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.
| __init__.py (pymol-open-source-2.2.0) | : | __init__.py (pymol-open-source-2.3.0) |
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| | |
| skipping to change at line 19 | | skipping to change at line 19 |
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| #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 os | | import os |
| import copy | | import copy |
|
| | import functools |
| | |
| # | | # |
| # Basic chempy types | | # Basic chempy types |
| # | | # |
| | |
|
| class Atom: | | @functools.total_ordering |
| | class Atom(object): |
| | |
| | def __reduce__(self): |
| | # for loading new-style class pickle with PyMOL <= 2.2 |
| | return (self.__class__, (), self.__dict__) |
| | |
| | def __setstate__(self, state): |
| | # for loading PyMOL <= 2.2 pickles |
| | self.__dict__.update(state) |
| | if 'resi' in state: |
| | self.resi = self.__dict__.pop('resi') |
| | |
| | @property |
| | def resi(self): |
| | return str(self.resi_number) + self.ins_code |
| | |
| | @resi.setter |
| | def resi(self, resi): |
| | if isinstance(resi, str) and resi and not resi[-1].isdigit(): |
| | self.ins_code = resi[-1] |
| | resi = resi[:-1] |
| | else: |
| | self.__dict__.pop('ins_code', None) |
| | self.resi_number = int(resi or 0) |
| | |
| # these must be immutables | | # these must be immutables |
| symbol = 'X' | | symbol = 'X' |
| name = '' | | name = '' |
| resn = 'UNK' | | resn = 'UNK' |
| resn_code = 'X' | | resn_code = 'X' |
|
| resi = '1' | | ins_code = '' |
| resi_number = 1 | | resi_number = 1 |
| b = 0.0 | | b = 0.0 |
| q = 1.0 | | q = 1.0 |
| vdw = 0.0 | | vdw = 0.0 |
| alt = '' | | alt = '' |
| hetatm = 1 | | hetatm = 1 |
| segi = '' | | segi = '' |
| chain = '' | | chain = '' |
| coord = (9999.999,9999.999,9999.999) | | coord = (9999.999,9999.999,9999.999) |
| formal_charge = 0.0 | | formal_charge = 0.0 |
| partial_charge = 0.0 | | partial_charge = 0.0 |
|
| | elec_radius = 0.0 |
| | custom = '' |
| # Flags | | # Flags |
| flags = 0 | | flags = 0 |
| # Force-fields | | # Force-fields |
| numeric_type = -9999 | | numeric_type = -9999 |
| text_type = '??' | | text_type = '??' |
| # MDL Mol-files | | # MDL Mol-files |
| stereo = 0 | | stereo = 0 |
| # Macromodel files | | # Macromodel files |
| color_code = 2 | | color_code = 2 |
| # Secondary structure | | # Secondary structure |
| | |
| skipping to change at line 90 | | skipping to change at line 117 |
|---|
| if self.segi == other.segi: | | if self.segi == other.segi: |
| return 1 | | return 1 |
| return 0 | | return 0 |
| | |
| def new_in_residue(self): | | def new_in_residue(self): |
| newat = Atom() | | newat = Atom() |
| if self.has('segi'): newat.segi = self.segi | | if self.has('segi'): newat.segi = self.segi |
| if self.has('chain'): newat.chain = self.chain | | if self.has('chain'): newat.chain = self.chain |
| if self.has('resn'): newat.resn = self.resn | | if self.has('resn'): newat.resn = self.resn |
| if self.has('resn_code'): newat.resn_code = self.resn_code | | if self.has('resn_code'): newat.resn_code = self.resn_code |
|
| if self.has('resi'): newat.resi = self.resi | | if self.has('ins_code'): newat.ins_code = self.ins_code |
| if self.has('resi_number'): newat.resi_number = self.resi_number | | if self.has('resi_number'): newat.resi_number = self.resi_number |
| if self.has('hetatm'): newat.hetatm = self.hetatm | | if self.has('hetatm'): newat.hetatm = self.hetatm |
| return newat | | return newat |
| | |
| def get_signature(self): | | def get_signature(self): |
| return ':'.join([self.segi, self.chain, self.resn, | | return ':'.join([self.segi, self.chain, self.resn, |
| self.resi, self.symbol, self.name]) | | self.resi, self.symbol, self.name]) |
| | |
| def __cmp__(self,other): | | def __cmp__(self,other): |
| return \ | | return \ |
| cmp(type(self), type(other)) or \ | | cmp(type(self), type(other)) or \ |
| cmp(self.segi, other.segi) or \ | | cmp(self.segi, other.segi) or \ |
| cmp(self.chain, other.chain) or \ | | cmp(self.chain, other.chain) or \ |
| cmp(self.resi_number, other.resi_number) or \ | | cmp(self.resi_number, other.resi_number) or \ |
|
| cmp(self.resi, other.resi) or \ | | cmp(self.ins_code, other.ins_code) or \ |
| cmp(self.resn, other.resn) or \ | | cmp(self.resn, other.resn) or \ |
| cmp(self.symbol, other.symbol) or \ | | cmp(self.symbol, other.symbol) or \ |
| cmp(self.name, other.name) or \ | | cmp(self.name, other.name) or \ |
| cmp(id(self), id(other)) | | cmp(id(self), id(other)) |
| | |
|
| | @staticmethod |
| | def _order(obj): |
| | return ( |
| | obj.segi, |
| | obj.chain, |
| | obj.resi_number, |
| | obj.ins_code, |
| | obj.resn, |
| | obj.symbol, |
| | obj.name, |
| | id(obj), |
| | ) |
| | |
| | def __gt__(self, other): |
| | return Atom._order(self) > Atom._order(other) |
| | |
| | def __eq__(self, other): |
| | return Atom._order(self) == Atom._order(other) |
| | |
| class Bond: | | class Bond: |
| | |
| order = 1 | | order = 1 |
| stereo = 0 | | stereo = 0 |
| | |
| def has(self,attr): | | def has(self,attr): |
| return attr in self.__dict__ | | return attr in self.__dict__ |
| | |
| class Molecule: | | class Molecule: |
| | |
| | | |
| End of changes. 7 change blocks. |
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| 4 lines changed or deleted | | 50 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 