"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/chempy/protein.py" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

About: PyMOL 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.

protein.py  (pymol-open-source-2.2.0)	:	protein.py  (pymol-open-source-2.3.0)
skipping to change at line 25		skipping to change at line 25
#		#
#		#
#		#
from __future__ import print_function		from __future__ import print_function
from . import bond_amber		from . import bond_amber
from . import protein_residues		from . import protein_residues
from . import protein_amber		from . import protein_amber
		import chempy.models
from chempy.neighbor import Neighbor		from chempy.neighbor import Neighbor
from chempy.models import Connected		from chempy.models import Connected
from chempy import Bond,place,feedback		from chempy import Bond,place,feedback
from chempy.cpv import *		from chempy.cpv import *
MAX_BOND_LEN = 2.2		MAX_BOND_LEN = 2.2
PEPT_CUTOFF = 1.7		PEPT_CUTOFF = 1.7
N_TERMINAL_ATOMS = ('HT','HT1','HT2','HT3','H1','H2','H3',		N_TERMINAL_ATOMS = ('HT','HT1','HT2','HT3','H1','H2','H3',
'1H','2H','3H','1HT','2HT','3HT')		'1H','2H','3H','1HT','2HT','3HT')
skipping to change at line 69		skipping to change at line 70
model.bond = new_bond		model.bond = new_bond
#------------------------------------------------------------------------------- --		#------------------------------------------------------------------------------- --
def assign_types(model, forcefield = protein_amber, histidine = 'HIE' ):		def assign_types(model, forcefield = protein_amber, histidine = 'HIE' ):
'''		'''
assigns types: takes HIS -> HID,HIE,HIP and CYS->CYX where appropriate		assigns types: takes HIS -> HID,HIE,HIP and CYS->CYX where appropriate
but does not add any bonds!		but does not add any bonds!
'''		'''
if feedback['actions']:		if feedback['actions']:
print(" "+str(__name__)+": assigning types...")		print(" "+str(__name__)+": assigning types...")
if str(model.__class__) != 'chempy.models.Indexed':		if not isinstance(model, chempy.models.Indexed):
raise ValueError('model is not an "Indexed" model object')		raise ValueError('model is not an "Indexed" model object')
if model.nAtom:		if model.nAtom:
crd = model.get_coord_list()		crd = model.get_coord_list()
nbr = Neighbor(crd,MAX_BOND_LEN)		nbr = Neighbor(crd,MAX_BOND_LEN)
res_list = model.get_residues()		res_list = model.get_residues()
if len(res_list):		if len(res_list):
for a in res_list:		for a in res_list:
base = model.atom[a[0]]		base = model.atom[a[0]]
if not base.hetatm:		if not base.hetatm:
resn = base.resn		resn = base.resn
skipping to change at line 167		skipping to change at line 168
def add_bonds(model, forcefield = protein_amber, histidine = 'HIE' ):		def add_bonds(model, forcefield = protein_amber, histidine = 'HIE' ):
'''		'''
add_bonds(model, forcefield = protein_amber, histidine = 'HIE' )		add_bonds(model, forcefield = protein_amber, histidine = 'HIE' )
(1) fixes aliases, assigns types, makes HIS into HIE,HID, or HIP		(1) fixes aliases, assigns types, makes HIS into HIE,HID, or HIP
and changes cystine to CYX		and changes cystine to CYX
(2) adds bonds between existing atoms		(2) adds bonds between existing atoms
'''		'''
if feedback['actions']:		if feedback['actions']:
print(" "+str(__name__)+": assigning types and bonds...")		print(" "+str(__name__)+": assigning types and bonds...")
if str(model.__class__) != 'chempy.models.Indexed':		if not isinstance(model, chempy.models.Indexed):
raise ValueError('model is not an "Indexed" model object')		raise ValueError('model is not an "Indexed" model object')
if model.nAtom:		if model.nAtom:
crd = model.get_coord_list()		crd = model.get_coord_list()
nbr = Neighbor(crd,MAX_BOND_LEN)		nbr = Neighbor(crd,MAX_BOND_LEN)
res_list = model.get_residues()		res_list = model.get_residues()
if len(res_list):		if len(res_list):
for a in res_list:		for a in res_list:
base = model.atom[a[0]]		base = model.atom[a[0]]
if not base.hetatm:		if not base.hetatm:
resn = base.resn		resn = base.resn
skipping to change at line 286		skipping to change at line 287
atx = model.atom [c]		atx = model.atom [c]
atx.resn = 'CYX'		atx.resn = 'CYX'
# since b>cur, a ssume assignment later on		# since b>cur, a ssume assignment later on
break		break
#------------------------------------------------------------------------------- --		#------------------------------------------------------------------------------- --
def add_hydrogens(model,forcefield=protein_amber,skip_sort=None):		def add_hydrogens(model,forcefield=protein_amber,skip_sort=None):
# assumes no bonds between non-hetatms		# assumes no bonds between non-hetatms
if feedback['actions']:		if feedback['actions']:
print(" "+str(__name__)+": adding hydrogens...")		print(" "+str(__name__)+": adding hydrogens...")
if str(model.__class__) != 'chempy.models.Connected':		if not isinstance(model, chempy.models.Connected):
raise ValueError('model is not a "Connected" model object')		raise ValueError('model is not a "Connected" model object')
if model.nAtom:		if model.nAtom:
if not model.index:		if not model.index:
model.update_index()		model.update_index()
res_list = model.get_residues()		res_list = model.get_residues()
if len(res_list):		if len(res_list):
for a in res_list:		for a in res_list:
base = model.atom[a[0]]		base = model.atom[a[0]]
if not base.hetatm:		if not base.hetatm:
resn = base.resn		resn = base.resn
End of changes. 4 change blocks.
3 lines changed or deleted		4 lines changed or added

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