import numpy as np
if len(sys.argv) < 5:
print( "USAGE:", sys.argv[0], "RESID1 CHAIN1 RESID2 CHAIN1 PDB_1 ...")
r1 = int( sys.argv[1] )
c1 = sys.argv[2]
r2 = int( sys.argv[3] )
c2 = sys.argv[4]
name = "CA"
for i in range( 5, len(sys.argv)):
with open( sys.argv[i] ) as f:
pos1 = []
pos2 = []
found1 = False
found2 = False
for l in f:
if ("ATOM" in l or "HETATM" in l) and pdb.chain(l) == c1 and pdb.resid(l) == r1 and pdb.atom_name(l) == name:
pos1 = pdb.position(l)
found1 = True
elif ("ATOM" in l or "HETATM" in l) and pdb.chain(l) == c2 and pdb.resid(l) == r2 and pdb.atom_name(l) == name:
pos2 = pdb.position(l)
found2 = True
if found1 and found2:
print( sys.argv[i], np.linalg.norm( pos1 - pos2 ) , end = ' ')
found1 = False
found2 = False
if l[:4] == "pose":
print( l.split()[-1] )
#!/usr/bin/python3
import numpy as np
import math, sys
import pdb_functions as pdb
import math_functions as m
if len(sys.argv) < 5:
print("USAGE:", sys.argv[0], "PDB X Y Z ANGLE optional:CHAIN1...")
exit(1)
axis = [float(x) for x in sys.argv[2:5]]
angle = float(sys.argv[5])
chains = []
if len(sys.argv) > 6:
chains = sys.argv[6:]
with open(sys.argv[1]) as f:
for l in f:
l = l.strip()
if l[:4] == "ATOM" and (len(chains) == 0 or pdb.chain(l) in chains):
pos = np.dot(m.rotation_matrix(axis, angle), pdb.position(l))
l = pdb.write_position(l, pos)
print(l)
else:
print(l)
#np.dot(rotation_matrix(axis, theta), v)
pdb_file = sys.argv[1]
mode = sys.argv[2] # 'atom' or chain, e.g. 'A'
atom_id = int(sys.argv[3])
distance = float( sys.argv[4] )
atom_types = []
if len(sys.argv) > 5:
atom_types = sys.argv[5:]
ref_pos = []
with open( pdb_file ) as r:
for l in r:
if ("ATOM" in l or "HETATM" in l) and ( ("at" in mode and atom_id == pdb.atom_id(l)) or (pdb.chain(l) == mode and atom_id == pdb.residue_id(l))) and "TIP3" not in l:
ref_pos.append( pdb.position(l))
print(l.strip())
print('\n',len(ref_pos), ' reference atoms found\n')
previous = -666
with open(pdb_file) as r:
for l in r:
if l[:4] == "ATOM" and ( len(atom_types) == 0 or pdb.atom_name(l) in atom_types):
if( previous != pdb.residue_id(l)):
#print( pdb.single_letter( pdb.residue_name(l) ) , end='')
previous = pdb.residue_id(l)
pos = pdb.position(l)
pose = sys.argv[1]
nr = int(sys.argv[2])
mins = [float(x) for x in sys.argv[3:6]]
maxs = [float(x) for x in sys.argv[6:]]
print(pose, nr, mins, maxs)
pid = pose.rfind(".")
head = pose[:pid]
tail = pose[pid + 1:]
pdb_lines = []
with open(pose) as f:
pdb_lines = f.readlines()
cms = at.CMS(pose)
for i in range(0, nr):
pos = [r.uniform(low, high) for low, high in zip(mins, maxs)]
axis = [r.uniform(-1.0, 1.0) for j in range(0, 3)]
angle = r.uniform(0, 2.0 * np.pi)
matrix = m.rotation_matrix(axis, angle)
filename = head + '_' + str(i) + '.' + tail
print(filename)
with open(filename, 'w') as w:
for l in pdb_lines:
if l[:4] == "ATOM":
x = np.dot(matrix, pdb.position(l) - cms)
l = pdb.write_position(l, x + pos)
w.write(l)
if len(sys.argv) < 2:
print( "USAGE: ", sys.argv[0], "PDB (optional: CHAIN1 ..)")
exit(1)
pos = []
chains = []
if len(sys.argv) > 2:
chains = sys.argv[2:]
with open( sys.argv[1]) as f:
for l in f:
if l[:4] != "ATOM" or (len(chains)>0 and pdb.chain(l) not in chains):
continue
pos.append( pdb.position(l) )
pos = np.array( pos)
print( 'first pos:', pos[0])
print( pos.shape)
pca = PCA(n_components=3)
newpos = pca.fit(pos)
print( pca.components_)
print( pca.explained_variance_)
### test by hand implementation: ###
print( 'first pos:', pos[0])
x1 = []
x2 = []
atoms = []
print sys.argv
with open( pdb_file ) as f:
for l in f:
if l[:4] != "ATOM" or l[21] != chain: continue
l_atom_name = pdb.atom_name( l )
l_resid = pdb.resid(l)
# calpha collection
if l_atom_name == atomname:
p = pdb.position(l)
if p[2] >= min_z and p[2] <= max_z:
atoms.append( [ chain , l_resid , p ] )
if l_resid != resid: continue
if l_atom_name == atom_name_1:
print l
x1 = pdb.position(l)
elif l_atom_name == atom_name_2:
print l
x2 = pdb.position(l)
sidechain = np.array(x2) - np.array(x1)
print len( atoms), atomname , "collected"
if len(sys.argv) < 3:
print "USAGE:", sys.argv[
0], " FIRST.pdb XSHIFT YSHIFT ZSHIFT optional:CHAIN_1 (...)"
print "move all or specified chains by x,y,z"
print "bye"
exit(1)
# to make this safe from HETATM section, use
#from Bio import Struct
#s = Struct.read('protein_A.pdb')
# p = s.as_protein() # strip off hetatms
first_file = sys.argv[1]
shift = np.array([float(sys.argv[2]), float(sys.argv[3]), float(sys.argv[4])])
chains = []
if len(sys.argv) > 5:
chains = sys.argv[5:]
with open(first_file) as f:
for l in f:
if len(l) > 50 and (l[0:4] == "ATOM" or l[0:6] == "HETATM") and (
len(chains) == 0 or pdb.chain(l) in chains):
pos = shift + pdb.position(l)
l = pdb.write_position(l, pos)
print l,
else:
print l,