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.
| measurement.py (pymol-v2.1.0.tar.bz2) | : | measurement.py (pymol-open-source-2.2.0) |
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| | |
| skipping to change at line 58 | | skipping to change at line 58 |
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| ] | | ] |
| object_mode_name = { | | object_mode_name = { |
| 'merge':'Merge With Previous', | | 'merge':'Merge With Previous', |
| 'overwr':'Replace Previous', | | 'overwr':'Replace Previous', |
| 'append':'Create New Object', | | 'append':'Create New Object', |
| } | | } |
| | |
| def __init__(self,_self=cmd): | | def __init__(self,_self=cmd): |
| Wizard.__init__(self,_self) | | Wizard.__init__(self,_self) |
| | |
|
| | self.pick_state = [0, 0, 0, 0] |
| | |
| self.cmd.unpick() | | self.cmd.unpick() |
| | |
| self.cutoff = self.cmd.get_setting_float("neighbor_cutoff") | | self.cutoff = self.cmd.get_setting_float("neighbor_cutoff") |
| self.heavy_neighbor_cutoff = self.cmd.get_setting_float("heavy_neighbor_
cutoff") | | self.heavy_neighbor_cutoff = self.cmd.get_setting_float("heavy_neighbor_
cutoff") |
| self.polar_neighbor_cutoff = self.cmd.get_setting_float("polar_neighbor_
cutoff") | | self.polar_neighbor_cutoff = self.cmd.get_setting_float("polar_neighbor_
cutoff") |
| self.hbond_cutoff = self.cmd.get_setting_float("h_bond_cutoff_center") | | self.hbond_cutoff = self.cmd.get_setting_float("h_bond_cutoff_center") |
| | |
| self.status = 0 # 0 no atoms selections, 1 atom selected, 2 atoms select
ed, 3 atoms selected | | self.status = 0 # 0 no atoms selections, 1 atom selected, 2 atoms select
ed, 3 atoms selected |
| self.error = None | | self.error = None |
| self.object_name = None | | self.object_name = None |
| | |
| skipping to change at line 291 | | skipping to change at line 293 |
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| """ | | """ |
| Corresponds to the "Delete All Measurements" menu button | | Corresponds to the "Delete All Measurements" menu button |
| """ | | """ |
| self.meas_count = 0 | | self.meas_count = 0 |
| self.cmd.delete(obj_prefix+"*") | | self.cmd.delete(obj_prefix+"*") |
| self.status=0 | | self.status=0 |
| self.error = None | | self.error = None |
| self.clear_input() | | self.clear_input() |
| self.cmd.refresh_wizard() | | self.cmd.refresh_wizard() |
| | |
|
| | def do_pick_state(self, state): |
| | self.pick_state[self.status] = state |
| | |
| def do_select(self,name): # map selects into picks | | def do_select(self,name): # map selects into picks |
| self.cmd.unpick() | | self.cmd.unpick() |
| try: | | try: |
| self.cmd.select("pk1", name + " and not " + sele_prefix + "*") # not
e, using new object name wildcards | | self.cmd.select("pk1", name + " and not " + sele_prefix + "*") # not
e, using new object name wildcards |
| self.cmd.delete(name) | | self.cmd.delete(name) |
| self.do_pick(0) | | self.do_pick(0) |
| except pymol.CmdException: | | except pymol.CmdException: |
| if self.status: | | if self.status: |
| sele_name = sele_prefix + str(self.status-1) | | sele_name = sele_prefix + str(self.status-1) |
| self.cmd.select(indi_sele, sele_name) | | self.cmd.select(indi_sele, sele_name) |
| | |
| skipping to change at line 313 | | skipping to change at line 318 |
|---|
| def do_pick(self,bondFlag): | | def do_pick(self,bondFlag): |
| # update pk1 based on current mouse mode | | # update pk1 based on current mouse mode |
| (what,code) = self.get_selection_name() | | (what,code) = self.get_selection_name() |
| self.cmd.select( "(pk1)", code + "(pk1)") | | self.cmd.select( "(pk1)", code + "(pk1)") |
| if bondFlag: | | if bondFlag: |
| self.error = "Error: please select an atom, not a bond." | | self.error = "Error: please select an atom, not a bond." |
| print(self.error) | | print(self.error) |
| else: | | else: |
| reset = 1 | | reset = 1 |
| sele_name = sele_prefix + str(self.status) | | sele_name = sele_prefix + str(self.status) |
|
| | state1, state2, state3, state4 = self.pick_state |
| | |
| if self.mode == 'pairs': | | if self.mode == 'pairs': |
| if self.status==0: | | if self.status==0: |
| self.cmd.select(sele_name,"(pk1)") | | self.cmd.select(sele_name,"(pk1)") |
| self.cmd.select(indi_sele, sele_name) | | self.cmd.select(indi_sele, sele_name) |
| self.cmd.enable(indi_sele) | | self.cmd.enable(indi_sele) |
| self.status = 1 | | self.status = 1 |
| self.error = None | | self.error = None |
| elif self.status==1: | | elif self.status==1: |
| obj_name = self.get_name((self.object_mode=='append'), | | obj_name = self.get_name((self.object_mode=='append'), |
| (self.object_mode=='append')) | | (self.object_mode=='append')) |
| if self.object_mode=='merge': | | if self.object_mode=='merge': |
| reset = 0 | | reset = 0 |
|
| self.cmd.dist(obj_name,"(v. and " + sele_prefix+"0)","(v. an | | |
| d (pk1))",reset=reset) | | if state1 == state2 and self.cmd.get_selection_state('?pk1') |
| | != 0: |
| | state1 = state2 = -3 |
| | |
| | self.cmd.dist(obj_name,"(v. and " + sele_prefix+"0)","(v. an |
| | d (pk1))",reset=reset, |
| | state1=state1, state2=state2) |
| | |
| self.cmd.enable(obj_name) | | self.cmd.enable(obj_name) |
| self.clear_input() | | self.clear_input() |
| self.status = 0 | | self.status = 0 |
| self.cmd.unpick() | | self.cmd.unpick() |
| elif self.mode == 'rings': | | elif self.mode == 'rings': |
| if self.status==0: | | if self.status==0: |
| self.cmd.select(sele_name,"(?pk1 | byring ?pk1)") | | self.cmd.select(sele_name,"(?pk1 | byring ?pk1)") |
| self.cmd.select(indi_sele, sele_name) | | self.cmd.select(indi_sele, sele_name) |
| self.cmd.enable(indi_sele) | | self.cmd.enable(indi_sele) |
| self.status = 1 | | self.status = 1 |
| self.error = None | | self.error = None |
| elif self.status==1: | | elif self.status==1: |
| obj_name = self.get_name((self.object_mode=='append'), | | obj_name = self.get_name((self.object_mode=='append'), |
| (self.object_mode=='append')) | | (self.object_mode=='append')) |
| if self.object_mode=='merge': | | if self.object_mode=='merge': |
| reset = 0 | | reset = 0 |
|
| | |
| | if state1 == state2 and self.cmd.get_selection_state('?pk1') |
| | != 0: |
| | state1 = state2 = -3 |
| | |
| self.cmd.distance(obj_name, | | self.cmd.distance(obj_name, |
| "?" + sele_prefix + "0", | | "?" + sele_prefix + "0", |
| "(?pk1 | byring ?pk1)", | | "(?pk1 | byring ?pk1)", |
|
| mode=4, reset=reset) | | mode=4, reset=reset, |
| | state1=state1, state2=state2) |
| self.cmd.enable(obj_name) | | self.cmd.enable(obj_name) |
| self.clear_input() | | self.clear_input() |
| self.status = 0 | | self.status = 0 |
| self.cmd.unpick() | | self.cmd.unpick() |
| elif self.mode == 'angle': | | elif self.mode == 'angle': |
| if self.status<2: | | if self.status<2: |
| self.cmd.select(sele_name,"(pk1)") | | self.cmd.select(sele_name,"(pk1)") |
| self.cmd.unpick() | | self.cmd.unpick() |
| self.cmd.select(indi_sele, sele_name) | | self.cmd.select(indi_sele, sele_name) |
| self.cmd.enable(indi_sele) | | self.cmd.enable(indi_sele) |
| self.status = self.status + 1 | | self.status = self.status + 1 |
| self.error = None | | self.error = None |
| else: | | else: |
| obj_name = self.get_name((self.object_mode=='append'), | | obj_name = self.get_name((self.object_mode=='append'), |
| (self.object_mode=='append')) | | (self.object_mode=='append')) |
| if self.object_mode=='merge': | | if self.object_mode=='merge': |
| reset = 0 | | reset = 0 |
|
| | |
| | if state1 == state2 == state3 and self.cmd.get_selection_sta |
| | te('?pk1') != 0: |
| | state1 = state2 = state3 = -3 |
| | |
| self.cmd.angle(obj_name, "(v. and " + sele_prefix+"0)", "(v.
and " + sele_prefix+"1)", | | self.cmd.angle(obj_name, "(v. and " + sele_prefix+"0)", "(v.
and " + sele_prefix+"1)", |
|
| "(v. and (pk1))", reset=reset) | | "(v. and (pk1))", reset=reset, |
| | state1=state1, state2=state2, state3=state3) |
| self.cmd.enable(obj_name) | | self.cmd.enable(obj_name) |
| self.clear_input() | | self.clear_input() |
| self.status = 0 | | self.status = 0 |
| self.cmd.unpick() | | self.cmd.unpick() |
| elif self.mode == 'dihed': | | elif self.mode == 'dihed': |
| if self.status<3: | | if self.status<3: |
| self.cmd.select(sele_name,"(pk1)") | | self.cmd.select(sele_name,"(pk1)") |
| self.cmd.unpick() | | self.cmd.unpick() |
| self.cmd.select(indi_sele, sele_name) | | self.cmd.select(indi_sele, sele_name) |
| self.cmd.enable(indi_sele) | | self.cmd.enable(indi_sele) |
| | | |
| End of changes. 8 change blocks. |
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| 4 lines changed or deleted | | 30 lines changed or added |
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