center, Float k, Float threshold, > Float capped_value) > } > > If we use Frido's smooth function, capped_value could default to > k*(threshold-center)^2, i.e. 2x the value at the threshold to give it space > to go smoothly to the value. And we could have Upper and symmetric versions > too (as that is little more code). > > > On Jan 8, 2009, at 3:44 AM, Davide Baú wrote: > > It's the exp() function of the standard cmath. > Performance is indeed another thing to be improved. > > Davide > > > > On Thu, Jan 8, 2009 at 12:37 PM, Friedrich Foerster < > foerster@biochem.mpg.de> wrote: > >> thanks. >> >> just for info: isn't the exp() a bit slow, or are you using some dodgy >> macro? >> >> best >> >> frido >> >> >> On Jan 8, 2009, at 12:05 PM, Davide Baú wrote: >> >> Hi Frido, >>> >>> these are the methods I implemented so far in a new class Morse.h. >>> >>> The first one returns a constant score if feature is greater then >>> threshold. At the moment the returned score is the Harmonic potential >>> calculated when feature >= threshold (i.e. when feature is >= threshold, the >>> returned score will always be Harmonic::evaluate(threshold) ). >>> The second one implements the Morse potential as described by Marc. >>> >>> These methods are still in a development phase since there are some >>> parameters which need to be better defined, such as the threshold to be >>> applied and the parameters that define the Morse potential. >>> >>> Regards, >>> Davide >>> >>> >>> // 1. a function that is a Harmonic for x<std and constant for x>std >>> /** If the feature is greater than or equal to the threshold, the score >>> is constant. >>> \param[in] feature Value of feature being tested. >>> \return Score >>> */ >>> virtual Float evaluate(Float feature) const { >>> Float k = Harmonic::get_k(); >>> Float mean = Harmonic::get_mean(); >>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>> if ( feature <= threshold ) { >>> return Harmonic::evaluate(feature); >>> } else { >>> return evaluate_with_derivative(threshold, k).first; >>> } >>> } >>> >>> >>> // 2. a function that is a Harmonic for x<std and asymptotically >>> approaches a constant value for x-> inf: >>> /** If the feature is greater than or equal to the threshold, apply the >>> Morse potential. >>> \param[in] feature Value of feature being tested. >>> \return Score >>> */ >>> virtual Float evaluate(Float feature) const { >>> Float mean = Harmonic::get_mean(); >>> Float k = Harmonic::get_k(); >>> Float threshold = 1.0 * mean + XYZRDecorator::get_radius(); >>> >>> // MORSE POTENTIAL PARAMETERS >>> Float var = 1.0/k; >>> Float alpha = 2.0; >>> Float De = 40.0; >>> Float beta = 1.0; >>> Float swf = 0.0; >>> >>> if ( feature <= threshold ) { >>> return Harmonic::evaluate(feature); >>> } else { >>> swf = beta * pow( ( 1.0 - exp( - sqrt( alpha/De ) * ( feature - >>> threshold )/2.0 ) ), 2 ); // MORSE POTENTIAL >>> return swf; >>> } >>> } >>> >>> >>> >>> >>> >>> On Thu, Jan 8, 2009 at 10:20 AM, Marc A. Marti-Renom mmarti@cipf.es >>> wrote: >>> Hi Frido, >>> >>> Indeed we are also in need of similar stuff. Davide Bau (a postdoc in my >>> lab and also in the IMP-Dev list) has already implemented a sort of a MORSE >>> potential in IMP restraints, which is not what you ask but may be similar. I >>> implemented many many many years ago something similar in CHARMM ( >>> http://sgu.bioinfo.cipf.es/martirenom/Thesis/pdf/Thesis.pdf, Chapter 4 >>> page 86). >>> >>> Unfortunately, we are NOT yet ready to commit the changes in the code to >>> the SVN since we are in the middle of production phase (ie, making models) >>> thus would prefer not to update IMP. But I am sure we could do soon. >>> >>> Davide, any comments? :-) >>> >>> m >>> >>> ------- >>> Marc A. Marti-Renom, Head of the Structural Genomics Unit >>> Bioinformatics & Genomics Department, Prince Felipe Research Center >>> Avda. Autopista del Saler, 16 , 46012 Valencia, Spain >>> Tel +34 96 328 96 80 (ext. 1015) Fax +34 96 328 97 01 >>> email mmarti@cipf.es web http://sgu.bioinfo.cipf.es >>> >>> *** Consider the environment. Print responsibly. *** >>> >>> On Jan 8, 2009, at 10:00 AM, Friedrich Foerster wrote: >>> >>> hi all, >>>> >>>> when dealing with experimental restraints i often feel that harmonic >>>> restraints are somewhat unsatisfactory: >>>> experimental data can be wrong and thus there is not necessarily a >>>> solution that fulfills all restraints (score=0). in those cases, a model >>>> with a lower score is not necessarily any more correct than a higher scoring >>>> one. thus, i think it'd be good to have an additional scoring function that >>>> levels off if the feature exceeds a certain value. for example, i'd suggest >>>> the following two functions alternatively to Harmonic: >>>> 1. a function that is a Harmonic for x<std and constant for x>std >>>> 2. a function that is a Harmonic for x<std and asymptotically approaches >>>> a constant value for x-> inf: >>>> e.g.: f=x^2 for x<1 and f=2-x^-2 for x>1 (would even be continuous in >>>> 1st derivative) >>>> >>>> is anyone else also interested in something like that? >>>> any better suggestions? >>>> is any IMP core expert interested and willing to code that (including >>>> analogous functions for Upper and Lower Harmonic)? probably i'd be one of >>>> the slowest and clumsiest persons in doing that... >>>> >>>> thanks >>>> >>>> frido >>>> >>>> >>>> -- >>>> >>>> Friedrich Foerster >>>> Max-Planck Institut fuer Biochemie >>>> Am Klopferspitz 18 >>>> D-82152 Martinsried >>>> >>>> Tel: +49 89 8578 2651 >>>> Fax: +49 89 8578 2641 >>>> >>>> foerster@biochem.mpg.de >>>> >>>> www.tomotronic.org >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> >> -- >> >> Friedrich Foerster >> Max-Planck Institut fuer Biochemie >> Am Klopferspitz 18 >> D-82152 Martinsried >> >> Tel: +49 89 8578 2651 >> Fax: +49 89 8578 2641 >> >> foerster@biochem.mpg.de >> >> www.tomotronic.org >> >> >> >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> > > > ___________ > *Carpe diem.* > > Chi non ride non è una persona seria. > Who does not laugh is not a serious person. > > *"Di solito non sono un uomo religioso, ma se tu sei lassu', salvami, > Superman!"* > > Homer Simpson > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >

On Jan 8, 2009, at 8:04 AM, Keren Lasker wrote:

> any thoughts on dealing with the derivatives at x=std? Just setting it to 0 should do for 1 as it is 0 infinitely close to std and we are doing floating point arithmetic. Or am I confused?

> > > On Thu, 8 Jan 2009, Friedrich Foerster wrote: > >> hi all, >> >> when dealing with experimental restraints i often feel that >> harmonic restraints are somewhat unsatisfactory: >> experimental data can be wrong and thus there is not necessarily a >> solution that fulfills all restraints (score=0). in those cases, a >> model with a lower score is not necessarily any more correct than a >> higher scoring one. thus, i think it'd be good to have an >> additional scoring function that levels off if the feature exceeds >> a certain value. for example, i'd suggest the following two >> functions alternatively to Harmonic: >> 1. a function that is a Harmonic for x<std and constant for x>std >> 2. a function that is a Harmonic for x<std and asymptotically >> approaches a constant value for x-> inf: >> e.g.: f=x^2 for x<1 and f=2-x^-2 for x>1 (would even be >> continuous in 1st derivative) >> >> is anyone else also interested in something like that? >> any better suggestions? >> is any IMP core expert interested and willing to code that >> (including analogous functions for Upper and Lower Harmonic)? >> probably i'd be one of the slowest and clumsiest persons in doing >> that... >> >> thanks >> >> frido >> >> >> -- >> >> Friedrich Foerster >> Max-Planck Institut fuer Biochemie >> Am Klopferspitz 18 >> D-82152 Martinsried >> >> Tel: +49 89 8578 2651 >> Fax: +49 89 8578 2641 >> >> foerster@biochem.mpg.de >> >> www.tomotronic.org >> >> >> >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev