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.
| hetatm.py (pymol-open-source-2.2.0) | : | hetatm.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* ------------------------------------------------------------------- |
| | |
| # | | # |
| # | | # |
| # | | # |
| | |
|
| | 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 | | from chempy import Bond |
| from chempy import place | | from chempy import place |
| | |
| MAX_BOND_LEN = 2.2 | | MAX_BOND_LEN = 2.2 |
| PEPT_CUTOFF = 1.7 | | PEPT_CUTOFF = 1.7 |
| | |
| #-------------------------------------------------------------------------------
-- | | #-------------------------------------------------------------------------------
-- |
| def generate(model, topology= None, forcefield = None ): | | def generate(model, topology= None, forcefield = None ): |
| | |
| add_bonds(model,topology=topology,forcefield=forcefield) | | add_bonds(model,topology=topology,forcefield=forcefield) |
| connected = model.convert_to_connected() | | connected = model.convert_to_connected() |
| add_hydrogens(connected,topology=topology,forcefield=forcefield) | | add_hydrogens(connected,topology=topology,forcefield=forcefield) |
| place.simple_unknowns(connected) | | place.simple_unknowns(connected) |
| return connected.convert_to_indexed() | | return connected.convert_to_indexed() |
| | |
| #-------------------------------------------------------------------------------
-- | | #-------------------------------------------------------------------------------
-- |
| def assign_types(model, topology = None, forcefield = None ): | | def assign_types(model, topology = None, forcefield = None ): |
|
| 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') |
| nAtom = model.nAtom | | nAtom = model.nAtom |
| if nAtom: | | if nAtom: |
| tmpl = topology.normal | | tmpl = topology.normal |
| ffld = forcefield.normal | | ffld = forcefield.normal |
| 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]] |
| resn = base.resn | | resn = base.resn |
| | |
| skipping to change at line 70 | | skipping to change at line 71 |
|---|
| if forcefield: | | if forcefield: |
| k = (resn,at.name) | | k = (resn,at.name) |
| if k in ffld: | | if k in ffld: |
| at.text_type = ffld[k]['type'] | | at.text_type = ffld[k]['type'] |
| at.partial_charge = ffld[k]['charge'] | | at.partial_charge = ffld[k]['charge'] |
| else: | | else: |
| raise RuntimeError("no parameters for '"+str(k)+
"'") | | raise RuntimeError("no parameters for '"+str(k)+
"'") |
| | |
| #-------------------------------------------------------------------------------
-- | | #-------------------------------------------------------------------------------
-- |
| def add_bonds(model, topology = None, forcefield = None ): | | def add_bonds(model, topology = None, forcefield = None ): |
|
| 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') |
| nAtom = model.nAtom | | nAtom = model.nAtom |
| if nAtom: | | if nAtom: |
| tmpl = topology.normal | | tmpl = topology.normal |
| ffld = forcefield.normal | | ffld = forcefield.normal |
| 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]] |
| resn = base.resn | | resn = base.resn |
| | |
| skipping to change at line 111 | | skipping to change at line 112 |
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| mbond = model.bond | | mbond = model.bond |
| for b in list(bonds.keys()): | | for b in list(bonds.keys()): |
| if b[0] in dict and b[1] in dict: | | if b[0] in dict and b[1] in dict: |
| bnd = Bond() | | bnd = Bond() |
| bnd.index = [ dict[b[0]], dict[b[1]] ] | | bnd.index = [ dict[b[0]], dict[b[1]] ] |
| bnd.order = bonds[b]['order'] | | bnd.order = bonds[b]['order'] |
| mbond.append(bnd) | | mbond.append(bnd) |
| | |
| #-------------------------------------------------------------------------------
-- | | #-------------------------------------------------------------------------------
-- |
| def add_hydrogens(model,topology=None,forcefield=None): | | def add_hydrogens(model,topology=None,forcefield=None): |
|
| 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') |
| nAtom = model.nAtom | | nAtom = model.nAtom |
| if nAtom: | | if nAtom: |
| if not model.index: | | if not model.index: |
| model.update_index() | | model.update_index() |
| ffld = forcefield.normal | | ffld = forcefield.normal |
| tmpl = topology.normal | | tmpl = topology.normal |
| 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: |
| | | |
| End of changes. 4 change blocks. |
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| 3 lines changed or deleted | | 4 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 