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Add lower threshold for pymol arrows #31

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Merged
dkoes merged 5 commits into from
Aug 8, 2019
Merged

Add lower threshold for pymol arrows #31

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b640181
Merge remote-tracking branch 'upstream/master'
RMeli Jul 10, 2019
a2549e8
open file in context
RMeli Aug 1, 2019
cbf9cd8
Merge remote-tracking branch 'upstream/master'
RMeli Aug 1, 2019
d679bc4
added optional lower threshold for arrow length
RMeli Aug 8, 2019
71212e1
reverted changes of another PR
RMeli Aug 8, 2019
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11 changes: 8 additions & 3 deletions pymol_arrows.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,13 @@
import argparse


def write_pymol_arrows(base, atoms, scale, color, radius):
def write_pymol_arrows(base, atoms, scale, color, radius, threshold):
pymol_file = base + '_arrows.pymol'
lines = []
lines.append('run cgo_arrow.py')
arrow_objs = []
t2 = threshold**2
s2 = scale**2
for i, atom in enumerate(atoms):
arrow_obj = base + '_arrow_' + str(i)
arrow_objs.append(arrow_obj)
Expand All @@ -25,7 +27,8 @@ def write_pymol_arrows(base, atoms, scale, color, radius):
if color:
line += ', color={}'.format(color)
line += ', name={}'.format(arrow_obj)
lines.append(line)
if( (dx**2 + dy**2 + dz**2)*s2 > t2 ): # Check threshold
lines.append(line)
arrow_group = base + '_arrows'
line = 'group {}, {}'.format(arrow_group, ' '.join(arrow_objs))
lines.append(line)
Expand Down Expand Up @@ -94,14 +97,16 @@ def parse_args():
help='Output a .pdb file where the b-factor is gradient magnitude')
parser.add_argument('--sum', action='store_true', default=False,
help='Sum gradient components instead of taking magnitude')
parser.add_argument('-t', '--threshold', type=float, default=0,
help="Lower thrashold for arrow length (scaled)")
return parser.parse_args()


if __name__ == '__main__':
args = parse_args()
atoms = read_xyz_file(args.xyz_file)
base_name = args.xyz_file.replace('.xyz', '')
write_pymol_arrows(base_name, atoms, args.scale, args.color, args.radius)
write_pymol_arrows(base_name, atoms, args.scale, args.color, args.radius, args.threshold)
if args.pdb_file:
pdb_file = base_name + '.pdb'
write_pdb_file(pdb_file, atoms, args.sum)
Expand Down