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.
| querying.py (pymol-open-source-2.2.0) | : | querying.py (pymol-open-source-2.3.0) |
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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 |
| | |
|
| if __name__=='pymol.querying': | | if True: |
| | |
| import time | | import time |
| from . import selector | | from . import selector |
| import pymol | | import pymol |
| cmd = __import__("sys").modules["pymol.cmd"] | | cmd = __import__("sys").modules["pymol.cmd"] |
| from .cmd import _cmd,lock,unlock,Shortcut, \ | | from .cmd import _cmd,lock,unlock,Shortcut, \ |
| _feedback,fb_module,fb_mask,is_list, \ | | _feedback,fb_module,fb_mask,is_list, \ |
| DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error | | DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error |
| | |
| def auto_measure(_self=cmd): | | def auto_measure(_self=cmd): |
| | |
| skipping to change at line 814 | | skipping to change at line 814 |
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| r = _cmd.export_dots(_self._COb,object,int(state)-1) | | r = _cmd.export_dots(_self._COb,object,int(state)-1) |
| finally: | | finally: |
| _self.unlock(r,_self) | | _self.unlock(r,_self) |
| if _raising(r,_self): raise pymol.CmdException | | if _raising(r,_self): raise pymol.CmdException |
| return r | | return r |
| | |
| def overlap(selection1, selection2, state1=1, state2=1, adjust=0.0, quiet=1,
_self=cmd): | | def overlap(selection1, selection2, state1=1, state2=1, adjust=0.0, quiet=1,
_self=cmd): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
|
| "overlap" is an unsupported command that may have something to do | | "overlap" is an unsupported command that sums up |
| with measuring the total amount of van der Waals overlap between | | [(VDWi + VDWj) - distance_ij]/2 between pairs of |
| two selections. | | selected atoms. |
| | |
| | PYMOL API |
| | |
| | cmd.overlap(string selection1, string selection2 [, int state1=1, int state2 |
| | =1, float adjust=0.0]) |
| | |
| NOTES | | NOTES |
| | |
|
| For best performance, use the smaller molecule as selection 1. | | It does not compute the volume overlap, |
| | selections with more atoms will have a larger |
| | sum. |
| | |
| ''' | | ''' |
| | |
| # preprocess selections | | # preprocess selections |
| selection1 = selector.process(selection1) | | selection1 = selector.process(selection1) |
| selection2 = selector.process(selection2) | | selection2 = selector.process(selection2) |
| # | | # |
| r = DEFAULT_ERROR | | r = DEFAULT_ERROR |
| try: | | try: |
| _self.lock(_self) | | _self.lock(_self) |
| | |
| skipping to change at line 1637 | | skipping to change at line 1643 |
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| DESCRIPTION | | DESCRIPTION |
| | |
| "get_raw_alignment" returns a list of lists of (object,index) | | "get_raw_alignment" returns a list of lists of (object,index) |
| tuples containing the raw per-atom alignment relationships | | tuples containing the raw per-atom alignment relationships |
| | |
| PYMOL API | | PYMOL API |
| | |
| cmd.get_raw_alignment(name) | | cmd.get_raw_alignment(name) |
| | |
| ''' | | ''' |
|
| | r = DEFAULT_ERROR |
| try: | | try: |
| _self.lock(_self) | | _self.lock(_self) |
| r = _cmd.get_raw_alignment(_self._COb,str(name),int(active_only)) | | r = _cmd.get_raw_alignment(_self._COb,str(name),int(active_only)) |
| finally: | | finally: |
| _self.unlock(r,_self) | | _self.unlock(r,_self) |
| if _raising(r,_self): raise pymol.CmdException | | if _raising(r,_self): raise pymol.CmdException |
| return r | | return r |
| | |
| def get_object_state(name, _self=cmd): | | def get_object_state(name, _self=cmd): |
| ''' | | ''' |
| | | |
| End of changes. 4 change blocks. |
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| 5 lines changed or deleted | | 13 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 