707 lines
16 KiB
Python
707 lines
16 KiB
Python
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#A* -------------------------------------------------------------------
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#B* This file contains source code for the PyMOL computer program
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#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
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#D* -------------------------------------------------------------------
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#E* It is unlawful to modify or remove this copyright notice.
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#F* -------------------------------------------------------------------
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#G* Please see the accompanying LICENSE file for further information.
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#H* -------------------------------------------------------------------
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#I* Additional authors of this source file include:
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#-*
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#-*
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#-*
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#Z* -------------------------------------------------------------------
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import os
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import copy
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import functools
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#
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# Basic chempy types
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#
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@functools.total_ordering
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class Atom(object):
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def __reduce__(self):
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# for loading new-style class pickle with PyMOL <= 2.2
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return (self.__class__, (), self.__dict__)
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def __setstate__(self, state):
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# for loading PyMOL <= 2.2 pickles
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self.__dict__.update(state)
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if 'resi' in state:
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self.resi = self.__dict__.pop('resi')
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@property
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def resi(self):
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return str(self.resi_number) + self.ins_code
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@resi.setter
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def resi(self, resi):
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if isinstance(resi, str) and resi and not resi[-1].isdigit():
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self.ins_code = resi[-1]
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resi = resi[:-1]
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else:
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self.__dict__.pop('ins_code', None)
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self.resi_number = int(resi or 0)
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# these must be immutables
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symbol = 'X'
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name = ''
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resn = 'UNK'
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resn_code = 'X'
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ins_code = ''
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resi_number = 1
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b = 0.0
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q = 1.0
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vdw = 0.0
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alt = ''
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hetatm = 1
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segi = ''
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chain = ''
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coord = (9999.999,9999.999,9999.999)
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formal_charge = 0.0
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partial_charge = 0.0
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elec_radius = 0.0
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custom = ''
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# Flags
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flags = 0
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# Force-fields
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numeric_type = -9999
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text_type = '??'
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# MDL Mol-files
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stereo = 0
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# Macromodel files
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color_code = 2
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# Secondary structure
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ss = ''
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def get_mass(self):
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'''Given the chemical symbol the atomic mass is returned'''
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return atomic_mass[self.symbol]
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def get_number(self):
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'''Given the chemical symbol the atomic number is returned'''
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return atomic_number[self.symbol]
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def get_implicit_valence(self):
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return implicit_valence[self.symbol]
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def get_free_valence(self, npaired):
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try:
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maxfree = implicit_valence[self.symbol][0]
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except KeyError:
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print("unknown implicit_valence for", self.symbol)
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return 0
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return max(0, maxfree - npaired + self.formal_charge)
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def has(self,attr):
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return attr in self.__dict__
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def in_same_residue(self,other):
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if self.resi == other.resi:
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if self.chain == other.chain:
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if self.segi == other.segi:
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return 1
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return 0
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def new_in_residue(self):
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newat = Atom()
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if self.has('segi'): newat.segi = self.segi
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if self.has('chain'): newat.chain = self.chain
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if self.has('resn'): newat.resn = self.resn
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if self.has('resn_code'): newat.resn_code = self.resn_code
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if self.has('ins_code'): newat.ins_code = self.ins_code
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if self.has('resi_number'): newat.resi_number = self.resi_number
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if self.has('hetatm'): newat.hetatm = self.hetatm
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return newat
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def get_signature(self):
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return ':'.join([self.segi, self.chain, self.resn,
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self.resi, self.symbol, self.name])
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def __cmp__(self,other):
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return \
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cmp(type(self), type(other)) or \
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cmp(self.segi, other.segi) or \
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cmp(self.chain, other.chain) or \
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cmp(self.resi_number, other.resi_number) or \
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cmp(self.ins_code, other.ins_code) or \
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cmp(self.resn, other.resn) or \
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cmp(self.symbol, other.symbol) or \
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cmp(self.name, other.name) or \
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cmp(id(self), id(other))
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@staticmethod
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def _order(obj):
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return (
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obj.segi,
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obj.chain,
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obj.resi_number,
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obj.ins_code,
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obj.resn,
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obj.symbol,
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obj.name,
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id(obj),
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)
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def __gt__(self, other):
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return Atom._order(self) > Atom._order(other)
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def __eq__(self, other):
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return Atom._order(self) == Atom._order(other)
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class Bond:
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order = 1
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stereo = 0 # deprecated
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symmetry_2 = "" # _geom_bond.site_symmetry_2
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def has(self,attr):
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return attr in self.__dict__
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class Molecule:
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defaults = {
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'dim_code' : '3D',
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'title' : 'untitled',
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'comments' : '',
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'chiral' : 1,
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'spacegroup' : 'P 1',
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'cell' : [1.0, 1.0, 1.0, 90.0, 90.0, 90.0],
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}
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def __getattr__(self,attr):
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if attr in Molecule.defaults:
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return Molecule.defaults[attr]
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else:
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raise AttributeError(attr)
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def has(self,attr):
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return attr in self.__dict__
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class Storage:
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def my_open(self,fname,mode='r'):
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if 'r' in mode and '://' in fname:
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import urllib.request as urllib
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return urllib.urlopen(fname)
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elif fname.endswith(".gz") or fname.endswith(".pze") or fname.endswith("pzw"):
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import gzip
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return gzip.open(fname, mode)
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else:
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return open(fname,mode)
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def updateFromList(self,indexed,**params):
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return NotImplementedError
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def fromList(self,**params):
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return NotImplementedError
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def toList(self,indexed,**params):
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return NotImplementedError
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def updateFromFile(self,indexed,fname,**params):
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fp = open(fname)
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result = self.updateFromList(indexed, fp.readlines(), **params)
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fp.close()
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def fromFile(self,fname,**params):
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if feedback['io']:
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print(' chempy: reading "%s".' % fname)
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fp = self.my_open(fname)
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result = self.fromList(fp.readlines(), **params)
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fp.close()
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return result
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def toFile(self,indexed,fname,**params):
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lines = self.toList(indexed, **params)
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if feedback['io']:
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print(' chempy: writing "%s".' % fname)
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fp = open(fname,'w')
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result = fp.writelines(lines)
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fp.close()
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class PseudoFile:
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def __init__(self,list=[]):
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self.list = copy.deepcopy(list)
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def write(self,st):
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self.list.append(str(st))
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def readline(self):
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try:
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return self.list.pop(0)
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except:
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return None
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def close(self):
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self.list = None
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feedback = { 'warnings': 1,
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'terse' : 1,
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'io' : 1,
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'actions' : 1,
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'tinker' : 1,
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'gamess' : 1,
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'atoms' : 0,
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'bonds' : 0,
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'verbose' : 0,
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'bmin' : 1,
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}
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if 'CHEMPY_DATA' in os.environ: #
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path = os.environ['CHEMPY_DATA'] + '/'
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elif 'PYMOL_DATA' in os.environ:
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path = os.environ['PYMOL_DATA'] + '/chempy/'
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elif 'PYMOL_PATH' in os.environ:
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path = os.environ['PYMOL_PATH'] + '/data/chempy/'
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else:
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path = ''
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# double check these values...
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#hvd values obtained from http://www.webelements.com/ and recorded to their
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# known accuracy.
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atomic_mass = {
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'H' : 1.00794,
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'He' : 4.002602,
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'HE' : 4.002602,
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'Li' : 6.941,
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'LI' : 6.941,
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'Be' : 9.012182,
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'BE' : 9.012182,
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'B' : 10.811,
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'C' : 12.0107,
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'N' : 14.0067,
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'O' : 15.9994,
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'F' : 18.9984032,
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'Ne' : 20.1797,
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'NE' : 20.1797,
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'Na' : 22.989770,
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'NA' : 22.989770,
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'Mg' : 24.3050,
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'MG' : 24.3050,
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'Al' : 26.981538,
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'AL' : 26.981538,
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'Si' : 28.0855,
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'SI' : 28.0855,
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'P' : 30.973761,
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'S' : 32.065,
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'Cl' : 35.453,
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'CL' : 35.453,
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'Ar' : 39.948,
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'AR' : 39.948,
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'K' : 39.0983,
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'Ca' : 40.078,
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'CA' : 40.078,
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'Sc' : 44.955910,
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'SC' : 44.955910,
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'Ti' : 47.867,
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'TI' : 47.867,
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'V' : 50.9415,
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'Cr' : 51.9961,
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'CR' : 51.9961,
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'Mn' : 54.938049,
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'MN' : 54.938049,
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'Fe' : 55.845,
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'FE' : 55.845,
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'Co' : 58.933200,
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'CO' : 58.933200,
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'Ni' : 58.6934,
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'NI' : 58.6934,
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'Cu' : 63.546,
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'CU' : 63.546,
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'Zn' : 65.39,
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'ZN' : 65.39,
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'Ga' : 69.723,
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'GA' : 69.723,
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'Ge' : 72.64,
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'GE' : 72.64,
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'As' : 74.92160,
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'AS' : 74.92160,
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'Se' : 78.96,
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'SE' : 78.96,
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'Br' : 79.904,
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'BR' : 79.904,
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'Kr' : 83.80,
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'KR' : 83.80,
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'Rb' : 85.4678,
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'RB' : 85.4678,
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'Sr' : 87.62,
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'SR' : 87.62,
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'Y' : 88.90585,
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'Zr' : 91.224,
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'ZR' : 91.224,
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'Nb' : 92.90638,
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'NB' : 92.90638,
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'Mo' : 95.94,
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'MO' : 95.94,
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'Tc' : 98,
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'TC' : 98,
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'Ru' : 101.07,
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'RU' : 101.07,
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'Rh' : 102.90550,
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'RH' : 102.90550,
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'Pd' : 106.42,
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'PD' : 106.42,
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'Ag' : 107.8682,
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'AG' : 107.8682,
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'Cd' : 112.411,
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'CD' : 112.411,
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'In' : 114.818,
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'IN' : 114.818,
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'Sn' : 118.710,
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'SN' : 118.710,
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'Sb' : 121.760,
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'SB' : 121.760,
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'Te' : 127.60,
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'TE' : 127.60,
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'I' : 126.90447,
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'Xe' : 131.293,
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'XE' : 131.293,
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'Cs' : 132.90545,
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'CS' : 132.90545,
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'Ba' : 137.327,
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'BA' : 137.327,
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'La' : 138.9055,
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'LA' : 138.9055,
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'Ce' : 140.116,
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'CE' : 140.116,
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'Pr' : 140.90765,
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'PR' : 140.90765,
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'Nd' : 144.24,
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'ND' : 144.24,
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'Pm' : 145,
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'PM' : 145,
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'Sm' : 150.36,
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'SM' : 150.36,
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'Eu' : 151.964,
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|
'EU' : 151.964,
|
||
|
|
'Gd' : 157.25,
|
||
|
|
'GD' : 157.25,
|
||
|
|
'Tb' : 158.92534,
|
||
|
|
'TB' : 158.92534,
|
||
|
|
'Dy' : 162.50,
|
||
|
|
'DY' : 162.50,
|
||
|
|
'Ho' : 164.93032,
|
||
|
|
'HO' : 164.93032,
|
||
|
|
'Er' : 167.259,
|
||
|
|
'ER' : 167.259,
|
||
|
|
'Tm' : 168.93421,
|
||
|
|
'TM' : 168.93421,
|
||
|
|
'Yb' : 173.04,
|
||
|
|
'YB' : 173.04,
|
||
|
|
'Lu' : 174.967,
|
||
|
|
'LU' : 174.967,
|
||
|
|
'Hf' : 178.49,
|
||
|
|
'HF' : 178.49,
|
||
|
|
'Ta' : 180.9479,
|
||
|
|
'TA' : 180.9479,
|
||
|
|
'W' : 183.84,
|
||
|
|
'Re' : 186.207,
|
||
|
|
'RE' : 186.207,
|
||
|
|
'Os' : 190.23,
|
||
|
|
'OS' : 190.23,
|
||
|
|
'Ir' : 192.217,
|
||
|
|
'IR' : 192.217,
|
||
|
|
'Pt' : 195.078,
|
||
|
|
'PT' : 195.078,
|
||
|
|
'Au' : 196.96655,
|
||
|
|
'AU' : 196.96655,
|
||
|
|
'Hg' : 200.59,
|
||
|
|
'HG' : 200.59,
|
||
|
|
'Tl' : 204.3833,
|
||
|
|
'TL' : 204.3833,
|
||
|
|
'Pb' : 207.2,
|
||
|
|
'PB' : 207.2,
|
||
|
|
'Bi' : 208.98038,
|
||
|
|
'BI' : 208.98038,
|
||
|
|
'Po' : 208.98,
|
||
|
|
'PO' : 208.98,
|
||
|
|
'At' : 209.99,
|
||
|
|
'AT' : 209.99,
|
||
|
|
'Rn' : 222.02,
|
||
|
|
'RN' : 222.02,
|
||
|
|
'Fr' : 223.02,
|
||
|
|
'FR' : 223.02,
|
||
|
|
'Ra' : 226.03,
|
||
|
|
'RA' : 226.03,
|
||
|
|
'Ac' : 227.03,
|
||
|
|
'AC' : 227.03,
|
||
|
|
'Th' : 232.0381,
|
||
|
|
'TH' : 232.0381,
|
||
|
|
'Pa' : 231.03588,
|
||
|
|
'PA' : 231.03588,
|
||
|
|
'U' : 238.02891,
|
||
|
|
'Np' : 237.05,
|
||
|
|
'NP' : 237.05,
|
||
|
|
'Pu' : 244.06,
|
||
|
|
'PU' : 244.06,
|
||
|
|
'Am' : 243.06,
|
||
|
|
'AM' : 243.06,
|
||
|
|
'Cm' : 247.07,
|
||
|
|
'CM' : 247.07,
|
||
|
|
'Bk' : 247.07,
|
||
|
|
'BK' : 247.07,
|
||
|
|
'Cf' : 251.08,
|
||
|
|
'CF' : 251.08,
|
||
|
|
'Es' : 252.08,
|
||
|
|
'ES' : 252.08,
|
||
|
|
'Fm' : 257.10,
|
||
|
|
'FM' : 257.10,
|
||
|
|
'Md' : 258.10,
|
||
|
|
'MD' : 258.10,
|
||
|
|
'No' : 259.10,
|
||
|
|
'NO' : 259.10,
|
||
|
|
'Lr' : 262.11,
|
||
|
|
'LR' : 262.11,
|
||
|
|
'Rf' : 261.11,
|
||
|
|
'RF' : 261.11,
|
||
|
|
'Db' : 262.11,
|
||
|
|
'DB' : 262.11,
|
||
|
|
'Sg' : 266.12,
|
||
|
|
'SG' : 266.12,
|
||
|
|
'Bh' : 264.12,
|
||
|
|
'BH' : 264.12,
|
||
|
|
'Hs' : 269.13,
|
||
|
|
'HS' : 269.13,
|
||
|
|
'Mt' : 268.14,
|
||
|
|
'MT' : 268.14,
|
||
|
|
}
|
||
|
|
|
||
|
|
atomic_number = {
|
||
|
|
'H' : 1,
|
||
|
|
'He' : 2,
|
||
|
|
'HE' : 2,
|
||
|
|
'Li' : 3,
|
||
|
|
'LI' : 3,
|
||
|
|
'Be' : 4,
|
||
|
|
'BE' : 4,
|
||
|
|
'B' : 5,
|
||
|
|
'C' : 6,
|
||
|
|
'N' : 7,
|
||
|
|
'O' : 8,
|
||
|
|
'F' : 9,
|
||
|
|
'Ne' : 10,
|
||
|
|
'NE' : 10,
|
||
|
|
'Na' : 11,
|
||
|
|
'NA' : 11,
|
||
|
|
'Mg' : 12,
|
||
|
|
'MG' : 12,
|
||
|
|
'Al' : 13,
|
||
|
|
'AL' : 13,
|
||
|
|
'Si' : 14,
|
||
|
|
'SI' : 14,
|
||
|
|
'P' : 15,
|
||
|
|
'S' : 16,
|
||
|
|
'Cl' : 17,
|
||
|
|
'CL' : 17,
|
||
|
|
'Ar' : 18,
|
||
|
|
'AR' : 18,
|
||
|
|
'K' : 19,
|
||
|
|
'Ca' : 20,
|
||
|
|
'CA' : 20,
|
||
|
|
'Sc' : 21,
|
||
|
|
'SC' : 21,
|
||
|
|
'Ti' : 22,
|
||
|
|
'TI' : 22,
|
||
|
|
'V' : 23,
|
||
|
|
'Cr' : 24,
|
||
|
|
'CR' : 24,
|
||
|
|
'Mn' : 25,
|
||
|
|
'MN' : 25,
|
||
|
|
'Fe' : 26,
|
||
|
|
'FE' : 26,
|
||
|
|
'Co' : 27,
|
||
|
|
'CO' : 27,
|
||
|
|
'Ni' : 28,
|
||
|
|
'NI' : 28,
|
||
|
|
'Cu' : 29,
|
||
|
|
'CU' : 29,
|
||
|
|
'Zn' : 30,
|
||
|
|
'ZN' : 30,
|
||
|
|
'Ga' : 31,
|
||
|
|
'GA' : 31,
|
||
|
|
'Ge' : 32,
|
||
|
|
'GE' : 32,
|
||
|
|
'As' : 33,
|
||
|
|
'AS' : 33,
|
||
|
|
'Se' : 34,
|
||
|
|
'SE' : 34,
|
||
|
|
'Br' : 35,
|
||
|
|
'BR' : 35,
|
||
|
|
'Kr' : 36,
|
||
|
|
'KR' : 36,
|
||
|
|
'Rb' : 37,
|
||
|
|
'RB' : 37,
|
||
|
|
'Sr' : 38,
|
||
|
|
'SR' : 38,
|
||
|
|
'Y' : 39,
|
||
|
|
'Zr' : 40,
|
||
|
|
'ZR' : 40,
|
||
|
|
'Nb' : 41,
|
||
|
|
'NB' : 41,
|
||
|
|
'Mo' : 42,
|
||
|
|
'MO' : 42,
|
||
|
|
'Tc' : 43,
|
||
|
|
'TC' : 43,
|
||
|
|
'Ru' : 44,
|
||
|
|
'RU' : 44,
|
||
|
|
'Rh' : 45,
|
||
|
|
'RH' : 45,
|
||
|
|
'Pd' : 46,
|
||
|
|
'PD' : 46,
|
||
|
|
'Ag' : 47,
|
||
|
|
'AG' : 47,
|
||
|
|
'Cd' : 48,
|
||
|
|
'CD' : 48,
|
||
|
|
'In' : 49,
|
||
|
|
'IN' : 49,
|
||
|
|
'Sn' : 50,
|
||
|
|
'SN' : 50,
|
||
|
|
'Sb' : 51,
|
||
|
|
'SB' : 51,
|
||
|
|
'Te' : 52,
|
||
|
|
'TE' : 52,
|
||
|
|
'I' : 53,
|
||
|
|
'Xe' : 54,
|
||
|
|
'XE' : 54,
|
||
|
|
'Cs' : 55,
|
||
|
|
'CS' : 55,
|
||
|
|
'Ba' : 56,
|
||
|
|
'BA' : 56,
|
||
|
|
'La' : 57,
|
||
|
|
'LA' : 57,
|
||
|
|
'Ce' : 58,
|
||
|
|
'CE' : 58,
|
||
|
|
'Pr' : 59,
|
||
|
|
'PR' : 59,
|
||
|
|
'Nd' : 60,
|
||
|
|
'ND' : 60,
|
||
|
|
'Pm' : 61,
|
||
|
|
'PM' : 61,
|
||
|
|
'Sm' : 62,
|
||
|
|
'SM' : 62,
|
||
|
|
'Eu' : 63,
|
||
|
|
'EU' : 63,
|
||
|
|
'Gd' : 64,
|
||
|
|
'GD' : 64,
|
||
|
|
'Tb' : 65,
|
||
|
|
'TB' : 65,
|
||
|
|
'Dy' : 66,
|
||
|
|
'DY' : 66,
|
||
|
|
'Ho' : 67,
|
||
|
|
'HO' : 67,
|
||
|
|
'Er' : 68,
|
||
|
|
'ER' : 68,
|
||
|
|
'Tm' : 69,
|
||
|
|
'TM' : 69,
|
||
|
|
'Yb' : 70,
|
||
|
|
'YB' : 70,
|
||
|
|
'Lu' : 71,
|
||
|
|
'LU' : 71,
|
||
|
|
'Hf' : 72,
|
||
|
|
'HF' : 72,
|
||
|
|
'Ta' : 73,
|
||
|
|
'TA' : 73,
|
||
|
|
'W' : 74,
|
||
|
|
'Re' : 75,
|
||
|
|
'RE' : 75,
|
||
|
|
'Os' : 76,
|
||
|
|
'OS' : 76,
|
||
|
|
'Ir' : 77,
|
||
|
|
'IR' : 77,
|
||
|
|
'Pt' : 78,
|
||
|
|
'PT' : 78,
|
||
|
|
'Au' : 79,
|
||
|
|
'AU' : 79,
|
||
|
|
'Hg' : 80,
|
||
|
|
'HG' : 80,
|
||
|
|
'Tl' : 81,
|
||
|
|
'TL' : 81,
|
||
|
|
'Pb' : 82,
|
||
|
|
'PB' : 82,
|
||
|
|
'Bi' : 83,
|
||
|
|
'BI' : 83,
|
||
|
|
'Po' : 84,
|
||
|
|
'PO' : 84,
|
||
|
|
'At' : 85,
|
||
|
|
'AT' : 85,
|
||
|
|
'Rn' : 86,
|
||
|
|
'RN' : 86,
|
||
|
|
'Fr' : 87,
|
||
|
|
'FR' : 87,
|
||
|
|
'Ra' : 88,
|
||
|
|
'RA' : 88,
|
||
|
|
'Ac' : 89,
|
||
|
|
'AC' : 89,
|
||
|
|
'Th' : 90,
|
||
|
|
'TH' : 90,
|
||
|
|
'Pa' : 91,
|
||
|
|
'PA' : 91,
|
||
|
|
'U' : 92,
|
||
|
|
'Np' : 93,
|
||
|
|
'NP' : 93,
|
||
|
|
'Pu' : 94,
|
||
|
|
'PU' : 94,
|
||
|
|
'Am' : 95,
|
||
|
|
'AM' : 95,
|
||
|
|
'Cm' : 96,
|
||
|
|
'CM' : 96,
|
||
|
|
'Bk' : 97,
|
||
|
|
'BK' : 97,
|
||
|
|
'Cf' : 98,
|
||
|
|
'CF' : 98,
|
||
|
|
'Es' : 99,
|
||
|
|
'ES' : 99,
|
||
|
|
'Fm' : 100,
|
||
|
|
'FM' : 100,
|
||
|
|
'Md' : 101,
|
||
|
|
'MD' : 101,
|
||
|
|
'No' : 102,
|
||
|
|
'NO' : 102,
|
||
|
|
'Lr' : 103,
|
||
|
|
'LR' : 103,
|
||
|
|
'Rf' : 104,
|
||
|
|
'RF' : 104,
|
||
|
|
'Db' : 105,
|
||
|
|
'DB' : 105,
|
||
|
|
'Sg' : 106,
|
||
|
|
'SG' : 106,
|
||
|
|
'Bh' : 107,
|
||
|
|
'BH' : 107,
|
||
|
|
'Hs' : 108,
|
||
|
|
'HS' : 108,
|
||
|
|
'Mt' : 109,
|
||
|
|
'MT' : 109
|
||
|
|
}
|
||
|
|
|
||
|
|
implicit_valence = {
|
||
|
|
'H' : {0:1,1:0},
|
||
|
|
'C' : {0:4,1:3,2:2,3:1,4:0},
|
||
|
|
'N' : {0:3,1:2,2:1,3:0,4:0},
|
||
|
|
'O' : {0:2,1:1,2:0},
|
||
|
|
'F' : {0:1,1:0},
|
||
|
|
'Cl' : {0:1,1:0},
|
||
|
|
'CL' : {0:1,1:0},
|
||
|
|
'Br' : {0:1,1:0},
|
||
|
|
'BR' : {0:1,1:0},
|
||
|
|
'I' : {0:1,1:0},
|
||
|
|
'S' : {0:2,1:2,2:0,3:1,4:0,5:1,6:0}, # ambiguity?
|
||
|
|
'K' : {0:0,1:0}, # as drawn
|
||
|
|
'Cu' : {0:0,1:0,2:0}, # as drawn
|
||
|
|
'CU' : {0:0,1:0,2:0}, # as drawn
|
||
|
|
'Zn' : {0:0,1:0,2:0,4:0}, # as drawn
|
||
|
|
'ZN' : {0:0,1:0,2:0,4:0}, # as drawn
|
||
|
|
'Mg' : {0:1,1:0},
|
||
|
|
'MG' : {0:1,1:0},
|
||
|
|
'Ca' : {0:1,1:0},
|
||
|
|
'CA' : {0:1,1:0},
|
||
|
|
'P' : {0:3,1:2,2:1,3:0,4:0,5:0,6:0},
|
||
|
|
}
|