Author: bugman
Date: Wed Feb 20 16:23:04 2013
New Revision: 18537
URL: http://svn.gna.org/viewcvs/relax?rev=18537&view=rev
Log:
Docstring whitespace fixes for the generic_fns.structure.pdb_* modules.
Modified:
trunk/generic_fns/structure/pdb_read.py
trunk/generic_fns/structure/pdb_write.py
Modified: trunk/generic_fns/structure/pdb_read.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/pdb_read.py?rev=18537&r1=18536&r2=18537&view=diff
==============================================================================
--- trunk/generic_fns/structure/pdb_read.py (original)
+++ trunk/generic_fns/structure/pdb_read.py Wed Feb 20 16:23:04 2013
@@ -82,8 +82,8 @@
- AltLoc is the place holder to indicate alternate conformation. The
alternate conformation can be in the entire polymer chain, or several
residues or partial residue (several atoms within one residue). If an atom is
provided in more than one position, then a non-blank alternate location
indicator must be used for each of the atomic positions. Within a residue,
all atoms that are associated with each other in a given conformation are
assigned the same alternate position indicator. There are two ways of
representing alternate conformation- either at atom level or at residue level
(see examples).
- For atoms that are in alternate sites indicated by the alternate site
indicator, sorting of atoms in the ATOM/HETATM list uses the following
general rules:
- - In the simple case that involves a few atoms or a few residues
with alternate sites, the coordinates occur one after the other in the
entry.
- - In the case of a large heterogen groups which are disordered, the
atoms for each conformer are listed together.
+ - In the simple case that involves a few atoms or a few residues
with alternate sites, the coordinates occur one after the other in the entry.
+ - In the case of a large heterogen groups which are disordered, the
atoms for each conformer are listed together.
- Alphabet letters are commonly used for insertion code. The insertion
code is used when two residues have the same numbering. The combination of
residue numbering and insertion code defines the unique residue.
- If the depositor provides the data, then the isotropic B value is
given for the temperature factor.
@@ -243,9 +243,9 @@
- CONECT records are present for:
- - Intra-residue connectivity within non-standard (HET) residues
(excluding water).
- - Inter-residue connectivity of HET groups to standard groups
(including water) or to other HET groups.
- - Disulfide bridges specified in the SSBOND records have
corresponding records.
+ - Intra-residue connectivity within non-standard (HET) residues
(excluding water).
+ - Inter-residue connectivity of HET groups to standard groups
(including water) or to other HET groups.
+ - Disulfide bridges specified in the SSBOND records have
corresponding records.
- No differentiation is made between atoms with delocalized charges
(excess negative or positive charge).
- Atoms specified in the CONECT records have the same numbers as given
in the coordinate section.
@@ -366,8 +366,8 @@
- The number of each atom type present immediately follows its chemical
symbol without an intervening blank space. There will be no number indicated
if there is only one atom for a particular atom type.
- Each set of SEQRES records and each HET group is assigned a component
number in an entry. These numbers are assigned serially, beginning with 1 for
the first set of SEQRES records. In addition:
- - If a HET group is presented on a SEQRES record its FORMUL is
assigned the component number of the chain in which it appears.
- - If the HET group occurs more than once and is not presented on
SEQRES records, the component number of its first occurrence is used.
+ - If a HET group is presented on a SEQRES record its FORMUL is
assigned the component number of the chain in which it appears.
+ - If the HET group occurs more than once and is not presented on
SEQRES records, the component number of its first occurrence is used.
- All occurrences of the HET group within a chain are grouped together
with a multiplier. The remaining occurrences are also grouped with a
multiplier. The sum of the multipliers is the number equaling the number of
times that that HET group appears in the entry.
- A continuation field is provided in the event that more space is
needed for the formula. Columns 17 - 18 are used in order to maintain
continuity with the existing format.
@@ -593,7 +593,7 @@
Details
=======
- - Each HET group is assigned a hetID of not more than three (3)
alphanumeric characters. The sequence number, chain identifier, insertion
code, and number of coordinate records are given for each occurrence of the
HET group in the entry. The chemical name of the HET group is given in the
HETNAM record and synonyms for the chemical name are given in the HETSYN
records, see ftp://ftp.wwpdb.org/pub/pdb/data/monomers .
+ - Each HET group is assigned a hetID of not more than three (3)
alphanumeric characters. The sequence number, chain identifier, insertion
code, and number of coordinate records are given for each occurrence of the
HET group in the entry. The chemical name of the HET group is given in the
HETNAM record and synonyms for the chemical name are given in the HETSYN
records, see ftp://ftp.wwpdb.org/pub/pdb/data/monomers.
- There is a separate HET record for each occurrence of the HET group in
an entry.
- A particular HET group is represented in the PDB archive with a unique
hetID.
- PDB entries do not have HET records for water molecules, deuterated
water, or methanol (when used as solvent).
Modified: trunk/generic_fns/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/pdb_write.py?rev=18537&r1=18536&r2=18537&view=diff
==============================================================================
--- trunk/generic_fns/structure/pdb_write.py (original)
+++ trunk/generic_fns/structure/pdb_write.py Wed Feb 20 16:23:04 2013
@@ -118,8 +118,8 @@
- AltLoc is the place holder to indicate alternate conformation. The
alternate conformation can be in the entire polymer chain, or several
residues or partial residue (several atoms within one residue). If an atom is
provided in more than one position, then a non-blank alternate location
indicator must be used for each of the atomic positions. Within a residue,
all atoms that are associated with each other in a given conformation are
assigned the same alternate position indicator. There are two ways of
representing alternate conformation- either at atom level or at residue level
(see examples).
- For atoms that are in alternate sites indicated by the alternate site
indicator, sorting of atoms in the ATOM/HETATM list uses the following
general rules:
- - In the simple case that involves a few atoms or a few residues
with alternate sites, the coordinates occur one after the other in the
entry.
- - In the case of a large heterogen groups which are disordered, the
atoms for each conformer are listed together.
+ - In the simple case that involves a few atoms or a few residues
with alternate sites, the coordinates occur one after the other in the entry.
+ - In the case of a large heterogen groups which are disordered, the
atoms for each conformer are listed together.
- Alphabet letters are commonly used for insertion code. The insertion
code is used when two residues have the same numbering. The combination of
residue numbering and insertion code defines the unique residue.
- If the depositor provides the data, then the isotropic B value is
given for the temperature factor.
@@ -283,9 +283,9 @@
- CONECT records are present for:
- - Intra-residue connectivity within non-standard (HET) residues
(excluding water).
- - Inter-residue connectivity of HET groups to standard groups
(including water) or to other HET groups.
- - Disulfide bridges specified in the SSBOND records have
corresponding records.
+ - Intra-residue connectivity within non-standard (HET) residues
(excluding water).
+ - Inter-residue connectivity of HET groups to standard groups
(including water) or to other HET groups.
+ - Disulfide bridges specified in the SSBOND records have
corresponding records.
- No differentiation is made between atoms with delocalized charges
(excess negative or positive charge).
- Atoms specified in the CONECT records have the same numbers as given
in the coordinate section.
@@ -385,7 +385,7 @@
Details
=======
- END is the final record of a coordinate entry.
+ - END is the final record of a coordinate entry.
Verification/Validation/Value Authority Control
@@ -450,9 +450,9 @@
Details
=======
- MODEL/ENDMDL records are used only when more than one structure is
presented in the entry, as is often the case with NMR entries.
- All the models in a multi-model entry must represent the same
structure.
- Every MODEL record has an associated ENDMDL record.
+ - MODEL/ENDMDL records are used only when more than one structure is
presented in the entry, as is often the case with NMR entries.
+ - All the models in a multi-model entry must represent the same
structure.
+ - Every MODEL record has an associated ENDMDL record.
Verification/Validation/Value Authority Control
@@ -541,8 +541,8 @@
- The number of each atom type present immediately follows its chemical
symbol without an intervening blank space. There will be no number indicated
if there is only one atom for a particular atom type.
- Each set of SEQRES records and each HET group is assigned a component
number in an entry. These numbers are assigned serially, beginning with 1 for
the first set of SEQRES records. In addition:
- - If a HET group is presented on a SEQRES record its FORMUL is
assigned the component number of the chain in which it appears.
- - If the HET group occurs more than once and is not presented on
SEQRES records, the component number of its first occurrence is used.
+ - If a HET group is presented on a SEQRES record its FORMUL is
assigned the component number of the chain in which it appears.
+ - If the HET group occurs more than once and is not presented on
SEQRES records, the component number of its first occurrence is used.
- All occurrences of the HET group within a chain are grouped together
with a multiplier. The remaining occurrences are also grouped with a
multiplier. The sum of the multipliers is the number equaling the number of
times that that HET group appears in the entry.
- A continuation field is provided in the event that more space is
needed for the formula. Columns 17 - 18 are used in order to maintain
continuity with the existing format.
@@ -788,7 +788,7 @@
Details
=======
- - Each HET group is assigned a hetID of not more than three (3)
alphanumeric characters. The sequence number, chain identifier, insertion
code, and number of coordinate records are given for each occurrence of the
HET group in the entry. The chemical name of the HET group is given in the
HETNAM record and synonyms for the chemical name are given in the HETSYN
records, see ftp://ftp.wwpdb.org/pub/pdb/data/monomers .
+ - Each HET group is assigned a hetID of not more than three (3)
alphanumeric characters. The sequence number, chain identifier, insertion
code, and number of coordinate records are given for each occurrence of the
HET group in the entry. The chemical name of the HET group is given in the
HETNAM record and synonyms for the chemical name are given in the HETSYN
records, see ftp://ftp.wwpdb.org/pub/pdb/data/monomers.
- There is a separate HET record for each occurrence of the HET group in
an entry.
- A particular HET group is represented in the PDB archive with a unique
hetID.
- PDB entries do not have HET records for water molecules, deuterated
water, or methanol (when used as solvent).
@@ -1132,8 +1132,8 @@
Details
=======
- MASTER gives checksums of the number of records in the entry, for
selected record types.
- MASTER records only the first model when there are multiple models
in the coordinates.
+ - MASTER gives checksums of the number of records in the entry, for
selected record types.
+ - MASTER records only the first model when there are multiple models in
the coordinates.
Verification/Validation/Value Authority Control
@@ -1402,7 +1402,6 @@
| 23 - 26 | Integer | initSeqNum | Sequence number of initial
residue in strand. |
| 27 | AChar | initICode | Insertion code of initial
residue in strand. |
| 29 - 31 | Residue name | endResName | Residue name of terminal
residue. |
-
| 33 | Character | endChainID | Chain identifier of terminal
residue. |
| 34 - 37 | Integer | endSeqNum | Sequence number of terminal
residue. |
| 38 | AChar | endICode | Insertion code of terminal
residue. |
r18537 - in /trunk/generic_fns/structure: pdb_read.py pdb_write.py