File size: 1,916 Bytes
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"""
read_msms.py: Read an msms output file that was output by MSMS (MSMS is the program we use to build a surface)
Pablo Gainza - LPDI STI EPFL 2019
Released under an Apache License 2.0
"""
def read_msms(file_root):
# read the surface from the msms output. MSMS outputs two files: {file_root}.vert and {file_root}.face
vertfile = open(file_root + ".vert")
meshdata = (vertfile.read().rstrip()).split("\n")
vertfile.close()
# Read number of vertices.
count = {}
header = meshdata[2].split()
count["vertices"] = int(header[0])
## Data Structures
vertices = np.zeros((count["vertices"], 3))
normalv = np.zeros((count["vertices"], 3))
atom_id = [""] * count["vertices"]
res_id = [""] * count["vertices"]
for i in range(3, len(meshdata)):
fields = meshdata[i].split()
vi = i - 3
vertices[vi][0] = float(fields[0])
vertices[vi][1] = float(fields[1])
vertices[vi][2] = float(fields[2])
normalv[vi][0] = float(fields[3])
normalv[vi][1] = float(fields[4])
normalv[vi][2] = float(fields[5])
atom_id[vi] = fields[7]
res_id[vi] = fields[9]
count["vertices"] -= 1
# Read faces.
facefile = open(file_root + ".face")
meshdata = (facefile.read().rstrip()).split("\n")
facefile.close()
# Read number of vertices.
header = meshdata[2].split()
count["faces"] = int(header[0])
faces = np.zeros((count["faces"], 3), dtype=int)
normalf = np.zeros((count["faces"], 3))
for i in range(3, len(meshdata)):
fi = i - 3
fields = meshdata[i].split()
faces[fi][0] = int(fields[0]) - 1
faces[fi][1] = int(fields[1]) - 1
faces[fi][2] = int(fields[2]) - 1
count["faces"] -= 1
assert count["vertices"] == 0
assert count["faces"] == 0
return vertices, faces, normalv, res_id
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