File size: 1,858 Bytes
10f2621 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | import pymesh
import numpy
"""
Modified from:
save_ply.py - MaSIF
Pablo Gainza - LPDI STI EPFL 2019
"""
"""
read_ply.py: Save a ply file to disk using pymesh and load the attributes used by MaSIF.
Pablo Gainza - LPDI STI EPFL 2019
Released under an Apache License 2.0
"""
def save_ply(
filename,
vertices,
faces=[],
normals=None,
charges=None,
vertex_cb=None,
hbond=None,
hphob=None,
iface=None,
si=None,
normalize_charges=False,
):
""" Save vertices, mesh in ply format.
vertices: coordinates of vertices
faces: mesh
"""
mesh = pymesh.form_mesh(vertices, faces)
if normals is not None:
n1 = normals[:, 0]
n2 = normals[:, 1]
n3 = normals[:, 2]
mesh.add_attribute("vertex_nx")
mesh.set_attribute("vertex_nx", n1)
mesh.add_attribute("vertex_ny")
mesh.set_attribute("vertex_ny", n2)
mesh.add_attribute("vertex_nz")
mesh.set_attribute("vertex_nz", n3)
if charges is not None:
mesh.add_attribute("charge")
if normalize_charges:
charges = charges / 10
mesh.set_attribute("charge", charges)
if hbond is not None:
mesh.add_attribute("hbond")
mesh.set_attribute("hbond", hbond)
if vertex_cb is not None:
mesh.add_attribute("vertex_cb")
mesh.set_attribute("vertex_cb", vertex_cb)
if hphob is not None:
mesh.add_attribute("vertex_hphob")
mesh.set_attribute("vertex_hphob", hphob)
if iface is not None:
mesh.add_attribute("vertex_iface")
mesh.set_attribute("vertex_iface", iface)
if si is not None:
mesh.add_attribute("vertex_si")
mesh.set_attribute("vertex_si", si)
pymesh.save_mesh(
filename, mesh, *mesh.get_attribute_names(), use_float=True, ascii=True
)
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