Functions
def	check_and_print_pdb (count, residue_buffer, residue_letter)

Variables
string	local_pdb_database = "/lab/shared/scaffolds/"
	set your scaffold source here ################################# More...

bool	keep_ligand = True

bool	shit_stat_insres = False

bool	shit_stat_altpos = False

bool	shit_stat_modres = False
	dont count MSEs as modiied residues (cos they're so common and get_pdb deal with them previosuly) More...

bool	shit_stat_misdns = False
	Print out the residue when the new line is for a new residue. More...

list	hetatm_list = []

bool	CA_MODEL = True

bool	NO_OCCUPANCY = True

string	fastaseq = ""

string	pdbfile = ""

	pdbname = argv[1]

	pdbcode = argv[1]

	chainid = argv[2]

	outfile = pdbname

int	nopdbout = 0

int	removechain = 0

int	ignorechain = 0

string	netpdbname = local_pdb_database + pdbname[1:3] + '/' + pdbname[0:4] + '/' + argv[1] + '_0.pdb'

	lines = popen( 'zcat '+netpdbname,'r').readlines()

string	oldresnum = ' '
	residue_invalid = True More...

int	count = 1;

string	modifiedres = ''

list	residue_buffer = []

string	residue_letter = ''

bool	residue_invalid = False

	line = lines[i]

	line_edit = line
	Is it a modified residue ? More...

bool	ok = False

	resnum = line_edit[22:27]
	if line_edit[13:14]=='P': #Nucleic acid? Skip. More...

	insres = line[26]

	altpos = line[16]

	longname = line_edit[17:20]

string	flag_altpos = "---"

string	flag_insres = "---"

string	flag_modres = "---"

string	flag_misdns = "---"

	nres = len(fastaseq)

string	flag_successful = "OK"

	outid = open( outfile, 'w')

	fastaid = stderr

Function Documentation

◆ check_and_print_pdb()

def clean_pdb_keep_ligand.check_and_print_pdb	(	count,
		residue_buffer,
		residue_letter
	)

References run_backbone.float, and ObjexxFCL.len().

Variable Documentation

◆ altpos

clean_pdb_keep_ligand.altpos = line[16]

◆ CA_MODEL

bool clean_pdb_keep_ligand.CA_MODEL = True

◆ chainid

string clean_pdb_keep_ligand.chainid = argv[2]

Referenced by MPInterfaceStatistics.get_size().

◆ count

int clean_pdb_keep_ligand.count = 1;

◆ fastaid

clean_pdb_keep_ligand.fastaid = stderr

◆ fastaseq

string clean_pdb_keep_ligand.fastaseq = ""

Referenced by main().

◆ flag_altpos

clean_pdb_keep_ligand.flag_altpos = "---"

◆ flag_insres

clean_pdb_keep_ligand.flag_insres = "---"

◆ flag_misdns

clean_pdb_keep_ligand.flag_misdns = "---"

◆ flag_modres

clean_pdb_keep_ligand.flag_modres = "---"

◆ flag_successful

string clean_pdb_keep_ligand.flag_successful = "OK"

◆ hetatm_list

list clean_pdb_keep_ligand.hetatm_list = []

◆ ignorechain

int clean_pdb_keep_ligand.ignorechain = 0

◆ insres

clean_pdb_keep_ligand.insres = line[26]

◆ keep_ligand

bool clean_pdb_keep_ligand.keep_ligand = True

◆ line

clean_pdb_keep_ligand.line = lines[i]

◆ line_edit

string clean_pdb_keep_ligand.line_edit = line

Is it a modified residue ?

What does this do ?

other substitution (of atoms mainly)

if so replace it with its canonical equivalent !

◆ lines

clean_pdb_keep_ligand.lines = popen( 'zcat '+netpdbname,'r').readlines()

◆ local_pdb_database

string clean_pdb_keep_ligand.local_pdb_database = "/lab/shared/scaffolds/"

set your scaffold source here #################################

◆ longname

clean_pdb_keep_ligand.longname = line_edit[17:20]

◆ modifiedres

string clean_pdb_keep_ligand.modifiedres = ''

◆ netpdbname

clean_pdb_keep_ligand.netpdbname = local_pdb_database + pdbname[1:3] + '/' + pdbname[0:4] + '/' + argv[1] + '_0.pdb'

◆ NO_OCCUPANCY

bool clean_pdb_keep_ligand.NO_OCCUPANCY = True

◆ nopdbout

int clean_pdb_keep_ligand.nopdbout = 0

◆ nres

clean_pdb_keep_ligand.nres = len(fastaseq)

◆ ok

bool clean_pdb_keep_ligand.ok = False

Referenced by ui::task::JobSubmit.on_rename_job_clicked(), and ui::viewers::ScoreFileView.update_ui_from_file_data().

◆ oldresnum

clean_pdb_keep_ligand.oldresnum = ' '

residue_invalid = True

◆ outfile

string clean_pdb_keep_ligand.outfile = pdbname

◆ outid

clean_pdb_keep_ligand.outid = open( outfile, 'w')

◆ pdbcode

clean_pdb_keep_ligand.pdbcode = argv[1]

Referenced by main().

◆ pdbfile

string clean_pdb_keep_ligand.pdbfile = ""

Referenced by densityTools(), main(), ReadCAsFromPDB(), relax_test(), run(), and spanfile_from_pdb().

◆ pdbname

clean_pdb_keep_ligand.pdbname = argv[1]

◆ removechain

int clean_pdb_keep_ligand.removechain = 0

◆ residue_buffer

list clean_pdb_keep_ligand.residue_buffer = []

◆ residue_invalid

bool clean_pdb_keep_ligand.residue_invalid = False

◆ residue_letter

string clean_pdb_keep_ligand.residue_letter = ''

◆ resnum

clean_pdb_keep_ligand.resnum = line_edit[22:27]

if line_edit[13:14]=='P': #Nucleic acid? Skip.

resnum = line_edit[23:26] oldresnum = resnum while (resnum == oldresnum): print "HERE" i += 1 line = lines[i] resnum = line_edit[23:26]

◆ shit_stat_altpos

clean_pdb_keep_ligand.shit_stat_altpos = False

◆ shit_stat_insres

clean_pdb_keep_ligand.shit_stat_insres = False

◆ shit_stat_misdns

bool clean_pdb_keep_ligand.shit_stat_misdns = False

Print out the residue when the new line is for a new residue.

if unsuccessful

is there a residue in the buffer ? If so print it out, then reinitialize

print "call from the loop:\n" ## new