Dimer update #14
Dimer update #14
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…rs are hard coded(see comments in draw_membrane2a. In the future, we need to add those parameters to the BornProfiler workflow.)
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Let's get this PR to the stage where draw_membrane2a
- has new command line options to generate a symmetric exclusion zone
- has documentation for the new options
- will by default work as before
As the next steps, can you write in a comment what you envisage the usage for draw_membrane2a should look like for your case: what additional data do you need to provide to the program in order for it to generate the correct dimer exclusion zones?
| /* bilayer or headgroup dielectric constant outside channel */ | ||
| *diel = (z >= M->z_h0 && z <= M->z_h1) ? M->mdie : M->idie; | ||
| if (R2 <= R_temp || R <= R_temp){ | ||
| //if (R2 <= R_temp) { // test the other protomer |
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| /* if dimer */ | ||
| else { | ||
| R = sqrt(SQR(x-M->x0_R) + SQR(y-M->y0_R)); /*better to use the Membrane struct for x2, y2*/ |
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| /* Draw symmetric exclusion zone for a dimer. */ | ||
| /* The zone is defined by x0_R, y0_R, dx_R, dy_R. */ | ||
| bool dimer = FALSE; /* New feature for CPA dimer. Set to FALSE as default*/ |
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Change formatting and comment.
| bool dimer = FALSE; /* New feature for CPA dimer. Set to FALSE as default*/ | |
| bool dimer=FALSE; /* dimeric proteins with symmetric exclusion zones. Set to FALSE as default*/ |
| /* For this test case, we are going to hard code the second zone center as:*/ | ||
| /* x0_R - 2 * dx_R */ | ||
| /* y0_R - 2 * dy_R */ | ||
| /* see core.py line 458*/ |
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Is this going to be replaced by an alternative way to set the position?
If so, what is needed as input to the program?
| /* Warning: this is the hard coded offset. Normally you should get them from core.py*/ | ||
| /* But the way wrote in core.py made it hard to do so. */ | ||
| dx_R = 20; | ||
| dy_R = -5; | ||
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Needs to be replaced with input.
| @@ -770,10 +819,21 @@ int main(int argc, char *argv[]) | |||
| Membrane.x0_p = x0_p; /* centre of the protein */ | |||
| Membrane.y0_p = y0_p; | |||
| Membrane.z0_p = z0_p; | |||
| Membrane.dimer = False; /*CPA hack*/ | |||
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Remove the comment... assuming that this value will be set from somewhere?
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| /* Manually add parameters for the second protomer. */ | ||
| if (dimer){ | ||
| printf("Dimer system detected. Turning on the hack mode."); |
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Maybe call it "symmetric dimer" mode? "Hack" sounds as if it's not really supposed to be here.
| @@ -770,10 +819,21 @@ int main(int argc, char *argv[]) | |||
| Membrane.x0_p = x0_p; /* centre of the protein */ | |||
| Membrane.y0_p = y0_p; | |||
| Membrane.z0_p = z0_p; | |||
| Membrane.dimer = False; /*CPA hack*/ | |||
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| /* Manually add parameters for the second protomer. */ | |||
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WHat is meant by the comment? Why "manually"?
Rolled back from #11 to separate the updates for GridData and drawmembrane2a.c.
Muted dimer option so that old code still works. Implementation of command line passing of dimer parameters is needed for next PR.
Updated Author list.