del ctx.minimizations del ctx.edit.minimizations del ctx.gen_sphere del ctx.params.gen_sphere del ctx.links.params_gen_sphere del ctx.links.code_gen_sphere ctx.texture_coords = cell("array").set_store("GL") ctx.triangle_texture_coords = cell("array").set_store("GL") #for now, load-ply must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.load_ply = cell(("cson", "seamless", "reactor_params")) ctx.links.params_load_ply = link(c, ".", "params-load-ply.cson") rc = ctx.load_ply = reactor(c) c = ctx.code.load_ply = cell(("text", "code", "python")) ctx.links.code_load_ply = link(c, ".", "cell-load-ply2.py") rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") ctx.load_ply.coordinates.connect(ctx.coordinates_prescale) ctx.load_ply.normals.connect(ctx.normals) ctx.load_ply.edges.connect(ctx.edges) ctx.load_ply.triangle_indices.connect(ctx.triangle_indices) ctx.load_ply.triangle_coordinates.connect(ctx.triangle_coordinates_prescale) ctx.load_ply.triangle_normals.connect(ctx.triangle_normals) ctx.load_ply.texture_coords.connect(ctx.texture_coords) ctx.load_ply.triangle_texture_coords.connect(ctx.triangle_texture_coords)
del ctx.subdivisions del ctx.edit.subdivisions del ctx.minimizations del ctx.edit.minimizations del ctx.gen_sphere del ctx.params.gen_sphere del ctx.links.params_gen_sphere del ctx.links.code_gen_sphere ctx.texture_coords = cell("array").set_store("GL") ctx.triangle_texture_coords = cell("array").set_store("GL") #for now, load-ply must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.load_ply = cell(("cson", "seamless", "reactor_params")) ctx.links.params_load_ply = link(c, ".", "params-load-ply.cson") rc = ctx.load_ply = reactor(c) c = ctx.code.load_ply = cell(("text", "code", "python")) ctx.links.code_load_ply = link(c, ".", "cell-load-ply2.py") rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") ctx.load_ply.coordinates.connect(ctx.coordinates_prescale) ctx.load_ply.normals.connect(ctx.normals) ctx.load_ply.edges.connect(ctx.edges) ctx.load_ply.triangle_indices.connect(ctx.triangle_indices) ctx.load_ply.triangle_coordinates.connect(ctx.triangle_coordinates_prescale) ctx.load_ply.triangle_normals.connect(ctx.triangle_normals) ctx.load_ply.texture_coords.connect(ctx.texture_coords) ctx.load_ply.triangle_texture_coords.connect(ctx.triangle_texture_coords)
from seamless import cell, pythoncell, context, reactor, transformer from seamless.silk import Silk import seamless.lib from seamless.lib.gui.basic_editor import edit from seamless.lib.gui.basic_display import display from seamless.lib import link from seamless.lib.gui.gl import glprogram ctx = context() file_dominant = False # Vertexdata Silk model ctx.silk_vertexdata = cell(("text", "code", "silk")) ctx.link_silk_vertexdata = link( ctx.silk_vertexdata, ".", "vertexdata.silk", file_dominant=file_dominant ) ctx.registrar.silk.register(ctx.silk_vertexdata) # Shaders ctx.vert_shader = cell(("text", "code", "vertexshader")) ctx.frag_shader = cell(("text", "code", "fragmentshader")) ctx.link_vert_shader = link(ctx.vert_shader, ".", "vert_shader.glsl", file_dominant=file_dominant) ctx.link_frag_shader = link(ctx.frag_shader, ".", "frag_shader.glsl", file_dominant=file_dominant) # Program template ctx.program_template = cell("cson") ctx.link_program_template = link(ctx.program_template,
del ctx.minimizations del ctx.edit.minimizations del ctx.gen_sphere del ctx.params.gen_sphere del ctx.links.params_gen_sphere del ctx.links.code_gen_sphere ctx.texture_coords = cell("array").set_store("GL") ctx.triangle_texture_coords = cell("array").set_store("GL") #for now, load-ply must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.load_ply = cell(("cson", "seamless", "reactor_params")) ctx.links.params_load_ply = link(c, ".", "params-load-ply.cson") rc = ctx.load_ply = reactor(c) c = ctx.code.load_ply = cell(("text", "code", "python")) ctx.links.code_load_ply = link(c, ".", "cell-load-ply2.py") rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") ctx.load_ply.coordinates.connect(ctx.coordinates_prescale) ctx.load_ply.normals.connect(ctx.normals) ctx.load_ply.edges.connect(ctx.edges) ctx.load_ply.triangle_indices.connect(ctx.triangle_indices) ctx.load_ply.triangle_coordinates.connect(ctx.triangle_coordinates_prescale) ctx.load_ply.triangle_normals.connect(ctx.triangle_normals) ctx.load_ply.texture_coords.connect(ctx.texture_coords) ctx.load_ply.triangle_texture_coords.connect(ctx.triangle_texture_coords)
from seamless.lib.gui.gl import glprogram, glwindow import numpy as np from scipy.spatial.distance import cdist ctx = context() ctx.params = context() ctx.links = context() ctx.code = context() file_dominant = True #for now, gen_sphere must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.gen_sphere = cell(("cson", "seamless", "reactor_params")) ctx.links.params_gen_sphere = link(c, ".", "params-gen-sphere.cson", file_dominant=file_dominant) rc = ctx.gen_sphere = reactor(c) c = ctx.code.gen_sphere = cell(("text", "code", "python")) ctx.links.code_gen_sphere = link(c, ".", "cell-gen-sphere.py", file_dominant=file_dominant) rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") do_scale_params = { "input":{"pin": "input", "dtype": "array"}, "scale":{"pin": "input", "dtype": "float"}, "output":{"pin": "output", "dtype": "array"} } ctx.subdivisions = cell("int").set(3) ctx.minimizations = cell("int").set(20) ctx.scale = cell("float").set(3.5)
from seamless import context, cell, transformer, reactor from seamless.lib import edit, display, link from seamless.lib.gui.gl import glprogram, glwindow import numpy as np ctx = context() ctx.params = context() ctx.links = context() ctx.code = context() #for now, gen_sphere must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.gen_sphere = cell(("cson", "seamless", "reactor_params")) ctx.links.params_gen_sphere = link(c, ".", "params-gen-sphere.cson") rc = ctx.gen_sphere = reactor(c) c = ctx.code.gen_sphere = cell(("text", "code", "python")) ctx.links.code_gen_sphere = link(c, ".", "cell-gen-sphere.py") rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") ctx.subdivisions = cell("int").set(3) ctx.minimizations = cell("int").set(20) ctx.coordinates = cell("array").set_store("GL") ctx.normals = cell("array").set_store("GL") ctx.edges = cell("array").set_store("GL") ctx.triangle_indices = cell("array").set_store("GL") ctx.triangle_normals = cell("array").set_store("GL") ctx.triangle_coordinates = cell("array").set_store("GL")
import seamless from seamless import context, cell from seamless.lib import link, browse from seamless.lib.plotly import plotly ctx = context() ctx.plotly = plotly(dynamic_html=True, mode="nxy") ctx.data = cell("text") ctx.link_data = link(ctx.data, ".", "data.csv") ctx.layout = cell("cson") ctx.link_layout = link(ctx.layout, ".", "layout.cson") ctx.attrib = cell("cson") ctx.link_attrib = link(ctx.attrib, ".", "attrib.cson") ctx.data.connect(ctx.plotly.data) ctx.attrib.connect(ctx.plotly.attrib) ctx.layout.connect(ctx.plotly.layout) ctx.html = cell(("text", "html")) ctx.plotly.html.connect(ctx.html) ctx.browser_static = browse(ctx.html, "Static HTML") ctx.dynamic_html = cell(("text", "html")) ctx.plotly.dynamic_html.connect(ctx.dynamic_html) ctx.browser_dynamic = browse(ctx.dynamic_html, "Dynamic HTML")
from seamless import context, cell, export, transformer from seamless.lib import edit, display, link, browse from seamless.slash import slash0 import sys #Stage 1 # Concatenate PDBs ctx = context() ctx.attract = cell(("text", "code", "slash-0")) # !touch "attract.slash" ctx.attract.fromfile("attract.slash") link(ctx.attract) ctx.attract.set(""" @input_doc pdbA @input_doc pdbB @intern pdb @intern result cat !pdbA !pdbB > pdb cat !pdb > result @export pdb @export result """) ctx.slash = slash0(ctx.attract) export(ctx.slash.pdbA) export(ctx.slash.pdbB) ctx.pdbA.fromfile("unbound/1AVXA.pdb") ctx.pdbB.fromfile("unbound/1AVXB.pdb") export(ctx.slash.pdb)
from seamless import context, cell, export, transformer from seamless.lib import edit, display, link, browse from seamless.slash import slash0 import sys #Stage 1 # Concatenate PDBs ctx = context() ctx.attract = cell(("text", "code", "slash-0")) # !touch "attract.slash" ctx.attract.fromfile("attract.slash") link(ctx.attract) ctx.attract.set(""" @input_doc pdbA @input_doc pdbB @intern pdb @intern result cat !pdbA !pdbB > pdb cat !pdb > result @export pdb @export result """) ctx.slash = slash0(ctx.attract) export(ctx.slash.pdbA) export(ctx.slash.pdbB) ctx.pdbA.fromfile("unbound/1AVXA.pdb") ctx.pdbB.fromfile("unbound/1AVXB.pdb") export(ctx.slash.pdb)
from seamless import context, cell, transformer, reactor from seamless.lib import edit, display, link from seamless.lib.gui.gl import glprogram, glwindow import numpy as np ctx = context() ctx.params = context() ctx.links = context() ctx.code = context() #for now, gen_sphere must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.gen_sphere = cell(("cson", "seamless", "reactor_params")) ctx.links.params_gen_sphere = link(c, ".", "params-gen-sphere.cson") rc = ctx.gen_sphere = reactor(c) c = ctx.code.gen_sphere = cell(("text", "code", "python")) ctx.links.code_gen_sphere = link(c, ".", "cell-gen-sphere.py") rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") ctx.subdivisions = cell("int").set(3) ctx.minimizations = cell("int").set(20) ctx.coordinates = cell("array").set_store("GL") ctx.normals = cell("array").set_store("GL") ctx.edges = cell("array").set_store("GL") ctx.triangle_indices = cell("array").set_store("GL") ctx.triangle_normals = cell("array").set_store("GL") ctx.triangle_coordinates = cell("array").set_store("GL")
""") ctx.pre_code.connect(gen_code.in_code) ctx.code = gen_code.out_code.cell() ctx.printer = transformer({"value": {"pin": "input", "dtype": "int"}}) ctx.printer.code.set("print('VALUE', value); return") ctx.equilibrate() p = ctx.slash0 = slash0(ctx.code) ctx.value = cell("int") p.value.connect(ctx.value) ctx.value.connect(ctx.printer.value) ctx.pulse_py = cell(("text", "code", "python")) ctx.pulse_py.connect(p.pulse_py) ctx.pulses = cell("int").set(3) ctx.pulses.connect(p.pulses) ctx.delay = cell("float").set(0.1) ctx.delay.connect(p.delay) link(ctx.pulse_py, ".", "pulse.py") ctx.equilibrate() print("... DONE", ctx.value.value) gen_code.monitor.set(True) ctx.equilibrate() print("... DONE", ctx.value.value) ctx.delay.set(0.5) ctx.pulses.set(10) edit(ctx.pulses, "Pulses") edit(ctx.delay, "Delay") display(ctx.value, "Value")
ctx = seamless.fromfile("test-sphere.seamless") del ctx.subdivisions del ctx.edit.subdivisions del ctx.minimizations del ctx.edit.minimizations del ctx.gen_sphere del ctx.params.gen_sphere del ctx.links.params_gen_sphere del ctx.links.code_gen_sphere #for now, load-ply must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.load_ply = cell(("cson", "seamless", "reactor_params")) ctx.links.params_load_ply = link(c, ".", "params-load-ply.cson") rc = ctx.load_ply = reactor(c) c = ctx.code.load_ply = cell(("text", "code", "python")) ctx.links.code_load_ply = link(c, ".", "cell-load-ply.py") rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") ctx.load_ply.coordinates.connect(ctx.coordinates_prescale) ctx.load_ply.normals.connect(ctx.normals) ctx.load_ply.edges.connect(ctx.edges) ctx.load_ply.triangle_indices.connect(ctx.triangle_indices) ctx.load_ply.triangle_coordinates.connect(ctx.triangle_coordinates_prescale) ctx.load_ply.triangle_normals.connect(ctx.triangle_normals) ctx.filename = cell("str") ctx.filename.connect(ctx.load_ply.filename)
import os, sys get_ipython().system('./load-test.sh') #Stage 1: display test dataset from seamless import context, cell, reactor, transformer, export from seamless.lib import link, browse from seamless.lib.plotly import plotly ctx = context() ctx.plotly = plotly(dynamic_html=True) ctx.plotly.values.width.set(800) ctx.plotly.values.height.set(600) c = export(ctx.plotly.data, "cson").fromfile("data.cson") link(c) c = export(ctx.plotly.attrib, "cson").fromfile("attrib.cson") link(c) c = export(ctx.plotly.layout, "cson").fromfile("layout.cson") link(c) c = export(ctx.plotly.html) link(c, ".", "plotly.html") browse(c, "Docking clusters") c = export(ctx.plotly.dynamic_html) link(c, ".", "plotly-dynamic.html") browse(c, "Docking clusters (dynamic)") #Stage 2: load real dataset get_ipython().system('./load-real.sh') #Stage 2a: perform (bound) docking, # (re)generating real dataset in cells data2, attrib2 import numpy as np ctx.attract = cell(("text", "code", "slash-0"))
import os, sys get_ipython().system('./load-test.sh') #Stage 1: display test dataset from seamless import context, cell, reactor, transformer, export from seamless.lib import link, browse from seamless.lib.plotly import plotly ctx = context() ctx.plotly = plotly(dynamic_html=True) ctx.plotly.values.width.set(800) ctx.plotly.values.height.set(600) c = export(ctx.plotly.data, "cson").fromfile("data.cson") link(c) c = export(ctx.plotly.attrib, "cson").fromfile("attrib.cson") link(c) c = export(ctx.plotly.layout, "cson").fromfile("layout.cson") link(c) c = export(ctx.plotly.html) link(c, ".", "plotly.html") browse(c, "Docking clusters") c = export(ctx.plotly.dynamic_html) link(c, ".", "plotly-dynamic.html") browse(c, "Docking clusters (dynamic)") #Stage 2: load real dataset get_ipython().system('./load-real.sh') #Stage 2a: perform (bound) docking, # (re)generating real dataset in cells data2, attrib2 import numpy as np ctx.attract = cell(("text", "code", "slash-0"))
ctx.pre_code.connect(gen_code.in_code) ctx.code = gen_code.out_code.cell() ctx.printer = transformer({"value": {"pin":"input", "dtype": "int"}}) ctx.printer.code.set("print('VALUE', value); return") ctx.equilibrate() p = ctx.slash0 = slash0(ctx.code) ctx.value = cell("int") p.value.connect(ctx.value) ctx.value.connect(ctx.printer.value) ctx.pulse_py = cell(("text", "code", "python")) ctx.pulse_py.connect(p.pulse_py) ctx.pulses = cell("int").set(3) ctx.pulses.connect(p.pulses) ctx.delay = cell("float").set(0.1) ctx.delay.connect(p.delay) link(ctx.pulse_py, ".", "pulse.py") ctx.equilibrate() print("... DONE", ctx.value.value) gen_code.monitor.set(True) ctx.equilibrate() print("... DONE", ctx.value.value) ctx.delay.set(0.5) ctx.pulses.set(10) edit(ctx.pulses, "Pulses") edit(ctx.delay, "Delay") display(ctx.value, "Value")
del ctx.subdivisions del ctx.edit.subdivisions del ctx.minimizations del ctx.edit.minimizations del ctx.gen_sphere del ctx.params.gen_sphere del ctx.links.params_gen_sphere del ctx.links.code_gen_sphere ctx.texture_coords = cell("array").set_store("GL") ctx.triangle_texture_coords = cell("array").set_store("GL") #for now, load-ply must be a reactor, because it has multiple outputs #TODO: make it a transformer in a future version of seamless c = ctx.params.load_ply = cell(("cson", "seamless", "reactor_params")) ctx.links.params_load_ply = link(c, ".", "params-load-ply.cson") rc = ctx.load_ply = reactor(c) c = ctx.code.load_ply = cell(("text", "code", "python")) ctx.links.code_load_ply = link(c, ".", "cell-load-ply2.py") rc.code_start.cell().set("") c.connect(rc.code_update) rc.code_stop.cell().set("") ctx.load_ply.coordinates.connect(ctx.coordinates_prescale) ctx.load_ply.normals.connect(ctx.normals) ctx.load_ply.edges.connect(ctx.edges) ctx.load_ply.triangle_indices.connect(ctx.triangle_indices) ctx.load_ply.triangle_coordinates.connect(ctx.triangle_coordinates_prescale) ctx.load_ply.triangle_normals.connect(ctx.triangle_normals) ctx.load_ply.texture_coords.connect(ctx.texture_coords) ctx.load_ply.triangle_texture_coords.connect(ctx.triangle_texture_coords)
from seamless import cell, pythoncell, context, reactor, transformer from seamless.silk import Silk import seamless.lib from seamless.lib.gui.basic_editor import edit from seamless.lib.gui.basic_display import display from seamless.lib import link from seamless.lib.gui.gl import glprogram ctx = context() file_dominant = False # Vertexdata Silk model ctx.silk_vertexdata = cell(("text", "code", "silk")) ctx.link_silk_vertexdata = link(ctx.silk_vertexdata, ".", "vertexdata.silk", file_dominant=file_dominant) ctx.registrar.silk.register(ctx.silk_vertexdata) # Shaders ctx.vert_shader = cell(("text", "code", "vertexshader")) ctx.frag_shader = cell(("text", "code", "fragmentshader")) ctx.link_vert_shader = link(ctx.vert_shader, ".", "vert_shader.glsl", file_dominant=file_dominant) ctx.link_frag_shader = link(ctx.frag_shader, ".", "frag_shader.glsl", file_dominant=file_dominant)