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cellblender_molmaker.py
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# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# ##### END GPL LICENSE BLOCK #####
### NOTE: Portions of this were intentionally written to be more "C-like" than "Pythonic"
# This code is based on text representation that looks like this:
"""
[0] = A (m) at (0,0,0) with peers [1, 2, 3, 4, 5, 6, 7]
[1] = a (c) at (0.009999999776482582,0.0,0.0) with peers [0] <7,0.0>
[2] = a (c) at (-0.009999999776482582,0.0,0.0) with peers [0] <7,0.0>
[3] = a (c) at (0.0,0.009999999776482582,0.0) with peers [0] <7,0.0>
[4] = a (c) at (0.0,-0.009999999776482582,0.0) with peers [0] <7,0.0>
[5] = a (c) at (0.0,0.0,0.009999999776482582) with peers [0] <7,0.0>
[6] = a (c) at (0.0,0.0,-0.009999999776482582) with peers [0, 9] <7,0.0>
[7] = a (k) at (0.0,0.0,0.03) with peers [0]
[8] = A (m) at (-6.12323385887182e-19,0.0,-0.019999999552965164) with peers [9, 10, 11, 12, 13, 14, 15]
[9] = a (c) at (0.0,0.0,-0.009999999776482582) with peers [8, 6] <15,0.0>
[10] = a (c) at (-1.224646771774364e-18,0.0,-0.029999999329447746) with peers [8] <15,0.0>
[11] = a (c) at (0.009999999776482582,6.123233858871821e-19,-0.019999999552965164) with peers [8] <15,0.0>
[12] = a (c) at (-0.009999999776482582,-6.123233858871821e-19,-0.019999999552965164) with peers [8] <15,0.0>
[13] = a (c) at (-1.224646771774364e-18,0.009999999776482582,-0.019999999552965164) with peers [8] <15,0.0>
[14] = a (c) at (9.62964972193618e-35,-0.009999999776482582,-0.019999999552965164) with peers [8, 17] <15,0.0>
[15] = a (k) at (-2.4492935846082116e-18,0.03,-0.019999999552965164) with peers [8]
[16] = A (m) at (-6.123233858871819e-19,-0.019999999552965164,-0.019999999552965164) with peers [17, 18, 19, 20, 21, 22, 23]
[17] = a (c) at (9.62964972193618e-35,-0.009999999776482582,-0.019999999552965164) with peers [16, 14] <23,0.0>
[18] = a (c) at (-1.224646771774364e-18,-0.029999999329447746,-0.019999999552965164) with peers [16] <23,0.0>
[19] = a (c) at (-1.224646771774364e-18,-0.019999999552965164,-0.029999999329447746) with peers [16] <23,0.0>
[20] = a (c) at (1.925929944387236e-34,-0.019999999552965164,-0.009999999776482582) with peers [16] <23,0.0>
[21] = a (c) at (-0.009999999776482582,-0.019999999552965164,-0.019999999552965164) with peers [16] <23,0.0>
[22] = a (c) at (0.009999999776482582,-0.019999999552965164,-0.019999999552965164) with peers [16] <23,0.0>
[23] = a (k) at (-0.03,-0.01999999955296516,-0.01999999955296516) with peers [16]
"""
# This example text was printed by CellBlender's MolMaker code.
# The format shown here can be used as an "interchange" format.
# This example shows a complex of 3 "A" molecules (each denoted with an "(m)").
# Each "A" molecule has 6 "normal" components and one "key" component (all named "a").
# Normal components are denoted with a "(c)" and key components are denoted with a "(k)".
# All final coordinate positions are relative to the molecule located at the origin (0,0,0).
# All molecules, components, and keys are related through their "peer" lists.
# All entries in any "peer" list refer to the item's index in the table (such as "[3]").
# Each molecule lists all of its components (both "normal" and "key") in its list of peers.
# All of a molecule's peers will be rotated and translated along with the molecule itself.
# Each non-molecule ("component" or "key") has a list of either 1 or 2 peers.
# The first peer of each non-molecule is an index to that item's molecule.
# The second peer of each non-molecule (if it exists) references a binding partner.
# The binding between molecules is done by co-locating the binding components.
# Any two bound molecules and their respective binding components are collinear.
# The angle brackets "<...>" define rotation angles about the collinear binding axis.
# A rotation angle is specified as "reference,angle" pair: <reference,angle>
# The "reference" in a rotation angle specification is an index into that molecule's table.
# A rotation "reference" may refer to either a component (c) or a key (k) in that molecule.
# Rotation Alignment Planes are defined by the ordered triplet: (molecule, component, reference).
# Rotation Alignment Planes must be defined (molecule, component, reference must not be collinear).
# Rotational Alignment between two molecules specifies an angle between their Alignment Planes.
# The binding angle between bound Alignment Planes is the sum of the two angles in each component.
# The rotation angle is interpreted as counter-clockwise viewed from its associated molecule.
# When both rotation angles are 0, the normals to the Rotation Alignment Planes are opposites.
import bpy
from bpy.props import StringProperty
from bpy.props import BoolProperty
from bpy.props import IntProperty
from bpy.props import FloatProperty
from bpy.props import EnumProperty
from bpy.props import FloatVectorProperty
from bpy.props import IntVectorProperty
from bpy.props import CollectionProperty
from bpy.props import PointerProperty
from bpy.app.handlers import persistent
import math
import mathutils
import cellblender
from . import data_model
bl_info = {
"name": "Molecule Maker",
"author": "Bob Kuczewski",
"version": (1,1,0),
"blender": (2,5,7),
"location": "View 3D > Edit Mode > Tool Shelf",
"description": "Generate a Molecule",
"warning" : "",
"wiki_url" : "http://mcell.org",
"tracker_url" : "",
"category": "Add Mesh",
}
def checked_print ( s ):
context = bpy.context
mcell = context.scene.mcell
molmaker = mcell.molmaker
if molmaker.print_debug:
print ( s )
def update_available_scripts ( molmaker ):
# Delete current scripts list
while molmaker.molecule_texts_list:
molmaker.molecule_texts_list.remove(0)
# Find the current internal scripts and add them to the list
for txt in bpy.data.texts:
checked_print ( "\n" + txt.name + "\n" + txt.as_string() + "\n" )
if True or (txt.name[-3:] == ".py"):
molmaker.molecule_texts_list.add()
index = len(molmaker.molecule_texts_list)-1
molmaker.molecule_texts_list[index].name = txt.name
while molmaker.comp_loc_texts_list:
molmaker.comp_loc_texts_list.remove(0)
# Find the current internal scripts and add them to the list
for txt in bpy.data.texts:
checked_print ( "\n" + txt.name + "\n" + txt.as_string() + "\n" )
if True or (txt.name[-3:] == ".py"):
molmaker.comp_loc_texts_list.add()
index = len(molmaker.comp_loc_texts_list)-1
molmaker.comp_loc_texts_list[index].name = txt.name
class MolMaker_OT_update_files(bpy.types.Operator):
bl_idname = "mol.update_files"
bl_label = "Refresh Files"
bl_description = "Refresh the list of available script files"
bl_options = {'REGISTER', 'UNDO'}
def execute(self, context):
molmaker = context.scene.mcell.molmaker
update_available_scripts ( molmaker )
return {'FINISHED'}
# This one is called by Build 2D and Build 3D
def read_molcomp_data_from_text ( fdata ):
ldata = [ l.strip() for l in fdata.split('\n') if len(l.strip()) > 0 ]
ldata = [ l for l in ldata if not l.startswith('#') ]
molcomp_list = []
for l in ldata:
mc = { # 'line':l,
'ftype':'c',
'has_coords':False,
'is_final':False,
'coords':[0,0,0],
'name':"",
'graph_string':"",
'peer_list':[],
'key_list':[],
'angle': 0,
}
mc['name'] = l.split("=")[1].split('(')[0].strip()
mc['ftype'] = l.split('(')[1][0] # Pull out the type (m or c or k)
mc['coords'] = eval ( '[' + l.split('(')[2].split(')')[0] + ']' )
peer_part = l.split('with peers')[1].strip()
if '[' in peer_part:
peers = peer_part.split('[')[1].split(']')[0].split(',')
peers = [ p for p in peers if len(p) > 0 ] # Remove any empty peers
for p in peers:
mc['peer_list'].append ( int(p) )
if '<' in peer_part:
keys = peer_part.split('<')[1].split('>')[0].split(',')
if mc['ftype'] == 'm':
# Molecules have a plain list of keys to be transformed along with the molecule
keys = [ k for k in keys if len(k) > 0 ] # Remove any empty keys
for k in keys:
mc['key_list'].append ( int(k) )
elif mc['ftype'] == 'c':
# Components have a key and an optional angle referenced to that key
if len(keys) == 1:
mc['key_list'].append ( int(keys[0]) )
mc['angle'] = 0.0
elif len(keys) == 2:
mc['key_list'].append ( int(keys[0]) )
mc['angle'] = ( float(keys[1]) )
else:
print ( "Expected <KeyIndex [, Angle]> for " + mc['name'] + ", but got " + peer_part.split('<')[1] )
molcomp_list.append ( mc )
return molcomp_list
'''
MolDef Text File Format:
# Type M C x y z rfx rfy rfz Unused
XYZRef T t 0.01 0.00 -0.007071067811865476 0 0 0 0
XYZRef T t -0.01 0.00 -0.007071067811865476 0 0 0 0
XYZRef T t 0.00 0.01 0.007071067811865476 0 0 0 0
XYZRef T t 0.00 -0.01 0.007071067811865476 0 0 0 0
XYZRef B t 0.01 0.00 -0.007071067811865476 0 0 0 0
XYZRef B t -0.01 0.00 -0.007071067811865476 0 0 0 0
XYZRef B t 0.00 0.01 0.007071067811865476 0 0 0 0
XYZRef B t 0.00 -0.01 0.007071067811865476 0 0 0 0
XYZRef C c 0.00 0.01 -0.002 0 0 0 0
XYZRef C c 0.00 -0.01 0.002 0 0 0 0
'''
def update_molcomp_list_from_defs ( context, molcomp_list, moldef_text, build_as_3D ):
mcell = context.scene.mcell
mcell_mols = mcell.molecules.molecule_list
molmaker = mcell.molmaker
if moldef_text == None:
# Try reading from a file
if molmaker.comp_loc_text_name in bpy.data.texts:
# There is a component location definition text
checked_print ( "Read component definition text named " + molmaker.comp_loc_text_name )
# Read the component definitions
moldef_text = bpy.data.texts[molmaker.comp_loc_text_name].as_string()
if moldef_text != None:
# There is a component location definition text
# Set the has_coords flag to false on each component of each molecule
for mc in molcomp_list:
if mc['ftype'] == 'm':
mc['coords'] = [0,0,0]
mc['has_coords'] = False
else:
mc['has_coords'] = False
# Read the component definitions
ldata = moldef_text
comploc_lines = [ l.strip() for l in ldata.split('\n') if len(l.strip()) > 0 ]
comploc_lines = [ l for l in comploc_lines if not l.startswith('#') ]
mol_comp_loc_dict = {}
for cll in comploc_lines:
cl_parts = [ p.strip() for p in cll.split() if len(p.strip()) > 0 ]
cl_type = cl_parts[0]
cl_mol_name = cl_parts[1]
cl_comp_name = cl_parts[2]
cl_x = float(cl_parts[3])
cl_y = float(cl_parts[4])
cl_z = float(cl_parts[5])
cl_refx = float(cl_parts[6])
cl_refy = float(cl_parts[7])
cl_refz = float(cl_parts[8])
if not build_as_3D:
checked_print ( "Setting z to zero for " + cl_mol_name + "." + cl_comp_name )
cl_z = 0.0
cl_refz = 0.0
if not (cl_mol_name in mol_comp_loc_dict):
# Make a list for this mol name
mol_comp_loc_dict[cl_mol_name] = []
# Append the current component definition to the list for this molecule
mol_comp_loc_dict[cl_mol_name].append ( { 'cname':cl_comp_name, 'coords':[cl_x, cl_y, cl_z], 'ref':[cl_refx, cl_refy, cl_refz], 'assigned':False } )
# Assign the component locations by molecule
for mc in molcomp_list:
# Only assign to components connected to molecules
if (mc['ftype']=='m') and (len(mc['peer_list']) > 0):
# Clear out the usage for this molecule in the component location table
for c in mol_comp_loc_dict[mc['name']]:
checked_print ( " Clearing assigned for " + c['cname'] + " with coords: " + str(c['coords']) )
c['assigned'] = False
# Sweep through all the components for this molecule
checked_print ( " Assigning coordinates to components in mol " + mc['name'] )
for pi in mc['peer_list']:
# Only assign to components that don't have coords
checked_print ( " Checking peer " + str(pi) )
if not molcomp_list[pi]['has_coords']:
# Sweep through the component name list looking for an unassigned match
for c in mol_comp_loc_dict[mc['name']]:
if not c['assigned']:
if c['cname'] == molcomp_list[pi]['name']:
molcomp_list[pi]['coords'] = [ cc for cc in c['coords'] ]
checked_print ( " Assigning coordinates: " + str(molcomp_list[pi]['coords']) )
molcomp_list[pi]['has_coords'] = True
c['assigned'] = True
break
# This is called directly by the "build as is" operator.
# The SphereCyl format is simpler and intended for rendering.
# The SphereCyl format only contains Spheres ("SphereList") and Cylinders ("CylList").
def read_molcomp_data_SphereCyl ( fdata ):
ldata = [ l.strip() for l in fdata.split('\n') if len(l.strip()) > 0 ]
ldata = [ l for l in ldata if not l.startswith('#') ]
SphereCyl_data = { 'Version':1.1, 'SphereList':[], 'CylList':[], 'FaceList':[] }
this_index = 0
for l in ldata:
checked_print ( "Line: " + l )
m = { 'name':'', 'loc':[0,0,0], 'r':1, 'c':'MolMaker_mol', 'ftype':'' }
m['name'] = l.split("=")[1].split('(')[0].strip()
m['ftype'] = l.split('(')[1][0] # Pull out the type (m or c or k)
if m['ftype'] == 'm':
m['r'] = 0.005
peer_part = l.split('with peers')[1].strip()
if '[' in peer_part:
peers = peer_part.split('[')[1].split(']')[0].split(',')
peers = [ p for p in peers if len(p) > 0 ] # Remove any empty peers
for p in peers:
SphereCyl_data['CylList'].append ( [this_index, int(p), 0.001] ) # Add the connecting bond cylinder
checked_print ( " Bond: " + str(this_index) + " " + p.strip() )
elif m['ftype'] == 'c':
m['r'] = 0.0025
m['c'] = 'MolMaker_comp'
elif m['ftype'] == 'k':
m['r'] = 0.0015
m['c'] = 'MolMaker_key'
m['loc'] = eval ( '[' + l.split('(')[2].split(')')[0] + ']' )
SphereCyl_data['SphereList'].append ( m )
this_index += 1
return SphereCyl_data
# This converts MolComp format to SphereCyl format for simple 3D rendering.
def MolComp_to_SphereCyl ( molcomp_list, build_as_3D ):
SphereCyl_data = { 'Version':1.1, 'SphereList':[], 'CylList':[], 'FaceList':[] }
this_index = 0
for mc in molcomp_list:
m = { 'name':mc['name'], 'loc':mc['coords'], 'r':1, 'c':'MolMaker_mol', 'ftype':mc['ftype'] }
if mc['ftype'] == 'm':
m['r'] = 0.005
if len(mc['peer_list']) > 0:
peers = mc['peer_list']
for p in peers:
if molcomp_list[int(p)]['ftype'] != 'k':
SphereCyl_data['CylList'].append ( [this_index, int(p), 0.001] ) # Add the connecting bond cylinder
if build_as_3D and len(molcomp_list[int(p)]['key_list']) > 0:
# This component has a key
k = molcomp_list[int(p)]['key_list'][0]
SphereCyl_data['FaceList'].append ( [ mc['coords'], molcomp_list[p]['coords'], molcomp_list[k]['coords'] ] ) # , [0.01,0.01,0.0 1] ] )
elif mc['ftype'] == 'c':
m['r'] = 0.0025
m['c'] = 'MolMaker_comp'
elif mc['ftype'] == 'k':
m['r'] = 0.0015
m['c'] = 'MolMaker_key'
SphereCyl_data['SphereList'].append ( m )
this_index += 1
return SphereCyl_data
def dump_molcomp_list ( molcomp_list ):
i = 0
for mc in molcomp_list:
mc_str = "[" + str(i) + "] = " + mc['name'] + " (" + mc['ftype'] + ") at (" + str(mc['coords'][0]) + "," + str(mc['coords'][1]) + "," + str(mc['coords'][2]) + ") with peers " + str(mc['peer_list'])
if len(mc['key_list']) > 0:
mc_str += " <" + str(mc['key_list'][0]) + "," + str(mc['angle']) + ">"
checked_print ( mc_str )
i += 1
class MolMaker_OT_build_as_is(bpy.types.Operator):
bl_idname = "mol.build_as_is"
bl_label = "Build As Is"
bl_description = "Build a molecule from the coordinates in the file"
bl_options = {'REGISTER', 'UNDO'}
def execute(self, context):
checked_print ( "Build Molecule from values in file" )
molmaker = context.scene.mcell.molmaker
fdata = bpy.data.texts[molmaker.molecule_text_name].as_string()
checked_print ( "Read:\n" + fdata )
mol_data = read_molcomp_data_SphereCyl ( fdata )
new_blender_mol_from_SphereCyl_data ( context, mol_data, show_key_planes=molmaker.show_key_planes )
return {'FINISHED'}
def get_distributed_sphere_points ( num_points ):
points = None
if num_points == 0: # Define the single point along the x axis
points = [ ]
elif num_points == 1: # Define the single point along the x axis
points = [ [ 1, 0, 0 ] ]
elif num_points == 2: # Define the two points along the x axis
points = [ [ 1, 0, 0 ], [ -1, 0, 0 ] ]
elif num_points == 3: # Define an equilateral triangle in the x-y plane with one point on x axis
sr3o2 = math.sqrt(3.0) / 2.0
points = [ [ 1, 0, 0 ], [ -0.5, sr3o2, 0 ], [ -0.5, -sr3o2, 0 ] ]
elif num_points == 4: # Define the points on a tetrahedron
oosr2 = 1.0 / math.sqrt(2.0)
points = [ [ 1, 0, -oosr2 ], [ -1, 0, -oosr2 ], [ 0, 1, oosr2 ], [ 0, -1, oosr2 ] ]
elif num_points == 5: # The "best" answer isn't clear, so place one on each pole and 3 around the "equator"
sr3o2 = math.sqrt(3.0) / 2.0
points = [ [ 0, 0, 1 ], [ 1, 0, 0 ], [ -0.5, sr3o2, 0 ], [ -0.5, -sr3o2, 0 ], [ 0, 0, -1 ] ]
elif num_points == 6: # Define 2 points on each axis (x, y, z)
points = [
[ 1, 0, 0 ],
[-1, 0, 0 ],
[ 0, 1, 0 ],
[ 0,-1, 0 ],
[ 0, 0, 1 ],
[ 0, 0,-1 ] ]
elif num_points == 8: # Define 8 points at the corners of a cube
d = 1.0 / math.sqrt(3)
points = [
[ d, d, d ],
[ d, d, -d ],
[ d, -d, d ],
[ d, -d, -d ],
[ -d, d, d ],
[ -d, d, -d ],
[ -d, -d, d ],
[ -d, -d, -d ] ]
else: # Use the Fibonacci Sphere Algorithm ("Golden Spiral") for any undefined number of points
points = [ [0,0,0] for i in range(num_points) ]
rnd = 1
offset = 2.0 / num_points
increment = math.pi * (3.0 - math.sqrt(5.0))
for i in range(num_points):
y = ((i * offset) -1) + (offset / 2)
r = math.sqrt ( 1 - math.pow(y,2) )
phi = ( (i+rnd) % num_points ) * increment
x = math.cos(phi) * r
z = math.sin(phi) * r
points[i][0] = x
points[i][1] = y
points[i][2] = z
return ( points )
def set_component_positions_3D ( mc ):
scale = 0.02;
for mi in range(len(mc)):
if mc[mi]['ftype'] == 'm':
#### fprintf ( stdout, "Setting component positions for %s\n", mc[mi].name );
mc[mi]['coords'] = [0,0,0]
# Because the molecule's peer list includes keys, they must be removed by creating a separate list of components only
component_index_list = [ ci for ci in range(len(mc[mi]['peer_list'])) if mc[mc[mi]['peer_list'][ci]]['ftype'] == 'c' ]
num_points = len(component_index_list)
points = get_distributed_sphere_points ( num_points )
for ci in component_index_list:
mc[mc[mi]['peer_list'][ci]]['coords'][0] = scale * points[ci][0];
mc[mc[mi]['peer_list'][ci]]['coords'][1] = scale * points[ci][1];
mc[mc[mi]['peer_list'][ci]]['coords'][2] = scale * points[ci][2];
#### fprintf ( stdout, " Component %s is at (%g,%g)\n", mc[mc[mi].peers[ci]].name, mc[mc[mi].peers[ci]].x, mc[mc[mi].peers[ci]].y );
elif mc[mi]['ftype'] == 'k':
# Set the rotation keys straight up in Z?
#mc[mi]['coords'][0] = 0
#mc[mi]['coords'][1] = 0
#mc[mi]['coords'][2] = 1 * scale
# Actually, do nothing while testing
pass
def set_component_positions_2D ( mc ):
scale = 0.02;
for mi in range(len(mc)):
if mc[mi]['ftype'] == 'm':
#### fprintf ( stdout, "Setting component positions for %s\n", mc[mi].name );
mc[mi]['coords'] = [0,0,0]
# Because the molecule's peer list includes keys, they must be removed by creating a separate list of components only
component_index_list = [ ci for ci in range(len(mc[mi]['peer_list'])) if mc[mc[mi]['peer_list'][ci]]['ftype'] == 'c' ]
for ci in component_index_list:
angle = 2 * math.pi * ci / len(component_index_list)
mc[mc[mi]['peer_list'][ci]]['coords'][0] = scale * math.cos(angle)
mc[mc[mi]['peer_list'][ci]]['coords'][1] = scale * math.sin(angle)
mc[mc[mi]['peer_list'][ci]]['coords'][2] = 0
#### fprintf ( stdout, " Component %s is at (%g,%g)\n", mc[mc[mi].peers[ci]].name, mc[mc[mi].peers[ci]].x, mc[mc[mi].peers[ci]].y );
elif mc[mi]['ftype'] == 'k':
# For 2D, the rotation keys should be straight up in Z
mc[mi]['coords'][0] = 0
mc[mi]['coords'][1] = 0
mc[mi]['coords'][2] = 1 * scale
def bind_molecules_at_components ( mc, fixed_comp_index, var_comp_index, build_as_3D, axial_rotation=True, bending_rotation=False ):
# Bind these two molecules by aligning their axes and shifting to align their components
# The "fixed" parts (components and molecules) will NOT have their locations changed.
# The "variable" parts (components and molecules) will be transformed to properly match up with the "fixed" parts.
# num_parts = len(mc)
checked_print ( " Binding " + str(mc[fixed_comp_index]['name']) + " to " + str(mc[var_comp_index]['name']) );
##### dump_molcomp_array(mc,num_parts);
fixed_mol_index = mc[fixed_comp_index]['peer_list'][0]
var_mol_index = mc[var_comp_index]['peer_list'][0]
# These vectors are either 2D (x,y) or 3D (x,y,z)
fixed_vec = []
var_vec = []
fixed_vec.append ( mc[fixed_comp_index]['coords'][0] - mc[fixed_mol_index]['coords'][0] )
fixed_vec.append ( mc[fixed_comp_index]['coords'][1] - mc[fixed_mol_index]['coords'][1] )
var_vec.append ( mc[ var_comp_index]['coords'][0] - mc[ var_mol_index]['coords'][0] )
var_vec.append ( mc[ var_comp_index]['coords'][1] - mc[ var_mol_index]['coords'][1] )
if build_as_3D:
fixed_vec.append ( mc[fixed_comp_index]['coords'][2] - mc[fixed_mol_index]['coords'][2] )
var_vec.append ( mc[ var_comp_index]['coords'][2] - mc[ var_mol_index]['coords'][2] )
fixed_mag = None
var_mag = None
if build_as_3D:
fixed_mag = math.sqrt ( (fixed_vec[0]*fixed_vec[0]) + (fixed_vec[1]*fixed_vec[1]) + (fixed_vec[2]*fixed_vec[2]) )
var_mag = math.sqrt ( ( var_vec[0]* var_vec[0]) + ( var_vec[1]* var_vec[1]) + ( var_vec[2]* var_vec[2]) )
else:
fixed_mag = math.sqrt ( (fixed_vec[0]*fixed_vec[0]) + (fixed_vec[1]*fixed_vec[1]) )
var_mag = math.sqrt ( ( var_vec[0]* var_vec[0]) + ( var_vec[1]* var_vec[1]) )
dot_prod = None
if build_as_3D:
dot_prod = (fixed_vec[0] * var_vec[0]) + (fixed_vec[1] * var_vec[1]) + (fixed_vec[2] * var_vec[2])
else:
dot_prod = (fixed_vec[0] * var_vec[0]) + (fixed_vec[1] * var_vec[1])
# In general, the magnitudes should be checked for 0.
# However, in this case, they were generated as non-zero.
norm_dot_prod = dot_prod / ( fixed_mag * var_mag )
# Ensure that the dot product is a legal argument for the "acos" function:
if norm_dot_prod > 1:
print ( "Numerical Warning: normalized dot product " + str( ) + " was greater than 1" )
norm_dot_prod = 1
if norm_dot_prod < -1:
print ( "Numerical Warning: normalized dot product " + str(norm_dot_prod) + " was less than 11" )
norm_dot_prod = -1
##### fprintf ( stdout, "norm_dot_prod = %g\n", norm_dot_prod );
angle = math.acos ( norm_dot_prod )
##### fprintf ( stdout, "Angle (from acos) = %g\n", angle );
if not build_as_3D:
# Try using a 2D "cross product" to fix the direction issue
##### fprintf ( stdout, "2D Cross of (%g,%g) X (%g,%g) = %g\n", fixed_vec[0], fixed_vec[1], var_vec[0], var_vec[1], (fixed_vec[0] * var_vec[1]) - (fixed_vec[1] * var_vec[0]) );
if ( (fixed_vec[0] * var_vec[1]) - (fixed_vec[1] * var_vec[0]) ) > 0:
angle = -angle
else:
# This seems to be required to get everything right:
angle = -angle
# Reverse the direction since we want the components attached to each other
angle = math.pi + angle;
# Bound the angle between -PI and PI
while angle > math.pi:
angle = angle - (2 * math.pi)
while angle <= -math.pi:
angle = angle + (2 * math.pi)
#angle = -angle;
##### fprintf ( stdout, "Final corrected angle = %g\n", angle );
##### fprintf ( stdout, "Binding between f(%s: %g,%g) and v(%s: %g,%g) is at angle %g deg\n", mc[fixed_comp_index].name, fixed_vec[0], fixed_vec[1], mc[var_comp_index].name, var_vec[0], var_vec[1], 180*angle/math.pi );
# Rotate all of the components of the var_mol_index by the angle
ca = math.cos(angle)
sa = math.sin(angle)
if build_as_3D:
cross_prod = [ (fixed_vec[1] * var_vec[2]) - (fixed_vec[2] * var_vec[1]),
(fixed_vec[2] * var_vec[0]) - (fixed_vec[0] * var_vec[2]),
(fixed_vec[0] * var_vec[1]) - (fixed_vec[1] * var_vec[0]) ]
norm_cross_prod = [ cp / ( fixed_mag * var_mag ) for cp in cross_prod ]
xpx = norm_cross_prod[0]
xpy = norm_cross_prod[1]
xpz = norm_cross_prod[2]
axis_length = math.sqrt( (xpx*xpx) + (xpy*xpy) + (xpz*xpz) )
R = None
if axis_length < 1e-30:
# Can't compute a meaningful unit vector to use for rotation matrix or quaternion
if norm_dot_prod < 0:
R = [ [ 1, 0, 0 ],
[ 0, 1, 0 ],
[ 0, 0, 1 ] ]
else:
R = [ [ -1, 0, 0 ],
[ 0, -1, 0 ],
[ 0, 0, -1 ] ]
else:
ux = xpx / axis_length
uy = xpy / axis_length
uz = xpz / axis_length
if True: # Build the rotation matrix directly
# Build a 3D rotation matrix
omca = 1 - ca
R = [ [ca + (ux*ux*omca), (ux*uy*omca) - (uz*sa), (ux*uz*omca) + (uy*sa)],
[(uy*ux*omca) + (uz*sa), ca + (uy*uy*omca), (uy*uz*omca) - (ux*sa)],
[(uz*ux*omca) - (uy*sa), (uz*uy*omca) + (ux*sa), ca + (uz*uz*omca)] ]
else: # Build the rotation matrix from a quaternion
s2 = math.sin(angle/2)
c2 = math.cos(angle/2)
q = [ c2, s2*ux, s2*uy, s2*uz ]
# qconj = [ c2, -s2*ux, -s2*uy, -s2*uz ]
# Create convenience variables for components and squares
qr = q[0]
qi = q[1]
qj = q[2]
qk = q[3]
qi2 = qi * qi
qj2 = qj * qj
qk2 = qk * qk
# Create the rotation matrix itself from the quaternion
R = [ [ 1-(2*(qj2+qk2)), 2*((qi*qj)-(qk*qr)), 2*((qi*qk)+(qj*qr)) ],
[ 2*((qi*qj)+(qk*qr)), 1-(2*(qi2+qk2)), 2*((qj*qk)-(qi*qr)) ],
[ 2*((qi*qk)-(qj*qr)), 2*((qj*qk)+(qi*qr)), 1-(2*(qi2+qj2)) ] ]
##### fprintf ( stdout, "Rotating component positions for %s by %g\n", mc[var_mol_index].name, 180*angle/math.pi );
# for (int ci=0; ci<mc[var_mol_index].num_peers; ci++) {
for ci in range ( len(mc[var_mol_index]['peer_list']) ):
##### fprintf ( stdout, " Component %s before is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
x = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][0]
y = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][1]
z = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][2]
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][0] = (R[0][0]*x) + (R[0][1]*y) + (R[0][2]*z)
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][1] = (R[1][0]*x) + (R[1][1]*y) + (R[1][2]*z)
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][2] = (R[2][0]*x) + (R[2][1]*y) + (R[2][2]*z)
##### fprintf ( stdout, " Component %s after is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
for ci in range ( len(mc[var_mol_index]['key_list']) ):
##### fprintf ( stdout, " Component %s before is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
x = mc[mc[var_mol_index]['key_list'][ci]]['coords'][0]
y = mc[mc[var_mol_index]['key_list'][ci]]['coords'][1]
z = mc[mc[var_mol_index]['key_list'][ci]]['coords'][2]
mc[mc[var_mol_index]['key_list'][ci]]['coords'][0] = (R[0][0]*x) + (R[0][1]*y) + (R[0][2]*z)
mc[mc[var_mol_index]['key_list'][ci]]['coords'][1] = (R[1][0]*x) + (R[1][1]*y) + (R[1][2]*z)
mc[mc[var_mol_index]['key_list'][ci]]['coords'][2] = (R[2][0]*x) + (R[2][1]*y) + (R[2][2]*z)
##### fprintf ( stdout, " Component %s after is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
else:
R = [ [ca, -sa],
[sa, ca] ]
##### fprintf ( stdout, "Rotating component positions for %s by %g\n", mc[var_mol_index].name, 180*angle/math.pi );
# for (int ci=0; ci<mc[var_mol_index].num_peers; ci++) {
for ci in range ( len(mc[var_mol_index]['peer_list']) ):
##### fprintf ( stdout, " Component %s before is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
x = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][0];
y = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][1];
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][0] = (R[0][0]*x) + (R[0][1]*y)
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][1] = (R[1][0]*x) + (R[1][1]*y)
##### fprintf ( stdout, " Component %s after is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
for ci in range ( len(mc[var_mol_index]['key_list']) ):
##### fprintf ( stdout, " Component %s before is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
x = mc[mc[var_mol_index]['key_list'][ci]]['coords'][0];
y = mc[mc[var_mol_index]['key_list'][ci]]['coords'][1];
mc[mc[var_mol_index]['key_list'][ci]]['coords'][0] = (R[0][0]*x) + (R[0][1]*y)
mc[mc[var_mol_index]['key_list'][ci]]['coords'][1] = (R[1][0]*x) + (R[1][1]*y)
##### fprintf ( stdout, " Component %s after is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
# Now the molecules are aligned as they should be except for rotation along their bonding axis or bending axis
if build_as_3D and axial_rotation:
# dump_molcomp_list ( mc )
# Rotate the variable molecule along its bonding axis to align based on the rotation key angle
checked_print ( "Axial Rotation:" )
checked_print ( " Fixed mol " + str(fixed_mol_index) + " binding to Var mol " + str(var_mol_index) )
checked_print ( " Fixed component " + str(fixed_comp_index) + " binding to Var component " + str(var_comp_index) )
fixed_key_index = int(mc[fixed_comp_index]['key_list'][0])
var_key_index = int(mc[var_comp_index]['key_list'][0])
checked_print ( " Fixed component key: " + str(fixed_key_index) + ", Var component key: " + str(var_key_index) )
fixed_req_bond_angle = mc[fixed_comp_index]['angle']
var_req_bond_angle = mc[var_comp_index]['angle']
checked_print ( " Fixed angle = " + str(fixed_req_bond_angle) + ", Var angle = " + str(var_req_bond_angle) )
# fixed_vcomp will be the vector from the fixed molecule to the fixed component
fixed_vcomp = []
for i in range(3):
fixed_vcomp.append ( mc[fixed_comp_index]['coords'][i] - mc[fixed_mol_index]['coords'][i] )
# var_vcomp will be the vector from the var molecule to the var component
var_vcomp = []
for i in range(3):
var_vcomp.append ( mc[var_comp_index]['coords'][i] - mc[var_mol_index]['coords'][i] )
# fixed_vkey will be the vector from the fixed molecule to the fixed key
fixed_vkey = []
for i in range(3):
fixed_vkey.append ( mc[fixed_key_index]['coords'][i] - mc[fixed_mol_index]['coords'][i] )
# var_vkey will be the vector from the var molecule to the var key
var_vkey = []
for i in range(3):
var_vkey.append ( mc[var_key_index]['coords'][i] - mc[var_mol_index]['coords'][i] )
checked_print ( " Fixed vcomp = " + str(fixed_vcomp) )
checked_print ( " Var vcomp = " + str(var_vcomp) )
checked_print ( " Fixed vkey = " + str(fixed_vkey) )
checked_print ( " Var vkey = " + str(var_vkey) )
# Use the cross product to get the normal to the fixed molecule-component-key plane
fixed_normal = [ (fixed_vcomp[1] * fixed_vkey[2]) - (fixed_vcomp[2] * fixed_vkey[1]),
(fixed_vcomp[2] * fixed_vkey[0]) - (fixed_vcomp[0] * fixed_vkey[2]),
(fixed_vcomp[0] * fixed_vkey[1]) - (fixed_vcomp[1] * fixed_vkey[0]) ]
# Use the cross product to get the normal to the variable molecule-component-key plane
var_normal = [ (var_vcomp[1] * var_vkey[2]) - (var_vcomp[2] * var_vkey[1]),
(var_vcomp[2] * var_vkey[0]) - (var_vcomp[0] * var_vkey[2]),
(var_vcomp[0] * var_vkey[1]) - (var_vcomp[1] * var_vkey[0]) ]
# Get the magnitudes of the two vectors for normalization
fixed_norm_mag = math.sqrt ( (fixed_normal[0]*fixed_normal[0]) + (fixed_normal[1]*fixed_normal[1]) + (fixed_normal[2]*fixed_normal[2]) )
var_norm_mag = math.sqrt ( ( var_normal[0]* var_normal[0]) + ( var_normal[1]* var_normal[1]) + ( var_normal[2]* var_normal[2]) )
# Calculate unit vectors
fixed_unit = [ cp / fixed_norm_mag for cp in fixed_normal ]
var_unit = [ cp / var_norm_mag for cp in var_normal ]
checked_print ( " Fixed unit = " + str(fixed_unit) )
checked_print ( " Var unit = " + str(var_unit) )
norm_dot_prod = (fixed_unit[0] * var_unit[0]) + (fixed_unit[1] * var_unit[1]) + (fixed_unit[2] * var_unit[2])
# Ensure that the dot product is a legal argument for the "acos" function:
if norm_dot_prod > 1:
print ( "Numerical Warning: normalized dot product " + str(norm_dot_prod) + " was greater than 1" )
norm_dot_prod = 1
if norm_dot_prod < -1:
print ( "Numerical Warning: normalized dot product " + str(norm_dot_prod) + " was less than -1" )
norm_dot_prod = -1
checked_print ( " Normalized Dot Product between fixed and var is " + str(norm_dot_prod) )
# Compute the amount of rotation to bring the planes into alignment offset by the requested bond angles
cur_key_plane_angle = math.acos ( norm_dot_prod )
checked_print ( "Current key plane angle = " + str(180*cur_key_plane_angle/math.pi) )
cross_prod = [ (fixed_unit[1] * var_unit[2]) - (fixed_unit[2] * var_unit[1]),
(fixed_unit[2] * var_unit[0]) - (fixed_unit[0] * var_unit[2]),
(fixed_unit[0] * var_unit[1]) - (fixed_unit[1] * var_unit[0]) ]
dot_cross_rot = (cross_prod[0] * var_vcomp[0]) + (cross_prod[1] * var_vcomp[1]) + (cross_prod[2] * var_vcomp[2])
if dot_cross_rot > 0:
cur_key_plane_angle = (2*math.pi) - cur_key_plane_angle
checked_print ( "Current key plane angle = " + str(180*cur_key_plane_angle/math.pi) + ", dot_cross_rot = " + str(dot_cross_rot) )
composite_rot_angle = math.pi + cur_key_plane_angle # The "math.pi" adds 180 degrees to make the components "line up"
if not bending_rotation:
# Only add the requested axial rotation if there is no bending
composite_rot_angle += (var_req_bond_angle + fixed_req_bond_angle)
checked_print ( " Fixed angle is = " + str(180 * fixed_req_bond_angle / math.pi) + " degrees" )
checked_print ( " Var angle is = " + str(180 * var_req_bond_angle / math.pi) + " degrees" )
checked_print ( " Current angle between keys is = " + str(180 * cur_key_plane_angle / math.pi) + " degrees" )
checked_print ( " Composite rotation angle is = " + str(180 * composite_rot_angle / math.pi) + " degrees" )
# Build a 3D rotation matrix along the axis of the molecule to the component
var_vcomp_mag = math.sqrt ( (var_vcomp[0]*var_vcomp[0]) + (var_vcomp[1]*var_vcomp[1]) + (var_vcomp[2]*var_vcomp[2]) )
var_rot_unit = [ v / var_vcomp_mag for v in var_vcomp ]
ux = var_rot_unit[0]
uy = var_rot_unit[1]
uz = var_rot_unit[2]
R = None
if True: # Build the rotation matrix directly
cca = math.cos(composite_rot_angle)
sca = math.sin(composite_rot_angle)
omcca = 1 - cca
R = [ [cca + (ux*ux*omcca), (ux*uy*omcca) - (uz*sca), (ux*uz*omcca) + (uy*sca)],
[(uy*ux*omcca) + (uz*sca), cca + (uy*uy*omcca), (uy*uz*omcca) - (ux*sca)],
[(uz*ux*omcca) - (uy*sca), (uz*uy*omcca) + (ux*sca), cca + (uz*uz*omcca)] ]
else: # Build the rotation matrix from a quaternion
s2 = math.sin(composite_rot_angle/2)
c2 = math.cos(composite_rot_angle/2)
q = [ c2, s2*ux, s2*uy, s2*uz ]
# qconj = [ c2, -s2*ux, -s2*uy, -s2*uz ]
# Create convenience variables for components and squares
qr = q[0]
qi = q[1]
qj = q[2]
qk = q[3]
qi2 = qi * qi
qj2 = qj * qj
qk2 = qk * qk
# Create the rotation matrix itself from the quaternion
R = [ [ 1-(2*(qj2+qk2)), 2*((qi*qj)-(qk*qr)), 2*((qi*qk)+(qj*qr)) ],
[ 2*((qi*qj)+(qk*qr)), 1-(2*(qi2+qk2)), 2*((qj*qk)-(qi*qr)) ],
[ 2*((qi*qk)-(qj*qr)), 2*((qj*qk)+(qi*qr)), 1-(2*(qi2+qj2)) ] ]
mm = bpy.context.scene.mcell.molmaker
if (not mm.skip_rotation) or (fixed_comp_index != mm.skip_fixed_comp_index) or (var_comp_index != mm.skip_var_comp_index):
# Apply the rotation matrix after subtracting the molecule center location from all components and keys
for ci in range ( len(mc[var_mol_index]['peer_list']) ):
##### fprintf ( stdout, " Component %s before is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
x = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][0] - mc[var_mol_index]['coords'][0]
y = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][1] - mc[var_mol_index]['coords'][1]
z = mc[mc[var_mol_index]['peer_list'][ci]]['coords'][2] - mc[var_mol_index]['coords'][2]
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][0] = (R[0][0]*x) + (R[0][1]*y) + (R[0][2]*z) + mc[var_mol_index]['coords'][0]
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][1] = (R[1][0]*x) + (R[1][1]*y) + (R[1][2]*z) + mc[var_mol_index]['coords'][1]
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][2] = (R[2][0]*x) + (R[2][1]*y) + (R[2][2]*z) + mc[var_mol_index]['coords'][2]
##### fprintf ( stdout, " Component %s after is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
for ci in range ( len(mc[var_mol_index]['key_list']) ):
##### fprintf ( stdout, " Component %s before is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
x = mc[mc[var_mol_index]['key_list'][ci]]['coords'][0] - mc[var_mol_index]['coords'][0]
y = mc[mc[var_mol_index]['key_list'][ci]]['coords'][1] - mc[var_mol_index]['coords'][1]
z = mc[mc[var_mol_index]['key_list'][ci]]['coords'][2] - mc[var_mol_index]['coords'][2]
mc[mc[var_mol_index]['key_list'][ci]]['coords'][0] = (R[0][0]*x) + (R[0][1]*y) + (R[0][2]*z) + mc[var_mol_index]['coords'][0]
mc[mc[var_mol_index]['key_list'][ci]]['coords'][1] = (R[1][0]*x) + (R[1][1]*y) + (R[1][2]*z) + mc[var_mol_index]['coords'][1]
mc[mc[var_mol_index]['key_list'][ci]]['coords'][2] = (R[2][0]*x) + (R[2][1]*y) + (R[2][2]*z) + mc[var_mol_index]['coords'][2]
##### fprintf ( stdout, " Component %s after is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]]['coords'][0], mc[mc[var_mol_index].peers[ci]]['coords'][1] );
if build_as_3D and bending_rotation:
# dump_molcomp_list ( mc )
# Rotate the variable molecule about an axis through its binding component and normal to the fixed molecule/component/key plane
# Rotate by an amount that puts the pre-axially rotated variable key in line with the binding component to fixed key vector
# Unfortunately, the location of the pre-axially rotated variable key is not available since the composite rotation angle included the arbitrary user-selected rotation
pass
##### dump_molcomp_array(mc,num_parts);
# Shift the var molecule location and the locations of all of its components by the difference of the binding components
dx = mc[fixed_comp_index]['coords'][0] - mc[var_comp_index]['coords'][0]
dy = mc[fixed_comp_index]['coords'][1] - mc[var_comp_index]['coords'][1]
dz = 0
if build_as_3D:
dz = mc[fixed_comp_index]['coords'][2] - mc[var_comp_index]['coords'][2]
##### fprintf ( stdout, "Shifting molecule and component positions for %s\n", mc[var_mol_index].name );
mc[var_mol_index]['coords'][0] += dx
mc[var_mol_index]['coords'][1] += dy
mc[var_mol_index]['coords'][2] += dz
#for (int ci=0; ci<mc[var_mol_index].num_peers; ci++) {
for ci in range ( len(mc[var_mol_index]['peer_list']) ):
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][0] += dx
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][1] += dy
mc[mc[var_mol_index]['peer_list'][ci]]['coords'][2] += dz
##### fprintf ( stdout, " Component %s is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]].x, mc[mc[var_mol_index].peers[ci]]['coords'][1] );
for ci in range ( len(mc[var_mol_index]['key_list']) ):
mc[mc[var_mol_index]['key_list'][ci]]['coords'][0] += dx
mc[mc[var_mol_index]['key_list'][ci]]['coords'][1] += dy
mc[mc[var_mol_index]['key_list'][ci]]['coords'][2] += dz
##### fprintf ( stdout, " Component %s is at (%g,%g)\n", mc[mc[var_mol_index].peers[ci]].name, mc[mc[var_mol_index].peers[ci]].x, mc[mc[var_mol_index].peers[ci]]['coords'][1] );
##### dump_molcomp_array(mc,num_parts);
##### fprintf ( stdout, "########## Done Binding %s to %s\n", mc[fixed_comp_index].name, mc[var_comp_index].name );
def bind_all_molecules ( molcomp_array, build_as_3D, axial_rotation=True, bending_rotation=False ):
context = bpy.context
mcell = context.scene.mcell
molmaker = mcell.molmaker
old_debug = molmaker.print_debug
## molmaker.print_debug = True
checked_print ( "======================================================================================" )
checked_print ( "===================================== bind_all_molecules =============================" )
checked_print ( "======================================================================================" )
dump_molcomp_list ( molcomp_array )
checked_print ( "======================================================================================" )
molmaker.print_debug = old_debug
# Compute positions for all molecules/components in a molcomp_array
num_parts = len(molcomp_array)
mi=0;
pi=0;
# Set all molecules and components to not final
for mi in range(num_parts):
molcomp_array[mi]['is_final'] = False
# Find first molecule
found_mol = False
for mi in range(num_parts):
if molcomp_array[mi]['ftype'] == 'm':
found_mol = True
break;
if found_mol:
# Set this first molecule and all of its components to final
molcomp_array[mi]['is_final'] = True
num_peers = len(molcomp_array[mi]['peer_list'])
for ci in range(num_peers):
molcomp_array[molcomp_array[mi]['peer_list'][ci]]['is_final'] = True
done = False
while not done:
# Look for a bond between a non-final and a final component
done = True
for mi in range(num_parts):
if molcomp_array[mi]['ftype'] == 'c':
# Only search components for bonds
if len(molcomp_array[mi]['peer_list']) > 1:
# This component has bonds, so search them
for ci in range(1,len(molcomp_array[mi]['peer_list'])): # for (int ci=1; ci<molcomp_array[mi].num_peers; ci++) {
pi = molcomp_array[mi]['peer_list'][ci] # Peer index
if molcomp_array[mi]['is_final'] != molcomp_array[pi]['is_final']:
done = False
# One of these is final and the other is not so join them and make them all final
fci=0 # Fixed Component Index
vci=0 # Variable Component Index
vmi=0 # Variable Molecule Index
# Figure out which is fixed and which is not
if molcomp_array[mi]['is_final']:
fci = mi;
vci = pi;
else:
fci = pi;
vci = mi;
# Set the variable molecule index for the bond based on the component
vmi = molcomp_array[vci]['peer_list'][0]
# Perform the bond (changes the locations)
bind_molecules_at_components ( molcomp_array, fci, vci, build_as_3D, axial_rotation, bending_rotation )
# The bonding process will have specified the placement of the variable molecule
# Set the variable molecule and all of its components to final
molcomp_array[vmi]['is_final'] = True
#for (int vmici=0; vmici<molcomp_array[vmi].num_peers; vmici++) {
for vmici in range(len(molcomp_array[vmi]['peer_list'])):
molcomp_array[molcomp_array[vmi]['peer_list'][vmici]]['is_final'] = True
old_debug = molmaker.print_debug
## molmaker.print_debug = True
checked_print ( "======================================================================================" )
dump_molcomp_list ( molcomp_array )
checked_print ( "======================================================================================" )
molmaker.print_debug = old_debug
def build_all_mols ( context, molcomp_list, build_as_3D=True, axial_rotation=True, bending_rotation=False ):
if build_as_3D:
checked_print ( "\n\nBuilding as 3D" )
else:
checked_print ( "\n\nBuilding as 2D" )
molmaker = context.scene.mcell.molmaker