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File export module that provides overloaded save commands with secondary
structure and crystal information header, as well as saving to trajectory
(c) 2010-2012 Thomas Holder and Steffen Schmidt, MPI for Developmental Biology
(c) 2009 Sean Law, Michigan State University (save2traj)
License: BSD-2-Clause
from __future__ import print_function
except NameError:
from io import FileIO as file
from pymol import cmd, CmdException
from pymol import selector
def _assert_package_import():
if not __name__.endswith('.exporting'):
raise CmdException("Must do 'import psico.exporting' instead of 'run ...'")
## trajectory stuff
def save_traj(filename, selection='(all)', format='', box=0, quiet=1):
Save coordinates of a multi-state object to a trajectory file (DCD OR CRD).
Based on by Sean Law
save_traj filename [, selection [, format ]]
filename = string: file path to be written
selection = string: atoms to save
format = string: 'dcd' or 'crd' (alias 'charmm' or 'amber') {default:
determined from filename extension)
from . import querying
box = int(box)
NATOMS = cmd.count_atoms(selection)
NSTATES = cmd.count_states(selection)
# Determine Trajectory Format
if format == '' and '.' in filename:
format = filename.rsplit('.', 1)[1]
format = format.lower()
if format in ['charmm', 'dcd']:
Outfile = DCDOutfile
elif format in ['amber', 'trj', 'crd']:
Outfile = CRDOutfile
elif format in ['rst', 'rst7']:
Outfile = RSTOutfile
print('Unknown format:', format)
raise CmdException
f = open(filename, 'wb')
# size of periodic box
if box:
boxdim = cmd.get_symmetry(selection)[0:3]
boxdim = [0,0,0]
boxdim = None
outfile = Outfile(filename, NSTATES, NATOMS, box=boxdim)
# Write Trajectory Coordinates
for state in range(1, NSTATES+1):
xyz = querying.get_coords(selection, state)
if not int(quiet):
fmt = 'Wrote trajectory in %s format with %d atoms and %d frames to file %s'
print(fmt % (format, NATOMS, NSTATES, filename))
class DCDOutfile(file):
def __init__(self, filename, nstates, natoms, vendor='PyMOL', box=None):
file.__init__(self, filename, 'wb')
self.natoms = natoms
self.fmt = '%df' % (natoms)
charmm = int(nstates > 0)
# Header
fmt='4s 9i d 9i'
header = [b'CORD', # 4s
nstates, 1, 1, 0, 0, 0, 0, 0, 0, # 9i
1.0, # d
0, 0, 0, 0, 0, 0, 0, 0, 0, # 9i
if charmm:
# DELTA is stored as a double with X-PLOR but as a float with CHARMm
fmt = '4s 9i f 10i'
header.append(24) # dummy charmm version number
# Title
fmt = 'i80s80s'
title = [2, # 1i
b'* TITLE'.ljust(80), # 80s
(b'* Created by ' + vendor.encode()).ljust(80), # 80s
def writeFortran(self, buffer, fmt, length=0):
Write FORTRAN unformatted binary record.
import struct
if length == 0:
length = struct.calcsize(fmt)
self.write(struct.pack('i', length))
self.write(struct.pack(fmt, *buffer))
self.write(struct.pack('i', length))
def writeCoordSet(self, xyz, transposed=0):
Write a 3xNATOMS coord matrix.
if not transposed:
xyz = list(zip(*xyz))
assert len(xyz) == 3, 'Wrong number of dimensions'
for coor in xyz:
assert len(coor) == self.natoms, 'Wrong number of atoms'
self.writeFortran(coor, self.fmt)
class CRDOutfile(file):
fmt = '%8.3f'
columns = 10
def __init__(self, filename, nstates=-1, natoms=-1, vendor='PyMOL', box=None):
file.__init__(self, filename, 'w')
self.natoms = natoms = box
# Write Trajectory Header Information
print('TITLE : Created by %s with %d atoms' % (vendor, natoms), file=self)
def writeCoordSet(self, xyz, transposed=0):
Write a NATOMSx3 coord matrix.
if transposed:
xyz = list(zip(*xyz))
if self.natoms > -1:
assert len(xyz) == self.natoms, 'Wrong number of atoms'
assert len(xyz[0]) == 3, 'Wrong number of dimensions'
f = self
count = 0
for coord in xyz:
for c in coord:
f.write(self.fmt % c)
count += 1
if count % self.columns == 0:
if count % self.columns != 0:
# size of periodic box
if is not None:
for c in
f.write(self.fmt % c)
class RSTOutfile(CRDOutfile):
fmt = '%12.7f'
columns = 6
def __init__(self, *args, **kwargs):
super(RSTOutfile, self).__init__(*args, **kwargs)
print('%5i%s' % (self.natoms, ' 0.0000000e+00' * 5), file=self)
## pdb header stuff
def get_pdb_sss(selection='(all)', state=-1, quiet=1):
API-only. Return the PDB "Secondary Structure Section" for a given
selection to put in the header section of a PDB file. Takes the "ss"
atom property of CA atoms.
selection = string: atom selection
state = int: object state {default: -1}
ss = {} # storing the secondary structure elements by
# {chain}{ss.type}[ start_atom_object,
# end_atom_object ]
# Get a list of CA atoms and read the secondary structure
# annotation This loop assumes that the atoms are in consecutive
# order i.e. sorted by chain & resi
for at in cmd.get_model( '(' + selection + ') and n. CA and polymer',
if == '': continue
# Init ss dictionary if key / ss doesn't exist
L = ss.setdefault(at.chain, {}).setdefault(, [])
# Check if a new ss has to be expanded (replace last atom in ss with at)
# or else a new ss will be appended
if len(L) and L[-1][1].resi_number == (at.resi_number - 1):
L[-1][1] = at
L.append([at, at])
ssstr = [] # the output string
# Iterate over stored secondary structures and add formatted
# string to ssstr
for chain in ss:
for s in ss[chain]:
for i, (atstart, atstop) in enumerate(ss[chain][s]):
# see
if s == 'H':
ssstr.append("HELIX %3d %3d %3s %1s %4s%1s %3s %s %4d%s%2d%30s %5d\n"%(
(i+1), (i+1),
atstart.resn, atstart.chain, atstart.resi_number, ' ',
atstop.resn, atstop.chain, atstop.resi_number, ' ',
1, ' ', (atstop.resi_number - atstart.resi_number + 1)))
elif s == 'S':
ssstr.append("SHEET %3d %3d%2d %3s %1s%4d%1s %3s %1s%4d%1s%2d\n"%(
(i+1), (i+1), 1,
atstart.resn, atstart.chain, atstart.resi_number, '',
atstop.resn, atstop.chain, atstop.resi_number, '',
return ''.join(ssstr)
def get_pdb_seqres(selection='all', quiet=1):
Get PDB SEQRES records for a given selection.
prev = [None, None]
sequences = []
def callback(modelchain, resi, resn):
if prev[0] != modelchain:
prev[0] = modelchain
sequences.append((modelchain[1], []))
elif prev[1] == resi:
# same residue
prev[1] = resi
cmd.iterate('polymer & (%s)' % selection,
'callback((model, chain), resi, resn)', space=locals())
buf = []
for (chain, seq) in sequences:
numRes = len(seq)
for i in range(0, numRes, 13):
buf.append('SEQRES %3i %1.1s %4i ' % ((i / 13) + 1, chain, numRes))
for j in range(i, min(i + 13, numRes)):
buf.append('%3.3s ' % seq[j])
buf = ''.join(buf)
if not int(quiet):
return buf
def save_pdb(filename, selection='(all)', state=-1, symm=1, ss=1, aniso=0, seqres=0, quiet=1):
Save the coordinates of a selection as pdb including the
secondary structure information and, if possible, the unit
cell. The latter requires the selction of a single object
save_pdb filename, selection [, state [, symm [, ss [, aniso ]]]]
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
Note: to include the unit cell information you
need to select a single object
state = integer: state to save {default: -1 (current state)}
symm = 0 or 1: save symmetry info if possible {default: 1}
ss = 0 or 1: save secondary structure info {default: 1}
aniso = 0 or 1: save ANISO records {default: 0}
from . import pymol_version
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
symm, ss = int(symm), int(ss)
filename = cmd.exp_path(filename)
f = open(filename, 'w')
print('REMARK 200 Generated with PyMOL and psico'.ljust(80), file=f)
# Write sequence
if int(seqres):
# Write the CRYST1 line if possible
if symm:
obj1 = cmd.get_object_list(selection)[0]
sym = cmd.get_symmetry(obj1)
if len(sym) != 7:
f.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-10s%4d\n" % tuple(sym + [1]))
if not quiet:
print(' Info: Wrote unit cell and space group info')
if not quiet:
print(' Info: No crystal information')
# Write secondary structure
if ss:
sss = get_pdb_sss(selection, state, quiet)
if not sss:
if not quiet:
print(' Info: Wrote secondary structure info')
if not quiet:
print(' Info: No secondary structure information')
# Write coordinates of selection
pdbstr = cmd.get_pdbstr(selection, state)
# fix END records
if state == 0 and pymol_version < 1.6:
pdbstr = '\n'.join(line for line in pdbstr.splitlines() if line != 'END') + '\nEND\n'
# anisotropic b-factors
if int(aniso) and pymol_version < 1.6 and \
cmd.get_model('first (%s)' % selection).atom[0].u_aniso[0] != 0.0:
def mergeaniso():
atom_it = iter(cmd.get_model(selection, state).atom)
for line in pdbstr.splitlines(True):
yield line
if line[:6] in ['ATOM ', 'HETATM']:
yield 'ANISOU' + line[6:28] + \
''.join('%7.0f' % (u*1e4) for u in next(atom_it).u_aniso) + \
pdbstr = ''.join(mergeaniso())
if not quiet:
print('Wrote PDB to \''+filename+'\'')
def save(filename, selection='(all)', state=-1, format='',
ref='', ref_state=-1, quiet=1, *args, **kwargs):
This is an overloaded version of the 'save' command that also saves
secondary structure and crystal information, if available.
if not (format == 'pdb' or format == '' and filename.endswith('.pdb')):
from pymol.exporting import save
return save(filename, selection, state, format, ref, ref_state, quiet, *args, **kwargs)
save_pdb(filename, selection, state, 1, 1, 0, quiet)
save.__doc__ = + save.__doc__
def unittouu(string, dpi=90.0):
API only. Returns pixel units given a string representation of units in
another system. Default unit is millimeter.
import re
uuconv = {'in':dpi, 'mm':dpi/25.4, 'cm':dpi/2.54}
unit = 'mm'
if isinstance(string, str) and string[-2:].isalpha():
string, unit = string[:-2], string[-2:]
retval = float(string)
raise ValueError("cannot parse value from: " + str(string))
if unit not in uuconv:
raise ValueError("unknown unit: " + str(unit))
return retval * uuconv[unit]
def paper_png(filename, width=100, height=0, dpi=300, ray=1):
Saves a PNG format image file of the current display.
Instead of pixel dimensions, physical dimensions for
printing (in millimeters) and DPI are specified.
paper_png filename [, width [, height [, dpi [, ray ]]]]
filename = string: filename
width = float: width in millimeters {default: 100 = 10cm}
width = string: width including unit (like: '10cm' or '100mm')
height = float or string, like "width" argument. If height=0, keep
aspect ratio {default: 0}
dpi = float: dots-per-inch {default: 300}
ray = 0 or 1: should ray be run first {default: 1 (yes)}
dpi, ray = float(dpi), int(ray)
width = unittouu(width, dpi)
height = unittouu(height, dpi)
cmd.png(filename, width, height, dpi, ray)
def save_pdb_without_ter(filename, selection, *args, **kwargs):
Save PDB file without TER records. External applications like TMalign and
DynDom stop reading PDB files at TER records, which might be undesired in
case of missing loops.
v = cmd.get_setting_boolean('pdb_use_ter_records')
if v: cmd.set('pdb_use_ter_records', 0), selection, *args, **kwargs)
if v: cmd.set('pdb_use_ter_records')
## pymol command stuff
cmd.extend('save_traj', save_traj)
cmd.extend('save_pdb', save_pdb)
cmd.extend('paper_png', paper_png)
('save_traj', cmd.auto_arg[1]['save']),
('save_pdb', cmd.auto_arg[1]['save']),
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