def get_reference_structure(path, selection_str, expected_num_res):
reference = parsePDB(path)
reference_structure = reference.select(selection_str)
writePDB("ref.pdb.chunk", reference_structure)
#The reference chunk must NOT have RESIDUE GAPS
assert expected_num_res == reference_structure.getHierView().numResidues(),\
"[ERROR] There are gaps in the reference structure inside this residue range.%d %d"%(options.final_res - options.initial_res +1, reference_structure.getHierView().numResidues())
def main():
parser = argparse.ArgumentParser(
description=
'Project the calpha coordinates of a PDB file by a projection matrix and output the new PDB file with only calpahs'
)
parser.add_argument('pdbFile', help='The pdb file')
parser.add_argument('P', help='the projection matrix')
parser.add_argument(
'-outputName',
help=
'name of the output file, default is beforeP_P_pdbFile and afterP_P_pdbFile'
)
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
assert os.path.isfile(args.pdbFile)
assert os.path.isfile(args.P)
if args.outputName:
outputName = args.outputName
else:
outputName = os.path.basename(args.P) + "_" + os.path.basename(
args.pdbFile)
# read files
pdbFile = parsePDB(args.pdbFile)
pdbFile_ca = pdbFile.select('calpha')
P = np.loadtxt(args.P)
writePDB("beforeP_" + outputName, pdbFile_ca)
coord_shape = pdbFile_ca.getCoords().shape
coords_P = P.dot(pdbFile_ca.getCoords().flatten())
coords_P = coords_P.reshape(coord_shape)
pdbFile_ca.setCoords(coords_P)
writePDB("afterP_" + outputName, pdbFile_ca)
referenceSegment = "R"
referenceOfComplex = pdbFile_ca.select('segment \"' + referenceSegment +
'.\"')
print "Center of fixed (receptor) frame is: ", calcCenter(
referenceOfComplex.select('calpha'))
print "calphas before projection written to: ", "beforeP_" + outputName
print "calphas after projection written to: ", "afterP_" + outputName
def writeSampleResults(self, basePath, experimentName, utils, cCase=None): np.set_printoptions(threshold=np.nan) utils.mkdir_p(basePath) utils.mkdir_p(basePath+experimentName+"/") if not cCase: path = basePath+experimentName+"/" else: path = basePath+experimentName+"/"+str(cCase)+"/" utils.mkdir_p(path) try: writePDB(path+"Ensemble.pdb", self.Ensemble) except AttributeError, err: print "Exception AttributeError occurred: ", err print traceback.format_exc()
else:
print "Correspondence not found for residue %d of template in pdb %s" % (
r_id, pdb_path)
index = index + 1
center = center / len(res_selection)
# Center coordinates
for i in range(num_res):
offset = i * 3
if sequence[i] != "GAP":
coords[offset] -= center[0]
coords[offset + 1] -= center[1]
coords[offset + 2] -= center[2]
sequences.append(sequence)
all_ca_coords.append(coords)
if options.chunk_path is not None:
pdb_name = os.path.basename(pdb_path)
# Extract the chunk
res_sel_string = "resid " + " ".join(
[str(residue_index) for residue_index in res_selection])
selected_residues_structure = pdb.select(res_sel_string)
writePDB(os.path.join(options.chunk_path, pdb_name + ".chunk"),
selected_residues_structure)
all_ca_coords = numpy.array(all_ca_coords)
numpy.savetxt("%s.coords" % (options.output), all_ca_coords, fmt="%.5f")
open("%s.seq" % (options.output),
"w").write("\n".join([" ".join(sequence) for sequence in sequences]))
for pdb_path in open(options.db_list).readlines():
sequence = []
pdb_path = pdb_path.rstrip('\r\n')
res_mapping = get_best_res_mapping(options.reference, pdb_path)
pdb = parsePDB(pdb_path)
angles, sequence, res_selection = get_angles_and_sequence_for_pdb_with_mapping(pdb, res_mapping, pdb_path, options)
sequences.append(sequence)
all_angles.append(angles)
# Extract the chunk
res_sel_string ="resid "+" ".join( [str(r_id) for r_id in res_selection])
selected_residues_structure = pdb.select(res_sel_string)
writePDB(pdb_path+".chunk", selected_residues_structure)
all_angles = numpy.array(all_angles)
# # Eliminate first column and change inf by mean values
# angle_means = get_means_for_non_inf(numpy.array(all_angles)) # <-- must be calculated with circular stats!
# all_new_angles = []
# for i in range(1, len(all_angles.T)):
# angles = all_angles.T[i]
# new_angles = []
# for j in range(len(angles)):
# if angles[j] == inf:
# new_angles.append( angle_means[i])
# else:
# new_angles.append( angles[j])
# all_new_angles.append(new_angles)
colors = sns.hls_palette(15, l=.3, s=.8)
# VMD execution template
template = open("/home/victor/git/PhD-GPCR/PhD-GPCR-2/data/load_script_representatives.tcl").read()
for line in open(options.input):
protein, drug, folder = line.strip().split()
# sorted clusters and same color generation always make the same cluster_id, color pair
representatives_file = os.path.join(folder, "representatives.pdb")
output_folder = os.path.join(options.output_folder, drug, protein)
create_directory(output_folder)
pdb = parsePDB(representatives_file)
writePDB(os.path.join(output_folder,"protein.pdb"), pdb.select("protein"), csets = [0])
writePDB(os.path.join(output_folder,"ligands.pdb"), pdb.select("resname %s"%drug))
num_clusters = pdb.numCoordsets()
clusters_file = open(os.path.join(output_folder,"cluster_colors"), "w")
for i in range(num_clusters):
clusters_file.write("%.2f %.2f %.2f%s"%( colors[i][0],
colors[i][1],
colors[i][2],
("\n" if i <(num_clusters-1) else "")))
clusters_file.close()
camera_settings = ""; camera_settings_zoomed = ""; option_camera = "#"; pre_render_file = ""; rendered_file = ""; option_zoom = "#"
if options.camera is not None:
camera_settings = camera[protein][0]
camera_settings_zoomed = camera[protein][1]
parser.error('You must define the results folder')
output = open(options.output,"w")
if not options.prototypes:
for line in open(options.input):
protein, drug, folder = line.strip().split()
files = glob.glob(os.path.join(folder, "cluster_*.pdb"))
results_folder = os.path.join(options.results, drug, protein)
create_directory(results_folder)
output.write("%s %s %s\n"%(protein, drug, results_folder))
for i, filename in enumerate(sorted(files)):
pdb = parsePDB(filename)
if i == 0:
# Extract first frame
prot = pdb.select("protein")
writePDB(os.path.join(results_folder, "%s.pdb"%protein), prot, csets=[0])
# Extract ligands
ligands = pdb.select("resname %s"%drug)
writePDB(os.path.join(results_folder, "ligand_%s"%os.path.basename(filename)), ligands)
else:
# Input file contains the folders with prototypes file
for line in open(options.input):
protein, drug, folder = line.strip().split()
filename = os.path.join(folder, "representatives.pdb")
results_folder = os.path.join(options.results, drug, protein)
# Look for "REMARK cluster id :"
# Parse once to get correct ordering of clusters
cluster_ids = []
for line in open(filename):
if "REMARK cluster id :" in line:
cluster_ids.append(line.split()[4])
'''
Created on Dec 10, 2015
@author: victor
'''
from prody.proteins.pdbfile import parsePDB, writePDB
import sys
from histogram import parse_motifs
import urllib
if __name__ == '__main__':
pdb = parsePDB(sys.argv[1])
motifs = parse_motifs(sys.argv[2])
prot_name = sys.argv[3]
for motif in motifs[prot_name]:
motif_struct = pdb.select("resid %d to %d"%motifs[prot_name][motif])
writePDB("%s.pdb"%urllib.quote(motif, safe=""),motif_struct)
print motif, sorted(list(set(motif_struct.getResnums())))