is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| sc_bb_dep.py (pymol-v1.8.6.0.tar.bz2) | : | sc_bb_dep.py (pymol-v2.1.0.tar.bz2) |
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| | |
| skipping to change at line 99 | | skipping to change at line 99 |
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| for line in lines: | | for line in lines: |
| field = line.split() | | field = line.split() |
| len_field = len(field) | | len_field = len(field) |
| if len_field>11: | | if len_field>11: |
| resn = field[0] | | resn = field[0] |
| phi = int(field[1]) | | phi = int(field[1]) |
| psi = int(field[2]) | | psi = int(field[2]) |
| if (((psi==(60*(psi/60))) and (phi==(60*(phi/60)))) or | | if (((psi==(60*(psi/60))) and (phi==(60*(phi/60)))) or |
| ((psi==(20*(psi/20))) and (phi==(20*(phi/20))) and (int(field[3]
)>0)) or | | ((psi==(20*(psi/20))) and (phi==(20*(phi/20))) and (int(field[3]
)>0)) or |
| ((psi==(10*(psi/10))) and (phi==(10*(phi/10))) and (int(field[3]
)>=250))): | | ((psi==(10*(psi/10))) and (phi==(10*(phi/10))) and (int(field[3]
)>=250))): |
|
| if not dd.has_key((phi,psi)): | | if (phi,psi) not in dd: |
| # print phi,psi | | # print phi,psi |
| dd[(phi,psi)]=1 | | dd[(phi,psi)]=1 |
| key = (resn, phi, psi) | | key = (resn, phi, psi) |
| list = output.get(key,[]) | | list = output.get(key,[]) |
| fsum = float(field[8]) | | fsum = float(field[8]) |
| dict = {} | | dict = {} |
| if total[key]>0.0: | | if total[key]>0.0: |
| freq = fsum/total[key] | | freq = fsum/total[key] |
| else: | | else: |
| freq = 0.0 | | freq = 0.0 |
| if freq>0.01: | | if freq>0.01: |
| dict['FREQ'] = freq | | dict['FREQ'] = freq |
|
| len_chi = len(chi[resn].keys()) | | len_chi = len(chi[resn]) |
| if len_chi>0: | | if len_chi>0: |
| chi1 = float(field[9]) | | chi1 = float(field[9]) |
| dict[chi[resn]['1']] = chi1 | | dict[chi[resn]['1']] = chi1 |
| if len_chi>1: | | if len_chi>1: |
| chi2 = float(field[10]) | | chi2 = float(field[10]) |
| dict[chi[resn]['2']] = chi2 | | dict[chi[resn]['2']] = chi2 |
| if len_chi>2: | | if len_chi>2: |
| chi3 = float(field[11]) | | chi3 = float(field[11]) |
| dict[chi[resn]['3']] = chi3 | | dict[chi[resn]['3']] = chi3 |
| if len_chi>3: | | if len_chi>3: |
| chi4 = float(field[12]) | | chi4 = float(field[12]) |
| dict[chi[resn]['4']] = chi4 | | dict[chi[resn]['4']] = chi4 |
| list.append((freq,dict)) | | list.append((freq,dict)) |
| output[key] = list | | output[key] = list |
| | |
| # sort by priority | | # sort by priority |
| | |
|
| for key in output.keys(): | | for key in list(output.keys()): |
| list = output[key] | | list = output[key] |
| list.sort() | | list.sort() |
| list.reverse() | | list.reverse() |
|
| output[key] = map(lambda x:x[1],list) | | output[key] = [x[1] for x in list] |
| | |
| #for key in output.keys(): | | #for key in output.keys(): |
| # | | # |
| # if key[0] == 'HIS': | | # if key[0] == 'HIS': |
| # output[( 'HIE', ) + key[1:]] = output[key] | | # output[( 'HIE', ) + key[1:]] = output[key] |
| # output[( 'HID', ) + key[1:]] = output[key] | | # output[( 'HID', ) + key[1:]] = output[key] |
| # output[( 'HIP', ) + key[1:]] = output[key] | | # output[( 'HIP', ) + key[1:]] = output[key] |
| # elif key[0] == 'CYS': | | # elif key[0] == 'CYS': |
| # output[( 'CYX', ) + key[1:]] = output[key] | | # output[( 'CYX', ) + key[1:]] = output[key] |
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| | | |
| End of changes. 4 change blocks. |
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| 4 lines changed or deleted | | 4 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 