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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.)
…dDataFormats in MDAnalysis.
orbeckst
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Jan 25, 2022
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orbeckst
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If you put the fix for analysis.py in a separate PR then I can merge it right away.
For drawmembrane we need
- remove hard coding of dimer option: use command line argument processing
- add documentation to the help for the new options
- list new options (e.g., -x, -y, -D)
- explain how the second cylinder position is computed (equation)
- state assumptions (e.g., would the box center need to be between the two cylinders??)
We can merge this without changing of the other code as long as it still works with the old code, i.e., the dimer option is off by default. Then in the next PR we change the Python code.
| float l_m=40, a0=0; | ||
| float z_m0=0, R_m0=0, R_m1=0, x0_R=NO_COORDINATE, y0_R=NO_COORDINATE; | ||
| float R, R_temp; | ||
| float R, R2, R_temp; /*11-2021 added R2*/ |
| char ext[]="m.dx"; | ||
| bool compression = FALSE; | ||
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| /*11-2021*/ |
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remove date from comment, that's available in the git log, rest of the comment is great
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| /* 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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remove comment when command line passing is implemented
| /*11-2021*/ | ||
| /* Draw symmetric exclusion zone for a dimer. */ | ||
| /* The zone is defined by x0_R, y0_R, dx_R, dy_R. */ | ||
| bool dimer = TRUE; /* New feature for CPA dimer. Set to FALSE as default*/ |
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| /*11-2021*/ | ||
| /* 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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replace with command line passing
| Membrane.x0_p = x0_p; /* centre of the protein */ | ||
| Membrane.y0_p = y0_p; | ||
| Membrane.z0_p = z0_p; | ||
| Membrane.dimer = TRUE; /*11-2021 CPA hack*/ |
| Membrane.z0_p = z0_p; | ||
| Membrane.dimer = TRUE; /*11-2021 CPA hack*/ | ||
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| /* 11-2021 */ |
| /* channel exclusion zone for ion accessibility */ | ||
| R = sqrt(SQR(x[k]-Membrane.x0_R) + SQR(y[j]-Membrane.y0_R)); | ||
| R_temp = (R_m1*(z[i]-Membrane.z_m0) - R_m0*(z[i]-Membrane.z_m1))/(Membrane.z_m1 - Membrane.z_m0); | ||
| /*If the system is not a dimer. 11-2021 added*/ |
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| if (z[i] <= Membrane.z_m1 && z[i] >= Membrane.z_m0 && R > R_temp) { | ||
| kk[cnt] = 0.0; /* Zero ion accessibility */ | ||
| /*11-2021*/ |
| R2 = sqrt(SQR(x[k]-x2_R) + SQR(y[j]-y2_R)); | ||
| R_temp = (R_m1*(z[i]-Membrane.z_m0) - R_m0*(z[i]-Membrane.z_m1))/(Membrane.z_m1 - Membrane.z_m0); | ||
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| //if (z[i] <= Membrane.z_m1 && z[i] >= Membrane.z_m0 && R > R_temp && R2 > R_temp) { |
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Updated bornprofiler/analysis.py to match current version of griddataformats.
Added dimer option for drawmembrane2a.c. Currently the dimer parameters are still hard coded. Need more work on this in the future.