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.
| util.py (pymol-v1.8.6.0.tar.bz2) | : | util.py (pymol-v2.1.0.tar.bz2) |
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| skipping to change at line 17 | | skipping to change at line 17 |
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| #G* Please see the accompanying LICENSE file for further information. | | #G* Please see the accompanying LICENSE file for further information. |
| #H* ------------------------------------------------------------------- | | #H* ------------------------------------------------------------------- |
| #I* Additional authors of this source file include: | | #I* Additional authors of this source file include: |
| #-* | | #-* |
| #-* | | #-* |
| #-* | | #-* |
| #Z* ------------------------------------------------------------------- | | #Z* ------------------------------------------------------------------- |
| | |
| from __future__ import print_function | | from __future__ import print_function |
| | |
|
| | import sys |
| | if sys.version_info[0] == 2: |
| | _next_method_name = 'next' |
| | else: |
| | _next_method_name = '__next__' |
| | |
| cmd = __import__("sys").modules["pymol.cmd"] | | cmd = __import__("sys").modules["pymol.cmd"] |
| import pymol | | import pymol |
| from pymol import movie | | from pymol import movie |
| # legacy mappings, remove in PyMOL 2.0 | | # legacy mappings, remove in PyMOL 2.0 |
| | |
| mload = movie.load | | mload = movie.load |
| mrock = movie.rock | | mrock = movie.rock |
| mroll = movie.roll | | mroll = movie.roll |
| | |
| # should match the list in layer1/Color.c: | | # should match the list in layer1/Color.c: |
| | |
| skipping to change at line 113 | | skipping to change at line 119 |
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| if orgN != tmpN: | | if orgN != tmpN: |
| raise pymol.CmdException('color_by_area failed') | | raise pymol.CmdException('color_by_area failed') |
| | |
| _self.set("dot_solvent", asa, tmpObj) | | _self.set("dot_solvent", asa, tmpObj) |
| _self.set("dot_density", 3, tmpObj) | | _self.set("dot_density", 3, tmpObj) |
| | |
| l = [] | | l = [] |
| _self.get_area(tmpSel, load_b=1) | | _self.get_area(tmpSel, load_b=1) |
| _self.spectrum("b", palette, tmpSel) | | _self.spectrum("b", palette, tmpSel) |
| _self.iterate(tmpSel, "l_a(color)", space={'l_a': l.append}) | | _self.iterate(tmpSel, "l_a(color)", space={'l_a': l.append}) |
|
| _self.alter(orgSel, "color=l_n()", space={'l_n': iter(l).__next__}) | | _self.alter(orgSel, "color=l_n()", space={'l_n': getattr(iter(l), _next_
method_name)}) |
| | |
| _self.recolor(orgSel) | | _self.recolor(orgSel) |
| finally: | | finally: |
| _self.delete(tmpSel) | | _self.delete(tmpSel) |
| _self.delete(tmpObj) | | _self.delete(tmpObj) |
| _self.delete(orgSel) | | _self.delete(orgSel) |
| | |
| def find_surface_residues(sele, name='', _self=cmd): | | def find_surface_residues(sele, name='', _self=cmd): |
| """ | | """ |
| DESCRIPTION | | DESCRIPTION |
| | |
| skipping to change at line 362 | | skipping to change at line 368 |
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| # make sure all atoms are included... | | # make sure all atoms are included... |
| cmd.alter(obj_name,"q=1.0",quiet=1) | | cmd.alter(obj_name,"q=1.0",quiet=1) |
| | |
| print(" Util: Fixing termini and assigning formal charges...") | | print(" Util: Fixing termini and assigning formal charges...") |
| | |
| assign.missing_c_termini(obj_name,quiet=1,_self=_self) | | assign.missing_c_termini(obj_name,quiet=1,_self=_self) |
| | |
| while not assign.formal_charges(obj_name,quiet=1,_self=_self): | | while not assign.formal_charges(obj_name,quiet=1,_self=_self): |
| print(" WARNING: unrecognized or incomplete residues are being deleted:"
) | | print(" WARNING: unrecognized or incomplete residues are being deleted:"
) |
| cmd.iterate("(byres ("+obj_name+" and flag 23)) and flag 31", | | cmd.iterate("(byres ("+obj_name+" and flag 23)) and flag 31", |
|
| 'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"
/"',quiet=1) | | 'print(" "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"
/")',quiet=1) |
| cmd.remove("byres ("+obj_name+" and flag 23)") # get rid of residues tha
t weren't assigned | | cmd.remove("byres ("+obj_name+" and flag 23)") # get rid of residues tha
t weren't assigned |
| assign.missing_c_termini(obj_name,quiet=1,_self=_self) | | assign.missing_c_termini(obj_name,quiet=1,_self=_self) |
| | |
| print(" Util: Assigning Amber 99 charges and radii...") | | print(" Util: Assigning Amber 99 charges and radii...") |
| | |
| cmd.h_add(obj_name) | | cmd.h_add(obj_name) |
| if not assign.amber99(obj_name,quiet=1,_self=_self): | | if not assign.amber99(obj_name,quiet=1,_self=_self): |
| print(" WARNING: some unassigned atoms are being deleted:") | | print(" WARNING: some unassigned atoms are being deleted:") |
| cmd.iterate("byres ("+obj_name+" and flag 23)", | | cmd.iterate("byres ("+obj_name+" and flag 23)", |
|
| 'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"
/"+name+"? ["+elem+"]"',quiet=1) | | 'print(" "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"
/"+name+"? ["+elem+"]")',quiet=1) |
| cmd.remove(obj_name+" and flag 23") # get rid of any atoms that weren't
assigned | | cmd.remove(obj_name+" and flag 23") # get rid of any atoms that weren't
assigned |
| | |
| # show the user what the net charges are... | | # show the user what the net charges are... |
| | |
| formal = sum_formal_charges(obj_name,quiet=0,_self=_self) | | formal = sum_formal_charges(obj_name,quiet=0,_self=_self) |
| partial = sum_partial_charges(obj_name,quiet=0,_self=_self) | | partial = sum_partial_charges(obj_name,quiet=0,_self=_self) |
| if round(formal)!=round(partial): | | if round(formal)!=round(partial): |
| print(" WARNING: formal and partial charge sums don't match -- there is
a problem!") | | print(" WARNING: formal and partial charge sums don't match -- there is
a problem!") |
| | |
| def protein_vacuum_esp(selection, mode=2, border=10.0, quiet = 1, _self=cmd): | | def protein_vacuum_esp(selection, mode=2, border=10.0, quiet = 1, _self=cmd): |
| | |
| skipping to change at line 813 | | skipping to change at line 819 |
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| c = (c + 1) % _color_cycle_len | | c = (c + 1) % _color_cycle_len |
| | |
| def color_deep(color, name='all', quiet=1, _self=cmd): | | def color_deep(color, name='all', quiet=1, _self=cmd): |
| ''' | | ''' |
| Unset all object and atom level (not global) color settings and | | Unset all object and atom level (not global) color settings and |
| apply given color. | | apply given color. |
| ''' | | ''' |
| from pymol.menu import rep_setting_lists | | from pymol.menu import rep_setting_lists |
| _self.unset_deep([s for L in rep_setting_lists for (r, s) in L if s], | | _self.unset_deep([s for L in rep_setting_lists for (r, s) in L if s], |
| name, updates=0, quiet=quiet) | | name, updates=0, quiet=quiet) |
|
| _self.color(color, name, quiet=quiet, _self=_self) | | _self.color(color, name, quiet=quiet) |
| | |
| def chainbow(selection='(all)', palette="rainbow", quiet=1, _self=cmd): | | def chainbow(selection='(all)', palette="rainbow", quiet=1, _self=cmd): |
| ''' | | ''' |
| Color all chains in rainbow | | Color all chains in rainbow |
| ''' | | ''' |
| for model in _self.get_object_list('(' + selection + ')'): | | for model in _self.get_object_list('(' + selection + ')'): |
| for a in _self.get_chains('model %s & (%s)' % (model, selection)) or [''
]: | | for a in _self.get_chains('model %s & (%s)' % (model, selection)) or [''
]: |
| _self.spectrum('count', palette, | | _self.spectrum('count', palette, |
| "(chain '%s' & model %s & (%s))" % (a, model, selection), | | "(chain '%s' & model %s & (%s))" % (a, model, selection), |
| byres=1, quiet=quiet) | | byres=1, quiet=quiet) |
| | |
| skipping to change at line 1686 | | skipping to change at line 1692 |
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| if vis: | | if vis: |
| _self.label('?%s & guide' % (sele), '"%.1f" % ' + var) | | _self.label('?%s & guide' % (sele), '"%.1f" % ' + var) |
| _self.spectrum(var, 'white blue', sele, minimum=0., maximum=1.) | | _self.spectrum(var, 'white blue', sele, minimum=0., maximum=1.) |
| | |
| finally: | | finally: |
| _self.set('dot_solvent', dot_solvent, updates=0) | | _self.set('dot_solvent', dot_solvent, updates=0) |
| _self.delete(sele) | | _self.delete(sele) |
| | |
| return resarea | | return resarea |
| | |
|
| def ligand_zoom(_self=cmd): | | def ligand_zoom(step=1, _self=cmd): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| Zoom to the next organic molecule (by residue identifier) | | Zoom to the next organic molecule (by residue identifier) |
| | |
| Bound to CTRL-L key. | | Bound to CTRL-L key. |
| ''' | | ''' |
| global _current_ligand | | global _current_ligand |
| | |
| s = {'ligand_set': set()} | | s = {'ligand_set': set()} |
| | |
| skipping to change at line 1708 | | skipping to change at line 1714 |
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| space=s) < 1: | | space=s) < 1: |
| return | | return |
| | |
| ligands = sorted(s["ligand_set"]) | | ligands = sorted(s["ligand_set"]) |
| | |
| try: | | try: |
| i = ligands.index(_current_ligand) | | i = ligands.index(_current_ligand) |
| except (ValueError, NameError): | | except (ValueError, NameError): |
| i = -1 | | i = -1 |
| | |
|
| i = (i + 1) % len(ligands) | | i = (i + int(step)) % len(ligands) |
| _current_ligand = ligands[i] | | _current_ligand = ligands[i] |
| | |
| # use "do" for feedback | | # use "do" for feedback |
| _self.do('zoom /%s/%s/%s & resi %s, animate=1, buffer=2' % ligands[i]) | | _self.do('zoom /%s/%s/%s & resi %s, animate=1, buffer=2' % ligands[i]) |
| | | |
| End of changes. 7 change blocks. |
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| 6 lines changed or deleted | | 12 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 